{"entity": "publications", "timestamp": "2026-06-12T20:10:36.781Z", "year": "2025", "links": {"self": {"href": "https://publications.scilifelab.se/publications/2025.json"}, "display": {"href": "https://publications.scilifelab.se/publications/2025"}}, "publications_count": 921, "full": true, "publications": [{"entity": "publication", "iuid": "e2b4725910744d92b8cdec06b890dec8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2b4725910744d92b8cdec06b890dec8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2b4725910744d92b8cdec06b890dec8"}}, "title": "Drugs that act on both GPCRs and kinases: Potentiation of effects, side effects and general aspects of drug pleiotropy", "authors": [{"family": "Ljunggren", "given": "Hampus", "initials": "H"}, {"family": "Sokolov", "given": "Aleksandr", "initials": "A"}, {"family": "Ballante", "given": "Flavio", "initials": "F"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Lagunas-Rangel", "given": "Francisco", "initials": "F"}, {"family": "Hauser", "given": "Alexander", "initials": "A"}, {"family": "Knapp", "given": "Stefan", "initials": "S"}, {"family": "Jonsson", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "posted-content", "published": "2025-12-31", "journal": {"issn-l": null}, "abstract": null, "doi": "10.22541/au.176718976.62475551/v1", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2026-03-17T14:08:01.780Z", "modified": "2026-03-17T14:08:01.780Z"}, {"entity": "publication", "iuid": "2c984cc0dbff42e6873efdc97db17297", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c984cc0dbff42e6873efdc97db17297.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c984cc0dbff42e6873efdc97db17297"}}, "title": "Impact of hydrogen peroxide photolysis on viable bacterial count and composition of in vivo dental biofilm-an ex vivo study.", "authors": [{"family": "Shirato", "given": "Midori", "initials": "M"}, {"family": "Lehrkinder", "given": "Anna", "initials": "A"}, {"family": "Nakamura", "given": "Keisuke", "initials": "K"}, {"family": "Kanno", "given": "Taro", "initials": "T"}, {"family": "Lingstr\u00f6m", "given": "Peter", "initials": "P"}, {"family": "\u00d6rtengren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2025-12-30", "journal": {"title": "BMC Oral Health", "issn": "1472-6831", "issn-l": null}, "abstract": null, "doi": "10.1186/s12903-025-07588-6", "pmid": "41469638", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12903-025-07588-6"}], "notes": [], "created": "2026-01-12T10:07:18.863Z", "modified": "2026-01-25T08:39:00.177Z"}, {"entity": "publication", "iuid": "457495686eaa4727b243b252d2f4e6fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/457495686eaa4727b243b252d2f4e6fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/457495686eaa4727b243b252d2f4e6fe"}}, "title": "Characterization of CTNND2-related neurodevelopmental disease, phenotype-genotype spectrum and WNT dynamics in early neurogenesis.", "authors": [{"family": "Shahsavani", "given": "Mansoureh", "initials": "M"}, {"family": "Wincent", "given": "Josephine", "initials": "J", "orcid": "0000-0002-1698-9605", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9777724444021924229d3fdc8673e.json"}}, {"family": "Reiter", "given": "Ricarda", "initials": "R"}, {"family": "Soltysova", "given": "Andrea", "initials": "A"}, {"family": "Schuy", "given": "Jakob", "initials": "J"}, {"family": "Helgadottir", "given": "Hafdis T", "initials": "HT", "orcid": "0000-0003-4352-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce4dc1001c944a9d9dfe4c092cfda497.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Ficek", "given": "Andrej", "initials": "A"}, {"family": "Druschke", "given": "Lotta", "initials": "L"}, {"family": "Kusikova", "given": "Katarina", "initials": "K"}, {"family": "Hsieh", "given": "Tzung-Chien", "initials": "TC"}, {"family": "Krichhoff", "given": "Aron", "initials": "A"}, {"family": "Krawitz", "given": "Peter", "initials": "P"}, {"family": "Li", "given": "Jing-Mei", "initials": "JM"}, {"family": "Webersinke", "given": "Gerald", "initials": "G"}, {"family": "Gorokhova", "given": "Svetlana", "initials": "S"}, {"family": "Missirian", "given": "Chantal", "initials": "C"}, {"family": "Riccardi", "given": "Florence", "initials": "F"}, {"family": "Pavinato", "given": "Lisa", "initials": "L"}, {"family": "Brusco", "given": "Alfredo", "initials": "A", "orcid": "0000-0002-8318-7231", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fa6038bda54597ac495d278d106511.json"}}, {"family": "Mandrile", "given": "Giorgia", "initials": "G"}, {"family": "Trajkova", "given": "Slavica", "initials": "S"}, {"family": "Pintus", "given": "Francesco", "initials": "F"}, {"family": "Gagachovska", "given": "Biljana", "initials": "B"}, {"family": "Waisfisz", "given": "Quinten", "initials": "Q"}, {"family": "van Hagen", "given": "Annet", "initials": "A"}, {"family": "Bedoukian", "given": "Emma", "initials": "E"}, {"family": "Izumi", "given": "Kosuke", "initials": "K"}, {"family": "Granger", "given": "Leslie", "initials": "L"}, {"family": "Petersen", "given": "Andrea", "initials": "A", "orcid": "0000-0003-3882-0867", "researcher": {"href": "https://publications.scilifelab.se/researcher/69701b12d455487a9dd1ab55f9904327.json"}}, {"family": "Oegema", "given": "Renske", "initials": "R", "orcid": "0000-0002-7146-617X", "researcher": {"href": "https://publications.scilifelab.se/researcher/246eec36818e410296fd2d6ea502483f.json"}}, {"family": "Huibers", "given": "Manon", "initials": "M"}, {"family": "Demurger", "given": "Florence", "initials": "F"}, {"family": "Brischoux-Boucher", "given": "Elise", "initials": "E"}, {"family": "Julia", "given": "Sophie", "initials": "S"}, {"family": "Banneau", "given": "Guillaume", "initials": "G"}, {"family": "Zavala", "given": "M Jesus", "initials": "MJ"}, {"family": "Lagos", "given": "Catalina", "initials": "C"}, {"family": "Repetto", "given": "Gabriela M", "initials": "GM"}, {"family": "Jouret", "given": "Guillaume", "initials": "G"}, {"family": "Kentros", "given": "Catherine", "initials": "C"}, {"family": "Ganapathi", "given": "Mythily", "initials": "M"}, {"family": "Chung", "given": "Wendy K", "initials": "WK"}, {"family": "May", "given": "Halie", "initials": "H"}, {"family": "Hiatt", "given": "Susan M", "initials": "SM"}, {"family": "Kelley", "given": "Whitley V", "initials": "WV"}, {"family": "F\u00f6rster", "given": "Alisa", "initials": "A"}, {"family": "Olfe", "given": "Lisa", "initials": "L"}, {"family": "Shillington", "given": "Amelle", "initials": "A"}, {"family": "Dauriat", "given": "Benjamin", "initials": "B"}, {"family": "Mercier", "given": "Sandra", "initials": "S"}, {"family": "Cogn\u00e9", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-5503-6292", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f0dea78166143c38c60c12206444207.json"}}, {"family": "Engel", "given": "Camille", "initials": "C"}, {"family": "Dahlen", "given": "Eric", "initials": "E"}, {"family": "Rosenberger", "given": "Georg", "initials": "G"}, {"family": "Sauvigny", "given": "Thomas", "initials": "T"}, {"family": "Abdallah", "given": "Hamza Hadj", "initials": "HH"}, {"family": "Courtin", "given": "Thomas", "initials": "T"}, {"family": "Stray-Pedersen", "given": "Asbj\u00f8rg", "initials": "A"}, {"family": "Bernat", "given": "John A", "initials": "JA"}, {"family": "Paolillo", "given": "Vitoria K", "initials": "VK"}, {"family": "Viso", "given": "Florencia Del", "initials": "FD"}, {"family": "Alaimo", "given": "Joseph T", "initials": "JT"}, {"family": "Thiffault", "given": "Isabelle", "initials": "I"}, {"family": "Farrow", "given": "Emily G", "initials": "EG"}, {"family": "Cohen", "given": "Ana S A", "initials": "ASA"}, {"family": "Weis", "given": "Serge", "initials": "S"}, {"family": "Duba", "given": "Hans-Christoph", "initials": "HC"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Falk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1634-8610", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b708dfb7f0548589bdee53d6e6b536e.json"}}, {"family": "Weis", "given": "Denisa", "initials": "D"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2025-12-30", "journal": {"title": "Res Sq", "issn": "2693-5015", "issn-l": null}, "abstract": "Heterozygous variants in CTNND2, encoding the brain-specific protein \u03b4-catenin, are associated with a broad spectrum of neurodevelopmental disorders, including dyslexia, attention deficit hyperactivity disorder, intellectual disability, and autism. Despite its clinical significance, the full phenotypic spectrum of CTNND2-associated disorders and the neurodevelopmental role of \u03b4-catenin, a key component of the cadherin-catenin cell adhesion complex, remain poorly defined.\n\nThrough international collaboration, we assembled the phenotypic and molecular information for 57 individuals, 42 previously unpublished, carrying heterozygous CTNND2 variants. All individuals were evaluated by local clinicians, and the variants were identified through exome or genome sequencing, clinical microarray, or karyotyping. To investigate the effects of \u03b4-catenin loss on early neurogenesis, we performed neural differentiation and transcriptomic profiling in three patient-derived neural stem cell lines and three CRISPR-Cas9-generated CTNND2 knockout lines. In one patient-derived line, we further analyzed cerebral organoid development and performed pathway modulation to assess phenotypic rescue.\n\nThe 41 CTNND2 variants included 12 previously reported loss-of-function- and one missense variant, and 28 novel variants comprising 10 missense and 18 predicted loss-of-function changes. Eight of the novel variants occurred de novo, and 12 were inherited from a parent with a neurodevelopmental phenotype. The most common clinical features were developmental delay (90%), intellectual disability (74%), and behavioral abnormalities (79%). Functional studies revealed impaired early neurogenesis in one patient-derived line, characterized by aberrant neural rosette formation. Transcriptome analysis showed dysregulated WNT signaling, and partial rescue of these defects was achieved by modulating the WNT pathway, highlighting \u03b4-catenin's role in early neural development.\n\nThis study defines the clinical symptoms of CTNND2-related neurodevelopmental disorders, outlining a recognizable yet variable phenotype that overlaps with other forms of intellectual disability and autism. Our findings provide preliminary evidence of genotype-phenotype correlations and highlight \u03b4-catenin's critical role in modulating WNT signaling during early neural development. These insights advance our understanding of CTNND2-associated disorders and support the importance of mechanistic studies to inform personalized diagnostics and therapies.", "doi": "10.21203/rs.3.rs-8224288/v1", "pmid": "41502569", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12772691"}, {"db": "pii", "key": "rs.3.rs-8224288"}], "notes": [], "created": "2026-01-13T10:29:57.427Z", "modified": "2026-01-25T08:39:21.323Z"}, {"entity": "publication", "iuid": "96f3d22ca79f4d718217e5f0af6a3865", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96f3d22ca79f4d718217e5f0af6a3865.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96f3d22ca79f4d718217e5f0af6a3865"}}, "title": "A north-south hemispheric migratory divide in the butterfly Vanessa cardui.", "authors": [{"family": "Garc\u00eda-Berro", "given": "Aurora", "initials": "A", "orcid": "0000-0002-2419-2516", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fdb6dd337074a89bf36e3b06458f042.json"}}, {"family": "Shipilina", "given": "Daria", "initials": "D", "orcid": "0000-0002-1145-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a7bdbc6654826ab7f06cf3938b5c3.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Suchan", "given": "Tomasz", "initials": "T", "orcid": "0000-0002-0811-8754", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b3c7df2089e4060a8ad426a5570654c.json"}}, {"family": "Palah\u00ed", "given": "Aleix", "initials": "A", "orcid": "0000-0002-1373-4949", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee01ff0f2c3746939dbf64a7fca04439.json"}}, {"family": "Collins", "given": "Steve C", "initials": "SC"}, {"family": "Martins", "given": "Dino J", "initials": "DJ"}, {"family": "Pierce", "given": "Naomi E", "initials": "NE", "orcid": "0000-0003-3366-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c1e6c94b58244ada2442e0541168252.json"}}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Talavera", "given": "Gerard", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}], "type": "journal article", "published": "2025-12-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "11341", "issn-l": "2041-1723"}, "abstract": "Reversed seasonality and distinct navigation cues in the Earth's two hemispheres may shape the evolution of migratory behaviour in animals. Migratory divides-contact zones where populations have evolved alternative migratory strategies-are well-documented in birds and typically occur longitudinally. We hypothesise that insect migratory divides are less likely to emerge longitudinally, but may exist latitudinally, driven by hemisphere-specific sensory adaptations that lead to spatial and temporal isolation. Here, we examine this hypothesis in the cosmopolitan painted lady butterfly (Vanessa cardui), whose Southern Hemisphere dynamics remain unexplored. Investigating the genomes of 300 individuals across Africa and Europe, we identify a 9 Mb chromosomal inversion on chromosome 8, which exhibits strong haplotype structure aligned with hemispheric origin, with a few potential heterozygotes near the equator. The inversion harbours 336 genes, including several directly relevant to migration. Notably, one inversion breakpoint intersects the gene encoding the GABA-B receptor, which responds to the neuropeptide \u03b3-aminobutyric acid (GABA), crucial for insect navigation. Our findings provide genomic evidence of a migratory divide in insects and highlight the role of inverted seasonality in the two hemispheres and genomic rearrangements as isolating barriers for highly mobile species.", "doi": "10.1038/s41467-025-67185-7", "pmid": "41469375", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12753642"}, {"db": "pii", "key": "10.1038/s41467-025-67185-7"}], "notes": [], "created": "2026-01-07T11:02:45.340Z", "modified": "2026-01-07T11:02:45.758Z"}, {"entity": "publication", "iuid": "8f8dca39f51246e399479b7a8829b62d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f8dca39f51246e399479b7a8829b62d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f8dca39f51246e399479b7a8829b62d"}}, "title": "Plasma protein profiling predicts cancer in patients with non-specific symptoms.", "authors": [{"family": "Wannberg", "given": "Fredrika", "initials": "F", "orcid": "0009-0001-8505-3122", "researcher": {"href": "https://publications.scilifelab.se/researcher/15572474779e45a7a64e439cca882a73.json"}}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Qvick", "given": "Alvida", "initials": "A", "orcid": "0000-0001-6688-947X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4be159eaa724d22982b7b1e24e9ba79.json"}}, {"family": "Pongracz", "given": "Tamas", "initials": "T", "orcid": "0000-0002-8089-4352", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bdf2f1b85954a1b872b59339838fa57.json"}}, {"family": "Aguilera", "given": "Katherina", "initials": "K"}, {"family": "Adolfsson", "given": "Emma", "initials": "E", "orcid": "0000-0002-7954-0696", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c790fe832ec4bf68608578c0c9d4552.json"}}, {"family": "Essehorn", "given": "Louise", "initials": "L"}, {"family": "Gordon", "given": "Max", "initials": "M", "orcid": "0000-0002-8080-5815", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3f1f5ca4e2a4f17bf9454cd7b5a259d.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Helenius", "given": "Gisela", "initials": "G"}, {"family": "Hjalmar", "given": "Viktoria", "initials": "V"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Rosell", "given": "Axel", "initials": "A", "orcid": "0000-0001-6280-0562", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcddaba7a96a406b994756ab71427baf.json"}}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C", "orcid": "0009-0008-9471-3234", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a1c3368c5314543bb4b2204f2938159.json"}}], "type": "journal article", "published": "2025-12-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "pages": "151", "issn-l": "2041-1723"}, "abstract": "Cancer detection is challenging, especially in patients with diffuse symptoms that overlap with non-malignant conditions. Here we show that plasma protein profiling can identify cancer among patients with non-specific symptoms. Using proximity extension assay-based proteomics of 1463 plasma proteins from 456 patients presenting with non-specific symptoms sampled prior to cancer diagnostic work-up and diagnosis, we identify 29 proteins associated with new cancer diagnoses. We develop a model able to stratify 160 cancer cases and 296 non-cancer cases with an area under the curve of 0.80, maintaining performance (0.82) in an independent replication cohort of 238 patients. The model also distinguishes cancer from autoimmune, inflammatory and infectious diseases. Designed as a triage tool, our model based on a blood test could help prioritize patients at higher cancer risk for rapid and highly sensitive diagnostic modalities such as positron emission tomography-computed tomography. These findings emphasize the potential of blood proteome profiling to support timely diagnosis and transform clinical medicine.", "doi": "10.1038/s41467-025-67688-3", "pmid": "41457066", "labels": {"Affinity Proteomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12774938"}, {"db": "pii", "key": "10.1038/s41467-025-67688-3"}], "notes": [], "created": "2026-01-09T16:47:14.250Z", "modified": "2026-03-05T09:10:04.784Z"}, {"entity": "publication", "iuid": "9f5bb0bc406e4e16ab66fb56a98eb3b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f5bb0bc406e4e16ab66fb56a98eb3b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f5bb0bc406e4e16ab66fb56a98eb3b5"}}, "title": "Mass spectrometric profiling reveals alterations in N-Glycans and O-Glycans in Tay-Sachs disease under Autophagy-Induced conditions.", "authors": [{"family": "Can", "given": "Melike", "initials": "M"}, {"family": "Basirli", "given": "Hande", "initials": "H"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Bojar", "given": "Daniel", "initials": "D"}, {"family": "Seyrantepe", "given": "Volkan", "initials": "V", "orcid": "0000-0002-0243-5011", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e3a38ecedab487a86e6a9fcf6c04f4f.json"}}], "type": "journal article", "published": "2025-12-29", "journal": {"title": "Glycoconj J", "issn": "1573-4986", "volume": "43", "issue": "1", "pages": "3", "issn-l": null}, "abstract": "Tay-Sachs disease is a rare neurodegenerative disorder caused by mutations in the HEXA gene. The HEXA gene encodes the \u03b1-subunit of the enzyme \u03b2-hexosaminidase A, which degrades GM2 ganglioside. Previously, we identified impaired autophagy in the brains of a mouse model of Tay-Sachs disease, which exhibited neuropathological and clinical abnormalities. Moreover, we demonstrated autophagosome clearance in Tay-Sachs cells under lithium-induced conditions. Here, we further aimed to evaluate N- and O-glycan changes in these cells and examine whether glycan alterations are linked to ER stress. The profiles of N- and O-glycans were analyzed using LC-MS/MS in fibroblasts and neuroglial cells from 5-month-old Hexa-/-Neu3-/- mice and neuroglial cells from Tay-Sachs patients under lithium induction and nutrient deprivation. The expression levels of ER stress-related markers were assessed using qRT-PCR and Western blot analyses. We demonstrated higher levels of high mannose and lower levels of complex types of N-glycans, along with increased O-glycan levels in Tay-Sachs cells. Compared to control groups, we observed upregulated expression of endoplasmic reticulum (ER) stress-related markers, CHOP and ATF-6, in Tay-Sachs cells. Our study demonstrated that autophagy induction causes the degradation of accumulated high-mannose N-glycans and O-glycans, which is associated with the downregulation of ER stress-related genes in Tay-Sachs cells. Our study is the first to show this phenomenon in Tay-Sachs cells and suggests the presence of ER stress-mediated autophagy. Therefore, targeting glycans through autophagy induction could offer therapeutic benefits to patients with Tay-Sachs disease in future studies.", "doi": "10.1007/s10719-025-10203-z", "pmid": "41460292", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s10719-025-10203-z"}], "notes": [], "created": "2026-01-27T13:23:35.091Z", "modified": "2026-01-27T13:23:35.202Z"}, {"entity": "publication", "iuid": "32a8f043a851424b897c3a1e3ae8c497", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32a8f043a851424b897c3a1e3ae8c497.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32a8f043a851424b897c3a1e3ae8c497"}}, "title": "Exploratory study linking plasma proteomics to cardiotoxicity in Hodgkin lymphoma.", "authors": [{"family": "Ulfstedt", "given": "Johan Mattsson", "initials": "JM"}, {"family": "Risebro", "given": "Ragnhild", "initials": "R"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Christersson", "given": "Christina", "initials": "C"}, {"family": "M\u00f6rth", "given": "Charlott", "initials": "C"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Robelius", "given": "Anna", "initials": "A"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Molin", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-12-26", "journal": {"title": "Cardiooncology", "issn": "2057-3804", "volume": "12", "issue": "1", "pages": "13", "issn-l": null}, "abstract": "Cardiovascular toxicity is a well-known complication of chemotherapy, especially doxorubicin (DXR), and irradiation of the mediastinum for classical Hodgkin lymphoma (cHL). Due to the excellent prognosis in cHL, the mortality rate in late toxicity historically exceeds that of relapse of lymphoma. This highlights the need for strategies to minimize toxicity.Our aim was to characterize the prevalence of cardiovascular diseases (CVDs) in our cohort of cHL patients treated with DXR with or without radiotherapy according to standard practice and to identify any plasma protein associations with preexisting or emerging CVD posttreatment.\n\nWe analyzed 182 different proteins in plasma samples from 56 cHL patients and 60 controls using Olink multiplex protein panels Oncology II and Cardiovascular III. The analysis was supplemented with separate analyses of N-terminal pro-brain natriuretic peptide (NTpro-BNP), troponin I and C-reactive protein (CRP). The patient samples were prospectively collected prior to, during and after treatment.\n\nOur analysis revealed a statistically significant association between the compound endpoint of heart failure and ischemic heart disease and the protein biomarkers cysteine rich protein 61 (CYR61), glycoprotein nonmetastatic melanoma protein B (GPNMB) and activated leukocyte cell adhesion molecule (ALCAM) in samples collected after treatment for cHL.\n\nThis exploratory study identified three new biomarkers reflecting different biological processes associated with CVD in patients treated for cHL. Adding biomarkers to risk prediction in this population has the potential to identify patients with a high risk of cardiovascular events who need focused follow-up.\n\nThe online version contains supplementary material available at 10.1186/s40959-025-00426-2.", "doi": "10.1186/s40959-025-00426-2", "pmid": "41449437", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12853685"}, {"db": "pii", "key": "10.1186/s40959-025-00426-2"}], "notes": [], "created": "2026-02-10T09:56:00.336Z", "modified": "2026-02-10T09:56:00.355Z"}, {"entity": "publication", "iuid": "eede36ef32fd4a6aac7dd2a2b9baa667", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eede36ef32fd4a6aac7dd2a2b9baa667.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eede36ef32fd4a6aac7dd2a2b9baa667"}}, "title": "The splicing genes SmEa and SmEb regulate plant development during vegetative growth in poplar.", "authors": [{"family": "Goretti", "given": "Daniela", "initials": "D", "orcid": "0000-0003-3996-0204", "researcher": {"href": "https://publications.scilifelab.se/researcher/cabe11cdf08446bda52aa5d2b62ea239.json"}}, {"family": "Collani", "given": "Silvio", "initials": "S", "orcid": "0000-0002-9603-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/0896530185b54e16824cd26658ccdfc8.json"}}, {"family": "Marcon", "given": "Alice", "initials": "A", "orcid": "0009-0006-9957-6115", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fb0b7d67e464160bda5a6acfdf96d95.json"}}, {"family": "Nilsson", "given": "Ove", "initials": "O", "orcid": "0000-0002-1033-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/729146afe5e24eb0a6f107db10e95e01.json"}}, {"family": "Schmid", "given": "Markus", "initials": "M", "orcid": "0000-0002-0068-2967", "researcher": {"href": "https://publications.scilifelab.se/researcher/8705d242aa8f4f92b930c2cdc23254f0.json"}}], "type": "journal article", "published": "2025-12-23", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "25", "issue": "1", "pages": "1723", "issn-l": "1471-2229"}, "abstract": "Spliceosomes are large evolutionary conserved ribonucleoprotein complexes containing at their core heptameric rings of Sm (or LSm) proteins and U-rich snRNAs. The role of Sm proteins in animal development is well established, and recent research has begun to link mutations in these genes to growth defects in plants. One of the most studied Sm genes is SmE1/PCP, mutants of which display a temperature-dependent phenotype in Arabidopsis thaliana.\n\nThis study provides a first glimpse into the function of a core splicing protein in the regulation of growth in a perennial species. Phylogenetic analysis identified two paralogous SmE genes in poplar, named SmEa and SmEb, that encode identical proteins and are orthologs of SmEs from Arabidopsis, as suggested by Y2H and in vivo experiments. CRISPR/Cas9 mutagenesis in hybrid aspen identified a role for SmEs in development in plants grown in an environment simulating seasonal photoperiod and temperature changes. Unlike in Arabidopsis, low temperatures had no or only a very minor effect on the development of sme mutants in aspen.\n\nWe identified specific aspects of SmE in poplar, highlighting the importance of examining the physiological and evolutionary differences that define this gene family in woody compared to herbaceous plants.\n\nThe online version contains supplementary material available at 10.1186/s12870-025-07676-3.", "doi": "10.1186/s12870-025-07676-3", "pmid": "41436944", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12729064"}, {"db": "pii", "key": "10.1186/s12870-025-07676-3"}], "notes": [], "created": "2026-01-07T11:04:57.648Z", "modified": "2026-01-07T11:04:57.822Z"}, {"entity": "publication", "iuid": "5717b69dac574afaa6ebf045b297c89b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5717b69dac574afaa6ebf045b297c89b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5717b69dac574afaa6ebf045b297c89b"}}, "title": "Comparative assessment of SNP genotyping assays for challenging forensic samples utilizing ancient DNA methods", "authors": [{"family": "Staadig", "given": "Adam", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Sidstedt", "given": "Maja", "initials": "M"}, {"family": "Kling", "given": "Daniel", "initials": "D"}, {"family": "Fagerholm", "given": "Siri Aili", "initials": "SA"}, {"family": "Ansell", "given": "Ricky", "initials": "R"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Tillmar", "given": "Andreas", "initials": "A"}], "type": "journal-article", "published": "2025-12-23", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "26", "issue": "1", "pages": "433", "issn-l": "1474-7596"}, "abstract": "The fields of ancient DNA research and forensic genetics share both methodological similarities and common challenges, particularly in the analysis of degraded DNA. Leveraging these overlaps, this study evaluates three single nucleotide polymorphisms (SNP)-based genotyping assays for analyzing challenging forensic samples: the FORCE-QIAseq SNP panel, the Twist ancient DNA hybridization capture panel, and whole-genome sequencing.\n\nWe analyze twenty skeletal bone and tooth samples from authentic missing person cases, where almost all samples are severely degraded and contain exceptionally low amounts of endogenous DNA, reflected by both reduced quantifiable DNA concentrations and lower proportions of human DNA reads than typically obtained from high-quality forensic samples. Despite these challenging sample characteristics, both the FORCE and Twist assays successfully generate a substantial number of genotypes across many samples, while whole-genome sequencing yields fewer SNP calls. However, techniques like probabilistic genotyping, increase sequencing depth or genotype imputation can further enhance the utility of WGS for forensic use.\n\nThis study highlights the effectiveness of incorporating ancient DNA methods into forensic genetics for the analysis of degraded samples. The findings are broadly applicable to both forensic and ancient DNA research disciplines, offering valuable insights into assay selection based on sample condition and investigative goals.", "doi": "10.1186/s13059-025-03912-z", "pmid": "41430704", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12723910"}, {"db": "pii", "key": "10.1186/s13059-025-03912-z"}], "notes": [], "created": "2026-01-07T11:00:22.743Z", "modified": "2026-01-09T07:55:19.944Z"}, {"entity": "publication", "iuid": "c70282615a154262b20d3bfd207d2419", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c70282615a154262b20d3bfd207d2419.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c70282615a154262b20d3bfd207d2419"}}, "title": "ZEB1, a novel junctional adhesion molecule A regulator, impacts sensitivity of pancreatic cancer-associated fibroblasts to reovirus.", "authors": [{"family": "Dam", "given": "Nicole", "initials": "N"}, {"family": "Harryvan", "given": "Tom J", "initials": "TJ"}, {"family": "Dang", "given": "Hao", "initials": "H"}, {"family": "Ioannidis", "given": "Gavriil", "initials": "G"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B"}, {"family": "Hawinkels", "given": "Lukas J A C", "initials": "LJAC"}, {"family": "Kemp", "given": "Vera", "initials": "V"}], "type": "journal article", "published": "2025-12-18", "journal": {"title": "Mol Ther Oncol", "issn": "2950-3299", "issn-l": null, "volume": "33", "issue": "4", "pages": "201071"}, "abstract": "Oncolytic virus (OV) therapy is a promising treatment for various tumors. However, in pancreatic ductal adenocarcinoma (PDAC), the high abundance of cancer-associated fibroblasts (CAFs) can limit OV therapy efficacy by impairing viral spread and anti-tumor immunity. We have previously shown that oncolytic reovirus infection of CAFs depends on the expression of the reovirus entry receptor junctional adhesion molecule A (JAM-A), which is not or lowly expressed in most PDAC CAFs. We propose that increasing JAM-A expression on CAFs will boost viral spread in a tumor. However, there are currently no known regulators of JAM-A expression. Therefore, we performed a genome-wide CRISPR-Cas9 knockout screen to identify novel regulators of JAM-A expression. Ablation of the top negative regulator, zinc finger E-box binding homeobox 1 (ZEB1), in pancreatic fibroblasts led to strong JAM-A upregulation. We show that ZEB1 directly regulates JAM-A expression by binding to the enhancer-box (E-box) regions located within the JAM-A promoter. Importantly, ZEB1 ablation increased the sensitivity of fibroblasts to reovirus infection and subsequent cell death. Our work provides a novel overview of genes regulating JAM-A expression and provides a rational approach of combining ZEB1 inhibition with reovirus therapy to target both CAFs and tumor cells in stroma-rich tumors such as PDAC.", "doi": "10.1016/j.omton.2025.201071", "pmid": "41244268", "labels": {"CRISPR Functional Genomics": "Service", "Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12617759"}, {"db": "pii", "key": "S2950-3299(25)00140-7"}], "notes": [], "created": "2025-11-25T08:36:19.443Z", "modified": "2025-12-19T13:03:44.572Z"}, {"entity": "publication", "iuid": "cc266f15720044ff97f0c84859c74dbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc266f15720044ff97f0c84859c74dbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc266f15720044ff97f0c84859c74dbf"}}, "title": "Airborne eDNA captures three decades of ecosystem biodiversity.", "authors": [{"family": "Sullivan", "given": "Alexis R", "initials": "AR"}, {"family": "Karlsson", "given": "Edvin", "initials": "E"}, {"family": "Svensson", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4476-9255", "researcher": {"href": "https://publications.scilifelab.se/researcher/75bc51f60237478abec1fb2969abc873.json"}}, {"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-8524-778X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75f852c1e5144ff3acda53bcec520001.json"}}, {"family": "Villegas", "given": "Jose Antonio", "initials": "JA"}, {"family": "Mikko", "given": "Amanda", "initials": "A", "orcid": "0009-0002-7701-8180", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bca394a219142d68195e45f756dd686.json"}}, {"family": "Bellieny", "given": "Daniel", "initials": "D"}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB", "orcid": "0000-0002-3178-523X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a19c155f873b4ec194a0ba07d9bbff92.json"}}, {"family": "Johansson", "given": "Anna-Mia", "initials": "AM"}, {"family": "Grahn", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-8936-3101", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5806ae054ec4cf1b67ee151bfd95b2f.json"}}, {"family": "Sundell", "given": "David", "initials": "D"}, {"family": "Norman", "given": "Anita", "initials": "A", "orcid": "0000-0002-9499-758X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1966d9c4e0f4c2c89702c8ef319264c.json"}}, {"family": "Esseen", "given": "Per-Anders", "initials": "PA"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Singh", "given": "Navinder J", "initials": "NJ", "orcid": "0000-0002-5131-0004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bae3b76bb4a4f95a77e41cd929637ff.json"}}, {"family": "Brodin", "given": "Tomas", "initials": "T", "orcid": "0000-0003-1086-7567", "researcher": {"href": "https://publications.scilifelab.se/researcher/8140649bc5e140369d031c78fc416ae2.json"}}, {"family": "Forsman", "given": "Mats", "initials": "M", "orcid": "0000-0002-4466-5325", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52b5a759a3e452b80728241c50c76dd.json"}}, {"family": "Stenberg", "given": "Per", "initials": "P", "orcid": "0000-0003-4738-4788", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e9b9949cf994f6c93d60261eb530d1b.json"}}], "type": "journal article", "published": "2025-12-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "11281", "issn-l": "2041-1723"}, "abstract": "Biodiversity loss threatens ecosystems and human well-being, making accurate, large-scale monitoring crucial. Environmental DNA (eDNA) has enabled species detection from substrates such as water, without the need for direct observation. Lately, airborne eDNA has been showing promise for tracking organisms from insects to mammals in terrestrial ecosystems. Conventional biodiversity assessments are often labor-intensive and limited in scope, leaving gaps in our understanding of ecosystem response to environmental change. Here, we demonstrate that airborne eDNA can detect organisms across the tree of life, quantify changes in abundance congruent with traditional monitoring, and reveal land-use induced regional decline of diversity in a northern boreal ecosystem over more than three decades. By analyzing 34 years of archived aerosol filters, we reconstruct weekly temporal relative abundance data for more than 2700 genera using non-targeted methods. This study provides unified, ecosystem-scale biodiversity surveillance spanning multiple decades, with data collected at weekly intervals on both the individual species and community level. Previously, large scale analyses of ecosystem changes, targeting all types of organisms, has been prohibitively expensive and difficult to attempt. Here, we present a way of holistically doing this type of analysis in a single framework.", "doi": "10.1038/s41467-025-67676-7", "pmid": "41413054", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12717267"}, {"db": "pii", "key": "10.1038/s41467-025-67676-7"}], "notes": [], "created": "2026-03-25T07:37:10.622Z", "modified": "2026-03-25T07:37:11.494Z"}, {"entity": "publication", "iuid": "2f040ec2230c4d4294c4dd7d17bf0d45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f040ec2230c4d4294c4dd7d17bf0d45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f040ec2230c4d4294c4dd7d17bf0d45"}}, "title": "Necessity of individual VDJ-databases for annotating antibody heavy chain characteristics in non-human primates.", "authors": [{"family": "Aartse", "given": "Aafke", "initials": "A"}, {"family": "Bakx", "given": "Jacco G J", "initials": "JGJ"}, {"family": "Mortier", "given": "Daniella", "initials": "D"}, {"family": "Hofman", "given": "Sam", "initials": "S"}, {"family": "Mooij", "given": "Petra", "initials": "P"}, {"family": "Claireaux", "given": "Mathieu", "initials": "M"}, {"family": "Eggink", "given": "Dirk", "initials": "D"}, {"family": "Bogers", "given": "Willy M", "initials": "WM"}, {"family": "Remarque", "given": "Edmond J", "initials": "EJ"}, {"family": "Corcoran", "given": "Martin M", "initials": "MM"}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB"}, {"family": "Bontrop", "given": "Ronald E", "initials": "RE"}, {"family": "van Gils", "given": "Marit J", "initials": "MJ"}, {"family": "Koopman", "given": "Gerrit", "initials": "G"}], "type": "journal article", "published": "2025-12-15", "journal": {"title": "Immunogenetics", "issn": "1432-1211", "volume": "77", "issue": "1", "pages": "35", "issn-l": "0093-7711"}, "abstract": "Non-human primates are important for preclinical vaccine evaluation. In depth characterization of the antibody response requires representative immunoglobulin (IG) germline gene databases for correct gene and allele assignments and assessment of affinity maturation of antigen-specific antibodies. Current IG-reference databases do not cover the genetic diversity observed in frequently used macaque species and it is unclear to what extent closely related animals express shared alleles at similar levels. Here, IG-germline alleles of sixteen cynomolgus macaques (CynoSet), some of which were related, were characterized and compared with previously described Mauritian and Indonesian origin cynomolgus macaque datasets. Although the CynoSet showed more overlap with the Mauritian origin dataset, compared to an Indonesian origin dataset, there were clear differences in allelic expression patterns, independent of family relationship. Calculation of somatic hypermutation levels in post-infection influenza hemagglutinin-specific B cells demonstrated the need for individualized IG-genotyping for accurate evaluation of the antigen-specific B cell response.", "doi": "10.1007/s00251-025-01392-w", "pmid": "41392054", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12702801"}, {"db": "pii", "key": "10.1007/s00251-025-01392-w"}], "notes": [], "created": "2026-01-22T13:22:00.965Z", "modified": "2026-01-22T13:22:00.976Z"}, {"entity": "publication", "iuid": "84576d4b89174b05be4e264f7d9736a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84576d4b89174b05be4e264f7d9736a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84576d4b89174b05be4e264f7d9736a6"}}, "title": "Accessing the proteome of extracellular vesicles via rapid acoustic isolation of a minute human blood plasma sample.", "authors": [{"family": "Havers", "given": "Megan", "initials": "M"}, {"family": "Scott", "given": "Aaron M", "initials": "AM"}, {"family": "Ortenl\u00f6f", "given": "Niklas", "initials": "N"}, {"family": "Welinder", "given": "Charlotte", "initials": "C"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S"}, {"family": "Baasch", "given": "Thierry", "initials": "T"}, {"family": "Evander", "given": "Mikael", "initials": "M"}, {"family": "Lenshof", "given": "Andreas", "initials": "A"}, {"family": "Gram", "given": "Magnus", "initials": "M"}, {"family": "Laurell", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2025-12-15", "journal": {"title": "Anal. Chim. Acta", "issn": "1873-4324", "volume": "1379", "pages": "344661", "issn-l": "0003-2670"}, "abstract": "Despite substantial progress in the field of mass spectrometry, there remain barriers to measuring the extracellular vesicles (EVs) proteome in blood plasma. Recent work has shown that isolating EVs can make it possible to detect proteins that have low abundance in plasma. Commonly used EV isolation methods either require large sample volumes and long ultracentrifugation times, or else result in population bias via targeted isolation. There is a great need for fast and easy methods to isolate EVs from small volumes of plasma, <10 \u03bcL, enabling biomarker discovery, e.g. in biobanked samples, where mass spectrometry can play an important role.\n\nWe unveil the extracellular vesicle proteome by using seed particle enhanced acoustic trapping to purify EVs from minute blood plasma samples (8 \u03bcL) in 6 min per sample. The differential mass spectrometry results find proteins which are significantly enriched (FDR-adjusted p-values<0.05) in acoustically trapped samples compared to raw (unprocessed) plasma, more than two thirds of those proteins have been associated with EVs previously. Additionally, we are able to increase the depth of analysis by detecting 51 low abundance proteins not detected in raw plasma, half of which are tagged with the gene ontology (GO) tag \"extracellular exosome\" (GO:0070062). Finally, we validate the novel use of neutrally charged silica seed particles paired with a washing flowrate of 200 \u03bcL/min, enabling the processing time to be halved and finding the same proteome as for tried-and-tested polystyrene seed particles with washing at 30 \u03bcL/min.\n\nOur microfluidics-based approach to EV isolation enables rapid processing of an individual minute blood plasma sample, demonstrating that personal proteomic information associated with EVs can be detected when acoustic trapping is used as a pre-processing step. By applying this technique to plasma from patient cohorts or mouse models, future studies may offer new insights into the role of EVs in the progression of diseases and reveal new diagnostic targets in the proteomic cargo of EVs.", "doi": "10.1016/j.aca.2025.344661", "pmid": "41167904", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-2670(25)01055-4"}], "notes": [], "created": "2025-11-28T10:03:49.935Z", "modified": "2025-11-28T10:03:49.946Z"}, {"entity": "publication", "iuid": "1550e72e72a54acd8a7b49fe497ce1b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1550e72e72a54acd8a7b49fe497ce1b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1550e72e72a54acd8a7b49fe497ce1b8"}}, "title": "Immune-stromal heterogeneity in breast cancer across diverse ancestries: impact on prognosis and treatment response.", "authors": [{"family": "Alamukii", "given": "Nanfizat A", "initials": "NA"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Raghavan", "given": "Sukanya", "initials": "S"}, {"family": "Ilio", "given": "Josefin", "initials": "J"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}], "type": "journal article", "published": "2025-12-12", "journal": {"title": "NPJ Breast Cancer", "issn": "2374-4677", "volume": "11", "issue": "1", "pages": "142", "issn-l": null}, "abstract": "Breast cancer immune phenotypes influence treatment response and clinical outcomes, yet their ancestry-specific variations remain underexplored. Here, we analyzed transcriptomic data from over 13,000 breast tumors across six ancestry groups to characterize immune-stromal profiles and their association with ancestry, biological features, treatment response, and survival outcomes. Expression patterns were validated by spatial proteomics and immunohistochemistry. K-means clustering consistently identified three immune phenotypes (Hot, Moderate, or Cold) that varied significantly by ancestry, age, molecular subtype, and prognosis. Logistic regression and ancestry-associated analyses revealed that while immune phenotypes were primarily driven by PAM50 subtype, age, and disease stage, notable ancestry-related differences persisted, with European ancestry generally exhibiting higher immune and stromal activity across breast cancer subtypes. Hot tumors, enriched in the Basal-like and HER2 subtypes, were associated with younger age, higher immune infiltration, and improved overall survival. African ancestry was linked to elevated immune scores and upregulation of BTLA-mediated T cell co-inhibition, suggesting sensitivity to immunotherapy. European and East Asian tumors showed stromal enrichment, particularly inflammatory and myofibroblastic cancer-associated fibroblasts, associated with poor prognosis. Core immune activation genes (e.g., CD3, CD2, and CXCL10) were conserved, while ancestry-specific signatures and chemokine signaling were identified. This study uncovers both shared and ancestry-specific immunogenomic features of breast cancer, highlighting the role of ancestry and other biological features in shaping the tumor immune microenvironment. These findings re-emphasize the need for population-informed approaches in breast cancer immunotherapy and biomarker development, to ensure equitable precision oncology strategies across global populations.", "doi": "10.1038/s41523-025-00881-1", "pmid": "41387728", "labels": {"Spatial Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12712059"}, {"db": "pii", "key": "10.1038/s41523-025-00881-1"}], "notes": [], "created": "2026-02-11T14:38:50.614Z", "modified": "2026-02-11T14:38:50.618Z"}, {"entity": "publication", "iuid": "c3f74b41f9be44d2ba332d6d5c86782a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3f74b41f9be44d2ba332d6d5c86782a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3f74b41f9be44d2ba332d6d5c86782a"}}, "title": "Copper ionophore elicits calpain-dependent paraptosis coincident with proteotoxic stress.", "authors": [{"family": "Sae-Fung", "given": "Apiwit", "initials": "A"}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2025-12-12", "journal": {"title": "Cell Commun Signal", "issn": "1478-811X", "volume": "24", "issue": "1", "pages": "47", "issn-l": null}, "abstract": "Copper is essential to all living organisms. However, too much copper is deleterious, and cellular copper content is therefore subject to tight control. Excess copper was recently found to perturb a set of metabolic enzymes in mitochondria, leading to the aggregation of these proteins and the demise of the cell. However, our understanding of the mechanism of copper-dependent cell death remains incomplete. Here, we report that copper ionophore (elesclomol)-induced cell death is calpain-dependent, featuring dilation of the endoplasmic reticulum along with perinuclear clustering of mitochondria. Moreover, elesclomol evoked proteotoxic stress, manifested as a disruption of ubiquitin and proteasome homeostasis, coupled with a conserved heat shock response. Overall, these results have shown that elesclomol promotes calpain-dependent paraptosis with the involvement of both mitochondrial and extramitochondrial compartments of the cell.", "doi": "10.1186/s12964-025-02558-5", "pmid": "41388416", "labels": {"Chemical Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12837948"}, {"db": "pii", "key": "10.1186/s12964-025-02558-5"}], "notes": [], "created": "2026-01-31T17:47:09.857Z", "modified": "2026-01-31T17:47:09.861Z"}, {"entity": "publication", "iuid": "bdaeb5bc238e46fcbec53a574a0e9f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdaeb5bc238e46fcbec53a574a0e9f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdaeb5bc238e46fcbec53a574a0e9f89"}}, "title": "A morphology-based machine learning model for scoring epithelial-mesenchymal plasticity using organelle dynamics.", "authors": [{"family": "Slager", "given": "Justin", "initials": "J", "orcid": "0009-0005-0481-8154", "researcher": {"href": "https://publications.scilifelab.se/researcher/b628fcc675354b86989c79e30cedc71a.json"}}, {"family": "Gatto", "given": "Francesca", "initials": "F"}, {"family": "Frey", "given": "Benjamin", "initials": "B", "orcid": "0009-0004-7649-8340", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e352dfc1f814b2abf8d38cde784557c.json"}}, {"family": "Shi", "given": "Wenyang", "initials": "W"}, {"family": "Porebski", "given": "Bartlomiej", "initials": "B"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Parniewska", "given": "Malgorzata Maria", "initials": "MM"}, {"family": "Fuxe", "given": "Jonas", "initials": "J", "orcid": "0000-0003-4576-9377", "researcher": {"href": "https://publications.scilifelab.se/researcher/df87648f16bc45b9999eb5c0da269a4e.json"}}], "type": "journal article", "published": "2025-12-10", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642"}, "abstract": "Re-activation of epithelial-mesenchymal transition (EMT), a key developmental process, contributes to cancer progression and therapy resistance. Modulating EMT could be attractive as a therapeutic strategy, but there is a lack of methods that can quantify EMT states, including hybrid phenotypes. Here, we developed a morphology-based machine learning approach to score EMT based on changes in organelle dynamics. Using the Cell Painting assay and high-throughput microscopy, we trained a histogram gradient boosting classifier to identify stage-specific organelle remodeling during a time course of TGF-\u03b21-induced EMT in mammary epithelial cells. The model achieved robust performance across datasets, capturing EMT kinetics, hybrid states, and reversal by mesenchymal-epithelial transition (MET). Importantly, the method accurately scored EMT in human breast cancer cells and lung cancer cells undergoing hypoxia-induced EMT, demonstrating cross-species, cross-inducer, and cross-cancer applicability. The results establish organelle morphology profiling as a scalable framework for quantifying epithelial-mesenchymal plasticity. The method offers a platform for drug discovery and identifying strategies to overcome EMT-associated resistance.", "doi": "10.1038/s42003-025-09326-8", "pmid": "41372576", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-025-09326-8"}], "notes": [], "created": "2025-12-11T16:08:39.796Z", "modified": "2025-12-11T16:08:40.050Z"}, {"entity": "publication", "iuid": "fdb2a58a717e4bbca202566f67f5792b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdb2a58a717e4bbca202566f67f5792b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdb2a58a717e4bbca202566f67f5792b"}}, "title": "A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7a545a218455fa134b3dd8bb1b895.json"}}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ"}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications.scilifelab.se/researcher/409de77af489419db6d2b599b590d02f.json"}}], "type": "journal-article", "published": "2025-12-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "pages": "41", "issn-l": "1471-2164"}, "abstract": "Long-term persistent symbiotic associations may result in co-speciation and can be inferred if species trees of hosts and symbionts are congruent in topology and divergence times. Co-speciation has been seen to occur relatively frequently in obligate associations, but is less common in parasitic or facultative ones, mainly due to the difference in horizontal transmission rates. The long-term vertical inheritance and close host association of obligate endosymbionts also generally result in smaller genomes than in facultative endosymbionts. Here, we investigate co-speciation and genome reduction using highly similar strains of the endosymbiont Wolbachia infecting Drosophila species from the willistoni and saltans groups, where only one strain, wPau, infecting D. paulistorum, is obligate.\n\nWe sequenced the Wolbachia genomes from five species of the willistoni and saltans groups and constructed phylogenies. Topological congruence was found between these Wolbachia strains and the nuclear DNA of their hosts, except for wPau and D. paulistorum, but full topological congruence was observed between Wolbachia and the host mitochondrial DNA. However, assuming temporal congruence, we estimated extremely low evolutionary rates in Wolbachia of 10- 10-10- 11 changes/site/year. Additionally, the obligate wPau strain was found to have a larger genome than closely related facultative strains, mainly due to an ongoing expansion of an IS4 element. Furthermore, wPau has lost a large proportion of its prophage WO genes, but the cif genes, known to be involved in the CI phenotype, are intact. Finally, nine of the eleven genes from the prophage WO-associated Undecim cluster are uniquely duplicated.\n\nThe congruent topologies between Wolbachia and their willistoni and saltans group hosts indicate co-speciation. However, the high similarity between Wolbachia strains, which results in low mutation rate estimates, challenges this interpretation. Contrary to the expectations of the genome reduction theory, we observed an increase in genome size in the obligate wPau strain, potentially driven by a decreased population size. Finally, the duplication of the Undecim cluster, despite a major loss of other prophage-associated genes, suggests that the genes in the Undecim cluster are under strong selection and potentially play a role in the obligate association between wPau and their D. paulistorum hosts.", "doi": "10.1186/s12864-025-12340-z", "pmid": "41366724", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12801941"}, {"db": "pii", "key": "10.1186/s12864-025-12340-z"}], "notes": [], "created": "2026-01-19T08:58:08.199Z", "modified": "2026-01-20T07:53:24.298Z"}, {"entity": "publication", "iuid": "310db69525be40ed9f4e569c00320568", "links": {"self": {"href": "https://publications.scilifelab.se/publication/310db69525be40ed9f4e569c00320568.json"}, "display": {"href": "https://publications.scilifelab.se/publication/310db69525be40ed9f4e569c00320568"}}, "title": "Ultra-large virtual screening unveils potent agonists of the neuromodulatory orphan receptor GPR139.", "authors": [{"family": "Cabeza de Vaca", "given": "Israel", "initials": "I", "orcid": "0000-0002-6208-1091", "researcher": {"href": "https://publications.scilifelab.se/researcher/65628edbdaa448b8ab37d5eb4e100aee.json"}}, {"family": "Trapkov", "given": "Boris", "initials": "B", "orcid": "0000-0003-1245-888X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dc796a7e85b4849ae92b2d3ce13a885.json"}}, {"family": "Shen", "given": "Ling", "initials": "L"}, {"family": "Vo", "given": "Duy Duc", "initials": "DD"}, {"family": "Zhang", "given": "Xiaoqun", "initials": "X", "orcid": "0000-0002-9461-8682", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f307c88103d43b1b0b893fa59a8e828.json"}}, {"family": "Yang", "given": "Yunting", "initials": "Y"}, {"family": "Pezeshki", "given": "Mitra", "initials": "M", "orcid": "0009-0001-0155-7463", "researcher": {"href": "https://publications.scilifelab.se/researcher/e51c7fe034b9477996d92c2dbddf6f21.json"}}, {"family": "Zhang", "given": "Xuehan", "initials": "X"}, {"family": "B\u00e4llgren", "given": "Frida", "initials": "F"}, {"family": "Saleh", "given": "Aljona", "initials": "A"}, {"family": "Tarnovskiy", "given": "Andrii V", "initials": "AV"}, {"family": "Radchenko", "given": "Dmytro S", "initials": "DS", "orcid": "0000-0001-5444-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/df4077c366bc4f4a8b422762c0be9cfe.json"}}, {"family": "Moroz", "given": "Yurii S", "initials": "YS", "orcid": "0000-0001-6073-002X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8586d3b69b4782bed34192411a02e5.json"}}, {"family": "Br\u00e4uner-Osborne", "given": "Hans", "initials": "H"}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9805d4f39cc48f79a6e6ba076917021.json"}}, {"family": "Liu", "given": "Zhi-Jie", "initials": "ZJ", "orcid": "0000-0001-7279-2893", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd5198c9a2924467bb85b451b99f381b.json"}}, {"family": "Hauser", "given": "Alexander Sebastian", "initials": "AS", "orcid": "0000-0003-1098-6419", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d10bc754dbc4fb49ae26994ab9fcff1.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7d91087358e46e38bb1b7110dc0b214.json"}}], "type": "journal article", "published": "2025-12-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "The orphan G protein-coupled receptor (GPCR) GPR139 attracts interest as a target for neuropsychiatric disorders. Whereas the physiological functions of GPR139 remain elusive, a high-resolution receptor structure is now available. To assess whether structural information enables ligand discovery, we computationally dock 235 million compounds to the GPR139 binding site. Of 68 top-ranked compounds evaluated experimentally, five are full agonists with potencies ranging from 160 nM to 3.6 \u00b5M. Structure-guided optimization identifies one of the most potent GPR139 agonists, and a cryo-EM structure of the receptor-ligand complex confirms the predicted binding mode. Functional characterization provides insights into GPR139 signalling, and one agonist elicits behavioural effects in mice. We also explore the potential to replace experimental structure determination with the deep-learning method AlphaFold3, revealing a limited capability of artificial intelligence to model receptor-ligand interactions for understudied GPCRs. The results demonstrate how high-resolution GPCR structures combined with large-library docking can accelerate drug discovery.", "doi": "10.1038/s41467-025-66845-y", "pmid": "41365886", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-66845-y"}], "notes": [], "created": "2025-12-15T10:13:02.964Z", "modified": "2025-12-15T10:13:04.219Z"}, {"entity": "publication", "iuid": "c998995ead0244f1b2aa6425b4c94d94", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c998995ead0244f1b2aa6425b4c94d94.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c998995ead0244f1b2aa6425b4c94d94"}}, "title": "Pharmacological activation of p53 induces dose-dependent changes in endothelial cell fate during angiogenic sprouting", "authors": [{"family": "Al-Radi", "given": "Omayma", "initials": "O"}, {"family": "Ingelshed", "given": "Katrine", "initials": "K"}, {"family": "Eichhorn", "given": "Lisa", "initials": "L"}, {"family": "Josefsson", "given": "Heidi", "initials": "H", "orcid": "0009-0001-0493-4877", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba8b17ae27f45ceb95d633757087213.json"}}, {"family": "Krkoska", "given": "Martin", "initials": "M"}, {"family": "Br\u00e4utigam", "given": "Lars", "initials": "L"}, {"family": "Lindstr\u00f6m", "given": "Susanne", "initials": "S", "orcid": "0009-0009-7396-9529", "researcher": {"href": "https://publications.scilifelab.se/researcher/fed14c3020094d9a8ca1ace96cbbe7b2.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Kheder", "given": "Sania", "initials": "S"}, {"family": "Cerrato", "given": "Carmine P", "initials": "CP"}, {"family": "Ferm\u00e9", "given": "Suzon", "initials": "S"}, {"family": "Bosdotter", "given": "Cecilia", "initials": "C"}, {"family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "researcher": {"href": "https://publications.scilifelab.se/researcher/98fffa8e99254fb597bf07dea61d8e37.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Vojtesek", "given": "Borivoj", "initials": "B"}, {"family": "Lane", "given": "David P", "initials": "DP"}, {"family": "Kannan", "given": "Pavitra", "initials": "P", "orcid": "0000-0002-9170-6062", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4f0b833cc604caf8dcff52dcbaa4fb9.json"}}], "type": "journal-article", "published": "2025-12-08", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "16", "issue": "1", "pages": "883", "issn-l": "2041-4889"}, "abstract": "The cell cycle is a key regulator of endothelial cell specification into tip and stalk cell phenotypes, which are essential for angiogenesis in both normal development and pathological conditions. While the tumor suppressor p53 is known to regulate the cell cycle and influence cell fate, its role in modulating the cell fate of these phenotypes remains unclear. Using non-genotoxic small molecule and stapled peptide compounds to pharmacologically activate p53 via MDM2 inhibition, we demonstrate that graded levels of p53 induce distinct cellular fates in normal endothelial cells. Low levels of p53 induce reversible cell cycle arrest by reducing DNA replication, while high levels induce senescence and cell death. Surprisingly, all tested levels of p53 activation reduced the growth of venous blood vessels in vitro and in zebrafish embryo models. This reduction in sprouting may stem from distinct cellular responses in tip-like and non-tip-like cells to pharmacological p53 activation: low p53 levels primarily reduced proliferation in non-tip-like cells, whereas high levels decreased the frequency of tip-like cells and the expression of genes associated with tip and stalk cell identities. Our findings show for the first time that pharmacological p53 activation modulates endothelial cell fate in a dose-dependent manner during sprouting angiogenesis. They also highlight the potential of using graded p53 modulation as a therapeutic strategy to target abnormal tip or stalk cell development in pathological angiogenesis, such as in cancer.", "doi": "10.1038/s41419-025-08292-7", "pmid": "41360924", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12698774"}, {"db": "pii", "key": "10.1038/s41419-025-08292-7"}], "notes": [], "created": "2025-12-12T12:24:13.109Z", "modified": "2026-01-09T07:55:39.395Z"}, {"entity": "publication", "iuid": "733bd4b2fcc74cb4882960d91b8e004a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/733bd4b2fcc74cb4882960d91b8e004a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/733bd4b2fcc74cb4882960d91b8e004a"}}, "title": "Synthetic cannabinoid receptor agonists inhibit the cardiac voltage-gated potassium channel hERG", "authors": [{"family": "Ottosson", "given": "Nina E", "initials": "NE", "orcid": "0000-0003-2159-6731", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e54acedff4e45bbaa661096b33f8f7c.json"}}, {"family": "Frampton", "given": "Damon J A", "initials": "DJA", "orcid": "0000-0003-0941-3330", "researcher": {"href": "https://publications.scilifelab.se/researcher/73c54f27d14e468d8ea0dc65bb71b5b3.json"}}, {"family": "Pipatpolkai", "given": "Tanadet", "initials": "T", "orcid": "0000-0001-5396-4784", "researcher": {"href": "https://publications.scilifelab.se/researcher/b629d00aa88d4db4a51692bd594e4117.json"}}, {"family": "Norman", "given": "Caitlyn", "initials": "C", "orcid": "0000-0003-2322-0367", "researcher": {"href": "https://publications.scilifelab.se/researcher/76236231afbf4ef5b43cb790ec4213fc.json"}}, {"family": "Karlsson", "given": "Urban", "initials": "U", "orcid": "0000-0002-9228-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb7fa0354374416ca2f928c56f4ffe81.json"}}, {"family": "Jauregi-Miguel", "given": "Amaia", "initials": "A", "orcid": "0000-0003-0938-7734", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd678c2b74f74975a83ca102fa473752.json"}}, {"family": "Venter", "given": "Maryke", "initials": "M", "orcid": "0009-0004-8319-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/e10766ad47d0470ab925b12c54e64bbe.json"}}, {"family": "Sridhar", "given": "Akshay", "initials": "A", "orcid": "0000-0003-0633-7707", "researcher": {"href": "https://publications.scilifelab.se/researcher/56c0ac56b98c43ff8b2a777b2424bd81.json"}}, {"family": "Larsson", "given": "H Peter", "initials": "HP"}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8015-5728", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d92037931f64b70b8d4bf78dab628b4.json"}}, {"family": "Liin", "given": "Sara I", "initials": "SI", "orcid": "0000-0001-8493-0114", "researcher": {"href": "https://publications.scilifelab.se/researcher/e82a591108f24dcabf50779d88fc8844.json"}}], "type": "posted-content", "published": "2025-12-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.64898/2025.12.03.692044", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-02-23T09:15:04.762Z", "modified": "2026-02-23T09:15:06.199Z"}, {"entity": "publication", "iuid": "27c51de324ea427da6d1ca7c145e1cb6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27c51de324ea427da6d1ca7c145e1cb6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27c51de324ea427da6d1ca7c145e1cb6"}}, "title": "Near-infrared MINFLUX imaging enabled by suppression of fluorophore blinking.", "authors": [{"family": "Srambickal", "given": "Chinmaya V", "initials": "CV", "orcid": "0009-0005-3541-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/83d10a808edf4d34a5ee39d5ae20bd49.json"}}, {"family": "Esmaeeli", "given": "Hanie M", "initials": "HM", "orcid": "0000-0003-3806-0255", "researcher": {"href": "https://publications.scilifelab.se/researcher/b00222b6b4f84c9987d4f30e778da180.json"}}, {"family": "Piguet", "given": "Joachim", "initials": "J", "orcid": "0000-0002-4762-4887", "researcher": {"href": "https://publications.scilifelab.se/researcher/3733dec61dc54d91a52d73b853dddc1d.json"}}, {"family": "Reinkensmeier", "given": "Lenny", "initials": "L", "orcid": "0009-0008-8315-6268", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b753b7873924481bbfdb7d03ce42de2.json"}}, {"family": "Siegmund", "given": "Ren\u00e9", "initials": "R", "orcid": "0009-0004-9010-6067", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1ee32987df6479f86e27cc8c79bb52d.json"}}, {"family": "Agostinho", "given": "Ana", "initials": "A", "orcid": "0000-0001-6270-7384", "researcher": {"href": "https://publications.scilifelab.se/researcher/b66ed948cad14e0c9bd35e487a48d330.json"}}, {"family": "Bates", "given": "Mark", "initials": "M", "orcid": "0000-0003-0668-5277", "researcher": {"href": "https://publications.scilifelab.se/researcher/681d6d1b70ad4879b3bb9a1e458d2960.json"}}, {"family": "Egner", "given": "Alexander", "initials": "A", "orcid": "0000-0001-5248-3858", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6b7bdedf9fa4c08b11701f9643d4f9c.json"}}, {"family": "Widengren", "given": "Jerker", "initials": "J", "orcid": "0000-0003-3200-0374", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5db653aece8408bb5aff6531edff22c.json"}}], "type": "journal article", "published": "2025-12-05", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "49", "pages": "eadw3149", "issn-l": "2375-2548"}, "abstract": "MINimal photon FLUXes (MINFLUX) offers nanometer localization precision, with lower fluorophore requirements than for other super-resolution microscopy (SRM) techniques. Nonetheless, low localization probabilities hamper its application, and use of less bright and photostable fluorophores, including near-infrared (NIR) fluorophores has been difficult to realize. Here, we devised strategies overcoming these limitations. We systematically studied the blinking properties of far-red and NIR cyanine fluorophores, followed by simulations of MINFLUX localizations, over typical time scales (microsecond to 10 milliseconds), sample and excitation conditions for MINFLUX imaging. We identified fluorophore blinking via photoisomerization and photoreduction as the main cause of localization errors, and that use of balanced redox buffers and repetitive excitation beam scans can suppress such errors. Implementing these strategies, we could demonstrate NIR-MINFLUX imaging with nanometer localization precision, thereby also presenting an overall strategy to design optimal sample and excitation conditions, for MINFLUX imaging and for SRM in general.", "doi": "10.1126/sciadv.adw3149", "pmid": "41348895", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-12-06T16:23:27.052Z", "modified": "2025-12-06T16:23:28.621Z"}, {"entity": "publication", "iuid": "837fd5a3e240418a922a7efe0a36c863", "links": {"self": {"href": "https://publications.scilifelab.se/publication/837fd5a3e240418a922a7efe0a36c863.json"}, "display": {"href": "https://publications.scilifelab.se/publication/837fd5a3e240418a922a7efe0a36c863"}}, "title": "Identification of Streptococcus pneumoniae-Specific Proteins by Surface-Shaving Proteomics.", "authors": [{"family": "Acha Alarcon", "given": "Leonarda", "initials": "L", "orcid": "0000-0002-9453-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fa254340a5b4ec39809654b54fd3481.json"}}, {"family": "Segu\u00ed", "given": "Guillem", "initials": "G"}, {"family": "Pi\u00f1eiro-Iglesias", "given": "Beatriz", "initials": "B"}, {"family": "Svetlicic", "given": "Ema", "initials": "E"}, {"family": "Kondori", "given": "Nahid", "initials": "N"}, {"family": "Gomila", "given": "Margarita", "initials": "M"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1c68436094391bfefd7de22757aba.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}], "type": "journal article", "published": "2025-12-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "24", "issue": "12", "pages": "6154-6173", "issn-l": "1535-3893"}, "abstract": "Streptococcus pneumoniae (pneumococcus) is a prominent cause of bacterial pneumonia, meningitis, and septicemia, causing high morbidity and high mortality, particularly in children and the elderly. In this study, proteomics- and genomics-based approaches were used for the identification of pneumococcal protein and peptide biomarkers of S. pneumoniae for diagnostics and prospective targets for treatment. Through a pan-genome analysis, 11 S. pneumoniae strains, demonstrating genetic variation within the species, were selected for proteomic characterization. Mass spectrometry-based proteomics, in combination with bacterial surface-shaving, were used to study the cell-surface proteome of S. pneumoniae. The data obtained from three biological replicates per strain were analyzed to identify and rank the proteins and peptides according to their presence in the strains, as well as their presence in all available S. pneumoniae proteomes (8,892) archived in public databases. Several highly ranked proteins have been described as \"species-specific\" for S. pneumoniae and as surface-associated virulence factors or demonstrate highly antigenic properties. Proteins (34) previously not recognized as S. pneumoniae-specific were proposed to be novel biomarkers, demonstrating high degrees of prevalence in all analyzed proteomes, with little or no sequence similarities to closely related species but common among the genetically diverse strains included in this study.", "doi": "10.1021/acs.jproteome.5c00716", "pmid": "41212599", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12687362"}], "notes": [], "created": "2025-11-20T18:17:19.599Z", "modified": "2026-01-26T15:08:00.860Z"}, {"entity": "publication", "iuid": "e42f9cac44624ea49439d8938a4dd87b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e42f9cac44624ea49439d8938a4dd87b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e42f9cac44624ea49439d8938a4dd87b"}}, "title": "Human oligodendrocyte progenitor cells mediate synapse elimination through TAM receptor activation.", "authors": [{"family": "Gkogka", "given": "Asimenia", "initials": "A", "orcid": "0009-0001-7892-0769", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5f6c80990684a2cb715a05e5dc6e830.json"}}, {"family": "Malwade", "given": "Susmita", "initials": "S", "orcid": "0000-0002-6756-018X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d254484412d4fcab1b65858d2d1d5bb.json"}}, {"family": "Koskuvi", "given": "Marja", "initials": "M"}, {"family": "Ohtonen", "given": "Sohvi", "initials": "S"}, {"family": "Molnar", "given": "Ellinor", "initials": "E"}, {"family": "Bose", "given": "Raj", "initials": "R", "orcid": "0009-0008-4039-862X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dfa265d83834453be680aed87c0f667.json"}}, {"family": "Ceccatelli", "given": "Sandra", "initials": "S", "orcid": "0000-0002-9367-8480", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee421983d86b46ac8b36dd0766c1f90d.json"}}, {"family": "Koistinaho", "given": "Jari", "initials": "J", "orcid": "0000-0001-6559-1153", "researcher": {"href": "https://publications.scilifelab.se/researcher/e92f575e61b244ec9a9f96190f0df35b.json"}}, {"family": "Tiihonen", "given": "Jari", "initials": "J", "orcid": "0000-0002-0400-6798", "researcher": {"href": "https://publications.scilifelab.se/researcher/d55a02bf2b1340878d23f0d594e778f2.json"}}, {"family": "Schalling", "given": "Martin", "initials": "M", "orcid": "0000-0001-5011-2922", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe1154f55d34051a41554d328bc8be3.json"}}, {"family": "Samudyata", "given": "Samudyata", "initials": "S", "orcid": "0000-0002-1062-2626", "researcher": {"href": "https://publications.scilifelab.se/researcher/4856a75f064f4e0f8726bfd4a6658ac6.json"}}, {"family": "Sellgren", "given": "Carl M", "initials": "CM", "orcid": "0000-0001-9103-2785", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c0740ddfd6d4c98988b2a19096a9814.json"}}], "type": "journal article", "published": "2025-12-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "10612", "issn-l": "2041-1723"}, "abstract": "Oligodendrocyte progenitor cells (OPCs) have been implicated in synaptic remodelling in animal models, but the underlying mechanisms and their relevance to human brain development remain unclear. Here, we generate a human multi-lineage forebrain organoid model in which OPCs, together with microglia, form close contacts with synapses and spontaneously internalize synaptic material. Single-nucleus transcriptomic profiling with unbiased cell-cell communication analysis identifies the growth arrest-specific gene 6 (GAS6)-TYRO3, AXL, and MERTK (TAM) receptor axis as a key signalling pathway, with neurons and microglia expressing GAS6 and a subset of OPCs expressing AXL. Further, dose-dependent pharmacological inhibition of TAM receptors demonstrates the importance of AXL, and targeted reduction of AXL expression in OPCs impairs synaptic uptake. These findings reveal a role for GAS6-AXL signalling in driving synaptic internalisation by AXL+ OPCs during early human brain development.", "doi": "10.1038/s41467-025-66521-1", "pmid": "41350273", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12680777"}, {"db": "pii", "key": "10.1038/s41467-025-66521-1"}], "notes": [], "created": "2026-01-07T15:28:15.485Z", "modified": "2026-01-07T15:28:16.609Z"}, {"entity": "publication", "iuid": "a37a5acc6c434e50afcfc8a6a13a8700", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a37a5acc6c434e50afcfc8a6a13a8700.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a37a5acc6c434e50afcfc8a6a13a8700"}}, "title": "Structural basis of specific lysine transport by Pseudomonas aeruginosa permease LysP.", "authors": [{"family": "Bicer", "given": "Deniz", "initials": "D"}, {"family": "Matsuoka", "given": "Rei", "initials": "R", "orcid": "0000-0001-6718-2572", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ff469bc61824dfdbd2f1bd2d9eda8fb.json"}}, {"family": "Moumbock", "given": "Aur\u00e9lien F A", "initials": "AFA", "orcid": "0000-0002-6034-2016", "researcher": {"href": "https://publications.scilifelab.se/researcher/d82e18423c15489da2e66f44bc546208.json"}}, {"family": "Sukumar", "given": "Preethi", "initials": "P"}, {"family": "Suades", "given": "Albert", "initials": "A"}, {"family": "Cheruvara", "given": "Harish", "initials": "H"}, {"family": "Quigley", "given": "Andrew", "initials": "A", "orcid": "0000-0002-5022-9845", "researcher": {"href": "https://publications.scilifelab.se/researcher/3463df3e436f4accbef2c85d631d535b.json"}}, {"family": "Drew", "given": "David", "initials": "D"}, {"family": "Pardon", "given": "Els", "initials": "E", "orcid": "0000-0002-2466-0172", "researcher": {"href": "https://publications.scilifelab.se/researcher/375719a54c844150a4d5cb2b4f3ebb57.json"}}, {"family": "Steyaert", "given": "Jan", "initials": "J", "orcid": "0000-0002-3825-874X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a13eb5511e1448fb982b5bd1bb1d6f1.json"}}, {"family": "Henderson", "given": "Peter J F", "initials": "PJF", "orcid": "0000-0002-9187-0938", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a039ab6f9b946079084fa5c5a1d73cb.json"}}, {"family": "Caffrey", "given": "Martin", "initials": "M", "orcid": "0000-0002-2931-4551", "researcher": {"href": "https://publications.scilifelab.se/researcher/4860054d06e24ccfb39fe781305f73d8.json"}}, {"family": "Griese", "given": "Julia J", "initials": "JJ", "orcid": "0000-0003-3686-3062", "researcher": {"href": "https://publications.scilifelab.se/researcher/308d2df438d8443ca932fb5111e4590e.json"}}, {"family": "Nji", "given": "Emmanuel", "initials": "E", "orcid": "0000-0001-6991-1046", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dfdecdfcb44a97b8513508e294aebd.json"}}], "type": "journal article", "published": "2025-12-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "Under conditions of extreme acidity, the lysine-specific permease, LysP, not only mediates the import of L-lysine it also interacts with the transcriptional regulator, CadC, to activate expression of the cadAB operon. This operon encodes the lysine decarboxylase, CadA, which converts lysine to cadaverine while consuming a cytoplasmic proton, and the antiporter, CadB, which exports protonated cadaverine in exchange for extracellular lysine. Together, these processes contribute to cytoplasmic pH homeostasis and support bacterial acid resistance - a mechanism essential for the survival of pathogenic bacteria in acidic host environments. Here, we present the cryo-EM structure of LysP from Pseudomonas aeruginosa in an inward-occluded conformation (3.2-5.3 \u00c5 resolution), bound to L-lysine and a nanobody. L-Lysine is coordinated by hydrophobic contacts, cation-\u03c0 interactions, and by hydrogen bonding mostly with polar uncharged residues. Reconstitution of LysP into proteoliposomes confirms specific L-lysine transport, which is competitively inhibited by L-4-thialysine. These findings provide a structural framework for understanding selective lysine recognition and inhibition, with implications for antibacterial drug design.", "doi": "10.1038/s41467-025-66618-7", "pmid": "41345107", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-66618-7"}], "notes": [], "created": "2025-12-09T13:04:51.180Z", "modified": "2025-12-09T13:04:57.345Z"}, {"entity": "publication", "iuid": "b8ca2a2dba2049ec8de7192c162898c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8ca2a2dba2049ec8de7192c162898c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8ca2a2dba2049ec8de7192c162898c4"}}, "title": "Homo sapiens-specific evolution unveiled by ancient southern African genomes.", "authors": [{"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C", "orcid": "0000-0002-3258-275X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fce67de4e14fa68c0edadfec0de085.json"}}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Hollfelder", "given": "Nina", "initials": "N", "orcid": "0000-0002-1567-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f81a63833c146999d73fa38f588ea06.json"}}, {"family": "Vicente", "given": "Mario", "initials": "M"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Brink", "given": "James", "initials": "J"}, {"family": "Zipfel", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-4251-884X", "researcher": {"href": "https://publications.scilifelab.se/researcher/74d1041d932a49c9bc2baca44273d4a4.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2025-12-03", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": null, "issue": null, "pages": null}, "abstract": "Homo sapiens evolved hundreds of thousands of years ago in Africa, later spreading across the globe1, but the early evolutionary process is debated2-6. Here we present whole-genome sequencing data for 28 ancient southern African individuals, including six individuals with 25\u00d7 to 7.2\u00d7 genome coverage, dated to between 10,200 and 150 calibrated years before present (cal. BP). All ancient southern Africans dated to more than 1,400 cal. BP show a genetic make-up that is outside the range of genetic variation in modern-day humans (including southern African Khoe-San people, although some retain up to 80% ancient southern African ancestry), manifesting in a large fraction of Homo sapiens-specific variants that are unique to ancient southern Africans. Homo sapiens-specific variants at amino acid-altering sites fixed for all humans-which are likely to have evolved rapidly on the Homo sapiens branch-were enriched for genes associated with kidney function. Some Homo sapiens-specific variants fixed in ancient southern Africans-which are likely to have adapted rapidly on the southern African branch-were enriched for genes associated with protection against ultraviolet light. The ancient southern Africans show little spatiotemporal stratification for 9,000 years, consistent with a large, stable Holocene population transcending archaeological phases. While southern Africa served as a long-standing geographical refugium, there is outward gene flow over 8,000 years ago; however, inward gene flow manifests only after around 1,400 years ago. The ancient genomes reported here are therefore key to the evolution of Homo sapiens, and are important for advancing our understanding of human genomic variation.", "doi": "10.1038/s41586-025-09811-4", "pmid": "41339558", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-025-09811-4"}], "notes": [], "created": "2025-12-04T08:12:48.745Z", "modified": "2025-12-05T10:16:26.469Z"}, {"entity": "publication", "iuid": "88ca53dd11f14b3191a5c1a38499a985", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88ca53dd11f14b3191a5c1a38499a985.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88ca53dd11f14b3191a5c1a38499a985"}}, "title": "Genome of the extinct Gotland cattle breed.", "authors": [{"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}], "type": "journal article", "published": "2025-12-03", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "1093", "issn-l": "1471-2164"}, "abstract": "The extinct cattle breed Gotland cattle lived on the island of Gotland in the Baltic Sea until the beginning of the 1950s. We sequenced the genomes of two Gotland cattle isolated from skulls from a local museum on Gotland.\n\nThe depth of coverage was 2.7X and 3.3X, respectively, with a breadth of coverage of 85% and 89%. Based on coverage of the sex chromosomes, both animals appeared to be female. We detected 19 million single nucleotide variants and 2.8 million indels in the joint dataset of Gotland cattle jointly called with modern Swedish cattle. In a principal component analysis, the two Gotland cattle placed the closest to Swedish Red cattle, rather than among the southern or northern traditional breeds. In terms of mitochondrial haplotypes, they were similar to clusters of related haplotypes involving multiple other breeds, including Swedish Mountain cattle, Swedish Red Polled and several Finnish cattle breeds.\n\nIn summary, our results suggest that Gotland cattle were genetically closer to the ancestors of Swedish Red cattle than to the extant traditional Swedish breeds.", "doi": "10.1186/s12864-025-12382-3", "pmid": "41340033", "labels": {"Ancient DNA": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-025-12382-3"}], "notes": [], "created": "2025-12-10T09:59:37.512Z", "modified": "2025-12-10T09:59:37.679Z"}, {"entity": "publication", "iuid": "148bff77b6a7405ba3d7dadd0c170a4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/148bff77b6a7405ba3d7dadd0c170a4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/148bff77b6a7405ba3d7dadd0c170a4a"}}, "title": "Gray wolves in an anthropogenic context on a small island in prehistoric Scandinavia.", "authors": [{"family": "Girdland-Flink", "given": "Linus", "initials": "L", "orcid": "0000-0001-6499-8728", "researcher": {"href": "https://publications.scilifelab.se/researcher/74574daaa4e340bca662b3e3bf4899e9.json"}}, {"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Apel", "given": "Jan", "initials": "J", "orcid": "0000-0002-8894-1985", "researcher": {"href": "https://publications.scilifelab.se/researcher/60265a0624a74b7aa01f278b7d53c608.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}], "type": "journal article", "published": "2025-12-02", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "122", "issue": "48", "pages": "e2421759122"}, "abstract": "Dogs were domesticated at least once from a yet-unidentified wolf population at least ~15,000 y ago. However, how domestication took place is a topic of ongoing debate, and the ability of human groups to manage wolves in their communities during early stages of domestication is poorly understood. Here, we report multiproxy data from two canids excavated from Late Neolithic and Bronze Age contexts in the Stora F\u00f6rvar cave on the island of Stora Karls\u00f6 in the Baltic Sea. The island is small (2.5 sq km) and, like the neighboring island of Gotland, carries no endemic populations of terrestrial mammals. Instead, the current consensus is that human introductions account for some mammal fauna on Gotland, and for the majority of that on Stora Karls\u00f6. Genome-wide data show that the two canids have ancestry indistinguishable from Eurasian wolves, with no shared ancestry with domestic dogs of the Canis familiaris lineage. Their genome-wide heterozygosity is lower than that observed in 72 previously published ancient wolf genomes, and instead comparable to dogs. Stable isotope data (\u03b413C and \u03b415N) reveals a diet rich in marine protein, which is consistent with habitation alongside the human groups who used Stora Karls\u00f6 as a seal-hunting, fowling, and sea fishing station, and in the Bronze Age probably also for grazing. Skeletal size is at the lower end of wolf variability, and one individual shows advanced pathology consistent with reduced mobility. While other scenarios are possible, a parsimonious explanation is that these wolves were brought to the island by humans and were possibly under human control.", "doi": "10.1073/pnas.2421759122", "pmid": "41284891", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-04T08:42:12.711Z", "modified": "2025-12-05T10:18:48.574Z"}, {"entity": "publication", "iuid": "7f1b78138d4747868212f404c4095ec3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f1b78138d4747868212f404c4095ec3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f1b78138d4747868212f404c4095ec3"}}, "title": "Engineered calcium-regulated affinity protein for efficient internalization and lysosomal toxin delivery.", "authors": [{"family": "J\u00f6nsson", "given": "Malin", "initials": "M", "orcid": "0000-0001-8706-5226", "researcher": {"href": "https://publications.scilifelab.se/researcher/785ec163f6f2413389d015e13dd9fe55.json"}}, {"family": "M\u00f6ller", "given": "Marit", "initials": "M", "orcid": "0000-0003-3138-6789", "researcher": {"href": "https://publications.scilifelab.se/researcher/05ce572b17b2456fad421fc3fb74e708.json"}}, {"family": "Schierholz", "given": "Leon", "initials": "L", "orcid": "0009-0000-4642-734X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e246375f672742c79c5befa26866c185.json"}}, {"family": "Dorka", "given": "Nicolai", "initials": "N"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9098-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c6ea8f5c456428db21b1085ad541538.json"}}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}], "type": "journal article", "published": "2025-12-02", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "48", "pages": "e2509081122", "issn-l": "0027-8424"}, "abstract": "The emerging strategy of protein-drug conjugates (PDCs) for targeted cancer therapy holds great potential to improve treatment efficacy by specifically targeting cancer biomarkers and delivering toxic payloads directly to tumor cells, minimizing off-target toxicity. The success of this approach depends on the internalization and retention of the payload in target cells. This study introduces a method using a small protein domain engineered for conditional target affinity, enabling lysosomal trafficking independent of the biological fate of the receptor. Specifically, we describe the development of an EGF receptor binder, CaRAEGFR, with calcium-regulated affinity (CaRA), meaning the target binding strength is tailored by the available calcium concentration. This allows for endosomal dissociation, as calcium levels are lower in endosomes than in the bloodstream. Affinity measurements and structural modeling reveal the molecular basis of the calcium modulated affinity. Live cell imaging demonstrates efficient internalization and lysosomal trafficking of the calcium-dependent domain, while the EGF receptor is recycled to the membrane. When used as a drug carrier, CaRAEGFR effectively delivers the toxin to the lysosomes, resulting in potent cytotoxicity with an IC50 of 0.8 nM in EGFR-expressing cancer cells.", "doi": "10.1073/pnas.2509081122", "pmid": "41289384", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T19:10:33.510Z", "modified": "2025-11-27T19:10:34.479Z"}, {"entity": "publication", "iuid": "317e66a79e9c40cebe92b74f879e04b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/317e66a79e9c40cebe92b74f879e04b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/317e66a79e9c40cebe92b74f879e04b3"}}, "title": "Structural diversity and conservation among CRESS-DNA bacilladnaviruses revealed through cryo-EM and computational modelling", "authors": [{"family": "Gebhard", "given": "L Johanna", "initials": "LJ", "orcid": "0000-0003-1986-5592", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfcf93d9677849078b6457464abf9ffa.json"}}, {"family": "Tomaru", "given": "Yuji", "initials": "Y", "orcid": "0000-0002-8164-6991", "researcher": {"href": "https://publications.scilifelab.se/researcher/85835893ee10481aafee34223ece859e.json"}}, {"family": "Okamoto", "given": "Kenta", "initials": "K", "orcid": "0000-0002-4858-1196", "researcher": {"href": "https://publications.scilifelab.se/researcher/9302e76f16a04afdbb72f00c805bffa4.json"}}, {"family": "Munke", "given": "Anna", "initials": "A", "orcid": "0000-0002-5510-2245", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd6d8030171420190aa65f3eb1ac4bd.json"}}], "type": "journal-article", "published": "2025-12-01", "journal": {"title": "Virol J", "issn": "1743-422X", "volume": "22", "issue": "1", "issn-l": "1743-422X"}, "abstract": null, "doi": "10.1186/s12985-025-03019-8", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-01T14:49:55.429Z", "modified": "2025-12-03T11:31:19.354Z"}, {"entity": "publication", "iuid": "d604787528614bb3a9cbc37e395c350b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d604787528614bb3a9cbc37e395c350b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d604787528614bb3a9cbc37e395c350b"}}, "title": "Sacrificial redox modulation by a secreted bacterial effector molecule mitigates oxidative stress and inflammation in vivo.", "authors": [{"family": "Andersson", "given": "Tilde", "initials": "T"}, {"family": "Anwaar", "given": "Shoaib", "initials": "S"}, {"family": "Fuentes-Lemus", "given": "Eduardo", "initials": "E"}, {"family": "Allhorn", "given": "Maria", "initials": "M"}, {"family": "Happonen", "given": "Lotta", "initials": "L"}, {"family": "Veitch", "given": "Margaret", "initials": "M"}, {"family": "Chew", "given": "Hui Yi", "initials": "HY"}, {"family": "Montes de Oca", "given": "Marcela", "initials": "M"}, {"family": "Tanner", "given": "Lloyd", "initials": "L"}, {"family": "Br\u00fcggemann", "given": "Holger", "initials": "H"}, {"family": "Nordenfelt", "given": "Pontus", "initials": "P"}, {"family": "Davies", "given": "Michael J", "initials": "MJ"}, {"family": "Wells", "given": "James W", "initials": "JW"}, {"family": "Lood", "given": "Rolf", "initials": "R"}], "type": "journal article", "published": "2025-12-01", "journal": {"title": "Free Radic. Biol. Med.", "issn": "1873-4596", "volume": "240", "pages": "339-346", "issn-l": "0891-5849"}, "abstract": "Human-bacterial interactions play a crucial role in several essential aspects of life. Here, we describe how a secreted protein from the skin commensal Cutibacterium acnes, RoxP, functions as a sacrificial redox effector molecule that facilitates beneficial interactions with its human host by counteracting oxidative stress and reducing stress-induced inflammation. Using a combination of structural mapping, biophysical binding studies, and in vivo experiments, we demonstrate how RoxP contributes to skin homeostasis by serving as a target for oxidative attack and influencing cytokine signaling. To our knowledge, this is the first in vivo mechanistic description of a secreted prokaryotic effector molecule modulating host redox balance through sacrificial oxidation, providing evidence of its role as a health-promoting factor.", "doi": "10.1016/j.freeradbiomed.2025.08.038", "pmid": "40849000", "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0891-5849(25)00925-6"}], "notes": [], "created": "2025-11-28T10:24:46.777Z", "modified": "2025-11-28T10:24:46.787Z"}, {"entity": "publication", "iuid": "258c731df5164d1d8f4e7fde8d07f2df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/258c731df5164d1d8f4e7fde8d07f2df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/258c731df5164d1d8f4e7fde8d07f2df"}}, "title": "Phenotypic variability in early-onset dementia segregating with a novel APP (p.I718M) variant.", "authors": [{"family": "Johansson", "given": "Charlotte", "initials": "C"}, {"family": "Rodriguez-Vieitez", "given": "Elena", "initials": "E"}, {"family": "Bluma", "given": "Marina", "initials": "M"}, {"family": "Nennesmo", "given": "Inger", "initials": "I", "orcid": "0009-0000-0871-1147", "researcher": {"href": "https://publications.scilifelab.se/researcher/7422a07a064648a5a1dfed8a9889503b.json"}}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0003-4503-4717", "researcher": {"href": "https://publications.scilifelab.se/researcher/481958db26a2433ea8d5cc786c3b2bca.json"}}, {"family": "Ullgren", "given": "Abbe", "initials": "A"}, {"family": "Jelic", "given": "Vesna", "initials": "V"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}, {"family": "Blennow", "given": "Kaj", "initials": "K", "orcid": "0000-0002-1890-4193", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e646be026ce42ecbfd4d62eca3f9bce.json"}}, {"family": "Nordberg", "given": "Agneta", "initials": "A"}, {"family": "Graff", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9949-2951", "researcher": {"href": "https://publications.scilifelab.se/researcher/3faadb7b187046b090d947f85d8c4dd1.json"}}], "type": "journal article", "published": "2025-12-01", "journal": {"title": "Alzheimers Res Ther", "issn": "1758-9193", "volume": "17", "issue": "1", "pages": "254", "issn-l": null}, "abstract": "Autosomal dominant Alzheimer disease (ADAD) is caused by pathogenic variants in the APP, PSEN1 and PSEN2 genes, but a substantial fraction of reported variants is of unknown clinical significance. Here we report a novel variant in the amyloid precursor protein gene (APP p.I718M).\n\nFive siblings from a family with a multi-generational history of cognitive disease were assessed for cognitive impairment at the memory clinic at Karolinska University Hospital. Data were included for genetic analysis, segregation analysis, phenotyping and fluid biomarker analysis. Biomarker analyses were performed in CSF (A\u03b238, A\u03b240, A\u03b242, t-tau, p-tau181, NfL) and plasma (p-tau181, p-tau217, GFAP, NfL). CSF and plasma biomarkers were compared cross-sectionally to non-carrier controls or mutation carriers from other ADAD families. Also, amyloid PET, brain MRI and neuropathological data were included.\n\nThe siblings fulfilled criteria of probable AD (N = 4) or mixed AD and dementia with Lewy bodies (AD/DLB) (N = 1). Median age at onset was 53 years (range 47 to 67). The genetic variant, APP p.I718M, classified as likely pathogenic based on segregation analysis, population frequency and in silico prediction of pathogenicity, was detected in all five siblings. CSF A\u03b242/40 and A\u03b242/38 ratios were decreased, and the CSF A\u03b238/40 ratio was increased compared to controls. Additionally, elevated plasma concentrations of GFAP, NfL and p-tau181 were observed in APP p.I718M and other ADAD mutation carriers.\n\nThe APP p.I718M variant is associated with ADAD. Also, concomitant Lewy body pathology was observed in one sibling. The increase in CSF A\u03b238/40 suggests a shift in APP processing product-lines, but functional experiments are needed to characterize further cellular mechanisms of the APP p.I718M variant and to confirm its pathogenicity.\n\nThe online version contains supplementary material available at 10.1186/s13195-025-01890-9.", "doi": "10.1186/s13195-025-01890-9", "pmid": "41327373", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12670831"}, {"db": "pii", "key": "10.1186/s13195-025-01890-9"}], "notes": [], "created": "2025-12-10T11:59:20.425Z", "modified": "2025-12-21T19:09:30.938Z"}, {"entity": "publication", "iuid": "bed19b398aa143d28064d622d7f4babf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bed19b398aa143d28064d622d7f4babf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bed19b398aa143d28064d622d7f4babf"}}, "title": "Holotype genome of the lesula provides insights into demography and evolution of a threatened primate lineage.", "authors": [{"family": "Jensen", "given": "Axel", "initials": "A", "orcid": "0000-0003-1766-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f139b7f3dac49e28ef6430637d88592.json"}}, {"family": "Horton", "given": "Emma R", "initials": "ER"}, {"family": "Koko", "given": "Mardoch\u00e9 B", "initials": "MB"}, {"family": "Detwiler", "given": "Kate M", "initials": "KM"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2025-12-01", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "26", "issue": "1", "pages": "408"}, "abstract": "The development of genome sequencing techniques has revolutionized evolutionary biology, facilitating the study of adaptation and speciation at the genome level. Genomic data has also become a cornerstone in conservation management, allowing inferences of population demography and genetic diversity.\n\nWe sequence the genome of the holotype specimen of the elusive lesula (Cercopithecus lomamiensis), a recently described member of the guenons (tribe Cercopithecini), endemic to the Democratic Republic of the Congo. Using published and novel genomic data, we explore the evolutionary and demographic history of C. lomamiensis and its sister species C. hamlyni. We estimate that the two species split ca. 3\u20134 million years ago, and find that they both show high genetic diversity despite being listed as Vulnerable on the IUCN Red List. We identify signatures of positive selection in genes involved in pelage coloration and immune functions, as well as skeletal morphology and locomotor behavior, potentially related to the terrestrial lifestyle of C. lomamiensis and C. hamlyni, which stand out among the otherwise arboreal Cercopithecus genus. We specifically explore whether introgression from more distantly related terrestrial guenons was involved in the evolution of terrestriality in the hamlyni group, but found low molecular convergence suggesting that putative terrestrial adaptations occurred largely independently.\n\nThis study provides insights into the demography and evolutionary history in a poorly known, threatened primate lineage. Furthermore, our results suggest that genomic erosion is not an imminent threat to these species, and that conservation management should prioritize actions to prevent further population decline.\n\nThe online version contains supplementary material available at 10.1186/s13059-025-03877-z.", "doi": "10.1186/s13059-025-03877-z", "pmid": "41327385", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12667059"}, {"db": "pii", "key": "10.1186/s13059-025-03877-z"}], "notes": [], "created": "2025-12-04T13:28:29.798Z", "modified": "2025-12-21T19:09:46.579Z"}, {"entity": "publication", "iuid": "2c0c707808dd4f1db74e1350424f7492", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c0c707808dd4f1db74e1350424f7492.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c0c707808dd4f1db74e1350424f7492"}}, "title": "Tree retention levels and prescribed burning effects on ectomycorrhizal fungal communities in a boreal Scots pine forest", "authors": [{"family": "Lariviere", "given": "Delphine", "initials": "D", "orcid": "0000-0002-1415-3476", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cdb62071ec5423ab4fd0be67b3b844a.json"}}, {"family": "Djupstr\u00f6m", "given": "Line", "initials": "L"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}, {"family": "Dahlberg", "given": "Anders", "initials": "A", "orcid": "0000-0002-3669-6797", "researcher": {"href": "https://publications.scilifelab.se/researcher/a62efad22b414d618531b66ad404f689.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Forest Ecology and Management", "issn": "0378-1127", "volume": "598", "pages": "123186", "issn-l": null}, "abstract": null, "doi": "10.1016/j.foreco.2025.123186", "pmid": null, "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T15:52:25.689Z", "modified": "2025-11-28T10:43:14.318Z"}, {"entity": "publication", "iuid": "3b697167fda749698f7675d0d2bccd4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b697167fda749698f7675d0d2bccd4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b697167fda749698f7675d0d2bccd4c"}}, "title": "Transforming solid-state nuclear magnetic resonance towards a chemistry-ready technique", "authors": [{"family": "Coulon", "given": "Rapha\u00eble", "initials": "R"}, {"family": "Gajan", "given": "David", "initials": "D"}, {"family": "Papawassiliou", "given": "Wassilios", "initials": "W"}, {"family": "Pell", "given": "Andrew J", "initials": "AJ", "orcid": "0000-0002-2542-8113", "researcher": {"href": "https://publications.scilifelab.se/researcher/47ef8c845de84d3ba40fddefbfb9511f.json"}}, {"family": "Schlagnitweit", "given": "Judith", "initials": "J"}, {"family": "Fayon", "given": "Franck", "initials": "F"}, {"family": "Florian", "given": "Pierre", "initials": "P"}, {"family": "Massiot", "given": "Dominique", "initials": "D"}, {"family": "Afrough", "given": "Armin", "initials": "A"}, {"family": "Juhl", "given": "Dennis W", "initials": "DW"}, {"family": "Vosegaard", "given": "Thomas", "initials": "T"}, {"family": "Cerofolini", "given": "Linda", "initials": "L"}, {"family": "Lelli", "given": "Moreno", "initials": "M"}, {"family": "Lucci", "given": "Massimo", "initials": "M"}, {"family": "Luchinat", "given": "Claudio", "initials": "C"}, {"family": "Aspers", "given": "Ruud L E G", "initials": "RLEG"}, {"family": "G\u00f3mez", "given": "Jennifer S", "initials": "JS"}, {"family": "Kentgens", "given": "Arno P M", "initials": "APM"}, {"family": "Lambregts", "given": "Sander F H", "initials": "SFH"}, {"family": "Angel Wong", "given": "Y T", "initials": "YT"}, {"family": "Mafra", "given": "Lu\u00eds", "initials": "L"}, {"family": "Marin-Montesinos", "given": "Ildefonso", "initials": "I"}, {"family": "Rocha", "given": "Jo\u00e3o", "initials": "J", "orcid": "0000-0001-5460-7615", "researcher": {"href": "https://publications.scilifelab.se/researcher/37e0a929cf884352bbdc844b4db86f28.json"}}, {"family": "Sardo", "given": "Mariana", "initials": "M"}, {"family": "Brath", "given": "Ulrika", "initials": "U"}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Pinon", "given": "Arthur C", "initials": "AC"}, {"family": "Schantz", "given": "Staffan", "initials": "S", "orcid": "0000-0002-0136-4856", "researcher": {"href": "https://publications.scilifelab.se/researcher/d80e21a364f4412db2e0b837853e870c.json"}}, {"family": "\u0160olt\u00e9sov\u00e1", "given": "M\u00e1ria", "initials": "M"}, {"family": "Bachmann", "given": "Stephanie", "initials": "S"}, {"family": "Brown", "given": "Steven P", "initials": "SP"}, {"family": "Iuga", "given": "Dinu", "initials": "D"}, {"family": "Trent Franks", "given": "W", "initials": "W"}, {"family": "Menakath", "given": "Anjali", "initials": "A"}, {"family": "Frydman", "given": "Lucio", "initials": "L"}, {"family": "Mentink-Vigier", "given": "Frederic", "initials": "F", "orcid": "0000-0002-3570-9787", "researcher": {"href": "https://publications.scilifelab.se/researcher/9048df8f85bc4013bfc1bc633cc7914d.json"}}, {"family": "Schurko", "given": "Robert W", "initials": "RW"}, {"family": "Grohe", "given": "Kristof", "initials": "K", "orcid": "0000-0002-3388-4741", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b0bb68ef1204e4d99fd4acee3fe5471.json"}}, {"family": "Engelke", "given": "Frank", "initials": "F", "orcid": "0000-0002-5673-1705", "researcher": {"href": "https://publications.scilifelab.se/researcher/77af0d191e65475fb24a088ad1ea8cae.json"}}, {"family": "Kempf", "given": "James", "initials": "J"}, {"family": "Purea", "given": "Armin", "initials": "A"}, {"family": "Reiter", "given": "Christian", "initials": "C"}, {"family": "Wegner", "given": "Sebastian", "initials": "S"}, {"family": "Castro", "given": "Vanessa", "initials": "V"}, {"family": "Cobas", "given": "Carlos", "initials": "C"}, {"family": "Jeannerat", "given": "Damien", "initials": "D"}, {"family": "Seoane", "given": "Felipe", "initials": "F"}, {"family": "Vaz", "given": "Esther", "initials": "E"}, {"family": "Jardon Alvarez", "given": "Daniel", "initials": "D"}, {"family": "Leskes", "given": "Michal", "initials": "M"}, {"family": "De Biasi", "given": "Federico", "initials": "F"}, {"family": "Pintacuda", "given": "Guido", "initials": "G"}, {"family": "Lesage", "given": "Anne", "initials": "A"}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Solid State Nuclear Magnetic Resonance", "issn": "0926-2040", "volume": "140", "pages": "102048", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ssnmr.2025.102048", "pmid": "41218242", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:02:43.878Z", "modified": "2025-12-21T19:09:59.568Z"}, {"entity": "publication", "iuid": "1713323a9169478392c8d609c08e7c95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1713323a9169478392c8d609c08e7c95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1713323a9169478392c8d609c08e7c95"}}, "title": "The utility of combining deep learning with metabarcoding to model biodiversity dynamics at a national scale", "authors": [{"family": "Baggstr\u00f6m", "given": "Adrian", "initials": "A"}, {"family": "Goodsell", "given": "Robert", "initials": "R", "orcid": "0000-0002-3349-1876", "researcher": {"href": "https://publications.scilifelab.se/researcher/84f42755a394403b95486707bf4a83bd.json"}}, {"family": "van Dijk", "given": "Laura", "initials": "L", "orcid": "0000-0003-1015-8496", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c9432c19234fd5bc5dfc0a037dae0f.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Miraldo", "given": "Andreia", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}, {"family": "Andermann", "given": "Tobias", "initials": "T"}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Ecological Informatics", "issn": "1574-9541", "volume": "90", "pages": "103318", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ecoinf.2025.103318", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:42:58.970Z", "modified": "2025-11-29T08:23:53.494Z"}, {"entity": "publication", "iuid": "7678fc793c294277b98ffb7946623a97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7678fc793c294277b98ffb7946623a97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7678fc793c294277b98ffb7946623a97"}}, "title": "The effect of glycerol and protein structure on chemical degradation through deamidation and isomerization", "authors": [{"family": "Ramm", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-8724-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/b53c54dfbdf24cd2b40d9448697f94fd.json"}}, {"family": "Diehl", "given": "Carl", "initials": "C", "orcid": "0000-0002-0959-6459", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0b423e48d94456c929cc3b4adf92fcd.json"}}, {"family": "V\u00e4stberg", "given": "Amanda", "initials": "A", "orcid": "0000-0001-7418-5587", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ddf3722885746c196aad03b8241c7a6.json"}}, {"family": "Markova", "given": "Natalia", "initials": "N"}, {"family": "Schagerl\u00f6f", "given": "Herje", "initials": "H", "orcid": "0000-0003-1048-5059", "researcher": {"href": "https://publications.scilifelab.se/researcher/30b45f41e7ee4a09b5213ceb0750ca1e.json"}}, {"family": "Wahlgren", "given": "Marie", "initials": "M", "orcid": "0000-0002-1705-3964", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2bb0f5208294feb8930acbe9cf7920b.json"}}, {"family": "Nilsson", "given": "Lars", "initials": "L", "orcid": "0000-0002-6769-2641", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a5b0a72dd74f88a93f09a7e52c503a.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "International Journal of Pharmaceutics", "issn": "0378-5173", "volume": "686", "pages": "126322", "issn-l": "0378-5173"}, "abstract": null, "doi": "10.1016/j.ijpharm.2025.126322", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:05:18.280Z", "modified": "2025-11-27T08:05:18.660Z"}, {"entity": "publication", "iuid": "39d27f777a814e6eb3ad7aa9db9e0df5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39d27f777a814e6eb3ad7aa9db9e0df5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39d27f777a814e6eb3ad7aa9db9e0df5"}}, "title": "Swapped domain orders in ZO-1 PDZ3 fusion proteins - implications for binding of established and novel targets.", "authors": [{"family": "Hamsikova", "given": "Marie", "initials": "M"}, {"family": "Hurdalek", "given": "Jan", "initials": "J"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Ptacek", "given": "Jakub", "initials": "J"}, {"family": "Vydra Bousova", "given": "Kristyna", "initials": "K"}, {"family": "Vondrasek", "given": "Jiri", "initials": "J"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}, {"family": "Zemanova", "given": "Lucie", "initials": "L"}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "Arch. Biochem. Biophys.", "issn": "1096-0384", "volume": "774", "pages": "110634", "issn-l": "0003-9861"}, "abstract": "PDZ domains play key roles in mediating protein-protein interactions by recognizing short PDZ-binding motifs, typically at the C-termini of target proteins. Zonula occludens 1 (ZO-1) is a scaffolding protein that links tight junction proteins to the actin cytoskeleton, and contains three PDZ domains. Here, we focus on its third PDZ (PDZ3_ZO-1) domain, which interacts with the C-terminus of junctional adhesion protein A as well as connexin 45. To investigate how the domain context of the PDZ3_ZO-1 domain affects its folding and function, we previously established two distinct fusions of PDZ3_ZO-1 and a Trp-cage mini-protein. These fusions with swapped domain order result in FD3A with Trp-cage fused C-terminally and FD4A with Trp-cage fused N-terminally. This study aims to explore the extent to which the distinct Trp-cage fusions affect the function of PDZ3_ZO-1 domain in peptide binding. We find that PDZ3_ZO-1 retains its function, interaction with the connexin 45 peptide, also as part of the fusion proteins. Furthermore, using a phage display approach, we identified a new PDZ3_ZO-1 binding peptide derived from the C-terminal region of methylcytosine dioxygenase TET3. Subsequent validation revealed a significantly higher affinity of PDZ3_ZO-1 for the TET3 peptide as compared to the connexin 45 peptide. Thermodynamic analyses revealed that the swapped domain order conferred distinct effects on the thermodynamic parameters. These results provide insights into the structural and functional adaptability of PDZ domains in engineered proteins, and offer useful principles for the rational design of functional fusion proteins.", "doi": "10.1016/j.abb.2025.110634", "pmid": "41047091", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-9861(25)00348-0"}], "notes": [], "created": "2025-11-19T09:52:22.470Z", "modified": "2025-11-19T09:52:22.474Z"}, {"entity": "publication", "iuid": "eb353a9bcb454a23b3db2a1ab4f3bdde", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb353a9bcb454a23b3db2a1ab4f3bdde.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb353a9bcb454a23b3db2a1ab4f3bdde"}}, "title": "Soil carbon and nitrogen near alder, birch and spruce trees in four mixed Norway spruce-dominated stands", "authors": [{"family": "Soronen", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0003-3524-1632", "researcher": {"href": "https://publications.scilifelab.se/researcher/27b897d52d2c4f6fb4577ad7ce89336a.json"}}, {"family": "J\u00e4mtg\u00e5rd", "given": "Sandra", "initials": "S", "orcid": "0000-0002-5222-7878", "researcher": {"href": "https://publications.scilifelab.se/researcher/84162671e5bf4570b9c6b4eec94e96b5.json"}}, {"family": "Myllym\u00e4ki", "given": "Mari", "initials": "M", "orcid": "0000-0002-2713-7088", "researcher": {"href": "https://publications.scilifelab.se/researcher/a86b4b9d35ce4d70ae567312665d94e3.json"}}, {"family": "Smolander", "given": "Aino", "initials": "A", "orcid": "0000-0002-0406-5069", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d92fe70a525428aa974fba3255c8e4a.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Forest Ecology and Management", "issn": "0378-1127", "volume": "598", "pages": "123224", "issn-l": null}, "abstract": null, "doi": "10.1016/j.foreco.2025.123224", "pmid": null, "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-19T10:50:53.668Z", "modified": "2025-11-19T10:50:53.840Z"}, {"entity": "publication", "iuid": "beaa141e5dae4c429a581c0a53d7fd9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/beaa141e5dae4c429a581c0a53d7fd9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/beaa141e5dae4c429a581c0a53d7fd9b"}}, "title": "Quantitative and chemical adaptation of exopolymeric substances formed by a river microbial consortium during exposure to the antibiotic trimethoprim", "authors": [{"family": "Duteil", "given": "Thibault", "initials": "T", "orcid": "0009-0008-3494-5949", "researcher": {"href": "https://publications.scilifelab.se/researcher/63a2e8cc983f46c69390628e8f1df8f9.json"}}, {"family": "Gorzs\u00e1s", "given": "Andras", "initials": "A", "orcid": "0000-0002-2298-8844", "researcher": {"href": "https://publications.scilifelab.se/researcher/8070792ccead4c809c89943d84cf0e03.json"}}, {"family": "Ramstedt", "given": "Madeleine", "initials": "M", "orcid": "0000-0003-2646-8501", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0fb139ad40341fd85e4ba6fe39eb7fe.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Biofilm", "issn": "2590-2075", "volume": "10", "pages": "100334", "issn-l": null}, "abstract": null, "doi": "10.1016/j.bioflm.2025.100334", "pmid": null, "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-26T14:11:14.229Z", "modified": "2025-11-29T08:24:35.095Z"}, {"entity": "publication", "iuid": "a77133b5c6e1485c8c39308492347e7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a77133b5c6e1485c8c39308492347e7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a77133b5c6e1485c8c39308492347e7f"}}, "title": "Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.", "authors": [{"family": "Clasen", "given": "Frederick", "initials": "F"}, {"family": "Yildirim", "given": "Suleyman", "initials": "S"}, {"family": "Ar\u0131kan", "given": "Muzaffer", "initials": "M"}, {"family": "Garcia-Guevara", "given": "Fernando", "initials": "F"}, {"family": "Hano\u011flu", "given": "L\u0171tf\u0171", "initials": "L"}, {"family": "Y\u0131lmaz", "given": "Nesrin H", "initials": "NH"}, {"family": "\u015een", "given": "Aysu", "initials": "A"}, {"family": "Celik", "given": "Handan Kaya", "initials": "HK"}, {"family": "Neslihan", "given": "Alagoz Aybala", "initials": "AA"}, {"family": "Demir", "given": "Tu\u01e7\u00e7e Kahraman", "initials": "TK"}, {"family": "Temel", "given": "Zeynep", "initials": "Z"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Moyes", "given": "David L", "initials": "DL"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Shoaie", "given": "Saeed", "initials": "S", "orcid": "0000-0001-5834-4533", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fcd41a9a3645c3b733564c99a97aea.json"}}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "Gut Microbes", "issn": "1949-0984", "volume": "17", "issue": "1", "pages": "2506843", "issn-l": null}, "abstract": "The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson's Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.", "doi": "10.1080/19490976.2025.2506843", "pmid": "40420833", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12118390"}], "notes": [], "created": "2025-11-21T15:28:41.143Z", "modified": "2025-11-21T15:28:41.197Z"}, {"entity": "publication", "iuid": "a1a66eb9378f48bcbb9c32923b5503e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1a66eb9378f48bcbb9c32923b5503e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1a66eb9378f48bcbb9c32923b5503e3"}}, "title": "Genome Variation in Three Anthophora Bee Species Reflects Divergent Demographic Histories", "authors": [{"family": "Taliadoros", "given": "Demetris", "initials": "D"}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER", "orcid": "0000-0002-7768-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/2270d42b20f6456a8db81f41503b0063.json"}}, {"family": "Dias", "given": "Guilherme", "initials": "G", "orcid": "0000-0002-1459-3148", "researcher": {"href": "https://publications.scilifelab.se/researcher/73778a1096e04b5d94f8d5c6f3584d99.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59d0c98de64ac1a62234792258ee62.json"}}, {"family": "Olsson", "given": "Anna", "initials": "A", "orcid": "0000-0002-5438-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/57ec91022afd4c1390433d6383a06fc0.json"}}, {"family": "Mosbech", "given": "Mai\u2010Britt", "initials": "M", "orcid": "0000-0002-6068-0971", "researcher": {"href": "https://publications.scilifelab.se/researcher/efde81e53e6e48cba694e82e6fa8d38c.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}}, {"family": "Lager", "given": "Nina", "initials": "N"}, {"family": "Strand", "given": "Anna\u2010Sofi", "initials": "A"}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Cederberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lindblad\u2010Toh", "given": "Kerstin", "initials": "K"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Mol Ecol", "issn": "0962-1083", "pages": "e70204", "volume": "34", "issue": "24", "issn-l": "0962-1083"}, "abstract": "Population genomics can reveal trends and drivers of biodiversity loss, but it is still unclear how best to use measures of genome variation to understand population vulnerability in insects. Here we study genome variation in three species of Anthophora bees that show contrasting population trends in northern Europe. Two species, Anthophora plagiata and Anthophora retusa , have experienced declines and recoveries of different magnitudes in the last 50 years, whereas a third species, Anthophora quadrimaculata , has relative population stability. We generate highly contiguous genome assemblies and use them to study genome variation in 136 samples of these species collected throughout Sweden. We find exceedingly low genetic variation in A. plagiata , which has experienced a severe recent bottleneck, but high genetic variation in A. retusa , despite a similar recent population trajectory. Fragmented populations of the threatened species A. plagiata appear isolated from each other, but in A. retusa, there is a lack of deep population structure among geographically separated subpopulations. We infer population size in the distant past using MSMC2 and recent past using GONE. These methods are remarkably concordant and indicate ancient fluctuations in population size dating back to the Pleistocene, with moderate expansions in the past century in all three species. These results are comparable to some other studies of endangered insects, which have experienced population declines that predate the modern era. We detect long blocks of identity-by-state in A. plagiata , indicative of severe recent inbreeding. Translocations between isolated populations of this species could have a positive effect on their resilience.", "doi": "10.1111/mec.70204", "pmid": "41387163", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Short read": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-17T11:40:16.625Z", "modified": "2025-12-21T19:08:10.173Z"}, {"entity": "publication", "iuid": "d0efba99df6248a3aee00ad4fb43df6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d0efba99df6248a3aee00ad4fb43df6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d0efba99df6248a3aee00ad4fb43df6a"}}, "title": "EphA2 and phosphoantigen-mediated selective killing of medulloblastoma by \u03b3\u03b4T cells preserves neuronal and stem cell integrity.", "authors": [{"family": "Boutin", "given": "Lola", "initials": "L", "orcid": "0000-0001-7928-6731", "researcher": {"href": "https://publications.scilifelab.se/researcher/371c988cc4be47cf86c2c777922e3557.json"}}, {"family": "Liu", "given": "Mingzhi", "initials": "M", "orcid": "0000-0001-5842-8307", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dc5d2bd77664158976f148e4088ae5c.json"}}, {"family": "D\u00e9chanet Merville", "given": "Julie", "initials": "J", "orcid": "0000-0001-7521-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/986ece668416414f806bf451c436de31.json"}}, {"family": "Bedoya-Reina", "given": "Oscar", "initials": "O", "orcid": "0009-0001-1703-2258", "researcher": {"href": "https://publications.scilifelab.se/researcher/94abfc2a001941cb8c33b64271618be9.json"}}, {"family": "Wilhelm", "given": "Margareta T", "initials": "MT", "orcid": "0000-0002-0516-9724", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0ccfc8178142e4954e05e25613d751.json"}}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "Oncoimmunology", "issn": "2162-402X", "volume": "14", "issue": "1", "pages": "2485535", "issn-l": "2162-4011"}, "abstract": "Medulloblastoma (MB) is a pediatric brain tumor that develops in the cerebellum, representing one of the most common malignant brain cancers in children. Standard treatments include surgery, chemotherapy, and radiation, but despite a 5-y survival rate of approximately 70%, these therapies often lead to significant neurological damage in the developing brain. This underscores the urgent need for less toxic, more effective therapeutic alternatives. Recent advancements in cancer immunotherapy, including immune checkpoint inhibitors and CAR-T cell therapy, have revolutionized cancer treatment. One promising avenue is the use of Gamma Delta (\u03b3\u03b4)T cells, a unique T cell population with potential advantages, such as non-alloreactivity, potent tumor cell lysis, and broad antigen recognition. However, their capacity to recognize and target MB cells remains underexplored. To investigate the therapeutic potential of \u03b3\u03b4T cells against MB, we analyzed the proportion and status of MB-infiltrated \u03b3\u03b4T cells within patient datasets. We next investigated the expression of \u03b3\u03b4T cell ligands on MB cells and identified the EphA2 receptor and the phosphoantigen/Butyrophilin complex as key ligands, activating V\u03b39 V\u03b41 and V\u03b39 V\u03b42 T cells, respectively, leading to significant MB cell lysis in both monolayer and spheroid models. Importantly, preliminary safety data showed that \u03b3\u03b4T cells did not target differentiated neurons or neuroepithelial stem cells derived from induced pluripotent stem cells, underscoring the selectivity and safety of this approach. In conclusion, \u03b3\u03b4T cells trigger an efficient and specific killing of MB and would offer a promising novel therapeutic strategy.", "doi": "10.1080/2162402X.2025.2485535", "pmid": "40190167", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11980450"}], "notes": [], "created": "2025-11-28T10:48:34.549Z", "modified": "2025-11-28T10:48:34.769Z"}, {"entity": "publication", "iuid": "cf1b91a85bc74e92ad44a2a472bf97b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf1b91a85bc74e92ad44a2a472bf97b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf1b91a85bc74e92ad44a2a472bf97b8"}}, "title": "Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis.", "authors": [{"family": "Zheng", "given": "Chao", "initials": "C"}, {"family": "Herv\u00e9", "given": "Bastien", "initials": "B", "orcid": "0000-0002-2610-8365", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd3c5f38fbf64b30828c15839db38448.json"}}, {"family": "Meijer", "given": "Mandy", "initials": "M"}, {"family": "Rubio Rodr\u00edguez-Kirby", "given": "Leslie Ann", "initials": "LA"}, {"family": "Guerreiro Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b824181455243b19f4aa145a4545870.json"}}, {"family": "Kukanja", "given": "Petra", "initials": "P", "orcid": "0000-0003-1228-5923", "researcher": {"href": "https://publications.scilifelab.se/researcher/082ef6e681214c14b8ca36cd0188722b.json"}}, {"family": "Kabbe", "given": "Mukund", "initials": "M"}, {"family": "Jimenez-Beristain", "given": "Tony", "initials": "T", "orcid": "0009-0005-3756-3354", "researcher": {"href": "https://publications.scilifelab.se/researcher/9717ea6f895441649166ea40aa34d2c3.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Agirre", "given": "Eneritz", "initials": "E", "orcid": "0000-0002-5012-0305", "researcher": {"href": "https://publications.scilifelab.se/researcher/a507b19745c64c3bb8ef5dce800c8687.json"}}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "28", "issue": "12", "pages": "2612-2627", "issn-l": "1097-6256"}, "abstract": "Multiple sclerosis (MS) is a chronic autoimmune disease that targets mature oligodendrocytes (MOLs) and their myelin. MOLs are heterogeneous and can transition to immune-like states in MS. However, the dynamics of this process remain unclear. Here, we used single-cell multiome assay for transposase-accessible chromatin and RNA sequencing targeting oligodendroglia (OLG) from the experimental autoimmune encephalomyelitis (EAE) MS mouse model at multiple disease stages. We found that immune OLG states appear at early disease stages and persist to late stages, which can be consistent with epigenetic memory of previous neuroinflammation. Transcription factor activity suggested immunosuppression in OLG at early disease stages. Different MOLs exhibit differential responsiveness to EAE, with MOL2 exhibiting a stronger transcriptional immune response than MOL5/MOL6, and showed divergent responses at the epigenetic level during disease evolution. Our single-cell multiomic resource highlights dynamic and subtype-specific responses of OLG to EAE, which might be amenable to modulation in MS.", "doi": "10.1038/s41593-025-02100-3", "pmid": "41249698", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-025-02100-3"}], "notes": [], "created": "2025-12-04T08:40:54.011Z", "modified": "2025-12-04T08:40:54.919Z"}, {"entity": "publication", "iuid": "1c5a6133d47f4a73ae56d921da61b6df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c5a6133d47f4a73ae56d921da61b6df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c5a6133d47f4a73ae56d921da61b6df"}}, "title": "Development of DARPin T cell engagers for specific targeting of tumor-associated HLA/peptide complexes", "authors": [{"family": "Venetz-Arenas", "given": "Natalia", "initials": "N"}, {"family": "Schulte", "given": "Tim", "initials": "T"}, {"family": "M\u00fcller", "given": "Sandra", "initials": "S"}, {"family": "Wallden", "given": "Karin", "initials": "K"}, {"family": "Fischer", "given": "Stefanie", "initials": "S"}, {"family": "Resink", "given": "Tom", "initials": "T"}, {"family": "Kadri", "given": "Nadir", "initials": "N", "orcid": "0000-0003-2623-4094", "researcher": {"href": "https://publications.scilifelab.se/researcher/70724b181f324c7aac42468a177dcff4.json"}}, {"family": "Paladino", "given": "Maria", "initials": "M"}, {"family": "Pina", "given": "Nicole", "initials": "N"}, {"family": "Radom", "given": "Filip", "initials": "F"}, {"family": "Villemagne", "given": "Denis", "initials": "D"}, {"family": "Bruckmaier", "given": "Sandra", "initials": "S"}, {"family": "Cornelius", "given": "Andreas", "initials": "A"}, {"family": "Hospodarsch", "given": "Tanja", "initials": "T"}, {"family": "Alici", "given": "Evren", "initials": "E", "orcid": "0000-0001-5307-6648", "researcher": {"href": "https://publications.scilifelab.se/researcher/94af705a738741dd928e90fe403b9475.json"}}, {"family": "Ljunggren", "given": "Hans Gustaf", "initials": "HG", "orcid": "0000-0003-0908-7387", "researcher": {"href": "https://publications.scilifelab.se/researcher/54d696167bca4a389807143f84baeafe.json"}}, {"family": "Chambers", "given": "Benedict J", "initials": "BJ", "orcid": "0000-0003-0437-8441", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bdd56cf648f4411945163135f9a7140.json"}}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Sun", "given": "Renhua", "initials": "R", "orcid": "0000-0002-8203-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/f639c1a9dca647c0b583ce74ab398f02.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Levitsky", "given": "Victor", "initials": "V"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T", "orcid": "0000-0002-7694-6420", "researcher": {"href": "https://publications.scilifelab.se/researcher/8adca17a49fc47b696cb2b2795f83e6f.json"}}, {"family": "Walser", "given": "Marcel", "initials": "M"}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39682601d1a24f5ba1d103bf74c9acbd.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "28", "issue": "12", "pages": "113926", "issn-l": "2589-0042"}, "abstract": null, "doi": "10.1016/j.isci.2025.113926", "pmid": null, "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-23T22:19:59.150Z", "modified": "2025-12-21T19:10:20.517Z"}, {"entity": "publication", "iuid": "1ab30d614fe645a9a36ab3b2cc26b2ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ab30d614fe645a9a36ab3b2cc26b2ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ab30d614fe645a9a36ab3b2cc26b2ca"}}, "title": "Detailed analysis of fungal communities in Norway spruce logs reveals stochastic fine-scale patterns of species and detects lichen forming fungi without their photobionts", "authors": [{"family": "Dahlberg", "given": "Anders", "initials": "A", "orcid": "0000-0002-3669-6797", "researcher": {"href": "https://publications.scilifelab.se/researcher/a62efad22b414d618531b66ad404f689.json"}}, {"family": "Pioli", "given": "Silvia", "initials": "S"}, {"family": "J\u00f6nsson", "given": "Mari", "initials": "M"}, {"family": "Barbi", "given": "Florian", "initials": "F"}, {"family": "Thor", "given": "G\u00f6ran", "initials": "G"}, {"family": "Nogerius", "given": "Veera Tuovinen", "initials": "VT"}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Fungal Ecology", "issn": "1754-5048", "volume": "78", "pages": "101458", "issn-l": "1878-0083"}, "abstract": null, "doi": "10.1016/j.funeco.2025.101458", "pmid": null, "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T15:47:23.003Z", "modified": "2025-11-07T15:47:23.051Z"}, {"entity": "publication", "iuid": "f4983b166ef34a648b931cc81cb2c9ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4983b166ef34a648b931cc81cb2c9ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4983b166ef34a648b931cc81cb2c9ff"}}, "title": "Changes in silver birch biochemical profiles and leaf-associated fungi across genetic markers induced by seed treatment with DBD plasma", "authors": [{"family": "\u010c\u0117snien\u0117", "given": "Ieva", "initials": "I"}, {"family": "\u010c\u0117sna", "given": "Vytautas", "initials": "V", "orcid": "0000-0001-8446-0044", "researcher": {"href": "https://publications.scilifelab.se/researcher/f335b19c60674a38830fd7d255034736.json"}}, {"family": "Milda\u017eien\u0117", "given": "Vida", "initials": "V"}, {"family": "Mi\u0161kelyt\u0117", "given": "Diana", "initials": "D"}, {"family": "Ivanauskas", "given": "Liudas", "initials": "L"}, {"family": "Marksa", "given": "Mindaugas", "initials": "M"}, {"family": "Menkis", "given": "Audrius", "initials": "A", "orcid": "0000-0002-6545-8907", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d4d16d281344b9f9cf2c3c27fb40f06.json"}}, {"family": "Koga", "given": "Kazunori", "initials": "K"}, {"family": "Shiratani", "given": "Masaharu", "initials": "M"}, {"family": "Sirgedait\u0117-\u0160\u0117\u017eien\u0117", "given": "Vaida", "initials": "V", "orcid": "0000-0002-1607-0551", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ae9d6c2f4e849deb02a11b4d2f524d6.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Plant Stress", "issn": "2667-064X", "volume": "18", "pages": "101077", "issn-l": null}, "abstract": null, "doi": "10.1016/j.stress.2025.101077", "pmid": null, "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T15:45:49.452Z", "modified": "2025-12-03T11:32:15.068Z"}, {"entity": "publication", "iuid": "33a7dec56443449cb830664f081e4efb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33a7dec56443449cb830664f081e4efb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33a7dec56443449cb830664f081e4efb"}}, "title": "Acylcarnitine enrichment as a characteristic of rheumatoid arthritis fibroblast-like synoviocyte metabolic fingerprint.", "authors": [{"family": "Vasileiadis", "given": "Georgios K", "initials": "GK"}, {"family": "Zhang", "given": "Yuan", "initials": "Y"}, {"family": "Laudette", "given": "Marion", "initials": "M"}, {"family": "Fatima", "given": "Tahzeeb", "initials": "T"}, {"family": "Hultg\u00e5rd Ekwall", "given": "Anna-Karin", "initials": "AK"}, {"family": "Sureshkumar", "given": "Reshmi", "initials": "R"}, {"family": "van Vollenhoven", "given": "Ronald", "initials": "R"}, {"family": "Lampa", "given": "Jon", "initials": "J"}, {"family": "Gudbjornsson", "given": "Bjorn", "initials": "B"}, {"family": "Haavardsholm", "given": "Espen A", "initials": "EA"}, {"family": "Nordstr\u00f6m", "given": "Dan", "initials": "D"}, {"family": "Gr\u00f6ndal", "given": "Gerdur", "initials": "G"}, {"family": "H\u00f8rslev-Petersen", "given": "Kim", "initials": "K"}, {"family": "Lend", "given": "Kristina", "initials": "K"}, {"family": "Hetland", "given": "Merete L", "initials": "ML"}, {"family": "Nurmohamed", "given": "Michael", "initials": "M"}, {"family": "\u00d8stergaard", "given": "Mikkel", "initials": "M"}, {"family": "Uhlig", "given": "Till", "initials": "T"}, {"family": "Sokka-Isler", "given": "Tuulikki", "initials": "T"}, {"family": "Rudin", "given": "Anna", "initials": "A"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Guma", "given": "Monica", "initials": "M"}, {"family": "Maglio", "given": "Cristina", "initials": "C"}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "J Transl Autoimmun", "issn": "2589-9090", "volume": "11", "pages": "100310", "issn-l": null}, "abstract": "In rheumatoid arthritis (RA), fibroblast-like synoviocytes (FLS) alter their metabolism to support their activation. We aimed to analyse the full spectrum of metabolic alterations associated with RA by performing untargeted metabolomics in RA FLS vs. non-inflamed (NI) FLS.\n\nUntargeted annotated metabolomics was performed using mass spectrometry on ten primary RA and seven NI FLS culture extracts and 220 serum samples from participants with early RA from the randomised controlled NORD-STAR trial. Carnitine-related proteins were measured with Western blot. FLS bioenergetic profile was assessed with a Seahorse flux analyser.\n\nMetabolomics analysis based on 138 annotated metabolites revealed a distinct metabolic fingerprint between RA and NI FLS. Of the 12 metabolites enriched in RA FLS, 11 were acylcarnitines. Pro-inflammatory stimulation of NI FLS also led to acylcarnitine accumulation. RA FLS exhibited lower levels of CD36, a fatty acid transporter, but similar levels of L-carnitine transporter, and carnitine palmitoyltransferase 1 A and 2 compared to NI FLS. Seahorse analyses showed no difference in fatty acid oxidation between RA and NI FLS; however, RA FLS displayed mitochondrial dysfunction and energetic impairment. Serum acylcarnitine content decreased after 24 weeks of treatment with methotrexate combined with abatacept or tocilizumab in patients with early RA achieving remission.\n\nAcylcarnitine accumulation is a characteristic of RA FLS metabolic fingerprint and could be linked to mitochondrial dysfunction. In patients with early RA, acylcarnitine content in serum decreases after successful anti-rheumatic treatment. These results indicate a dysregulation in acylcarnitine metabolism in RA at the joint level and systemically.", "doi": "10.1016/j.jtauto.2025.100310", "pmid": "40894250", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12398893"}, {"db": "pii", "key": "S2589-9090(25)00045-0"}], "notes": [], "created": "2025-11-18T12:16:29.903Z", "modified": "2025-11-18T12:16:29.922Z"}, {"entity": "publication", "iuid": "7b0b2860d88b4862949004c3f62ec09a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b0b2860d88b4862949004c3f62ec09a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b0b2860d88b4862949004c3f62ec09a"}}, "title": "A nonlocal multiscale model for Brownian particles: Application to hindered deposition in microfluidic systems", "authors": [{"family": "Michael", "given": "Anand Joseph", "initials": "AJ", "orcid": "0009-0007-8405-3124", "researcher": {"href": "https://publications.scilifelab.se/researcher/68bc8ba52c12444bbc1ef722076de494.json"}}, {"family": "Mark", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0038-3307", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa2ef51b30a4a0b8a75d5f21f072d55.json"}}, {"family": "Sasic", "given": "Srdjan", "initials": "S"}, {"family": "Str\u00f6m", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8581-5174", "researcher": {"href": "https://publications.scilifelab.se/researcher/31cc6fcd18204618867df71bb45adb81.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "International Journal of Multiphase Flow", "issn": "0301-9322", "volume": "193", "pages": "105421", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ijmultiphaseflow.2025.105421", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:43:34.653Z", "modified": "2025-11-28T10:43:34.847Z"}, {"entity": "publication", "iuid": "52e091fbbc604aaab3844a78dc652c29", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52e091fbbc604aaab3844a78dc652c29.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52e091fbbc604aaab3844a78dc652c29"}}, "title": "Mapping Interactions Between Cytokines, Chemokines, Growth Factors, and Conventional Biomarkers in COVID-19 ICU-Patients", "authors": [{"family": "Eriksson", "given": "Mats B", "initials": "MB", "orcid": "0000-0002-3178-4210", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfcf6caaeeea422997c259d802e7e6f8.json"}}, {"family": "Marks-Hultstr\u00f6m", "given": "Michael", "initials": "M", "orcid": "0000-0003-4675-1099", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a74d3380a24c31930e6e671e685b5b.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Lipcsey", "given": "Mikl\u00f3s", "initials": "M", "orcid": "0000-0002-1976-4129", "researcher": {"href": "https://publications.scilifelab.se/researcher/81805f2324634628abefcf0ab6ce6a15.json"}}, {"family": "Frithiof", "given": "Robert", "initials": "R", "orcid": "0000-0003-2278-7951", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fec11dd18f941b7842610ad14237a35.json"}}, {"family": "Larsson", "given": "Anders O", "initials": "AO", "orcid": "0000-0003-3161-0402", "researcher": {"href": "https://publications.scilifelab.se/researcher/2276de26382b402aa384ac231f30f156.json"}}], "type": "journal-article", "published": "2025-11-26", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "23", "pages": "11419", "issn-l": null}, "abstract": null, "doi": "10.3390/ijms262311419", "pmid": null, "labels": {"Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-26T13:51:26.247Z", "modified": "2025-11-26T13:51:37.193Z"}, {"entity": "publication", "iuid": "81a8ff1347b741339d840038298a8e71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81a8ff1347b741339d840038298a8e71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81a8ff1347b741339d840038298a8e71"}}, "title": "Seal milk oligosaccharides rival human milk complexity and exhibit functional dynamics during lactation.", "authors": [{"family": "Jin", "given": "Chunsheng", "initials": "C", "orcid": "0000-0002-0229-102X", "researcher": {"href": "https://publications.scilifelab.se/researcher/458804f3f7274b8a9efe7a90469d0e56.json"}}, {"family": "Lundstr\u00f8m", "given": "Jon", "initials": "J", "orcid": "0000-0003-2733-7124", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9b642f0bae4a19ba21ed3db3e14d85.json"}}, {"family": "Cori", "given": "Carmen R", "initials": "CR"}, {"family": "Guu", "given": "Shih-Yun", "initials": "SY"}, {"family": "Bennett", "given": "Alexander R", "initials": "AR", "orcid": "0000-0003-4869-9132", "researcher": {"href": "https://publications.scilifelab.se/researcher/becd350a3553463bb37530cc639f281d.json"}}, {"family": "Dannborg", "given": "Mirjam", "initials": "M"}, {"family": "Pomeroy", "given": "Patrick P", "initials": "PP", "orcid": "0000-0003-1603-5630", "researcher": {"href": "https://publications.scilifelab.se/researcher/834269bd43b74cd8bc42aaa3600de72b.json"}}, {"family": "Kennedy", "given": "Malcolm W", "initials": "MW", "orcid": "0000-0002-0970-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1fc8fbe5d748c78ab9fdd182796176.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/267ff77d11e04a30bacdd0ae7492bea8.json"}}, {"family": "Hevey", "given": "Rachel", "initials": "R", "orcid": "0000-0002-2649-3427", "researcher": {"href": "https://publications.scilifelab.se/researcher/020432b915a84ec7a643efdfc8ec9e95.json"}}, {"family": "Khoo", "given": "Kay-Hooi", "initials": "KH"}, {"family": "Bojar", "given": "Daniel", "initials": "D", "orcid": "0000-0002-3008-7851", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a9b04a70e34849b1a54b8db3252807.json"}}], "type": "journal article", "published": "2025-11-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "10067", "issn-l": "2041-1723"}, "abstract": "Milk oligosaccharides are crucial for neonatal development and health in mammals. Yet most milk research focuses on humans, or on domesticated mammals that are poor in milk oligosaccharide complexity. Here, we perform an exhaustive mass spectrometry-driven structural characterization of milk oligosaccharides in a wild mammal, female Atlantic grey seals (Halichoerus grypus), throughout their lactation period. Characterizing and quantifying 332 milk oligosaccharides, including 166 unreported structures, we reveal seals to rival human milk in complexity. We report seal free oligosaccharides to reach up to 28 monosaccharides in size. Paired glycomics and metabolomics time course analysis establishes a concerted regulatory process reshaping the seal milk glycome throughout lactation, similar to human milk. Functional analysis of the structures we here characterized reveals anti-biofilm effects and immunomodulatory functions of seal milk oligosaccharides. Our findings challenge long-held assumptions about milk complexity of non-human mammals and enable insights into the functional relevance of complex carbohydrates in milk.", "doi": "10.1038/s41467-025-66075-2", "pmid": "41290693", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12647773"}, {"db": "pii", "key": "10.1038/s41467-025-66075-2"}], "notes": [], "created": "2026-01-27T13:07:39.913Z", "modified": "2026-01-27T13:07:41.170Z"}, {"entity": "publication", "iuid": "638e3981672c479bb5ffcd2ac87dc4d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/638e3981672c479bb5ffcd2ac87dc4d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/638e3981672c479bb5ffcd2ac87dc4d5"}}, "title": "Blood biomarkers of Alzheimer's disease and progression across different stages of cognitive decline in the community.", "authors": [{"family": "Valletta", "given": "Martina", "initials": "M", "orcid": "0000-0003-0139-8287", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa01849f48049c78eef04747ab1797a.json"}}, {"family": "Vetrano", "given": "Davide Liborio", "initials": "DL", "orcid": "0000-0002-3099-4830", "researcher": {"href": "https://publications.scilifelab.se/researcher/06867644d5f14eef958737353517f53d.json"}}, {"family": "Gregorio", "given": "Caterina", "initials": "C", "orcid": "0000-0002-8163-1634", "researcher": {"href": "https://publications.scilifelab.se/researcher/21265a4e63634efba72a5ee676156baa.json"}}, {"family": "Rizzuto", "given": "Debora", "initials": "D"}, {"family": "Winblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-0011-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/73185a13ca474153b66415e6a2dfff0f.json"}}, {"family": "Canevelli", "given": "Marco", "initials": "M"}, {"family": "Andersson", "given": "Sarah", "initials": "S"}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Laukka", "given": "Erika J", "initials": "EJ"}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "Grande", "given": "Giulia", "initials": "G", "orcid": "0000-0001-6312-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6fc0b0bad8243059965a2b828321c14.json"}}], "type": "journal article", "published": "2025-11-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "Blood biomarkers of Alzheimer's disease (AD) are promising for dementia prediction, but their association with progression across intermediate stages of cognitive decline in the general population remains unclear. We followed 2148 dementia-free individuals from a Swedish population-based cohort for up to 16 years. Associations between baseline AD blood biomarkers and transitions between normal cognition, mild cognitive impairment (MCI), and dementia were examined. Lower amyloid-\u03b242/40 ratio and higher phosphorylated-tau181 (p-tau181), p-tau217, total-tau, neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) were associated with faster progression from MCI to all-cause and AD dementia, with the strongest associations for NfL and p-tau217. Elevated NfL and GFAP were linked to reduced MCI reversion to normal cognition, whereas no biomarker was associated with MCI development from normal cognition. These findings show robust group-level associations and indicate that AD blood biomarkers may help stratify dementia risk at the MCI stage in the community.", "doi": "10.1038/s41467-025-66728-2", "pmid": "41276530", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-66728-2"}], "notes": [], "created": "2025-11-24T16:43:44.175Z", "modified": "2025-11-24T16:43:44.720Z"}, {"entity": "publication", "iuid": "61f674feb9bb47cc945261f439654003", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61f674feb9bb47cc945261f439654003.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61f674feb9bb47cc945261f439654003"}}, "title": "Single cell long read whole genome sequencing reveals somatic transposon activity in human brain.", "authors": [{"family": "Izydorczyk", "given": "Michal B", "initials": "MB"}, {"family": "Kalef-Ezra", "given": "Ester", "initials": "E", "orcid": "0000-0002-1297-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/7872b77059a7463a9d70214941f2da4e.json"}}, {"family": "Horner", "given": "Dominic W", "initials": "DW", "orcid": "0009-0002-1988-3838", "researcher": {"href": "https://publications.scilifelab.se/researcher/44931007770f44ce8e7f4d71ee2e0f53.json"}}, {"family": "Zheng", "given": "Xinchang", "initials": "X"}, {"family": "Holmes", "given": "Nadine", "initials": "N"}, {"family": "Toffoli", "given": "Marco", "initials": "M", "orcid": "0000-0002-3255-9648", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a1af99369b43d39dd36408491f25c2.json"}}, {"family": "Sahin", "given": "Zeliha", "initials": "Z"}, {"family": "Han", "given": "Yi", "initials": "Y", "orcid": "0000-0001-7605-8979", "researcher": {"href": "https://publications.scilifelab.se/researcher/2773c1d2c94f468fa78eed048bd13d3a.json"}}, {"family": "Mehta", "given": "Heer H", "initials": "HH"}, {"family": "Scholz", "given": "Sonja W", "initials": "SW", "orcid": "0000-0002-6623-0429", "researcher": {"href": "https://publications.scilifelab.se/researcher/7600f820a52a4e99b9b01480e8848669.json"}}, {"family": "Dalgard", "given": "Clifton L", "initials": "CL", "orcid": "0000-0003-2025-8239", "researcher": {"href": "https://publications.scilifelab.se/researcher/5476c12921064b89bd069f7942c40b71.json"}}, {"family": "Muzny", "given": "Donna M", "initials": "DM"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ", "orcid": "0000-0001-6040-2691", "researcher": {"href": "https://publications.scilifelab.se/researcher/28f940f4fb8b47ec8acb7ba04ca3890b.json"}}, {"family": "Proukakis", "given": "Christos", "initials": "C", "orcid": "0000-0001-6423-6539", "researcher": {"href": "https://publications.scilifelab.se/researcher/c159214a80944c8fa64910a0023d8c42.json"}}], "type": "journal article", "published": "2025-11-20", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "1627", "issn-l": "2399-3642"}, "abstract": "The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound impact. In this work we discover previously uncharacterized genomic dynamics in 18 cells from three human brains utilizing single cell long-read whole genome sequencing. This provides key insights into the dynamic of the genomes of individual cells and further highlights brain specific activity of transposable elements, but requires validation in larger studies.", "doi": "10.1038/s42003-025-08805-2", "pmid": "41266782", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Long read": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-025-08805-2"}], "notes": [], "created": "2025-11-21T06:20:40.789Z", "modified": "2025-11-21T06:20:42.030Z"}, {"entity": "publication", "iuid": "5aa825a515bd4748afa8d655ebf3d0ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5aa825a515bd4748afa8d655ebf3d0ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5aa825a515bd4748afa8d655ebf3d0ac"}}, "title": "NUDT5 regulates the global efficacy of nucleoside analog drugs by coordinating purine synthesis and PRPP allocation", "authors": [{"family": "Valerie", "given": "Nicholas C K", "initials": "NCK", "orcid": "0000-0002-9423-964X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d90c5a1f924c8b97409934dec74b0b.json"}}, {"family": "Alam", "given": "Seher", "initials": "S", "orcid": "0000-0002-8494-832X", "researcher": {"href": "https://publications.scilifelab.se/researcher/034588861fbc437bafe9cf7074ecd7ab.json"}}, {"family": "Hormann", "given": "Femke M", "initials": "FM", "orcid": "0000-0001-5164-3047", "researcher": {"href": "https://publications.scilifelab.se/researcher/79446287545b419aa569359af34b23ce.json"}}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Bostr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0001-5252-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af59464d2c74c27af7a43fb5d1a670e.json"}}, {"family": "Rudd", "given": "Sean G", "initials": "SG", "orcid": "0000-0002-4368-3855", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1e23d9748e4868a4b5e966e423b1a9.json"}}, {"family": "Arvidsson", "given": "Per I", "initials": "PI", "orcid": "0000-0002-9453-6812", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae064b90b750457e80e974947f2dfc7a.json"}}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}], "type": "posted-content", "published": "2025-11-20", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.11.20.689348", "pmid": null, "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T16:34:20.317Z", "modified": "2025-12-18T18:33:55.727Z"}, {"entity": "publication", "iuid": "d555a8f47fca4675abe9efcfa8dbb103", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d555a8f47fca4675abe9efcfa8dbb103.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d555a8f47fca4675abe9efcfa8dbb103"}}, "title": "PTBP1 variants displaying altered nucleocytoplasmic distribution are responsible for a neurodevelopmental disorder with skeletal dysplasia.", "authors": [{"family": "Masson", "given": "Aymeric", "initials": "A"}, {"family": "Paccaud", "given": "Julien", "initials": "J"}, {"family": "Orefice", "given": "Martina", "initials": "M"}, {"family": "Colin", "given": "Estelle", "initials": "E"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "Cormier-Daire", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Relator", "given": "Raissa", "initials": "R"}, {"family": "Ghosh", "given": "Sourav", "initials": "S"}, {"family": "Strub", "given": "Jean-Marc", "initials": "JM"}, {"family": "Schaeffer-Reiss", "given": "Christine", "initials": "C"}, {"family": "Marcelis", "given": "Carlo", "initials": "C"}, {"family": "Koolen", "given": "David A", "initials": "DA"}, {"family": "Pfundt", "given": "Rolph", "initials": "R"}, {"family": "de Boer", "given": "Elke", "initials": "E"}, {"family": "Vissers", "given": "Lisenka Elm", "initials": "LE"}, {"family": "Gardeitchik", "given": "Thatjana", "initials": "T"}, {"family": "Aarts", "given": "Lonneke Am", "initials": "LA"}, {"family": "Rinne", "given": "Tuula", "initials": "T"}, {"family": "Terhal", "given": "Paulien A", "initials": "PA"}, {"family": "Verbeek", "given": "Nienke E", "initials": "NE"}, {"family": "Zuurbier", "given": "Linda C", "initials": "LC"}, {"family": "Plomp", "given": "Astrid S", "initials": "AS"}, {"family": "Wessels", "given": "Marja W", "initials": "MW"}, {"family": "de Man", "given": "Stella A", "initials": "SA"}, {"family": "Bouman", "given": "Arjan", "initials": "A"}, {"family": "Bird", "given": "Lynne M", "initials": "LM"}, {"family": "Saadeh-Haddad", "given": "Reem", "initials": "R"}, {"family": "Guillen Sacoto", "given": "Maria J", "initials": "MJ"}, {"family": "Person", "given": "Richard", "initials": "R"}, {"family": "Gooch", "given": "Catherine", "initials": "C"}, {"family": "Hurst", "given": "Anna Ce", "initials": "AC"}, {"family": "Thompson", "given": "Michelle L", "initials": "ML"}, {"family": "Hiatt", "given": "Susan M", "initials": "SM"}, {"family": "Littlejohn", "given": "Rebecca O", "initials": "RO"}, {"family": "Roeder", "given": "Elizabeth R", "initials": "ER"}, {"family": "Mori", "given": "Mari", "initials": "M"}, {"family": "Hickey", "given": "Scott E", "initials": "SE"}, {"family": "Hunter", "given": "Jesse M", "initials": "JM"}, {"family": "Lee", "given": "Kristy", "initials": "K"}, {"family": "Osman", "given": "Khaled", "initials": "K"}, {"family": "Halloun", "given": "Rana", "initials": "R"}, {"family": "Bachmann-Gagescu", "given": "Ruxandra", "initials": "R"}, {"family": "Rauch", "given": "Anita", "initials": "A"}, {"family": "Wieczorek", "given": "Dagmar", "initials": "D"}, {"family": "Platzer", "given": "Konrad", "initials": "K"}, {"family": "Luppe", "given": "Johannes", "initials": "J"}, {"family": "Duplomb-Jego", "given": "Laurence", "initials": "L"}, {"family": "El It", "given": "Fatima", "initials": "F"}, {"family": "Duffourd", "given": "Yannis", "initials": "Y"}, {"family": "Tran Mau-Them", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}, {"family": "Huber", "given": "Celine", "initials": "C"}, {"family": "Gordon", "given": "Christopher T", "initials": "CT"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "M\u00e4kitie", "given": "Riikka E", "initials": "RE"}, {"family": "Costantini", "given": "Alice", "initials": "A"}, {"family": "Valta", "given": "Helena", "initials": "H"}, {"family": "Robertson", "given": "Stephen", "initials": "S"}, {"family": "Poke", "given": "Gemma", "initials": "G"}, {"family": "Francoise", "given": "Michel", "initials": "M"}, {"family": "Ciolfi", "given": "Andrea", "initials": "A"}, {"family": "Tartaglia", "given": "Marco", "initials": "M"}, {"family": "Ekhilevitch", "given": "Nina", "initials": "N"}, {"family": "Zaid", "given": "Rinat", "initials": "R"}, {"family": "Levy", "given": "Michael A", "initials": "MA"}, {"family": "Kerkhof", "given": "Jennifer", "initials": "J"}, {"family": "McConkey", "given": "Haley", "initials": "H"}, {"family": "Delanne", "given": "Julian", "initials": "J"}, {"family": "Chevarin", "given": "Martin", "initials": "M"}, {"family": "Vautrot", "given": "Valentin", "initials": "V"}, {"family": "Bourgeois", "given": "Valentin", "initials": "V"}, {"family": "Nguyen", "given": "Sylvie", "initials": "S"}, {"family": "Marle", "given": "Nathalie", "initials": "N"}, {"family": "Callier", "given": "Patrick", "initials": "P"}, {"family": "Safraou", "given": "Hana", "initials": "H"}, {"family": "Morgan", "given": "Angela", "initials": "A"}, {"family": "Amor", "given": "David J", "initials": "DJ"}, {"family": "Hildebrand", "given": "Michael S", "initials": "MS"}, {"family": "Coman", "given": "David", "initials": "D"}, {"family": "Aubert Mucca", "given": "Marion", "initials": "M"}, {"family": "Thevenon", "given": "Julien", "initials": "J"}, {"family": "Laffargue", "given": "Fanny", "initials": "F"}, {"family": "Bilan", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}, {"family": "Pebrel-Richard", "given": "C\u00e9line", "initials": "C"}, {"family": "Yoon", "given": "Grace", "initials": "G"}, {"family": "Axford", "given": "Michelle M", "initials": "MM"}, {"family": "P\u00e9rez-Jurado", "given": "Luis A", "initials": "LA"}, {"family": "Sevilla-Porras", "given": "Marta", "initials": "M"}, {"family": "Black", "given": "Douglas L", "initials": "DL"}, {"family": "Philippe", "given": "Christophe", "initials": "C"}, {"family": "Sadikovic", "given": "Bekim", "initials": "B"}, {"family": "Thauvin-Robinet", "given": "Christel", "initials": "C"}, {"family": "Olivier-Faivre", "given": "Laurence", "initials": "L"}, {"family": "Ori", "given": "Michela", "initials": "M"}, {"family": "Thomas", "given": "Quentin", "initials": "Q"}, {"family": "Vitobello", "given": "Antonio", "initials": "A"}], "type": "journal article", "published": "2025-11-17", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "135", "issue": "22", "issn-l": "0021-9738"}, "abstract": "Polypyrimidine tract-binding protein 1 (PTBP1) is a heterogeneous nuclear ribonucleoprotein primarily known for its alternative splicing activity. It shuttles between the nucleus and cytoplasm via partially overlapping N-terminal nuclear localization (NLS) and export (NES) signals. Despite its fundamental role in cell growth and differentiation, its involvement in human disease remains poorly understood. We identified 27 individuals from 25 families harboring de novo or inherited pathogenic variants - predominantly start-loss (89%) and, to a lesser extent, missense (11%) - affecting NES/NLS motifs. Affected individuals presented with a syndromic neurodevelopmental disorder and variable skeletal dysplasia with disproportionate short stature with short limbs. Intellectual functioning ranged from normal to moderately delayed. Start-loss variants led to translation initiation from an alternative downstream in-frame methionine, resulting in loss of the NES and the first half of the bipartite NLS, and increased cytoplasmic stability. Start-loss and missense variants shared a DNA methylation episignature in peripheral blood and altered nucleocytoplasmic distribution in vitro and in vivo with preferential accumulation in processing bodies, causing aberrant gene expression but normal RNA splicing. Transcriptomic analysis of patient-derived fibroblasts revealed dysregulated pathways involved in osteochondrogenesis and neurodevelopment. Overall, our findings highlight a cytoplasmic role for PTBP1 in RNA stability and disease pathogenesis.", "doi": "10.1172/JCI182100", "pmid": "40965981", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12618068"}, {"db": "pii", "key": "182100"}], "notes": [], "created": "2025-11-20T20:36:03.867Z", "modified": "2025-11-20T20:36:03.881Z"}, {"entity": "publication", "iuid": "1760e26a9d4c48d7b1cab8cc140eb637", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1760e26a9d4c48d7b1cab8cc140eb637.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1760e26a9d4c48d7b1cab8cc140eb637"}}, "title": "Correcting CFTR mRNA splicing defects with the plant cytokine kinetin and its analogues.", "authors": [{"family": "Rimoldi", "given": "Valeria", "initials": "V"}, {"family": "Sold\u00e0", "given": "Giulia", "initials": "G"}, {"family": "Capalbo", "given": "Anita", "initials": "A"}, {"family": "Saba", "given": "Elena", "initials": "E"}, {"family": "Giannone", "given": "Valentina", "initials": "V"}, {"family": "Capurro", "given": "Valeria", "initials": "V"}, {"family": "Lentini", "given": "Laura", "initials": "L"}, {"family": "Melfi", "given": "Raffaella", "initials": "R"}, {"family": "Lazzeri", "given": "Massimo", "initials": "M"}, {"family": "Porcaro", "given": "Luigi", "initials": "L"}, {"family": "Seia", "given": "Manuela", "initials": "M"}, {"family": "Aureli", "given": "Massimo", "initials": "M"}, {"family": "Pedemonte", "given": "Nicoletta", "initials": "N"}, {"family": "Duga", "given": "Stefano", "initials": "S"}, {"family": "Orrenius", "given": "Christian", "initials": "C"}, {"family": "Asselta", "given": "Rosanna", "initials": "R"}, {"family": "Straniero", "given": "Letizia", "initials": "L"}], "type": "journal article", "published": "2025-11-15", "journal": {"title": "J Cyst Fibros", "issn": "1873-5010", "issn-l": null}, "abstract": "Cystic Fibrosis (CF) results from CFTR gene mutations, including splicing defects such as the polymorphic TGnTm repeat, which disrupts exon-10 inclusion and contributes to CF monosymptomatic forms. While recent advances in CF treatment have led to targeted therapies for specific CFTR defects, most splicing variants remain without an effective treatment. Small molecules, like the plant cytokine kinetin, have shown promise in correcting splicing defects in other genetic diseases, offering potential for personalized CF therapies.\n\nThis study evaluated the efficacy of kinetin and its analogue, RECTAS, in correcting CFTR exon-10 splicing defects caused by TGnTm repeats. Cell models and patient-derived cells were treated with both compounds to assess their ability to enhance exon-10 inclusion. The impact of these treatments on splicing correction and CFTR protein expression was analyzed using molecular and cellular assays.\n\nBoth kinetin and RECTAS improved exon-10 inclusion, with RECTAS demonstrating superior efficacy, achieving up to a four-fold increase in patient-derived cells compared to kinetin. Additionally, RECTAS consistently rescued exon-10 splicing across various TG-T alleles and successfully restored CFTR protein expression, highlighting its potential as a more potent therapeutic option.\n\nThese findings identify RECTAS as an effective modulator of CFTR splicing. Rather than stand-alone therapeutics, kinetin and its analogues may act as transcript amplifiers, thereby possibly enhancing the efficacy of existing CFTR modulators. This approach could broaden treatment options for splicing-related CFTR variants and other genetic disorders.", "doi": "10.1016/j.jcf.2025.11.006", "pmid": "41242903", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service"}, "xrefs": [{"db": "pii", "key": "S1569-1993(25)02502-0"}], "notes": [], "created": "2025-11-18T17:30:11.530Z", "modified": "2025-11-18T17:30:11.566Z"}, {"entity": "publication", "iuid": "823c71158dcd4b9fb085d01e55d13e48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/823c71158dcd4b9fb085d01e55d13e48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/823c71158dcd4b9fb085d01e55d13e48"}}, "title": "scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.", "authors": [{"family": "Yadav", "given": "Ram Prakash", "initials": "RP"}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Hollander", "given": "Peter", "initials": "P"}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Xie", "given": "Minglu", "initials": "M"}, {"family": "Salehi", "given": "Maede", "initials": "M"}, {"family": "Torell", "given": "Emma", "initials": "E"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}, {"family": "Swartling", "given": "Fredrik Johansson", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Glimelius", "given": "Ingrid", "initials": "I"}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "10022", "issn-l": "2041-1723"}, "abstract": "Formalin-fixed paraffin-embedded (FFPE) samples are the gold standard for tissue preservation in clinical and research settings. Current single-cell chromatin accessibility technologies cannot resolve cell-type-specific epigenetic profiles in FFPE tissues due to extensive DNA damage. We present scFFPE-ATAC, a high-throughput single-cell chromatin accessibility assay for FFPE samples that integrates an FFPE-adapted Tn5 transposase, ultra-high-throughput DNA barcoding (>56 million barcodes per run), T7 promoter-mediated DNA damage repair, and in vitro transcription. We benchmark scFFPE-ATAC on FFPE mouse spleen and validate its performance against fresh tissue. We apply it to human lymph node samples archived for 8-12 years and to lung cancer FFPE tissues, revealing distinct regulatory trajectories between tumor center and invasive edge. Analysis of archived follicular lymphoma and transformed diffuse large B-cell lymphoma samples identifies relapse- and transformation-associated epigenetic dynamics. scFFPE-ATAC enables retrospective, spatial, and mechanistic epigenetic studies in long-term archived specimens.", "doi": "10.1038/s41467-025-66170-4", "pmid": "41238550", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-66170-4"}, {"db": "pmc", "key": "PMC12618699"}], "notes": [], "created": "2025-11-17T09:00:46.632Z", "modified": "2025-11-17T09:00:47.092Z"}, {"entity": "publication", "iuid": "e7e4997a81904bfca3075b1e45f9cb0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7e4997a81904bfca3075b1e45f9cb0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7e4997a81904bfca3075b1e45f9cb0e"}}, "title": "Validation of a Genetic Risk Score Combined with Clinical Variables for Predicting Pulmonary Fibrosis in early Rheumatoid Arthritis.", "authors": [{"family": "Brink", "given": "Mikael", "initials": "M", "orcid": "0000-0001-7675-3488", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecbce4cc891249c5b96f71b6586aa777.json"}}, {"family": "Wheeler", "given": "Austin", "initials": "A", "orcid": "0000-0002-8816-7782", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcae89f571644e0c9aeb200574256acb.json"}}, {"family": "England", "given": "Bryant R", "initials": "BR", "orcid": "0000-0002-9649-3588", "researcher": {"href": "https://publications.scilifelab.se/researcher/3197cc141bd449728e5e65659fc2cada.json"}}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "Arthritis Care Res (Hoboken)", "issn": "2151-4658", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Pulmonary fibrosis (PF) is a severe extra-articular manifestation of rheumatoid arthritis (RA). The study aimed to externally validate a genetic risk score (GRS) and a combined risk score for predicting the risk of RA-associated PF in an independent cohort of early-RA patients.\r\n\r\nThis study utilized an inception cohort of 1118 patients diagnosed with RA from northern Sweden between 1996 and 2016. Clinical data were systematically collected, and genotyping was performed for 12 single-nucleotide polymorphisms (SNPs) associated with idiopathic pulmonary fibrosis. Statistical analyses, including logistic regression and area under the curve (AUC) assessments, were conducted to evaluate the performance of the GRS and in combination with clinical data as combined risk score in predicting RA-PF development.\r\n\r\nOf the 1115 patients with complete data, 60 (5.6%) were diagnosed with PF. PF was significantly associated with age, rheumatoid factor positivity, disease activity, and MUC5B (rs35705950) and FAM13A(rs2609255) SNPs. The GRS demonstrated a significant association with RA-PF (odds ratio 2.6, (95%CI 1.6, 4.5), while the combined risk score exhibited superior performance (AUC 0.75, p<0.001) compared to the GRS alone (AUC 0.62). The combined risk score outperformed the GRS in discriminating RA-PF, indicating its potential utility in clinical practice.\r\n\r\nThis study provides external validation of the VARA-ILD-GRS and VARA-ILD combined risk score in an RA cohort, demonstrating their generalizability and effectiveness in identifying high-risk individuals for RA-ILD. The findings support the integration of genetic and clinical data in risk stratification models, which could significantly improve screening strategies for RA patients at risk of developing PF.", "doi": "10.1002/acr.25696", "pmid": "41236136", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Ume\u00e5": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-26T09:18:10.968Z", "modified": "2026-02-10T09:57:37.145Z"}, {"entity": "publication", "iuid": "4aa787602e4e4678988c48ce41e25ce7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4aa787602e4e4678988c48ce41e25ce7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4aa787602e4e4678988c48ce41e25ce7"}}, "title": "Ancient RNA expression profiles from the extinct woolly mammoth.", "authors": [{"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E"}, {"family": "Fromm", "given": "Bastian", "initials": "B"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Aslanzadeh", "given": "Morteza", "initials": "M"}, {"family": "Bozlak", "given": "Elif", "initials": "E"}, {"family": "Brown", "given": "Katherine", "initials": "K"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Furug\u00e5rd", "given": "Cecilia", "initials": "C"}, {"family": "Plotnikov", "given": "Valeri", "initials": "V"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Peterson", "given": "Kevin J", "initials": "KJ"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": null, "issue": null, "pages": null}, "abstract": "Ancient DNA has revolutionized the study of extinct and extant organisms that lived up to 2 million years ago, enabling the reconstruction of genomes from multiple extinct species, as well as the ecosystems where they once thrived. However, current DNA sequencing techniques alone cannot directly provide insights into tissue identity, gene expression dynamics, or transcriptional regulation, as these are encoded in the RNA fraction. Here, we report transcriptional profiles from 10 Late Pleistocene woolly mammoths. One of these, dated to be \u223c39,000 years old, yielded sufficient detail to recover tissue-specific regulatory mechanisms and biological functions essential for skeletal muscle metabolism, representing the oldest ancient RNA sequences recorded to date. We showcase the potential to study ancient RNA molecules beyond preconceived limitations, providing an analytical framework for validating and decoding preserved transcriptomes through time. With our findings, we anticipate the emergence of integrative paleo-studies combining genomics, proteomics, and transcriptomics.", "doi": "10.1016/j.cell.2025.10.025", "pmid": "41240910", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)01231-0"}], "notes": [], "created": "2025-11-17T15:01:06.080Z", "modified": "2025-11-19T07:44:17.391Z"}, {"entity": "publication", "iuid": "5087e22117c64ebbbc4b4299bfc98b9a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5087e22117c64ebbbc4b4299bfc98b9a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5087e22117c64ebbbc4b4299bfc98b9a"}}, "title": "A [11C]PBR28 PET study on the associations between sleep health and microglial density.", "authors": [{"family": "Balter", "given": "Leonie Jt", "initials": "LJ"}, {"family": "Malmros", "given": "Jonatan", "initials": "J"}, {"family": "Stenkrona", "given": "Per", "initials": "P"}, {"family": "Varrone", "given": "Andrea", "initials": "A"}, {"family": "Forsberg", "given": "Anton", "initials": "A"}, {"family": "Gustavsson", "given": "Erik", "initials": "E"}, {"family": "Mouyobo", "given": "Cedrique E", "initials": "CE"}, {"family": "Kalpouzos", "given": "Gr\u00e9goria", "initials": "G"}, {"family": "Papenberg", "given": "Goran", "initials": "G"}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "J Neuroinflammation", "issn": "1742-2094", "volume": "22", "issue": "1", "pages": "270", "issn-l": "1742-2094"}, "abstract": "Sleep disturbances and inflammation are interconnected through shared regulatory mechanisms and are both implicated in age-related diseases. However, their connection at the level of brain-specific inflammation remains underexamined in humans. This study investigated whether specific dimensions of sleep are associated with microglial density, as measured by translocator protein (TSPO) levels, a biomarker of neuroinflammation. TSPO levels were measured using a single [11C]PBR28 positron emission tomography (PET) scan in 39 healthy adults aged 50-81 years (Mage = 66.7, SD = 8.9; 19 females, 20 males). Sleep dimensions were assessed using the Karolinska Sleep Questionnaire on three occasions over five years, twice before and once around the time of PET imaging. Shorter sleep, more frequent napping, daytime fatigue, and sleep insufficiency were associated with higher TSPO levels in the middle frontal cortex (MFC). Conversely, longer sleep was associated with higher TSPO levels in the hippocampus and putamen. Exploratory factor analysis and bootstrapping confirmed a negative association between a factor representing shorter sleep and MFC TSPO levels. Additionally, a greater deviation from optimal sleep duration over the five years, in either direction from eight hours, was associated with higher current TSPO levels in all but one examined brain regions. Peripheral C-reactive protein levels did not significantly correlate with the sleep variables or TSPO levels in any of the brain regions. Analyses were adjusted for age and sex. These findings suggest that insufficient and prolonged sleep durations are associated with elevated microglial density in frontostriatal and limbic systems, respectively, among healthy middle-aged and older adults, without any associations with peripheral inflammation. Further longitudinal studies are needed to clarify directionality and whether changes in sleep duration over time may serve as early indicators of brain health.", "doi": "10.1186/s12974-025-03613-1", "pmid": "41239401", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12619189"}, {"db": "pii", "key": "10.1186/s12974-025-03613-1"}], "notes": [], "created": "2025-11-18T15:39:15.446Z", "modified": "2025-11-18T15:39:15.465Z"}, {"entity": "publication", "iuid": "22942ea7e4604351ab779e9dac5bcad1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22942ea7e4604351ab779e9dac5bcad1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22942ea7e4604351ab779e9dac5bcad1"}}, "title": "That's So Last Season: Unraveling the Genomic Consequences of Fur Farming in Arctic Foxes (Vulpes lagopus).", "authors": [{"family": "Cockerill", "given": "Christopher A", "initials": "CA", "orcid": "0000-0001-9776-3183", "researcher": {"href": "https://publications.scilifelab.se/researcher/43a0788d687045f7b0257996a55327b0.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Bj\u00f6rklund", "given": "Gabriella", "initials": "G"}, {"family": "Hasselgren", "given": "Malin", "initials": "M", "orcid": "0000-0002-4875-4413", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e7f1368a98040f4a683c3d082483079.json"}}, {"family": "Wall\u00e9n", "given": "Johan", "initials": "J"}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Fuglei", "given": "Eva", "initials": "E"}, {"family": "Unnsteinsdottir", "given": "Ester Rut", "initials": "ER"}, {"family": "White", "given": "Paula", "initials": "P"}, {"family": "Samelius", "given": "Gustaf", "initials": "G"}, {"family": "Alisauskas", "given": "Ray", "initials": "R"}, {"family": "Berteaux", "given": "Dominique", "initials": "D"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Landa", "given": "Arild", "initials": "A"}, {"family": "Eide", "given": "Nina E", "initials": "NE"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "P\u00e1lsson", "given": "Sn\u00e6bj\u00f6rn", "initials": "S", "orcid": "0000-0002-4297-3500", "researcher": {"href": "https://publications.scilifelab.se/researcher/44a3d48564f04b5ea53d14f19bb623cc.json"}}, {"family": "Magn\u00fasson", "given": "Kristinn P\u00e9tur", "initials": "KP"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K", "orcid": "0000-0002-9707-5206", "researcher": {"href": "https://publications.scilifelab.se/researcher/40450a7e8cda45ba8292b9a677b3fb29.json"}}], "type": "journal article", "published": "2025-11-13", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": null, "issue": null, "pages": "e70166"}, "abstract": "Humans have relied on animal fur for centuries, yet fur farming only began recently during the mid-19th Century. Little is known about this incipient domestication or the genomic processes involved. Domestication may involve founder effects, population bottlenecks and low population size, which, when combined with intense artificial selection, lead to inbreeding, a limited gene pool and reduced fitness. The arctic fox (Vulpes lagopus) has been farmed intensively since the early 1900s and has been artificially selected for economic phenotypes. We investigated the origin of these lineages and the genomic consequences of intensive farming by comparing the genomes of farmed and wild arctic foxes from across their range. Our research indicates recent inbreeding through long Runs of Homozygosity and reduced genomic variation in farmed foxes relative to their respective wild populations. We identified a coastal ecotype origin for all Fennoscandian farmed arctic foxes, aligning them phylogenetically with the wild Icelandic population, a geographically isolated and phenotypically distinct coastal lineage. The depleted genome-wide heterozygosity and increased recent inbreeding in farmed fox lineages is consistent with a heavy consequence of domestication, shedding light on the demographic history and genomic consequences of human manipulation. We highlight the need for increased genomic investigations into fur farm populations to understand the incipient domestication process and uncover the cost of intense farming. The genomic consequences of domestication must be considered in the management of fur farms, with actionable steps needed to prevent descendants of escaped farmed foxes from polluting the gene pool in the wild through introgression.", "doi": "10.1111/mec.70166", "pmid": "41229383", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Long read": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-16T14:58:28.536Z", "modified": "2025-11-19T07:43:38.634Z"}, {"entity": "publication", "iuid": "ea689d9e74e64cb4b41ca1602aa8832b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea689d9e74e64cb4b41ca1602aa8832b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea689d9e74e64cb4b41ca1602aa8832b"}}, "title": "Glucosinolate diversity in seven field-collected Brassicaceae species.", "authors": [{"family": "Pormetter", "given": "Lisa", "initials": "L"}, {"family": "Pfalz", "given": "Marina", "initials": "M"}, {"family": "Kagho", "given": "Mervic D", "initials": "MD", "orcid": "0000-0003-3714-7738", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0d7812a50e942f09ec2df8bb7d6e287.json"}}, {"family": "Klahn", "given": "Philipp", "initials": "P", "orcid": "0000-0003-4713-2345", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c6f067dc85a4e12b3593401e34e36d6.json"}}, {"family": "Vogel", "given": "Heiko", "initials": "H"}, {"family": "Kroymann", "given": "Juergen", "initials": "J", "orcid": "0000-0002-4573-6498", "researcher": {"href": "https://publications.scilifelab.se/researcher/3054f0bc1428466ea02890db7a2258f1.json"}}, {"family": "Wittstock", "given": "Ute", "initials": "U", "orcid": "0000-0002-0914-8453", "researcher": {"href": "https://publications.scilifelab.se/researcher/016de873c14341b0b9778de1d5cb7cf9.json"}}], "type": "journal article", "published": "2025-11-13", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "11", "pages": "e0336172", "issn-l": "1932-6203"}, "abstract": "The glucosinolate-myrosinase system is a well-known chemical defense in the Brassicales order, which has been extensively studied in Arabidopsis thaliana. Here, we assessed natural variation of leaf glucosinolate content and profiles in seven species of the Brassicaceae family, using over 300 cauline leaf samples collected from wild populations in Germany and France. Total glucosinolate content varied substantially among individuals, populations and species. Analysis of glucosinolate profiles identified two types of profiles each for Cardamine amara and C. pratensis, and three profile types for C. impatiens. One profile type for each Cardamine species showed glucosinolate compositions distinct from previously described profile types. In contrast, the glucosinolate profiles of the other four species - Lepidium draba, Lunaria rediviva, Hesperis matronalis, and Descurainia sophia - were less variable. The obtained dataset paves the way for more detailed analyses of the genetic basis of glucosinolate biosynthesis in these species. Our data indicate that, among plutellid species whose larvae feed exclusively on cruciferous host plants, the oligophagous Eidophasia messingiella and Rhigognostis senilella are exposed to a diverse array of glucosinolate structures. In contrast, Plutella porrectella primarily encounters only a limited set of unusual glucosinolates when feeding on its preferred host plant, H. matronalis. Future research is required to evaluate whether this has led to specialized adaptations in this Lepidopteran herbivore. Furthermore, our study indicates that the unpredictable variation in total glucosinolate content as detected in our field-collected samples might pose a substantial challenge even to adapted herbivores.", "doi": "10.1371/journal.pone.0336172", "pmid": "41231778", "labels": {"Swedish NMR Centre": "Service", "Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12614607"}, {"db": "pii", "key": "PONE-D-25-13852"}], "notes": [], "created": "2025-11-27T08:05:23.538Z", "modified": "2026-01-27T13:36:50.874Z"}, {"entity": "publication", "iuid": "558da5213cd248b6a7ab633e36fd8c6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/558da5213cd248b6a7ab633e36fd8c6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/558da5213cd248b6a7ab633e36fd8c6e"}}, "title": "Ancient host-associated microbes obtained from mammoth remains.", "authors": [{"family": "Guinet", "given": "Benjamin", "initials": "B"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Moreland", "given": "Kelsey", "initials": "K"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Danilov", "given": "Gleb", "initials": "G"}, {"family": "Kanellidou", "given": "Foteini", "initials": "F"}, {"family": "Kitchener", "given": "Andrew C", "initials": "AC"}, {"family": "Muller", "given": "H\u00e9lo\u00efse", "initials": "H"}, {"family": "Plotnikov", "given": "Valerii", "initials": "V"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Tikhonov", "given": "Alexei", "initials": "A"}, {"family": "Termes", "given": "Laura", "initials": "L"}, {"family": "Zazula", "given": "Grant", "initials": "G"}, {"family": "Mortensen", "given": "Peter", "initials": "P"}, {"family": "Grigorieva", "given": "Lena", "initials": "L"}, {"family": "Richards", "given": "Michael", "initials": "M"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Lister", "given": "Adrian M", "initials": "AM"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}], "type": "journal article", "published": "2025-11-13", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "188", "issue": "23", "pages": "6606-6619.e24"}, "abstract": "Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix. Some of these clades contained putative virulence factors, including a Pasteurella-related bacterium that had previously been linked to the deaths of African elephants. Notably, we reconstructed partial genomes of Erysipelothrix from the oldest mammoth sample, representing the oldest authenticated host-associated microbial DNA to date. This work demonstrates the potential of obtaining ancient animal microbiomes, which can inform further paleoecological and evolutionary research.", "doi": "10.1016/j.cell.2025.08.003", "pmid": "40902595", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)00917-1"}], "notes": [], "created": "2025-09-30T13:54:45.200Z", "modified": "2025-11-28T10:42:10.971Z"}, {"entity": "publication", "iuid": "e962bd7ef8824c55975d40adb2d41799", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e962bd7ef8824c55975d40adb2d41799.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e962bd7ef8824c55975d40adb2d41799"}}, "title": "Oligodendroglia as functional effectors of Multiple Sclerosis risk variants", "authors": [{"family": "Carlstr\u00f6m", "given": "Karl E", "initials": "KE", "orcid": "0000-0002-3001-2403", "researcher": {"href": "https://publications.scilifelab.se/researcher/3aa5f65acad34b5790a2b9f607521825.json"}}, {"family": "Agirre", "given": "Eneritz", "initials": "E"}, {"family": "Sun", "given": "Ting", "initials": "T", "orcid": "0000-0002-7104-7215", "researcher": {"href": "https://publications.scilifelab.se/researcher/521fca43267242fca06da0f5fc823e6a.json"}}, {"family": "Dumral", "given": "\u00d6zge", "initials": "\u00d6"}, {"family": "Kabbe", "given": "Mukund", "initials": "M"}, {"family": "Mahmud", "given": "Neemat", "initials": "N"}, {"family": "Kit Lor", "given": "Yuk", "initials": "Y"}, {"family": "Pahlevan Kakhki", "given": "Majid", "initials": "M", "orcid": "0000-0002-5407-3147", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f376c85cfbe4711ae41d9ee5ade8f09.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Goldman", "given": "Steve A", "initials": "SA", "orcid": "0000-0002-5498-4303", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a78fe500aa54369b3716c70792dee90.json"}}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "posted-content", "published": "2025-11-12", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.11.11.687640", "pmid": null, "labels": {"CRISPR Functional Genomics": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-19T09:35:53.525Z", "modified": "2025-12-18T18:35:03.301Z"}, {"entity": "publication", "iuid": "05f686d75d0343e0a27bd5e6fb686ba1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05f686d75d0343e0a27bd5e6fb686ba1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05f686d75d0343e0a27bd5e6fb686ba1"}}, "title": "Stable clonal contribution of lineage-restricted stem cells to human hematopoiesis.", "authors": [{"family": "Yoshizato", "given": "Tetsuichi", "initials": "T", "orcid": "0000-0003-4283-2983", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6f499e339d2444b817a81ab2712b9e5.json"}}, {"family": "Nilsson", "given": "Christer", "initials": "C", "orcid": "0000-0003-0695-0050", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f78180b33fa48cd86474d5c3cdaa852.json"}}, {"family": "Grasso", "given": "Francesca", "initials": "F"}, {"family": "H\u00f6gstrand", "given": "Kari", "initials": "K"}, {"family": "Mazzi", "given": "Stefania", "initials": "S", "orcid": "0009-0009-2676-5232", "researcher": {"href": "https://publications.scilifelab.se/researcher/83dc55ff218049b287e650588772cbfd.json"}}, {"family": "Winroth", "given": "Axel", "initials": "A", "orcid": "0009-0002-3314-7781", "researcher": {"href": "https://publications.scilifelab.se/researcher/63fae66620a04a79bb642b29703a5aaf.json"}}, {"family": "Lehander", "given": "Madeleine", "initials": "M"}, {"family": "Barbosa", "given": "Indira", "initials": "I", "orcid": "0009-0004-1171-2932", "researcher": {"href": "https://publications.scilifelab.se/researcher/20efd8770db84811a240a8bb70c43939.json"}}, {"family": "Waldin", "given": "Gunilla", "initials": "G"}, {"family": "Mortera-Blanco", "given": "Teresa", "initials": "T"}, {"family": "Jansson", "given": "Monika", "initials": "M"}, {"family": "Widfeldt", "given": "Mikaela Hillberg", "initials": "MH"}, {"family": "Aliouat", "given": "Affaf", "initials": "A"}, {"family": "Brennan", "given": "Margs S", "initials": "MS", "orcid": "0000-0002-8864-4147", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b684863566a420bb894bbd7265d938e.json"}}, {"family": "Markljung", "given": "Ellen", "initials": "E"}, {"family": "Hillen", "given": "Amy", "initials": "A", "orcid": "0000-0002-8567-1545", "researcher": {"href": "https://publications.scilifelab.se/researcher/fba7f6c5a2f04d71816a8381ede8a615.json"}}, {"family": "Chari", "given": "Edwin", "initials": "E"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-7839-3743", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf8d52e24234fa8b348ad08f58d1d48.json"}}, {"family": "Kretzschmar", "given": "Warren W", "initials": "WW", "orcid": "0000-0002-2575-0807", "researcher": {"href": "https://publications.scilifelab.se/researcher/a67389ef276a47cfacec7cbe50da37a7.json"}}, {"family": "Woll", "given": "Petter S", "initials": "PS", "orcid": "0000-0002-2340-2526", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ae0c1d2cf5461894c6d0d80ed42f68.json"}}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW", "orcid": "0000-0002-1362-3659", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fc5e4f49e4330b095c26cd965cc98.json"}}], "type": "journal article", "published": "2025-11-11", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "issn-l": "1061-4036"}, "abstract": "Dynamic steady-state lineage contribution of human hematopoietic stem cell (HSC) clones needs to be assessed over time. However, clonal contribution of HSCs has only been investigated at single time points and without assessing the critical erythroid and platelet lineages. Here we screened for somatic mutations in healthy aged individuals, identifying expanded HSC clones accessible for lineage tracing of all major blood cell lineages. In addition to HSC clones with balanced contribution to all lineages, we identified clones with all myeloid lineages but no or few B and T lymphocytes or all myeloid lineages and B cells but no T cells. No other lineage restriction patterns were reproducibly observed. Retrospective phylogenetic inferences uncovered a 'hierarchical' pattern of descendant subclones more lineage biased than their ancestral clone and a more common 'stable' pattern with descendant subclones showing highly concordant lineage contributions with their ancestral clone, despite decades of separation. Prospective lineage tracing confirmed remarkable stability over years of HSC clones with distinct lineage replenishment patterns.", "doi": "10.1038/s41588-025-02405-w", "pmid": "41219528", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-025-02405-w"}], "notes": [], "created": "2025-11-21T14:18:19.115Z", "modified": "2025-11-21T14:18:20.018Z"}, {"entity": "publication", "iuid": "fae720ef3a8d42dc85bccd01c23b2bd4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fae720ef3a8d42dc85bccd01c23b2bd4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fae720ef3a8d42dc85bccd01c23b2bd4"}}, "title": "Persistence-Directed Testing of Chemicals Discharged from Offshore Oil Platforms Combined with Nontargeted Analysis", "authors": [{"family": "M\u00f8ller", "given": "Mette T", "initials": "MT", "orcid": "0000-0003-2216-6514", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5f327145efe4adca7b27f0318b0133c.json"}}, {"family": "Birch", "given": "Heidi", "initials": "H", "orcid": "0000-0002-7152-3832", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7a299dcbf7b4e6981b452007d3cac14.json"}}, {"family": "Sj\u00f8holm", "given": "Karina K", "initials": "KK", "orcid": "0000-0002-2964-3849", "researcher": {"href": "https://publications.scilifelab.se/researcher/e493845fefff470dbf37c9d10dd4fce5.json"}}, {"family": "Papazian", "given": "Stefano", "initials": "S", "orcid": "0000-0003-2538-8702", "researcher": {"href": "https://publications.scilifelab.se/researcher/5de990c59ec4460e92c414dbc0ed0b16.json"}}, {"family": "Wennberg", "given": "Aina C", "initials": "AC", "orcid": "0000-0003-3798-6574", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fce082bcb7c4ecd8d2fe898e31226f0.json"}}, {"family": "Bonnefille", "given": "B\u00e9nilde", "initials": "B", "orcid": "0000-0001-5141-7111", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb5cae7e57b1443a8b296824dc186b04.json"}}, {"family": "Kronsbein", "given": "Pia M", "initials": "PM"}, {"family": "Kelland", "given": "Malcolm A", "initials": "MA", "orcid": "0000-0003-2295-5804", "researcher": {"href": "https://publications.scilifelab.se/researcher/1da5b7716bfd4d84950219be6d0eea63.json"}}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications.scilifelab.se/researcher/f275a68856cb459ebbc933b18c3e315d.json"}}, {"family": "Mayer", "given": "Philipp", "initials": "P", "orcid": "0000-0001-5138-7506", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f103ddb642445e8a83d8f36d35f8aec.json"}}], "type": "journal-article", "published": "2025-11-11", "journal": {"title": "Environ. Sci. Technol.", "issn": "0013-936X", "volume": "59", "issue": "44", "pages": "24000-24011", "issn-l": null}, "abstract": "Persistent chemicals discharged into the sea can pose long-term, irreversible risks. New approaches are needed to elucidate the number and type of persistent chemicals, particularly in complex mixtures and high-volume discharges. We introduce a novel \"Persistence-Directed Testing\" approach that combines environmentally relevant biodegradation tests with nontarget analytical methods. Complex produced waters from two offshore oil platforms in the North Sea served as case studies. In the biodegradation tests, produced waters were diluted 1:200 with seawater from the site of discharge (inoculum). Biotic test systems and abiotic controls were incubated at 9 \u00b0C. At day 60 nontarget analyses were performed by Solid Phase Microextraction coupled to GC-MS and Solid Phase Extraction coupled to LC-HRMS. Primary biodegradation and persistence were determined based on biotic/abiotic peak area ratios. Over 600 chemicals passed the quality control filtering criteria, and the persistent fraction of chemicals discovered by GC-MS was 4% and that discovered by LC-HRMS was 32-44%. Spectral library matches and computational modeling of the LC-HRMS data annotated several persistent chemicals as N-substituted aromatic ring structures. These findings demonstrate the value of a persistence-directed approach in uncovering the hidden burden of unidentified persistent chemicals in environmental discharges and highlight the urgent need for enhanced treatment of produced water discharges.", "doi": "10.1021/acs.est.5c08802", "pmid": "41160886", "labels": {"Exposomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-30T08:48:01.502Z", "modified": "2026-02-02T16:53:06.335Z"}, {"entity": "publication", "iuid": "6176a29337eb4648a2c736c7849ce6b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6176a29337eb4648a2c736c7849ce6b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6176a29337eb4648a2c736c7849ce6b6"}}, "title": "Linking nutrient availability and community size to stochasticity in microbial community assembly.", "authors": [{"family": "Bick", "given": "Berenike", "initials": "B", "orcid": "0000-0001-9445-9266", "researcher": {"href": "https://publications.scilifelab.se/researcher/58373f9528d04f4bbcceebb2d14f4b20.json"}}, {"family": "Lumpi", "given": "Theresa", "initials": "T"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES", "orcid": "0000-0001-8920-3071", "researcher": {"href": "https://publications.scilifelab.se/researcher/9290d334ce5a4488b8afd2af511e02ad.json"}}, {"family": "Langenheder", "given": "Silke", "initials": "S"}], "type": "journal article", "published": "2025-11-11", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "101", "issue": "12", "issn-l": "0168-6496"}, "abstract": "Both deterministic (e.g. species-environment interactions) and stochastic processes (e.g. random birth and death events) shape communities, but it remains poorly understood, which environmental conditions promote stochasticity. Here, we investigated interactive effects of nutrient availability and community size on stochasticity in order to predict how eutrophication and biomass loss shift the balance between predictable and random community dynamics. For this, we used freshwater bacterial communities in a microcosm experiment, where communities were diluted to varying sizes and exposed to low, intermediate, and high nutrient concentrations. Stochasticity was estimated with null modelling and as beta-diversity among replicate communities. At low nutrient concentrations, deterministic processes dominated, especially in smaller communities, which had the lowest diversity and abundance. Whereas, higher nutrient concentrations increased stochasticity. In contrast to theoretical predictions, this was particularly the case in larger communities with the highest diversity and abundance, likely due to stochastic initial growth. The findings underline how nutrient availability and community size jointly influence stochastic assembly processes, with important consequences for bacterial diversity and ecosystem functioning under environmental change.", "doi": "10.1093/femsec/fiaf110", "pmid": "41147699", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12603558"}, {"db": "pii", "key": "8305078"}], "notes": [], "created": "2025-12-05T11:46:56.250Z", "modified": "2025-12-05T11:46:56.438Z"}, {"entity": "publication", "iuid": "c7b4c0e889ea4415b8cbaa01eccb847b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7b4c0e889ea4415b8cbaa01eccb847b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7b4c0e889ea4415b8cbaa01eccb847b"}}, "title": "ALC1 Finds a New Foothold on the Nucleosome\u2019s Super-Groove", "authors": [{"family": "Bridges", "given": "Hannah R", "initials": "HR", "orcid": "0000-0001-6890-6050", "researcher": {"href": "https://publications.scilifelab.se/researcher/87b42fbd72ad4a25949e7bb7113dd0b1.json"}}, {"family": "Bacic", "given": "Luka", "initials": "L", "orcid": "0000-0001-6896-3506", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bcd56cafd294116870c894ba344cf12.json"}}, {"family": "Deindl", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-6807-8654", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e45e8288a3445e2b346f29b73141738.json"}}, {"family": "Gaullier", "given": "Guillaume", "initials": "G", "orcid": "0000-0003-3405-6021", "researcher": {"href": "https://publications.scilifelab.se/researcher/26bde2020c164cff8216338fb2d6d652.json"}}], "type": "posted-content", "published": "2025-11-10", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.11.10.687450", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-17T10:09:15.163Z", "modified": "2025-12-18T18:59:43.530Z"}, {"entity": "publication", "iuid": "56bb0412feda48beadd0c63b3e769d3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56bb0412feda48beadd0c63b3e769d3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56bb0412feda48beadd0c63b3e769d3a"}}, "title": "Metabolomics and glucose tolerance in pregnancy and postpartum: The PONCH study", "authors": [{"family": "Andersson-Hall", "given": "Ulrika", "initials": "U", "orcid": "0000-0003-3722-3454", "researcher": {"href": "https://publications.scilifelab.se/researcher/843efce412cc42b2ad63bc9eccf31b44.json"}}, {"family": "Nord", "given": "Anders Bay", "initials": "AB"}, {"family": "Malmodin", "given": "Daniel", "initials": "D", "orcid": "0000-0001-8528-0141", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4aceb81db18460c819c81a7319bbe61.json"}}, {"family": "Holm\u00e4ng", "given": "Agneta", "initials": "A"}], "type": "journal-article", "published": "2025-11-07", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "11", "pages": "e0335708", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0335708", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:02:49.433Z", "modified": "2025-11-27T08:02:49.514Z"}, {"entity": "publication", "iuid": "9ae3301ccdfd4c4e9458bd60287cead9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ae3301ccdfd4c4e9458bd60287cead9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ae3301ccdfd4c4e9458bd60287cead9"}}, "title": "Preclinical Validation of [177Lu]Lu-AKIR001, a CD44v6-Targeted Radiotherapeutic Entering First-in-Human Trials.", "authors": [{"family": "Mortensen", "given": "Anja C L", "initials": "ACL"}, {"family": "Mohajershojai", "given": "Tabassom", "initials": "T", "orcid": "0000-0002-7364-5470", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a193b44e7c4c85997ec74c0fee29ae.json"}}, {"family": "Gustafsson", "given": "Amanda", "initials": "A"}, {"family": "Berglund", "given": "Hanna", "initials": "H", "orcid": "0009-0007-1754-1822", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad08d24abc17454dafb1415b1400a038.json"}}, {"family": "Selvaraju", "given": "Ram Kumar", "initials": "RK"}, {"family": "Hofstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}, {"family": "Tran", "given": "Thuy A", "initials": "TA"}, {"family": "Mor\u00e9n", "given": "Anton Forsberg", "initials": "AF"}, {"family": "Ochniewicz", "given": "Piotr", "initials": "P"}, {"family": "Zedenius", "given": "Jan", "initials": "J", "orcid": "0000-0003-2833-3758", "researcher": {"href": "https://publications.scilifelab.se/researcher/319fe27b84674ea3829d2e0c0e0ab966.json"}}, {"family": "Bernhardt", "given": "Peter", "initials": "P"}, {"family": "Frejd", "given": "Fredrik Y", "initials": "FY"}, {"family": "Nestor", "given": "Marika", "initials": "M", "orcid": "0000-0003-4662-3142", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e9ff7b0cad949c48c808a1dedec7fe4.json"}}], "type": "journal article", "published": "2025-11-06", "journal": {"title": "J Nucl Med", "issn": "1535-5667", "issn-l": null}, "abstract": "Targeted radionuclide therapy is an emerging potent therapeutic strategy in oncology. The cell surface antigen CD44v6 is a potential pan-cancer target for radionuclide therapy. This study aimed to evaluate the therapeutic efficacy, biodistribution, dosimetry, and safety profile of AKIR001, an antibody targeting CD44v6 labeled with 177Lu. Methods: The biodistribution and preclinical dosimetry of [177Lu]Lu-AKIR001 were calculated in the highly CD44v6-expressing A431 murine xenograft model, with subsequent extrapolation to predict human dosimetry. Therapeutic efficacy was evaluated across 3 xenograft models, 2 with high and 1 with moderate levels of CD44v6, using multiple dosing levels, fractionation regimens, and combinations with cisplatin. Preclinical toxicology was evaluated in a cross-reactive rabbit model and complemented by a PET imaging study using 68Ga-labeled AKIR001 in a cynomolgus macaque. Results: Biodistribution studies confirmed the high and selective tumor uptake of [177Lu]Lu-AKIR001, resulting in favorable dosimetry predictions for clinical application. Therapeutic evaluations demonstrated significant dose-dependent efficacy in all tested xenograft models, with fractionated dosing (2 doses) resulting in complete tumor regression in 80% of the animals in a radioresistant xenograft model. Biodistribution in rabbits demonstrated low uptake in normal tissues, and a good-laboratory-practice study using an excessive dose of AKIR001 was well tolerated, with no signs of adverse effects. PET imaging in a cynomolgus macaque corroborated these findings. Conclusion: Collectively, these data strongly support the therapeutic efficacy, safety, and dosimetry of [177Lu]Lu-AKIR001, justifying its advancement into clinical trials. A phase 1 clinical trial of [177Lu]Lu-AKIR001for CD44v6-positive solid cancers (NCT06639191) is currently recruiting patients.", "doi": "10.2967/jnumed.125.270782", "pmid": "41198237", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "jnumed.125.270782"}, {"db": "ClinicalTrials.gov", "key": "NCT06639191"}], "notes": [], "created": "2025-11-14T08:35:37.291Z", "modified": "2025-11-14T09:53:35.556Z"}, {"entity": "publication", "iuid": "91db8e6db9aa49efbc40237fa90ee147", "links": {"self": {"href": "https://publications.scilifelab.se/publication/91db8e6db9aa49efbc40237fa90ee147.json"}, "display": {"href": "https://publications.scilifelab.se/publication/91db8e6db9aa49efbc40237fa90ee147"}}, "title": "Spatial single-cell atlas reveals regional variations in healthy and diseased human lung.", "authors": [{"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Marco Salas", "given": "Sergio", "initials": "S", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Kuemmerle", "given": "Louis B", "initials": "LB"}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications.scilifelab.se/researcher/944b78e930df40ee8cd5d590638cd4d9.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Mahbubani", "given": "Krishnaa T", "initials": "KT", "orcid": "0000-0002-1327-2334", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f378366e0594e8da4d56704215fc31c.json"}}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Alonso Galicia", "given": "Leire", "initials": "L"}, {"family": "Liontos", "given": "Andreas", "initials": "A"}, {"family": "Balassa", "given": "Tam\u00e1s", "initials": "T"}, {"family": "Kovacs", "given": "Ferenc", "initials": "F", "orcid": "0000-0003-4512-4448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8d63cee27914cc19796e7c6502d5f01.json"}}, {"family": "Horvath", "given": "Peter", "initials": "P"}, {"family": "Chen", "given": "Yuexin", "initials": "Y"}, {"family": "Gote-Schniering", "given": "Janine", "initials": "J", "orcid": "0000-0001-7869-4936", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e3e12bc834b4699b4675e3ff6043f5b.json"}}, {"family": "Stoleriu", "given": "Mircea-Gabriel", "initials": "MG"}, {"family": "Behr", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Meyer", "given": "Kerstin B", "initials": "KB", "orcid": "0000-0001-5906-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc26138d52fe4534a58ed24165e3370d.json"}}, {"family": "Timens", "given": "Wim", "initials": "W", "orcid": "0000-0002-4146-6363", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29a8a5f02a14b3095d02444ad631598.json"}}, {"family": "Schiller", "given": "Herbert B", "initials": "HB"}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b82068719d43448992741da54e00bd.json"}}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Nawijn", "given": "Martijn C", "initials": "MC", "orcid": "0000-0003-3372-6521", "researcher": {"href": "https://publications.scilifelab.se/researcher/61646a2dcd43478d955d0e9c5a3e5025.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}], "type": "journal article", "published": "2025-11-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9745", "issn-l": "2041-1723"}, "abstract": "Integration of scRNA-seq data from millions of cells revealed a high diversity of cell types in the healthy and diseased human lung. In a large and complex organ, constantly exposed to external agents, it is crucial to understand the influence of lung tissue topography or external factors on gene expression variability within cell types. Here, we apply three spatial transcriptomics approaches, to: (i) localize the majority of lung cell types, including rare epithelial cells within the tissue topography, (ii) describe consistent anatomical and regional gene expression variability within and across cell types, and (iii) reveal distinct cellular neighborhoods in specific anatomical regions and examine gene expression variations in them. We thus provide a spatially resolved tissue reference atlas in three representative regions of the healthy human lung. We further demonstrate its utility by defining previously unknown imbalances of epithelial cell type compositions in chronic obstructive pulmonary disease lungs. Our topographic atlas enables a precise description of characteristic regional cellular responses upon experimental perturbations or during disease progression.", "doi": "10.1038/s41467-025-65704-0", "pmid": "41193468", "labels": {"In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12589588"}, {"db": "pii", "key": "10.1038/s41467-025-65704-0"}], "notes": [], "created": "2025-11-28T06:52:42.945Z", "modified": "2025-11-28T06:52:43.158Z"}, {"entity": "publication", "iuid": "383fc2f557f74c5ca9961f9823a9c2e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/383fc2f557f74c5ca9961f9823a9c2e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/383fc2f557f74c5ca9961f9823a9c2e0"}}, "title": "Parallel clines of chromosomal inversion frequencies in seaweed flies are associated with thermal variation.", "authors": [{"family": "Nicolas", "given": "L\u00e9a A", "initials": "LA", "orcid": "0009-0007-2292-8431", "researcher": {"href": "https://publications.scilifelab.se/researcher/400196db3fb04ab0911f28029b922598.json"}}, {"family": "Berdan", "given": "Emma L", "initials": "EL", "orcid": "0000-0002-6435-4604", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f65066e9a744b95b25ec0597b4b8e23.json"}}, {"family": "Wellenreuther", "given": "Maren", "initials": "M", "orcid": "0000-0002-2764-8291", "researcher": {"href": "https://publications.scilifelab.se/researcher/82e9b593bf0f4535a7b9231608b1e27d.json"}}, {"family": "Colinet", "given": "Herv\u00e9", "initials": "H"}, {"family": "Clouard", "given": "Andr\u00e9a", "initials": "A"}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S"}, {"family": "M\u00e9rot", "given": "Claire", "initials": "C"}], "type": "journal article", "published": "2025-11-05", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "issn-l": "0018-067X"}, "abstract": "Chromosomal inversion supergenes, which form blocks of linked genes, are increasingly recognized for their role in maintaining intra-specific diversity. They are predicted to be relevant genetic architectures for local adaptation in the face of gene flow. However, pinpointing the underlying traits and functional mechanisms under selection remains challenging. The seaweed fly Coelopa frigida harbors several large polymorphic inversions, of which the Cf-Inv(4.1) inversion displays a latitudinal cline of frequencies along the North American Atlantic Coast, suggesting a putative role in adaptation along the eco-climatic gradient. To investigate this hypothesis, we designed a molecular marker for karyotyping and studied natural and experimental populations from North America and Europe. We confirmed that this inversion is also polymorphic in Europe, and displays parallel latitudinal clines across continents, providing strong indirect support that Cf-Inv(4.1) is under natural selection along similar environmental gradients. We found that Cf-Inv(4.1) had a significant impact on egg-to-adult survival and fecundity under different thermal conditions. However, no effect on cold tolerance could be determined using supercooling point and chill coma recovery time. We speculate that fitness associated with Cf-Inv(4.1) is shaped by subtle life-history differences whose relative advantage depends on climate. While our experimental approaches provided insights into genotype-phenotype associations, it is worth noting that selection acts on the overall fitness, involving complex sets of traits. This is especially relevant for inversions linking hundreds of genes. This multi-gene property also explains why inversions are frequently involved in repeated parallel adaptation to environmental gradients, as demonstrated here in the seaweed fly.", "doi": "10.1038/s41437-025-00808-3", "pmid": "41193615", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-025-00808-3"}], "notes": [], "created": "2025-11-19T07:41:34.155Z", "modified": "2025-11-19T07:41:34.300Z"}, {"entity": "publication", "iuid": "91f883543fd7455c9bb15fc44808b0d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/91f883543fd7455c9bb15fc44808b0d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/91f883543fd7455c9bb15fc44808b0d4"}}, "title": "Improving Triplet-Triplet Annihilation Upconversion Output by a Triplet Mediator Approach: Mechanistic Insights on Homo and Hetero-Annihilation in Three-Component Systems.", "authors": [{"family": "Kandappa", "given": "Sunil Kumar", "initials": "SK"}, {"family": "Gray", "given": "Victor", "initials": "V", "orcid": "0000-0001-6583-8654", "researcher": {"href": "https://publications.scilifelab.se/researcher/872f4084ae9e429ab74e0e346f2420bd.json"}}], "type": "journal article", "published": "2025-11-05", "journal": {"title": "J. Am. Chem. Soc.", "issn": "1520-5126", "volume": "147", "issue": "44", "pages": "40214-40224", "issn-l": "0002-7863"}, "abstract": "Triplet-triplet annihilation photon upconversion (TTA-UC) is a promising strategy for converting low-energy photons into higher-energy emission, with potential applications in solar energy harvesting, bioimaging, and photocatalysis. A challenge in TTA-UC systems is minimizing the reabsorption of upconverted photons by the annihilator molecules. To address this, we present a mediator-assisted TTA-UC approach utilizing a neutral mediator molecule to facilitate upconversion in the ultraviolet (UV) and visible regions. Our study introduces a general protocol, and through detailed kinetic modeling, we elucidate the underlying mechanism, highlighting the role of hetero-TTA (triplet-triplet annihilation between the mediator and annihilator). Notably, we report the first estimation of a hetero-TTA rate constant, which exceeds the homo-TTA rate by a factor of 2. This work broadens the design space for TTA-UC systems by enabling the use of neutral, noncovalently linked mediators, expanding beyond the conventional reliance on charged or covalently tethered species.", "doi": "10.1021/jacs.5c09906", "pmid": "41135045", "labels": {"Spatial Mass Spectrometry": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12593377"}], "notes": [], "created": "2025-11-21T10:01:32.431Z", "modified": "2025-11-21T10:01:32.519Z"}, {"entity": "publication", "iuid": "02b3955223f04da1b7d8470ef00171e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02b3955223f04da1b7d8470ef00171e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02b3955223f04da1b7d8470ef00171e2"}}, "title": "Cold-induced serum short-chain fatty acids act as markers of brown adipose tissue metabolism in humans.", "authors": [{"family": "Monfort-Pires", "given": "Milena", "initials": "M", "orcid": "0000-0002-1652-8083", "researcher": {"href": "https://publications.scilifelab.se/researcher/128d4268cabc4117bff0065b9960a648.json"}}, {"family": "U-Din", "given": "Mueez", "initials": "M"}, {"family": "de Mello", "given": "Vanessa", "initials": "V"}, {"family": "Saari", "given": "Teemu", "initials": "T", "orcid": "0000-0002-3212-6906", "researcher": {"href": "https://publications.scilifelab.se/researcher/871d414babfb4a158e5bb77f66cfbe72.json"}}, {"family": "Raiko", "given": "Juho", "initials": "J"}, {"family": "Kerminen", "given": "Edla", "initials": "E"}, {"family": "Rajander", "given": "Johan", "initials": "J"}, {"family": "Hanhineva", "given": "Kati", "initials": "K"}, {"family": "Fromme", "given": "Tobias", "initials": "T"}, {"family": "Landberg", "given": "Rikard", "initials": "R", "orcid": "0000-0002-6399-7608", "researcher": {"href": "https://publications.scilifelab.se/researcher/4472ec17986146d1a095acdb202815e6.json"}}, {"family": "Klingenspor", "given": "Martin", "initials": "M"}, {"family": "Virtanen", "given": "Kirsi A", "initials": "KA"}], "type": "journal article", "published": "2025-11-05", "journal": {"title": "J. Clin. Endocrinol. Metab.", "issn": "1945-7197", "issn-l": "0021-972X"}, "abstract": "Short-chain fatty acids (SCFAs) produced from dietary fibre fermentation can regulate adipose tissue metabolism through signalling pathways involving G-protein-coupled receptors and histone deacetylase inhibition. While preclinical studies suggest they enhance thermogenesis, their role in human brown adipose tissue (BAT) under different thermal conditions remains unclear.\n\nThis study explores the associations between circulating SCFAs and human BAT metabolism at room temperature and after cold exposure.\n\nThis cross-sectional study included data from 71 adults (20-55 years, BMI 19-44 kg/m\u00b2). Dynamic [15O]O2, [15O]H2O, [\u00b9\u2078F]FDG, and [\u00b9\u2078F]FTHA PET/CT scans were used to assess BAT metabolism. Serum SCFAs were quantified using LC-MS, and gene expression in biopsy-excised BAT samples (n=14) was analysed. Participants were stratified into low- and high-BAT groups based on [\u00b9\u2078F]FDG or [\u00b9\u2078F]FTHA uptakes.\n\nCold-induced acetate and propionate were positively associated with key in vivo BAT metabolism indicators, namely non-esterified fatty acids (NEFA) uptake and oxygen consumption. Only in the high-BAT group were circulating SCFAs maintained after cold exposure. BAT transcriptome revealed that genes involved in SCFA metabolism (such as conversion to acetyl-CoA) correlated with thermogenic and lipid metabolism genes exclusively in the high-BAT group, suggesting a distinct molecular link between SCFA pathways and BAT function.\n\nCirculating SCFAs are linked with BAT oxidative metabolism and NEFA uptake during cold exposure. The observed correlations between SCFA catabolic genes and thermogenic markers suggest that metabolically active BAT may selectively engage SCFA-related pathways, pointing to a potential mechanistic role of SCFAs in supporting BAT function in humans.", "doi": "10.1210/clinem/dgaf607", "pmid": "41206219", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "8315282"}], "notes": [], "created": "2025-12-01T05:42:30.155Z", "modified": "2025-12-01T05:42:30.603Z"}, {"entity": "publication", "iuid": "f3a1b1396edb4101b0575fbc43ec7415", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3a1b1396edb4101b0575fbc43ec7415.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3a1b1396edb4101b0575fbc43ec7415"}}, "title": "Comparative evaluation of Olink Explore 3072 and mass spectrometry with peptide fractionation for plasma proteomics.", "authors": [{"family": "Sissala", "given": "Noora", "initials": "N", "orcid": "0009-0000-0758-8140", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a96666a6a2e478fbdd3cf33d7db1e74.json"}}, {"family": "Baba\u010di\u0107", "given": "Haris", "initials": "H", "orcid": "0000-0003-0813-0005", "researcher": {"href": "https://publications.scilifelab.se/researcher/45a1c5d3d2d34a9e96d112877632784c.json"}}, {"family": "Leo", "given": "Isabelle R", "initials": "IR", "orcid": "0000-0002-7627-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/21185d9c6a2343f189397cbbb95c6e71.json"}}, {"family": "Cao", "given": "Xiaofang", "initials": "X"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "Eriksson", "given": "Lars E", "initials": "LE", "orcid": "0000-0001-5121-5325", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebb717a9972245a5b2427a4b8421fe6f.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}], "type": "journal article", "published": "2025-11-04", "journal": {"title": "Commun Chem", "issn": "2399-3669", "issn-l": null, "volume": "8", "issue": "1", "pages": "327"}, "abstract": "Plasma proteomics technologies are advancing rapidly, offering new opportunities for biomarker discovery and precision medicine. Direct comparisons of available technologies are needed to understand how platform selection affects downstream findings. We compared the performance of a peptide fractionation-based mass spectrometry method (HiRIEF LC-MS/MS) and the Olink Explore 3072 proximity extension assays on 88 plasma samples, analyzing 1129 proteins with both methods. The platforms exhibited complementary proteome coverage, high precision, and concordance in estimating sex differences in protein levels. Quantitative agreement between platforms was moderate (median correlation 0.59, interquartile range 0.33-0.75), mainly influenced by technical factors. Finally, we present a publicly available tool for peptide-level analysis of platform agreement and demonstrate its utility in clarifying cross-platform discrepancies in protein and proteoform measurements. Our findings provide insights for platform selection and study design, and highlight the value of combining mass spectrometry and affinity-based approaches for more comprehensive and reliable plasma proteome profiling.", "doi": "10.1038/s42004-025-01753-2", "pmid": "41188494", "labels": {"National Genomics Infrastructure": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Affinity Proteomics Stockholm": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12586489"}, {"db": "pii", "key": "10.1038/s42004-025-01753-2"}], "notes": [], "created": "2025-11-07T07:35:27.214Z", "modified": "2025-11-27T13:03:30.885Z"}, {"entity": "publication", "iuid": "b9b0683a2605480fa566e3f16876d804", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9b0683a2605480fa566e3f16876d804.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9b0683a2605480fa566e3f16876d804"}}, "title": "T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population.", "authors": [{"family": "Schmitz", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4480-891X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b1d0c4505854c7d9ab7a2ed3116b7ae.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}], "type": "journal article", "published": "2025-11-03", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "35", "issue": "11", "pages": "2377-2388", "issn-l": "1088-9051"}, "abstract": "The T2T-CHM13 reference genome, released in March 2022, fills in the 8% of the human genome that was not resolved in GRCh38 and reconstructs large parts of the known genome. The more accurate and complete reference genome is expected to improve the quality of read mapping and variant calling. Even though whole-genome sequencing (WGS)-based approaches have become the gold standard in medical genetics, the extent of the benefits of the improved reference genome remains unclear. In this study, we aim to evaluate alignment and variant call performance with T2T-CHM13 as a reference using a cross-sectional Swedish cohort (SweGen) comprising 1000 individuals with short-read Illumina WGS data available. Remapping and variant calling is performed using the nf-core/sarek pipeline. T2T-CHM13 improves a wide range of mapping- and variant calling-related metrics, including a higher fraction of properly paired reads, lower mismatch rate, and more uniform coverage of coding regions. Moreover, the fraction of ambiguous alignments is higher, reflecting segmental duplications that were incorrectly collapsed in GRCh37 and GRCh38. In comparison to GRCh38, we identify 10 million additional variants in the cohort, including 5.5 million singletons, and observe an increased sensitivity for rare variants. SnpEff assigns impact ratings of moderate or high to 13% more variants in T2T-CHM13 than GRCh38. In summary, we conclude that T2T-CHM13 improves alignment metrics with higher alignment quality, better variant calling performance, and confidence, including for rare and deleterious variants. The T2T-CHM13 genome reference thus facilitates enhanced discovery of new disease-causing variation, benefiting, for example, rare-disease diagnostics.", "doi": "10.1101/gr.279320.124", "pmid": "40957660", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12581843"}, {"db": "pii", "key": "gr.279320.124"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2025-11-03T08:37:12.674Z", "modified": "2025-11-28T10:50:30.060Z"}, {"entity": "publication", "iuid": "e8c58caebc5a495ab34dffe3cbaea1a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8c58caebc5a495ab34dffe3cbaea1a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8c58caebc5a495ab34dffe3cbaea1a0"}}, "title": "Single recipient cell tracking of tellurium-labeled extracellular vesicle proteomes (TeLEV) identifies EV-driven immunomodulation", "authors": [{"family": "Bachurski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9168-9680", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3955354a5b4db1975680eafdc2c997.json"}}, {"family": "Gholamipoorfard", "given": "Rahil", "initials": "R", "orcid": "0000-0001-8207-7295", "researcher": {"href": "https://publications.scilifelab.se/researcher/943864a091c1466795e02edacb855fe2.json"}}, {"family": "Bu", "given": "Yong Jia", "initials": "YJ", "orcid": "0000-0001-9390-0494", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5d00f647d72480b846148683f141be2.json"}}, {"family": "Hoelker", "given": "Patrick", "initials": "P"}, {"family": "Wessendorf", "given": "Lisa", "initials": "L"}, {"family": "Jestrabek", "given": "Hendrik", "initials": "H"}, {"family": "Schreurs", "given": "Luca D", "initials": "LD"}, {"family": "Stahl", "given": "David", "initials": "D"}, {"family": "Mokhlesi", "given": "Amin", "initials": "A"}, {"family": "G\u00f6del", "given": "Philipp", "initials": "P"}, {"family": "Gaedke", "given": "Felix", "initials": "F"}, {"family": "Ranjbari", "given": "Elias", "initials": "E"}, {"family": "Seyhan", "given": "Selen", "initials": "S"}, {"family": "Resch", "given": "Ulrike", "initials": "U"}, {"family": "Schmidt", "given": "Luisa Marie", "initials": "LM"}, {"family": "Tertel", "given": "Tobias", "initials": "T", "orcid": "0000-0001-8659-8610", "researcher": {"href": "https://publications.scilifelab.se/researcher/af482bab6f514bf3b81e5efb0d2b47c5.json"}}, {"family": "Rose", "given": "France", "initials": "F"}, {"family": "Pinheiro", "given": "Cl\u00e1udio", "initials": "C"}, {"family": "Corona", "given": "Maribel L", "initials": "ML"}, {"family": "von Lom", "given": "Anton", "initials": "A"}, {"family": "vom Stein", "given": "Alexander Frederik", "initials": "AF", "orcid": "0000-0002-6910-7792", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ecdaf193d1b4930bf5dfb65cf6920ab.json"}}, {"family": "Nguyen", "given": "Phuong Hien", "initials": "PH", "orcid": "0000-0002-3249-7264", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea3272b8f7b4433950fd70c01d15f49.json"}}, {"family": "Reiners", "given": "Katrin S", "initials": "KS"}, {"family": "Hendrix", "given": "An", "initials": "A"}, {"family": "van Niel", "given": "Guillaume", "initials": "G", "orcid": "0000-0002-8651-9705", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a1d365f0f0a4152af6c8ead53f71d77.json"}}, {"family": "Kr\u00fcger", "given": "Marcus", "initials": "M"}, {"family": "Bozek", "given": "Katarzyna", "initials": "K"}, {"family": "Meder", "given": "Lydia", "initials": "L"}, {"family": "Malmberg", "given": "Per", "initials": "P"}, {"family": "Cramer", "given": "Paula", "initials": "P"}, {"family": "Eichhorst", "given": "Barbara", "initials": "B"}, {"family": "Peifer", "given": "Martin", "initials": "M"}, {"family": "Ullrich", "given": "Roland T", "initials": "RT"}, {"family": "Schauss", "given": "Astrid", "initials": "A"}, {"family": "Pallasch", "given": "Christian", "initials": "C"}, {"family": "Br\u00f6ckelmann", "given": "Paul J", "initials": "PJ", "orcid": "0000-0001-9662-9900", "researcher": {"href": "https://publications.scilifelab.se/researcher/507ee132e2ff444790ab2eedf0863689.json"}}, {"family": "Jachimowicz", "given": "Ron D", "initials": "RD"}, {"family": "Preu\u00dfer", "given": "Christian", "initials": "C"}, {"family": "Giebel", "given": "Bernd", "initials": "B"}, {"family": "von Strandmann", "given": "Elke Pogge", "initials": "EP"}, {"family": "Nitz", "given": "Mark", "initials": "M", "orcid": "0000-0001-8078-2265", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fb8811e7d964a439d3c4d610d811cde.json"}}, {"family": "Hallek", "given": "Michael", "initials": "M", "orcid": "0000-0002-7425-4455", "researcher": {"href": "https://publications.scilifelab.se/researcher/491a1b4cafe6445d98f5371258d2601c.json"}}, {"family": "Abedpour", "given": "Nima", "initials": "N"}], "type": "posted-content", "published": "2025-11-03", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.11.01.685872", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "NanoSIMS": "Service"}, "xrefs": [], "notes": [], "created": "2026-03-10T07:23:40.873Z", "modified": "2026-03-10T14:20:37.651Z"}, {"entity": "publication", "iuid": "ff23b886460946f8b866e1a1db68e6a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff23b886460946f8b866e1a1db68e6a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff23b886460946f8b866e1a1db68e6a3"}}, "title": "Ancient DNA and dating evidence for the dispersal of hippos into central Europe during the last glacial.", "authors": [{"family": "Arnold", "given": "Patrick", "initials": "P"}, {"family": "D\u00f6ppes", "given": "Doris", "initials": "D"}, {"family": "Alberti", "given": "Federica", "initials": "F"}, {"family": "F\u00fcglistaler", "given": "Andreas", "initials": "A"}, {"family": "Lindauer", "given": "Susanne", "initials": "S"}, {"family": "Hoselmann", "given": "Christian", "initials": "C"}, {"family": "Friedrich", "given": "Ronny", "initials": "R"}, {"family": "Hajdas", "given": "Irka", "initials": "I"}, {"family": "Dickinson", "given": "Marc", "initials": "M"}, {"family": "Menger", "given": "Frank", "initials": "F"}, {"family": "Paijmans", "given": "Johanna L A", "initials": "JLA"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Wegmann", "given": "Daniel", "initials": "D"}, {"family": "Penkman", "given": "Kirsty E H", "initials": "KEH"}, {"family": "Barlow", "given": "Axel", "initials": "A"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2025-11-03", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "35", "issue": "21", "pages": "5363-5371.e6", "issn-l": "0960-9822"}, "abstract": "Late Pleistocene hippo fossils (Hippopotamus amphibius) from Europe have generally been associated with the last interglacial period (Eemian, 129-115 thousand years ago [kya]).1,2,3,4 As a widely accepted indicator species for temperate climate conditions, it was assumed they went extinct with the onset of the last glacial (Weichselian) around 115 kya.2,5 Their origin and relationships to extant African common hippos and the exact age of their extinction in central Europe, however, remain unclear. Here, we address these questions using an integrated approach applied to hippos from the Upper Rhine Graben in central Europe. By sequencing the paleogenome of a European hippo, we reveal its close genetic links to modern hippos from Africa. Six additional partial mitochondrial genomes confirm that European representatives were part of the same, once widespread species that is today restricted to sub-Saharan Africa. Surprisingly, radiocarbon dating shows that hippos were present in central Europe during the middle Weichselian (a period spanning from earlier than 47 kya until \u223c31 kya), i.e., well into the last glacial. Similar radiocarbon dates for woolly mammoth and woolly rhino fossils from the same sites imply the presence of both faunas during this period. Despite the paleogenome's low coverage, we are able to confidently estimate its genome-wide diversity by recalibrating the sequencing quality scores and assessing post-mortem damage. The low genome-wide diversity recovered suggests that it belonged to a small, isolated population. Overall, our combined data imply that hippos inhabited the Upper Rhine Graben refugium during temperate phases of the middle Weichselian.", "doi": "10.1016/j.cub.2025.09.035", "pmid": "41067227", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(25)01205-9"}], "notes": [], "created": "2025-11-19T09:56:40.454Z", "modified": "2025-11-19T09:56:40.458Z"}, {"entity": "publication", "iuid": "9e18ef322a3d4b42a45a7bbe96686990", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e18ef322a3d4b42a45a7bbe96686990.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e18ef322a3d4b42a45a7bbe96686990"}}, "title": "Studying macromolecular composition in cell-cell interfaces using 3D membrane reconstitution systems", "authors": [{"family": "Ragaller", "given": "Franziska", "initials": "F", "orcid": "0000-0002-4148-262X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ead87aca17f476b9febf3f020567c4b.json"}}, {"family": "Schneider", "given": "Amelie Maribel", "initials": "AM"}, {"family": "Sjule", "given": "Ellen", "initials": "E", "orcid": "0000-0003-0166-2826", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e0fd8926ef843a0a8db936df7209107.json"}}, {"family": "Sun", "given": "Renhua", "initials": "R", "orcid": "0000-0002-8203-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/f639c1a9dca647c0b583ce74ab398f02.json"}}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Jenkins", "given": "Edward", "initials": "E"}, {"family": "Dustin", "given": "Michael", "initials": "M"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}], "type": "posted-content", "published": "2025-11-02", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.11.01.686034", "pmid": null, "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-05T10:03:39.995Z", "modified": "2025-12-18T19:00:09.690Z"}, {"entity": "publication", "iuid": "3821dab294014f708369e1c7a88fe9f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3821dab294014f708369e1c7a88fe9f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3821dab294014f708369e1c7a88fe9f0"}}, "title": "Open and closed forms of assembled henipavirus nucleoprotein suggest structural basis of genome access", "authors": [{"family": "Jayachandran", "given": "Rupesh Balaji", "initials": "RB", "orcid": "0009-0000-4969-6991", "researcher": {"href": "https://publications.scilifelab.se/researcher/871970f1ea9641518a8e76e8c4d9e028.json"}}, {"family": "Quignon", "given": "Erwan", "initials": "E", "orcid": "0000-0001-7929-8847", "researcher": {"href": "https://publications.scilifelab.se/researcher/87589236770e400bbe113139d9c04d62.json"}}, {"family": "Renner", "given": "Max", "initials": "M", "orcid": "0000-0001-9885-8256", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dec10d9f96e400b800647eb4437a6c9.json"}}], "type": "posted-content", "published": "2025-11-02", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.11.02.686081", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-13T09:05:45.619Z", "modified": "2025-12-18T19:00:32.996Z"}, {"entity": "publication", "iuid": "0391dd2cb5aa4435bc12f0ff1b3683c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0391dd2cb5aa4435bc12f0ff1b3683c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0391dd2cb5aa4435bc12f0ff1b3683c5"}}, "title": "Metabolomic biomarkers associated with trismus and dysphagia, radiation therapy, tumour stage and location in patients with head and neck cancer", "authors": [{"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Tuomi", "given": "Lisa", "initials": "L"}, {"family": "Karlsson", "given": "Therese", "initials": "T", "orcid": "0000-0002-8558-8338", "researcher": {"href": "https://publications.scilifelab.se/researcher/99864d3a4c2d46958a6e97c6e2090227.json"}}, {"family": "Finizia", "given": "Caterina", "initials": "C"}, {"family": "Skiljic", "given": "Dragana", "initials": "D", "orcid": "0000-0002-9220-7767", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c67d0b4d6f849a2b3fffc1eee6cab83.json"}}], "type": "journal-article", "published": "2025-11-02", "journal": {"title": "Acta Otolaryngol.", "issn": "0001-6489", "volume": "145", "issue": "11", "pages": "1109-1121", "issn-l": null}, "abstract": null, "doi": "10.1080/00016489.2025.2561911", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:05:09.402Z", "modified": "2025-11-27T08:05:09.524Z"}, {"entity": "publication", "iuid": "b6b00054f2834df095a407814eb3b50c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6b00054f2834df095a407814eb3b50c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6b00054f2834df095a407814eb3b50c"}}, "title": "Cryo-EM exposes diverse polymorphism in IAPP mutants to guide the rational design of peptide-based therapeutics.", "authors": [{"family": "Ooi", "given": "Saik Ann", "initials": "SA"}, {"family": "Valli", "given": "Dylan", "initials": "D"}, {"family": "Kuska", "given": "Miko\u0142aj I", "initials": "MI"}, {"family": "Mar\u00ed", "given": "Helena", "initials": "H"}, {"family": "Chaudhary", "given": "Himanshu", "initials": "H"}, {"family": "Wahlgren", "given": "Weixiao Yuan", "initials": "WY"}, {"family": "Westenhoff", "given": "Sebastian", "initials": "S"}, {"family": "Tietze", "given": "Alesia A", "initials": "AA"}, {"family": "Novials", "given": "Anna", "initials": "A"}, {"family": "Servitja", "given": "Joan-Marc", "initials": "JM"}, {"family": "Maj", "given": "Micha\u0142", "initials": "M"}], "type": "journal article", "published": "2025-11-01", "journal": {"title": "J. Mol. Biol.", "issn": "1089-8638", "volume": "437", "issue": "21", "pages": "169405", "issn-l": "0022-2836"}, "abstract": "In the pursuit of potential therapeutic agents for type 2 diabetes, non-amyloidogenic forms of the human Islet Amyloid Polypeptide (hIAPP) containing site-specific mutations are of significant interest. In the present study, we dissect the three proline mutations present in the core region of the non-amyloidogenic rat IAPP into single-point mutations at A25P, S28P, and S29P sites. We apply high-resolution cryo-electron microscopy and solve the structures of 6 polymorphs formed by these mutants, revealing the peptide's self-assembly patterns and identifying critical interactions that reinforce these structures in the presence of the \u03b2-sheet breaker. A unique trimeric aggregate with C3 symmetry was identified in the A25P mutant, which we resolved with a 3.05 \u00c5 resolution, while asymmetric trimeric assemblies were observed in the other mutants. Guided by the high-resolution structural models of A25P and S28P fibrils obtained in our study, we successfully designed novel non-amyloidogenic mutants of IAPP with potential therapeutic value. Our findings demonstrate the immense potential of structure-based approaches in developing effective therapeutics against amyloid diseases.", "doi": "10.1016/j.jmb.2025.169405", "pmid": "40850490", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "Cryo-EM": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0022-2836(25)00471-1"}], "notes": [], "created": "2025-11-05T13:58:49.739Z", "modified": "2025-11-28T10:44:05.239Z"}, {"entity": "publication", "iuid": "2b2c9cd55b354c8c805f7b3f3749f406", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b2c9cd55b354c8c805f7b3f3749f406.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b2c9cd55b354c8c805f7b3f3749f406"}}, "title": "Warming-Induced Effects on Microbial Communities and Nitrogen Cycling Capacity in Tundra Litter Are Modulated by Herb Abundance and Litter Quality.", "authors": [{"family": "Jeanbille", "given": "Mathilde", "initials": "M", "orcid": "0000-0002-7758-8928", "researcher": {"href": "https://publications.scilifelab.se/researcher/aec9e57ba006483381b852b505728277.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Juhanson", "given": "Jaanis", "initials": "J", "orcid": "0000-0003-3799-2819", "researcher": {"href": "https://publications.scilifelab.se/researcher/43736fc1dba8405285b1143f5ba3f170.json"}}, {"family": "Michelsen", "given": "Anders", "initials": "A", "orcid": "0000-0002-9541-8658", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1ae80fdcd1949869986ad85c68a5586.json"}}, {"family": "Alatalo", "given": "Juha", "initials": "J", "orcid": "0000-0001-5084-850X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e31e5ef78cd941ffb26abd000ea418c1.json"}}, {"family": "Cooper", "given": "Elisabeth J", "initials": "EJ", "orcid": "0000-0002-0634-1282", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e24fe660b0540ea9b977e022b22a82d.json"}}, {"family": "Henry", "given": "Greg H R", "initials": "GHR", "orcid": "0000-0002-2606-9650", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec146a7b05534922b90d3205f12b5716.json"}}, {"family": "Hofgaard", "given": "Annika", "initials": "A", "orcid": "0000-0001-6919-5537", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cb3c8abbf684418a75b41492e83ad5c.json"}}, {"family": "Hollister", "given": "Robert D", "initials": "RD", "orcid": "0000-0002-4764-7691", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e541fcf014f49e38fccb53eeb989b64.json"}}, {"family": "J\u00f3nsd\u00f3ttir", "given": "Ingibj\u00f6rg S", "initials": "IS", "orcid": "0000-0003-3804-7077", "researcher": {"href": "https://publications.scilifelab.se/researcher/89fc1fd6b2b84dba86483c9e25d2a214.json"}}, {"family": "Klanderud", "given": "Kari", "initials": "K", "orcid": "0000-0003-1049-7025", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f070d4cdfa40e3addf23592be1c840.json"}}, {"family": "Tolvanen", "given": "Anne", "initials": "A", "orcid": "0000-0002-5304-7510", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ea61db4d29d428091e2bce0ae8d00a9.json"}}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Glob Chang Biol", "issn": "1365-2486", "issn-l": "1354-1013", "volume": "31", "issue": "11", "pages": "e70582"}, "abstract": "Climate warming is changing tundra vegetation in the Arctic, with implications for plant litter properties. Warming may thus modify bacterial and fungal communities and their nitrogen (N) cycling capacity in the litter layer, which in turn can affect plant N availability. To address potential warming effects, we characterized the responses of bacterial and fungal communities and their genetically encoded capacity for inorganic N-transformations in the litter layer, as well as 15N natural abundance in the underlying soil layer as an integrated measure of N processes in the soil, in 16 long-term alpine and Arctic tundra warming experiments distributed across 12 circumpolar locations. Although abundance, diversity, and composition of microbial communities were structured by the local conditions rather than experimental warming, warming indirectly modified microbial communities and their capacity for N transformations through changes in litter quality. Specifically, experimental warming resulted in stronger connections between the capacity for nitrification, denitrification and N-fixation in the litter and the \u03b415N signature in the soil. These warming-induced connections were mainly mediated by increased dominance of herbs but also increased litter mass. These findings suggest accelerated inorganic N cycling in the litter layer with warming, particularly coupled to local abundance of herbs, which can create positive feedback on plant growth as well as ecosystem respiration. Thus, microbial communities in the litter may contribute to an intensification of ongoing vegetation shifts across the tundra biome.", "doi": "10.1111/gcb.70582", "pmid": "41221642", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC12606403"}], "notes": [], "created": "2025-11-16T14:52:02.241Z", "modified": "2025-11-21T14:19:43.976Z"}, {"entity": "publication", "iuid": "bd866b3980e5400ca69a83689661ebfd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd866b3980e5400ca69a83689661ebfd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd866b3980e5400ca69a83689661ebfd"}}, "title": "The circulating dihydrotestosterone/testosterone ratio is increased by gut microbial 5\u03b1-reductase activity in females.", "authors": [{"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Li", "given": "Lei", "initials": "L"}, {"family": "Horkeby", "given": "Karin", "initials": "K"}, {"family": "Lawenius", "given": "Lina", "initials": "L"}, {"family": "Colld\u00e9n", "given": "Hannah", "initials": "H"}, {"family": "Sj\u00f6gren", "given": "Klara", "initials": "K"}, {"family": "Baldanzi", "given": "Gabriel", "initials": "G"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Grahnemo", "given": "Louise", "initials": "L"}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "121", "pages": "105978", "issn-l": "2352-3964"}, "abstract": "Dihydrotestosterone (DHT), the most potent ligand to the androgen receptor, is synthesised from testosterone (T) by 5\u03b1-reductase type 1 and 2. While type 1 is expressed in several non-reproductive tissues in both sexes, men also express high levels of the high-affinity type 2 isoform in reproductive tissues; yet women have a higher circulating DHT to T (DHT/T) ratio than men. We hypothesised that the high DHT/T ratio in women is caused by high gut microbiota (GM) 5\u03b1-reductase activity or altered \u03b2-glucuronidase-induced androgen reabsorption from the gut.\n\nWe used a large cross-sectional subsample of the Swedish CArdioPulmonary bioImage Study (2897 women and 4338 men, 50-65 years of age) with GM composition and functionality determined by metagenome sequencing and circulating androgens determined by liquid chromatography-tandem mass spectrometry.\n\nWe confirmed that women had higher (+194%) circulating DHT/T ratio than men. The relative abundance of microbial genes for 5\u03b1-reductase type 1 (P = 3 \u00d7 10-4), but not \u03b2-glucuronidase, was positively associated with the DHT/T ratio in women. In women, the GM relative abundances of Odoribacter splanchnicus and Parabacteroides distasonis were positively associated with the relative abundance of microbial genes for 5\u03b1-reductase type 1 (P < 2 \u00d7 10-149) and the circulating DHT/T ratio (O. splanchnicus P = 3 \u00d7 10-6; P. distasonis P = 5 \u00d7 10-5). In mechanistic studies, we observed very high DHT/T ratio in intestinal content of female conventionally-raised but not germ-free mice. In female mice, the DHT/T ratio was 86.9% higher in serum from the portal vein than in inferior vena cava (P = 0.007).\n\nThese findings demonstrate that the circulating DHT/T ratio is increased by GM 5\u03b1-reductase activity in females. We propose that the GM acts as an endocrine organ influencing the androgenic status in females.\n\nSee Acknowledgements.", "doi": "10.1016/j.ebiom.2025.105978", "pmid": "41124778", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12589954"}, {"db": "pii", "key": "S2352-3964(25)00422-0"}], "notes": [], "created": "2025-11-28T10:42:53.955Z", "modified": "2025-11-28T10:42:53.959Z"}, {"entity": "publication", "iuid": "92f0abc9e79944d2bebd0d108d67ca04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92f0abc9e79944d2bebd0d108d67ca04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92f0abc9e79944d2bebd0d108d67ca04"}}, "title": "Spatiotemporal gene expression and cellular dynamics of the developing human heart.", "authors": [{"family": "L\u00e1z\u00e1r", "given": "Enik\u0151", "initials": "E", "orcid": "0000-0001-8664-7531", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd94abaf66dd407da5056c04174fc62d.json"}}, {"family": "Mauron", "given": "Rapha\u00ebl", "initials": "R", "orcid": "0009-0004-0909-3554", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0b2662f1bc40b682ff6923c797877e.json"}}, {"family": "Andrusivov\u00e1", "given": "\u017daneta", "initials": "\u017d"}, {"family": "Foyer", "given": "Julia", "initials": "J"}, {"family": "He", "given": "Mengxiao", "initials": "M", "orcid": "0000-0001-5905-8467", "researcher": {"href": "https://publications.scilifelab.se/researcher/79045a6ac62b4f8ea64233619eb6bfc9.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Shakari", "given": "Nick", "initials": "N", "orcid": "0009-0003-2192-769X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c36fc495bd4e16829c53630137b3c2.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Sariyar", "given": "Sanem", "initials": "S"}, {"family": "Hansen", "given": "Jan Niklas", "initials": "JN", "orcid": "0000-0002-0489-7535", "researcher": {"href": "https://publications.scilifelab.se/researcher/272dfc4476064018bc7ed0235b7d3e55.json"}}, {"family": "Vicari", "given": "Marco", "initials": "M"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Bergmann", "given": "Olaf", "initials": "O", "orcid": "0000-0003-1065-4107", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb61ad666a3427193e07c6274e8c3a1.json"}}, {"family": "Sylv\u00e9n", "given": "Christer", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "issn-l": "1061-4036", "volume": "57", "issue": "11", "pages": "2756-2771"}, "abstract": "Heart development relies on topologically orchestrated cellular transitions and interactions, many of which remain poorly characterized in humans. Here, we combined unbiased spatial and single-cell transcriptomics with imaging-based validation across postconceptional weeks 5.5 to 14 to uncover the molecular landscape of human early cardiogenesis. We present a high-resolution transcriptomic map of the developing human heart, revealing the spatial arrangements of 31 coarse-grained and 72 fine-grained cell states organized into distinct functional niches. Our findings illuminate key insights into the formation of the cardiac pacemaker-conduction system, heart valves and atrial septum, and uncover unexpected diversity among cardiac mesenchymal cells. We also trace the emergence of autonomic innervation and provide the first spatial account of chromaffin cells in the fetal heart. Our study, supported by an open-access spatially centric interactive viewer, offers a unique resource to explore the cellular and molecular blueprint of human heart development, offering links to genetic causes of heart disease.", "doi": "10.1038/s41588-025-02352-6", "pmid": "41162788", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12597827"}, {"db": "pii", "key": "10.1038/s41588-025-02352-6"}], "notes": [], "created": "2025-11-24T12:14:25.565Z", "modified": "2025-11-24T12:48:57.768Z"}, {"entity": "publication", "iuid": "fdfce138b5554e72a4f6cf82097b08e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdfce138b5554e72a4f6cf82097b08e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdfce138b5554e72a4f6cf82097b08e2"}}, "title": "Reticulate and Hybrid Speciation is Promoted by Environmental Instability in an Indo-Pacific Species Complex of Whistlers (Aves: Pachycephala).", "authors": [{"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Guinet", "given": "Benjamin", "initials": "B"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "21", "pages": "e70018", "issn-l": "0962-1083"}, "abstract": "Genomic studies have revealed introgressive hybridisation as a common phenomenon across the tree of life, particularly among young radiations. As incipient speciation tends to be induced by vicariance events, it is assumed that introgressive hybridisation is more frequent in young radiations in which allopatrically distributed species have a high probability of coming into secondary contact. In this study, we use whole genomic data to investigate spatio-temporal introgression patterns in a songbird radiation that has colonised a highly dynamic island region in the Indo-Pacific. Some taxa within this radiation have colonised remote oceanic islands whereas others occur on landmasses and islands in the Sahul region that were periodically connected during Pleistocene periods of lower sea levels. Our results show that introgressive hybridisation has been pervasive within this young radiation, despite prominent plumage differences between taxa. Geographical proximity has been an important factor for hybridisation and we further find that species occupying islands in the environmentally unstable Sahul region exhibit particularly high signatures of introgressive hybridisation. Yet, one species appears to have been shielded from hybridisation, perhaps due to specific ecological specialisations. Finally, we identify a hybrid species on an island where two oceanic radiations meet. Our results also caution against relying solely on analyses that only detect asymmetric introgression when examining systems with complex introgression histories. Collectively, our results support a growing body of literature that suggests that reticulate speciation is more common than previously thought. This has implications for our understanding of species formation and their persistence through time.", "doi": "10.1111/mec.70018", "pmid": "40650490", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573736"}], "notes": [], "created": "2025-11-19T08:33:24.398Z", "modified": "2025-11-19T08:33:24.490Z"}, {"entity": "publication", "iuid": "7f52e3a6678e478fa8713a395977ad99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f52e3a6678e478fa8713a395977ad99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f52e3a6678e478fa8713a395977ad99"}}, "title": "Reproductive Isolation due to Divergent Ecological Selection Is Accompanied by Vast Genomic Instability in Experimentally Evolved Yeast Populations.", "authors": [{"family": "Bendixsen", "given": "Devin P", "initials": "DP", "orcid": "0000-0003-0831-7646", "researcher": {"href": "https://publications.scilifelab.se/researcher/533f0c534a214ee68a037b243a63a028.json"}}, {"family": "Gilchrist", "given": "Ciaran", "initials": "C", "orcid": "0000-0002-7639-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/44917102032e428998899b3e63e5c4df.json"}}, {"family": "Haberkorn", "given": "Chlo\u00e9", "initials": "C", "orcid": "0000-0002-7371-9177", "researcher": {"href": "https://publications.scilifelab.se/researcher/099838e4d3b94ee1af5cdfbf8ffea5d2.json"}}, {"family": "Persson", "given": "Karl", "initials": "K", "orcid": "0000-0002-2173-8165", "researcher": {"href": "https://publications.scilifelab.se/researcher/e13a27bed91340bf997f179e1c2c6c3b.json"}}, {"family": "Geijer", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-4158-2938", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad8eab8b087d47c4bce77ee2661628fb.json"}}, {"family": "Warringer", "given": "Jonas", "initials": "J", "orcid": "0000-0001-6144-2740", "researcher": {"href": "https://publications.scilifelab.se/researcher/864cb0fde85a4aaeb68627f67e97d283.json"}}, {"family": "Stelkens", "given": "Rike", "initials": "R", "orcid": "0000-0002-8530-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3449c244a4c13b8610e401f4cbef4.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "22", "pages": "e70110", "issn-l": "0962-1083"}, "abstract": "Populations evolving independently in divergent environments accumulate genetic differences and potentially evolve reproductive isolation as a by-product of divergence. The speed and mechanisms underlying this process are difficult to investigate because we rarely get the opportunity to witness them in natural settings, and histories of selection and gene flow between populations are often unknown. Here, we experimentally evolved yeast for 1000 generations of evolution in both divergent and parallel environments. At regular time points during experimental evolution, we made crosses between parallel- and divergent-evolving populations to measure postzygotic reproductive isolation (gamete viability). We used whole genome population sequencing to determine the mutational load, the number and types of structural variation, and other genomic features of the parent, F1 and F2 intraspecific hybrids. We found evidence for large-scale phenotypic and genome-wide differentiation in response to divergent laboratory selection. Divergent-selected populations produced hybrids with reduced gamete viability-a classic signature of postzygotic reproductive isolation in the form of hybrid breakdown. Parallel-selected populations, on the other hand, remained more reproductively compatible (with exceptions). We found that F2 hybrid genomes contained vast genomic instability, that is, new structural variants (especially insertions, deletions and interchromosomal translocations) that were not observed in parent and F1 genomes, which is likely a result of chromosome missegregation and recombination errors in hybrid meiosis. Our results provide phenotypic and genomic evidence that partial reproductive isolation evolved due to adaptation to divergent environments, consistent with predictions of ecological speciation theory.", "doi": "10.1111/mec.70110", "pmid": "40960070", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12617035"}], "notes": [], "created": "2025-11-19T09:48:26.950Z", "modified": "2025-11-19T09:48:27.465Z"}, {"entity": "publication", "iuid": "26bfae29afd14c7bb2a1a265f49ac622", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26bfae29afd14c7bb2a1a265f49ac622.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26bfae29afd14c7bb2a1a265f49ac622"}}, "title": "Probing physicochemical properties of a mixed-anion protic ionic liquid based on [TFSI] and [NO3]", "authors": [{"family": "Abdou", "given": "Nicole", "initials": "N", "orcid": "0009-0003-0907-7725", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f1406e1686740939cad716c9ab894d9.json"}}, {"family": "Pipertzis", "given": "Achilleas", "initials": "A", "orcid": "0009-0001-8569-6670", "researcher": {"href": "https://publications.scilifelab.se/researcher/736fa3a4a56e47de983e9c5d7cc8267c.json"}}, {"family": "Swenson", "given": "Jan", "initials": "J", "orcid": "0000-0001-5640-4766", "researcher": {"href": "https://publications.scilifelab.se/researcher/20791829da1540ed9327857790d65940.json"}}, {"family": "Martinelli", "given": "Anna", "initials": "A", "orcid": "0000-0001-9885-5901", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4adbd00ead04caaaa107e57fbe67c7b.json"}}], "type": "journal-article", "published": "2025-11-00", "journal": {"title": "Journal of Molecular Liquids", "issn": "0167-7322", "volume": "437", "pages": "128418", "issn-l": null}, "abstract": null, "doi": "10.1016/j.molliq.2025.128418", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:06:35.374Z", "modified": "2025-11-27T08:06:35.734Z"}, {"entity": "publication", "iuid": "696f138df66747158e7f0f9a47bbd9ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/696f138df66747158e7f0f9a47bbd9ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/696f138df66747158e7f0f9a47bbd9ae"}}, "title": "Paleogenomic evidence on the temporal continuity of indigenous goat exploitation in the Canary Islands", "authors": [{"family": "D\u00edaz-P\u00e9rez", "given": "Clara", "initials": "C"}, {"family": "Santana", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-9615-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a4f0fc23b847b98e0d57d22a8a756d.json"}}, {"family": "Daly", "given": "Kevin G", "initials": "KG"}, {"family": "Ord\u00f3\u00f1ez", "given": "Alejandra C", "initials": "AC"}, {"family": "Serrano", "given": "Javier G", "initials": "JG"}, {"family": "Armas-Quintana", "given": "Sara B", "initials": "SB"}, {"family": "Vacas-Fumero", "given": "Emilio", "initials": "E"}, {"family": "Brito-Mayor", "given": "Aitor", "initials": "A"}, {"family": "Gilson", "given": "Simon Pierre", "initials": "SP"}, {"family": "Morales", "given": "Jacob", "initials": "J"}, {"family": "Marrero Salas", "given": "Efra\u00edn", "initials": "E"}, {"family": "Hern\u00e1ndez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Alberto", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Moreno", "given": "Marco", "initials": "M"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Hern\u00e1ndez", "given": "Mariano", "initials": "M"}, {"family": "Arnay", "given": "Matilde", "initials": "M"}, {"family": "Fregel", "given": "Rosa", "initials": "R", "orcid": "0000-0002-2951-6508", "researcher": {"href": "https://publications.scilifelab.se/researcher/abfbfec4ddea49f8b4eedcf1e04e01c2.json"}}], "type": "journal-article", "published": "2025-11-00", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "28", "issue": "11", "pages": "113771"}, "abstract": null, "doi": "10.1016/j.isci.2025.113771", "pmid": null, "labels": {"Ancient DNA": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2025-11-05T07:40:52.150Z", "modified": "2025-11-19T07:57:42.304Z"}, {"entity": "publication", "iuid": "0df16491ad2f48b098d8d2d47ab51a40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0df16491ad2f48b098d8d2d47ab51a40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0df16491ad2f48b098d8d2d47ab51a40"}}, "title": "Novel protein targets for type 2 diabetes prevention and their mediating role in the diet-disease relationship: evidence from 2 population-based cohorts and a Mendelian randomization analysis.", "authors": [{"family": "Shi", "given": "Lin", "initials": "L"}, {"family": "Zheng", "given": "Rui", "initials": "R"}, {"family": "Brunius", "given": "Carl", "initials": "C"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Baron", "given": "John A", "initials": "JA"}, {"family": "Wolk", "given": "Alicja", "initials": "A"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Am. J. Clin. Nutr.", "issn": "1938-3207", "volume": "122", "issue": "5", "pages": "1400-1412", "issn-l": "0002-9165"}, "abstract": "Circulating proteins are associated with type 2 diabetes (T2D) but causality has often not been investigated. Whether plasma proteins could be suitable targets for T2D prevention remains uncertain.\n\nWe aimed to identify causal associations between plasma proteins and incident T2D and discover whether proteins may mediate associations between diet and T2D risk.\n\nWe measured 276 plasma proteins in 2 Swedish prospective cohorts. The discovery cohort consisted of 4103 females, and the replication cohort consisted of 1017 females and 4124 males. During follow-up, 189 females in the discovery cohort and 297 participants in the replication cohort developed T2D. Associations between proteins with incident T2D were estimated using Cox proportional hazards models. Mendelian randomization analyses using cis-protein quantitative trait loci were conducted to assess causal relevance, along with colocalization analyses to examine shared causal variants between proteins and T2D. We further assessed whether proteins could mediate associations between dietary patterns (DPs) derived from principle component analysis and incident T2D.\n\nOverall, 112 proteins were associated with incident T2D independent of age, sex and lifestyle factors in 2 cohorts. Genetically raised levels of tyrosine-protein kinase receptor TYRO3, intercellular adhesion molecule 2, sortilin (SORT1), and sialomucin core protein 24 were associated with increased T2D risk, whereas catechol O-methyltransferase, CD2-associated protein, matrix metalloproteinase-12, nectin-2 (NECTIN2), reticulon-4 receptor (RTN4R), and fibroblast growth factor 21 were inversely associated (false discovery rate-adjusted P < 0.05). Strong evidence (posterior hypothesis 4 of colocalization > 0.8) of shared genetic variants of NECTIN2, RTN4R, and SORT1 with T2D was found. Phenome-wide association investigation at the gene level confirmed associations of proteins with T2D traits. We identified a mediating role of proteins with genetic evidence in the association between a healthy DP (i.e., high consumption of vegetables, fruits, nuts, and whole grains) and T2D.\n\nWe provide novel and robust findings of proteins causally linked to T2D and their associations with habitual diet. These findings may guide nutritional strategies for T2D prevention.", "doi": "10.1016/j.ajcnut.2025.07.015", "pmid": "41193035", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9165(25)00431-9"}], "notes": [], "created": "2025-11-25T19:21:40.129Z", "modified": "2025-11-25T19:21:40.143Z"}, {"entity": "publication", "iuid": "7bf8cac9d52640798fd53ad7a662d223", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7bf8cac9d52640798fd53ad7a662d223.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7bf8cac9d52640798fd53ad7a662d223"}}, "title": "Impact of Shared Facilities in Advancing Solid-State NMR Research: 2025 Edition", "authors": [{"family": "Schurko", "given": "Robert W", "initials": "RW"}, {"family": "Rienstra", "given": "Chad M", "initials": "CM"}, {"family": "Jaroniec", "given": "Christopher P", "initials": "CP"}, {"family": "Hansen", "given": "Alexandar L", "initials": "AL"}, {"family": "Franks", "given": "W Trent", "initials": "WT"}, {"family": "Bryce", "given": "David L", "initials": "DL"}, {"family": "Brinkmann", "given": "Andreas", "initials": "A"}, {"family": "Terskikh", "given": "Victor", "initials": "V"}, {"family": "Brown", "given": "Steven P", "initials": "SP"}, {"family": "Iuga", "given": "Dinu", "initials": "D"}, {"family": "van Heijenoort", "given": "Carine", "initials": "C"}, {"family": "Fayon", "given": "Franck", "initials": "F"}, {"family": "Bertaina", "given": "Sylvain", "initials": "S"}, {"family": "Alfonso", "given": "Carlos", "initials": "C"}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Gr\u00f6bner", "given": "Gerhard", "initials": "G"}, {"family": "Potrzebowski", "given": "Marek J", "initials": "MJ"}, {"family": "Cerofolini", "given": "Linda", "initials": "L"}, {"family": "Ravera", "given": "Enrico", "initials": "E"}, {"family": "Fragai", "given": "Marco", "initials": "M"}, {"family": "Lelli", "given": "Moreno", "initials": "M"}, {"family": "Lesage", "given": "Anne", "initials": "A"}, {"family": "Pintacuda", "given": "Guido", "initials": "G"}, {"family": "Pons", "given": "Miquel", "initials": "M"}, {"family": "Mafra", "given": "Lu\u00eds", "initials": "L"}, {"family": "Schneider", "given": "Jos\u00e9 F", "initials": "JF"}, {"family": "Monti", "given": "Gustavo A", "initials": "GA"}, {"family": "Acosta", "given": "Rodolfo H", "initials": "RH"}, {"family": "Pastawski", "given": "Horacio M", "initials": "HM"}, {"family": "Thomas", "given": "Brijith", "initials": "B"}, {"family": "Kolyagin", "given": "Yury G", "initials": "YG"}, {"family": "Agarwal", "given": "Vipin", "initials": "V"}, {"family": "Hou", "given": "Guangjin", "initials": "G"}, {"family": "Deng", "given": "Feng", "initials": "F"}, {"family": "Xue", "given": "Kai", "initials": "K"}, {"family": "Kigawa", "given": "Takanori", "initials": "T"}, {"family": "Manjunatha Reddy", "given": "G N", "initials": "GN", "orcid": "0000-0002-8283-2462", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbb04e62fb2548f98f72289528e16647.json"}}], "type": "journal-article", "published": "2025-11-00", "journal": {"title": "Solid State Nuclear Magnetic Resonance", "issn": "0926-2040", "pages": "102053", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ssnmr.2025.102053", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-12-03T14:42:43.231Z", "modified": "2025-12-03T14:42:43.429Z"}, {"entity": "publication", "iuid": "edba25a5b1e54a32865c02915ee9ff5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edba25a5b1e54a32865c02915ee9ff5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edba25a5b1e54a32865c02915ee9ff5e"}}, "title": "Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.", "authors": [{"family": "Moraitou", "given": "Markella", "initials": "M", "orcid": "0000-0003-0860-5920", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f3b54ad837e4860a81b0bd5a886b416.json"}}, {"family": "Richards", "given": "John L", "initials": "JL", "orcid": "0000-0003-4428-1580", "researcher": {"href": "https://publications.scilifelab.se/researcher/23d3051397fd422b94afdb6eb8be17c4.json"}}, {"family": "Bolyos", "given": "Chanah", "initials": "C"}, {"family": "Saliari", "given": "Konstantina", "initials": "K", "orcid": "0000-0002-1344-0756", "researcher": {"href": "https://publications.scilifelab.se/researcher/b32afde8cb454fa3bb0e880e2cff5d0b.json"}}, {"family": "Gilissen", "given": "Emmanuel", "initials": "E"}, {"family": "Timmons", "given": "Zena", "initials": "Z"}, {"family": "Kitchener", "given": "Andrew C", "initials": "AC"}, {"family": "Pauwels", "given": "Olivier S G", "initials": "OSG"}, {"family": "Sabin", "given": "Richard", "initials": "R", "orcid": "0000-0003-0699-7596", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7d0503256fd45e687c1eebc9ce0c797.json"}}, {"family": "Kokkini", "given": "Phaedra", "initials": "P", "orcid": "0000-0002-7652-0956", "researcher": {"href": "https://publications.scilifelab.se/researcher/223e41a72db2480aa5fbfd015702b525.json"}}, {"family": "Portela Miguez", "given": "Roberto", "initials": "R", "orcid": "0000-0003-3094-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/103b88f38bcb494e8b42096d632e9f71.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": "25", "issue": "8", "pages": "e70039"}, "abstract": "Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.", "doi": "10.1111/1755-0998.70039", "pmid": "40889349", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12550474"}], "notes": [], "created": "2025-09-08T07:07:00.224Z", "modified": "2025-11-28T10:50:40.774Z"}, {"entity": "publication", "iuid": "394d345f587e4a8fa382227d3718c80e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/394d345f587e4a8fa382227d3718c80e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/394d345f587e4a8fa382227d3718c80e"}}, "title": "HAPP: High-accuracy pipeline for processing deep metabarcoding data.", "authors": [{"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Granqvist", "given": "Emma", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "van Dijk", "given": "Laura J A", "initials": "LJA"}, {"family": "Goodsell", "given": "Robert", "initials": "R"}, {"family": "Godeiro", "given": "Nerivania N", "initials": "NN", "orcid": "0000-0002-1669-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/990e5c3362f94d76af29742ab5876a8a.json"}}, {"family": "Bellini", "given": "Bruno C", "initials": "BC"}, {"family": "Orsholm", "given": "Johanna", "initials": "J"}, {"family": "\u0141ukasik", "given": "Piotr", "initials": "P"}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "PLoS Comput. Biol.", "issn": "1553-7358", "issn-l": "1553-734X", "volume": "21", "issue": "11", "pages": "e1013558"}, "abstract": "Deep metabarcoding offers an efficient and reproducible approach to biodiversity monitoring, but noisy data and incomplete reference databases challenge accurate diversity estimation and taxonomic annotation. Here, we introduce a novel algorithm, NEEAT, for removing spurious operational taxonomic units (OTUs) originating from nuclear-embedded mitochondrial DNA sequences (NUMTs) or sequencing errors. It integrates 'echo' signals across samples with the identification of unusual evolutionary patterns among similar DNA sequences. We also extensively benchmark current tools for chimera removal, taxonomic annotation and OTU clustering of deep metabarcoding data. The best performing tools/parameter settings are integrated into HAPP, a high-accuracy pipeline for processing deep metabarcoding data. Tests using CO1 data from BOLD and large-scale metabarcoding data on insects demonstrate that HAPP significantly outperforms existing methods, while enabling efficient analysis of extensive datasets by parallelizing computations across taxonomic groups.", "doi": "10.1371/journal.pcbi.1013558", "pmid": "41202092", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12622834"}, {"db": "pii", "key": "PCOMPBIOL-D-25-00687"}], "notes": [], "created": "2025-11-21T11:45:11.315Z", "modified": "2025-11-21T12:27:09.804Z"}, {"entity": "publication", "iuid": "ca5a160aa916465286ca5da0958e09ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca5a160aa916465286ca5da0958e09ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca5a160aa916465286ca5da0958e09ea"}}, "title": "Growth failure in aggrecan deficiency is due to decreased extracellular matrix and impaired growth plate chondrocyte hypertrophy.", "authors": [{"family": "Bendre", "given": "Ameya", "initials": "A"}, {"family": "Ottosson", "given": "Lars", "initials": "L"}, {"family": "Baroncelli", "given": "Marta", "initials": "M"}, {"family": "Dou", "given": "Zelong", "initials": "Z"}, {"family": "Nilsson", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Bone", "issn": "1873-2763", "volume": "200", "pages": "117594", "issn-l": null}, "abstract": "Heterozygous loss-of-function mutations in the aggrecan (ACAN) gene cause autosomal dominant short stature often associated with advanced bone age, early-onset osteoarthritis and intervertebral disc disease (SSOAOD). These mutations are relatively common in patients with idiopathic short stature. However, the pathogenic mechanism of growth failure in this condition is not fully understood. Here, we studied the heterozygous cartilage matrix deficiency mouse (Acan+/-), which harbors a 7 bp microdeletion in aggrecan and develops postnatal growth cessation despite being born of normal size. Using detailed histomorphometric analysis, we found that the growth failure was primarily due to decreased extracellular matrix and impaired chondrocyte hypertrophy, whereas proliferation was largely unaffected. Furthermore, single-cell transcriptomic profiling revealed decreased total Acan mRNA expression in the Acan+/- chondrocytes. Notably, Akt signalling, which is important for hypertrophic differentiation was suppressed in Acan+/- pre-hypertrophic and hypertrophic chondrocytes. The decreased Akt signalling was associated with increased expression of calcium-calmodulin dependent protein kinase 1D (Camk1D), which negatively regulates Akt signalling, thereby providing a potential mechanism for the impaired hypertrophic differentiation. These findings reveal key cellular and molecular causes of growth failure in aggrecan deficiency and suggest that boosting proteoglycan expression and Akt signalling may help restore growth.", "doi": "10.1016/j.bone.2025.117594", "pmid": "40685060", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S8756-3282(25)00206-6"}], "notes": [], "created": "2025-10-16T17:17:25.970Z", "modified": "2025-10-16T17:17:25.976Z"}, {"entity": "publication", "iuid": "4dc8a8e86bb54b9a94855d45c97c5265", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4dc8a8e86bb54b9a94855d45c97c5265.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4dc8a8e86bb54b9a94855d45c97c5265"}}, "title": "Genomic analysis of a Neisseria meningitidis patient isolate causing a false-positive result in the Abbott Alinity m STI, Sweden: a case report.", "authors": [{"family": "Herrmann", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-8729-2306", "researcher": {"href": "https://publications.scilifelab.se/researcher/163a6af6acb643aeb6faf96b93ae9b10.json"}}, {"family": "S\u00e4ll\u00e9ber", "given": "Andreas", "initials": "A"}, {"family": "Kaden", "given": "Rene", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications.scilifelab.se/researcher/018870b1d0034ee09552a3ae451d5504.json"}}], "type": "case reports", "published": "2025-11-00", "journal": {"title": "ASM Case Rep", "issn": "2996-2684", "volume": "1", "issue": "6", "issn-l": null}, "abstract": "Diagnostics of sexually transmitted infections, such as Neisseria gonorrhoeae (NG), are often performed using high-volume test systems, often in combination with other targets. This report examines the occurrence of two false-positive NG results from pharyngeal samples in the Abbott Alinity m STI assay, cleared by the Food and Drug Administration.\n\nAnalysis of pharyngeal samples from two men who have sex with men was positive for NG in the Abbott Alinity m STI assay, but negative upon confirmation testing with the Cepheid Xpert CT/NG assay. A pharyngeal culture isolate was obtained from one of the two men. The isolate tested negative for being NG in four different commercial nucleic acid amplification tests. A laboratory-developed PCR based on two targets gave inconclusive results, with positive detection for the opa gene but no detection for the porA gene. The isolate was identified as Neisseria meningitidis (NM) in MALDI-TOF analysis. Whole-genome sequencing revealed 322 diverse virulence genes, of which 314 were typical for NM and 8 for NG. Phylogenetic analysis showed a taxonomic delineation for NM.\n\nConfirmatory tests with alternative targets are essential for accurate analysis of NG, especially in low-prevalence settings. Evaluation of diagnostic tools to ensure accurate detection of NG is also needed.", "doi": "10.1128/asmcr.00143-25", "pmid": "41244285", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12584176"}, {"db": "pii", "key": "asmcr00143-25"}], "notes": [], "created": "2025-11-26T14:14:35.611Z", "modified": "2025-11-26T14:14:35.729Z"}, {"entity": "publication", "iuid": "ee9a4f95a65047b6b653d5c9247a378c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee9a4f95a65047b6b653d5c9247a378c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee9a4f95a65047b6b653d5c9247a378c"}}, "title": "Genomic Landscape of Divergence in Ballan Wrasse (Labrus bergylta).", "authors": [{"family": "Jansson", "given": "Eeva", "initials": "E", "orcid": "0000-0002-7840-7201", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d9b75e0780c43f8ac26d9a7a0418555.json"}}, {"family": "Ayllon", "given": "Fernando", "initials": "F", "orcid": "0009-0005-6051-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/beb3c127a1fe47ec874dca9fe6f3ffd4.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Casas", "given": "Laura", "initials": "L", "orcid": "0000-0001-6617-8731", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5189f1f7c74aad9b8a2af7f47ad4f3.json"}}, {"family": "Saborido-Rey", "given": "Fran", "initials": "F", "orcid": "0000-0002-2760-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/74db5d050f844f6a944e2393d83728b9.json"}}, {"family": "Furmanek", "given": "Tomasz", "initials": "T"}, {"family": "Brieuc", "given": "Marine S O", "initials": "MSO", "orcid": "0000-0001-8601-2122", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef26450b493a412faac6b9b0b4a1a857.json"}}, {"family": "Villegas-Rios", "given": "David", "initials": "D", "orcid": "0000-0001-5660-5322", "researcher": {"href": "https://publications.scilifelab.se/researcher/0038fd6eb1234894a0b1938c0e862a36.json"}}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M", "orcid": "0000-0003-4762-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b95d1205db043108756e235bcb25c84.json"}}, {"family": "Edvardsen", "given": "Rolf B", "initials": "RB", "orcid": "0000-0001-8430-8042", "researcher": {"href": "https://publications.scilifelab.se/researcher/07efd6f7e7b04bbd8af5221f78e982c7.json"}}, {"family": "Lille-Lang\u00f8y", "given": "Roger", "initials": "R", "orcid": "0000-0002-8010-8542", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea677d3afed44519b9a3e5406c721735.json"}}, {"family": "Glover", "given": "Kevin A", "initials": "KA"}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e17732"}, "abstract": "The architecture underpinning genomic divergence is still a largely uncharted territory and likely case-dependent. Here, we investigated genome-wide variation in Ballan wrasse, a northeastern Atlantic fish species that displays two sympatric colour morphs, spotty and plain, that have been suggested to represent subspecies. We produced a chromosome-level reference genome and thereafter investigated genomic divergence among 152 individuals including both morphs, from two localities in Spain and Norway each and one in France. Differences between morphs dominated in Spain in accordance with sympatric divergence, whereas in Norway allopatric differentiation was prominent and repeated genomic signals of local divergence were found. Chromosomes had large low-recombining areas shared across all populations. Within the Spanish morphs, these areas contained large islands of divergence, totalling ~11% of the genome, and showed high morph specificity and strong selection. The same regions showed frequent admixture in the French morphs and no differentiation in Norway. In contrast, divergent regions observed between sampling localities in Norway were shorter and found throughout the genome. High inbreeding and lower diversity were observed in the Norwegian samples, consistent with the proposed recolonisation bottleneck and subsequent drift. Several genomic regions were significantly associated with morphs and contained tens of genes of diverse functions, suggesting that colouration is unlikely to be the sole driver of divergence. Our results do not support the hypothesis of shared larger genomic features underlying intraspecific colour divergence. Instead, we observe gradual accumulation of differences into low-recombining regions, likely when additional factors like assortative mating and/or lack of gene flow favour their development.", "doi": "10.1111/mec.17732", "pmid": "40095420", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null, "NGI Other": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573741"}], "notes": [], "created": "2025-08-19T13:31:21.967Z", "modified": "2025-11-28T10:51:26.963Z"}, {"entity": "publication", "iuid": "abaf1e9bf72441a4a14b06619ce812b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abaf1e9bf72441a4a14b06619ce812b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abaf1e9bf72441a4a14b06619ce812b3"}}, "title": "Genome sequencing in a cohort of 32 fetuses with genetic skeletal disorders.", "authors": [{"family": "Lindel\u00f6f", "given": "Hillevi", "initials": "H"}, {"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A"}, {"family": "Voss", "given": "Ulrika", "initials": "U"}, {"family": "Gaetana Piticchio", "given": "Serena", "initials": "S"}, {"family": "Conner", "given": "Peter", "initials": "P"}, {"family": "Papadogiannakis", "given": "Nikos", "initials": "N"}, {"family": "Batkovskyte", "given": "Dominyka", "initials": "D", "orcid": "0000-0002-0492-1259", "researcher": {"href": "https://publications.scilifelab.se/researcher/017749b78ac540a6b2a36303130606f2.json"}}, {"family": "Orellana", "given": "Laura", "initials": "L", "orcid": "0000-0003-1927-555X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c614cf477d9044e28ae901600cc84e7d.json"}}, {"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Malmgren", "given": "Helena", "initials": "H"}, {"family": "Lagerstedt Robinson", "given": "Kristina", "initials": "K"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Nishimura", "given": "Gen", "initials": "G"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G", "orcid": "0000-0001-9601-3137", "researcher": {"href": "https://publications.scilifelab.se/researcher/684864357acd490cb627f38fed3b82a4.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "volume": "33", "issue": "11", "pages": "1474-1483", "issn-l": "1018-4813"}, "abstract": "Approximately 200 genetic skeletal disorders can present prenatally, detectable through ultrasound abnormalities during pregnancy. Severe forms are typically identified during the first or second trimester, whereas milder phenotypes are recognized later, in the third trimester. Diagnosing skeletal dysplasia prenatally is challenging due to the large number of disorders and the overlapping clinical findings that can be detected by ultrasound. This study, conducted at Karolinska University Hospital between 2015 and 2022, examines the genetic and radiographic findings in 32 fetuses (14 female and 18 male, from unrelated families) with skeletal abnormalities detected on prenatal ultrasound and confirmed by radiographs at birth or after pregnancy termination. Fetal DNA samples from all 32 fetuses underwent singleton genome sequencing using an in silico skeletal dysplasia gene panel. As a second step, for six fetuses with molecularly unsolved diagnoses, trio genome sequencing analysis involving the fetus and both parents was performed. The diagnostic yield of genome sequencing was 72%, with pathogenic or likely pathogenic variants identified in 23 of the 32 fetuses. Additionally, four variants of uncertain significance, strongly suspected to be causative based on clinical and radiographic features, as well as structural protein analyses, were identified in four fetuses with autosomal recessive conditions. The diagnoses of five fetuses remain molecularly unsolved. In conclusion, by combining detailed phenotypic data with singleton genome sequencing we were able to reach a genetic diagnosis in 72% of 32 fetal genetic skeletal disorder cases investigated at the Karolinska University Hospital.", "doi": "10.1038/s41431-025-01886-x", "pmid": "40500351", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12583725"}, {"db": "pii", "key": "10.1038/s41431-025-01886-x"}], "notes": [], "created": "2025-11-18T20:45:58.654Z", "modified": "2025-11-28T18:04:38.525Z"}, {"entity": "publication", "iuid": "4454335dc4504444ac7197bda2a143ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4454335dc4504444ac7197bda2a143ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4454335dc4504444ac7197bda2a143ad"}}, "title": "Genetic mapping in the red mason bee implicates ANTSR as an ancient sex-determining locus in bees and ants.", "authors": [{"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T"}, {"family": "Taliadoros", "given": "Demetris", "initials": "D"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Magnusson", "given": "Sara", "initials": "S"}, {"family": "Huser", "given": "Linn", "initials": "L"}, {"family": "Nor Fuad", "given": "Muhammad Nafiz Ikhwan Bin", "initials": "MNIB"}, {"family": "Everitt", "given": "Turid", "initials": "T"}, {"family": "Mart\u00edn-Hern\u00e1ndez", "given": "Giselle C", "initials": "GC"}, {"family": "Theodorou", "given": "Panagiotis", "initials": "P"}, {"family": "Cederberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Paxton", "given": "Robert J", "initials": "RJ"}, {"family": "Seidelmann", "given": "Karsten", "initials": "K"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "volume": "23", "issue": "11", "pages": "e3003458", "issn-l": "1544-9173"}, "abstract": "Haplodiploid inheritance, in which females are diploid and males are haploid, is found in all species of Hymenoptera. Sex in haplodiploids is commonly determined by the alleles present at a complementary sex determination (CSD) locus, with heterozygosity triggering the female developmental pathway. The identity of this locus differs among taxa and is only known in a few species. Here, we map a single CSD locus to a 2 kbp region in the genome of the red mason bee Osmia bicornis. It overlaps the long noncoding RNA ANTSR, which has been identified as the sex-determining gene in the invasive ant Linepithema humile. This locus is homozygous in diploid males and exhibits extremely high levels of haplotype diversity, consistent with the action of frequency-dependent selection. The elevated levels of heterozygosity in the CSD locus enable us to fine-map potentially functional genetic variation within it. We also identify elevated levels of genetic diversity in the ortholog of the CSD locus in five other bee and ant genera, suggesting that it may govern sex determination widely in Hymenoptera. Our data are consistent with the hypothesis that ANTSR evolved a role in sex determination over 150 million years ago and is the ancestral sex-determination locus of bees and ants.", "doi": "10.1371/journal.pbio.3003458", "pmid": "41183133", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12594375"}, {"db": "pii", "key": "PBIOLOGY-D-25-02082"}], "notes": [], "created": "2025-11-21T13:19:56.177Z", "modified": "2025-11-21T13:19:56.233Z"}, {"entity": "publication", "iuid": "72cefc191b884104801e8e6a814331a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72cefc191b884104801e8e6a814331a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72cefc191b884104801e8e6a814331a3"}}, "title": "Epigenetic alterations facilitate transcriptional and translational programs in hypoxia.", "authors": [{"family": "Watt", "given": "Kathleen", "initials": "K"}, {"family": "Dauber", "given": "Bianca", "initials": "B", "orcid": "0009-0006-6755-3840", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd42e74de22e49a4a1b279ba43048c9a.json"}}, {"family": "Szkop", "given": "Krzysztof J", "initials": "KJ"}, {"family": "Lee", "given": "Laura", "initials": "L"}, {"family": "Jovanovic", "given": "Predrag", "initials": "P", "orcid": "0000-0002-0090-0047", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9428a0025a74362a8ada196e0a9292d.json"}}, {"family": "Chen", "given": "Shan", "initials": "S"}, {"family": "Palia", "given": "Ranveer", "initials": "R"}, {"family": "Vassalakis", "given": "Julia A", "initials": "JA"}, {"family": "Cooper", "given": "Tyler T", "initials": "TT"}, {"family": "Papadopoli", "given": "David", "initials": "D"}, {"family": "Masvidal", "given": "La\u00eca", "initials": "L"}, {"family": "Jewer", "given": "Michael", "initials": "M"}, {"family": "Tandoc", "given": "Kristofferson", "initials": "K"}, {"family": "Plummer", "given": "Hannah", "initials": "H"}, {"family": "Lajoie", "given": "Gilles A", "initials": "GA"}, {"family": "Topisirovic", "given": "Ivan", "initials": "I", "orcid": "0000-0002-5510-9762", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cc0d0d273054042b1ef202ea6174f0d.json"}}, {"family": "Larsson", "given": "Ola", "initials": "O", "orcid": "0000-0003-1412-1308", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8d18c6429ac46d094a81a3049b7f478.json"}}, {"family": "Postovit", "given": "Lynne-Marie", "initials": "LM", "orcid": "0000-0002-8088-4197", "researcher": {"href": "https://publications.scilifelab.se/researcher/21ec312efc1846938b6f3c62e493c307.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Nat Cell Biol", "issn": "1476-4679", "volume": "27", "issue": "11", "pages": "1965-1981", "issn-l": null}, "abstract": "Adaptation to cellular stresses entails an incompletely understood coordination of transcriptional and post-transcriptional gene expression programs. Here, by quantifying hypoxia-dependent transcriptomes, epigenomes and translatomes in T47D breast cancer cells and H9 human embryonic stem cells, we show pervasive changes in transcription start site (TSS) selection associated with nucleosome repositioning and alterations in H3K4me3 distribution. Notably, hypoxia-associated TSS switching was induced or reversed via pharmacological modulation of H3K4me3 in the absence of hypoxia, defining a role for H3K4me3 in TSS selection independent of HIF1-transcriptional programs. By remodelling 5'UTRs, TSS switching selectively alters protein synthesis, including enhanced translation of messenger RNAs encoding pyruvate dehydrogenase kinase 1, which is essential for metabolic adaptation to hypoxia. These results demonstrate a previously unappreciated mechanism of translational regulation during hypoxia driven by epigenetic reprogramming of the 5'UTRome.", "doi": "10.1038/s41556-025-01786-8", "pmid": "41102449", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12611764"}, {"db": "pii", "key": "10.1038/s41556-025-01786-8"}], "notes": [], "created": "2025-10-29T10:04:31.556Z", "modified": "2025-11-28T10:46:16.259Z"}, {"entity": "publication", "iuid": "0577c5369a1d4893bc7f6fb121420f6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0577c5369a1d4893bc7f6fb121420f6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0577c5369a1d4893bc7f6fb121420f6f"}}, "title": "Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes).", "authors": [{"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Rajan", "given": "Samyuktha", "initials": "S"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V"}, {"family": "Smith", "given": "Brian Tilston", "initials": "BT"}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Iova", "given": "Bulisa", "initials": "B"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e17760"}, "abstract": "Speciation is a fundamental concept in evolutionary biology, and understanding the mechanisms driving speciation remains the foremost research topic within this field. Hybridisation is often involved in speciation and can influence its rates, potentially accelerating, decelerating or even reversing the process. This study investigates the evolutionary history of the New Guinean bird genus Melidectes, consisting of six species that inhabit various montane regions at different elevations. While most Melidectes species have allopatric distributions, two species overlap in the central mountain range and hybridise. However, plumage differences and elevational adaptations are assumed to maintain the species' boundaries. Utilising specimens from natural history collections and comprehensive genomic analyses, including a de novo genome assembly, we characterise allopatric speciation patterns within the genus and highlight how future speciation could potentially be driven by climate change. Contrary to previous hypotheses, our findings suggest that in the two distributionally overlapping species, phenotypic differences do not prevent gene flow. We find limited acoustic differentiation and extensive admixture across most of their distributions. Divergence and admixture levels conform poorly to the current taxonomy and follow a geographical pattern in which the most isolated populations at the ends of the distributions are most divergent and show least admixture. However, in contrast, their mitochondrial genomes do group in accordance with species identity, namely, into two deeply divergent lineages. We propose that this system demonstrates the ephemeral nature of speciation, in which two incipient species have started mixing extensively as they came into secondary contact, resulting in nearly complete fusion into a single lineage.", "doi": "10.1111/mec.17760", "pmid": "40219608", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573753"}], "notes": [], "created": "2025-11-19T08:27:00.806Z", "modified": "2025-11-19T09:18:52.732Z"}, {"entity": "publication", "iuid": "23d74f5bf04c40f0822bf72e5bdf7753", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23d74f5bf04c40f0822bf72e5bdf7753.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23d74f5bf04c40f0822bf72e5bdf7753"}}, "title": "Early prediction of subsequent peg-asparaginase inactivation in acute lymphoblastic leukaemia patients-A NOPHO ALL2008 study.", "authors": [{"family": "Dam", "given": "Merete", "initials": "M", "orcid": "0000-0002-8857-8629", "researcher": {"href": "https://publications.scilifelab.se/researcher/36bf1a873bf94505ac4621e2cb6ae7ea.json"}}, {"family": "Centanni", "given": "Maddalena", "initials": "M"}, {"family": "Centanni", "given": "Daniel", "initials": "D"}, {"family": "Friberg", "given": "Lena E", "initials": "LE"}, {"family": "Karlsson", "given": "Mats O", "initials": "MO"}, {"family": "Lynggaard", "given": "Line S", "initials": "LS"}, {"family": "Johannsdottir", "given": "Inga M", "initials": "IM"}, {"family": "Lepik", "given": "Kristi", "initials": "K"}, {"family": "Vaitkeviciene", "given": "Goda E", "initials": "GE"}, {"family": "Griskevicius", "given": "Laimonas", "initials": "L"}, {"family": "P\u00f6yh\u00f6nen", "given": "Tuuli", "initials": "T"}, {"family": "Py\u00f6r\u00e4l\u00e4", "given": "Marja", "initials": "M"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur G", "initials": "\u00d3G"}, {"family": "Quist-Paulsen", "given": "Petter", "initials": "P"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Christoforaki", "given": "Tania", "initials": "T"}, {"family": "Overgaard", "given": "Ulrik", "initials": "U"}, {"family": "Hansen", "given": "Stefan N", "initials": "SN"}, {"family": "Albertsen", "given": "Birgitte K", "initials": "BK"}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Br. J. Haematol.", "issn": "1365-2141", "volume": "207", "issue": "5", "pages": "1920-1929", "issn-l": "0007-1048"}, "abstract": "Polyethylene glycol (peg)-asparaginase plays a crucial role in acute lymphoblastic leukaemia (ALL) treatment, yet its associated toxicity often leads to treatment discontinuation, elevating relapse risk. Hypersensitivity with inactivation of asparaginase is common and often associated with severe allergic reactions. This study aims to comprehensively analyse asparaginase enzyme activity (AEA) pharmacokinetics, validate a previously developed pharmacokinetic model based on intravenous administration and evaluate its capability to detect changes in clearance before inactivation in patients treated with intramuscular peg-asparaginase. The study, covering 644 patients aged 1-45 with ALL under the Nordic Society of Paediatric Haematology and Oncology (NOPHO) ALL2008 Protocol (February 2017-December 2022, in Nordic and Baltic countries), included 3003 AEA samples. Sampling occurred 14 days post peg-asparaginase doses, with additional sampling between doses. The incidence of inactivation was 15.2%. Utilizing the pharmacokinetic model, estimates revealed an 87.8% sensitivity and 65.5% specificity for detecting increased peg-asparaginase clearance over time in patients experiencing inactivation. Identification of increased clearance preceding inactivation in the NOPHO ALL2008 dataset highlights the potential of pharmacokinetic sampling to predict inactivation and enable timely intervention before clinical manifestation, with further refinement and inclusion of additional protocols into a unified model offering the promise of improving clinicians' ability to assess individual patient risk.", "doi": "10.1111/bjh.70145", "pmid": "40916350", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12624184"}], "notes": [], "created": "2025-11-28T10:51:01.336Z", "modified": "2025-11-28T10:51:01.391Z"}, {"entity": "publication", "iuid": "10591e3d44e348ae915ead7ea930d86d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10591e3d44e348ae915ead7ea930d86d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10591e3d44e348ae915ead7ea930d86d"}}, "title": "Depression Polygenicity and Disease Activity and Disability Worsening in Multiple Sclerosis.", "authors": [{"family": "Manouchehrinia", "given": "Ali", "initials": "A", "orcid": "0000-0003-4857-5762", "researcher": {"href": "https://publications.scilifelab.se/researcher/766e4d714e3042e4ae90d750ce82f7a7.json"}}, {"family": "Fitzgerald", "given": "Kathryn C", "initials": "KC", "orcid": "0000-0003-3137-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/40befe8eee6041638b4965633a08c8c6.json"}}, {"family": "Salter", "given": "Amber", "initials": "A", "orcid": "0000-0002-1088-110X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e42f735de154b4e8bc37333f48fda14.json"}}, {"family": "Marrie", "given": "Ruth Ann", "initials": "RA"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Bernstein", "given": "Charles N", "initials": "CN"}, {"family": "Bolton", "given": "James M", "initials": "JM"}, {"family": "Cutter", "given": "Gary", "initials": "G"}, {"family": "Fisk", "given": "John D", "initials": "JD"}, {"family": "Graff", "given": "Lesley A", "initials": "LA"}, {"family": "Hitchon", "given": "Carol A", "initials": "CA"}, {"family": "Hillert", "given": "Jan", "initials": "J"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Lublin", "given": "Fred D", "initials": "FD"}, {"family": "McKay", "given": "Kyla", "initials": "K", "orcid": "0000-0002-9081-1522", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a3879af6e44ba08514eccba217cfa9.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Patten", "given": "Scott", "initials": "S"}, {"family": "Patki", "given": "Amit", "initials": "A"}, {"family": "Riel", "given": "Hayley", "initials": "H"}, {"family": "Shchetynsky", "given": "Klementy", "initials": "K"}, {"family": "Stridh", "given": "Pernilla", "initials": "P"}, {"family": "Tiwari", "given": "Hemant K", "initials": "HK"}, {"family": "Wolinsky", "given": "Jerry S", "initials": "JS", "orcid": "0000-0002-8197-2762", "researcher": {"href": "https://publications.scilifelab.se/researcher/728aee2d34af46ebb8a8f7d831f3209b.json"}}, {"family": "Kowalec", "given": "Kaarina", "initials": "K", "orcid": "0000-0003-3928-9879", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf9da956e23e4a63a823d9bad0c1d21c.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Ann Neurol", "issn": "1531-8249", "volume": "98", "issue": "5", "pages": "1057-1069", "issn-l": null}, "abstract": "A better understanding of factors associated with multiple sclerosis (MS) disease activity and disability is needed. Given the strong link between comorbid depression and MS disease activity and disability, we aimed to determine whether the depression genetic burden, as modelled using its polygenic score, is associated with MS disease activity and disability worsening.\n\nIn this cohort study, we used samples from neurologist-defined adult people with MS (PwMS) followed in clinical care or during a clinical trial from existing cohorts: Canada, the United States (US), and Sweden with extensive longitudinal phenotypes. We computed the depression polygenic score (PGS) and tested its association with annualized relapse rate and worsening disability. In the US cohort, we additionally explored the time to relapse, number of enhancing lesions, and confirmed Expanded Disability Status Scale (EDSS) worsening during the study period.\n\nWe included 3,420 relapsing-onset PwMS of European genetic ancestry with a median follow-up of 3 to 5 years. Meta-analyses revealed for each 1-standard deviation increase in the depression PGS, the relapse rate increased (incidence rate ratio: 1.23, 95% confidence interval [CI] = 1.01-1.50). In the US cohort, higher depression PGS was associated with protocol-defined relapses (hazard ratio [HR] = 1.58, 95% CI = 1.03-2.43), and time to confirmed EDSS worsening (HR = 1.51, 95% CI = 1.03-2.22) with this effect largely direct.\n\nMeta-analyses showed a higher depression genetic burden was associated with increased MS disease activity. In the US clinical trial cohort only, we found a significant association between higher depression PGS and time to relapse and confirmed EDSS worsening. These findings may provide insights into MS disease activity and disability worsening. ANN NEUROL 2025;98:1057-1069.", "doi": "10.1002/ana.70020", "pmid": "40772555", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12577672"}], "notes": [], "created": "2025-11-28T10:39:49.074Z", "modified": "2025-11-28T10:39:49.506Z"}, {"entity": "publication", "iuid": "fe4fbf54443842c687e997679feba32e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe4fbf54443842c687e997679feba32e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe4fbf54443842c687e997679feba32e"}}, "title": "Cytomegalovirus infection is common in prostate cancer and antiviral therapies inhibit progression in disease models.", "authors": [{"family": "Classon", "given": "Johanna", "initials": "J", "orcid": "0000-0003-0392-7605", "researcher": {"href": "https://publications.scilifelab.se/researcher/641cf9db52e64f9fb8eee60a977a88be.json"}}, {"family": "Stenudd", "given": "Moa", "initials": "M"}, {"family": "Zamboni", "given": "Margherita", "initials": "M"}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Eriksson", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Pedersen", "given": "Lars", "initials": "L"}, {"family": "Sch\u00f6rling", "given": "Alrik", "initials": "A"}, {"family": "Thoss", "given": "Anna", "initials": "A"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "Wikstr\u00f6m", "given": "Pernilla", "initials": "P", "orcid": "0000-0002-6347-1999", "researcher": {"href": "https://publications.scilifelab.se/researcher/66e1e640e83948a4a3f8a1ddd49bd953.json"}}, {"family": "Adami", "given": "Hans-Olov", "initials": "HO"}, {"family": "S\u00f8rensen", "given": "Henrik Toft", "initials": "HT"}, {"family": "Druid", "given": "Henrik", "initials": "H"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "19", "issue": "11", "pages": "3035-3059", "issn-l": "1574-7891"}, "abstract": "Metastatic prostate cancer is incurable, and new therapeutic targets and drugs are urgently needed. Viral infections are associated with several cancer types, but a link between viruses and prostate oncogenesis has not been established. Only recently, an association between human cytomegalovirus (CMV) seropositivity and increased risk of prostate cancer mortality was demonstrated. Here, we show that CMV infection is common in the normal prostate epithelium and in prostate tumor tissue, with 70-92% of tumors being infected. Additionally, we report that commonly studied prostate cancer cell lines are CMV infected. Loss-of-function experiments demonstrate that CMV promotes cell survival, proliferation, and androgen receptor signaling, identifying it as a therapeutic target in castration-sensitive and castration-resistant prostate cancer. Several anti-CMV pharmaceutical compounds in clinical use inhibited cell expansion in prostate cancer models both in vitro and in vivo. We conclude that CMV is common in prostate cancer, promotes core prostate cancer cell programs, and can be inhibited by well-tolerated drugs. These findings motivate investigation into potential clinical benefits of CMV inhibition in the treatment of prostate cancer.", "doi": "10.1002/1878-0261.70073", "pmid": "40493023", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12591316"}], "notes": [], "created": "2025-11-28T10:39:38.461Z", "modified": "2025-11-28T10:39:38.586Z"}, {"entity": "publication", "iuid": "7b5288037215436796bda7010f8cde84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b5288037215436796bda7010f8cde84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b5288037215436796bda7010f8cde84"}}, "title": "Characterisation of airway inflammation and proteomes associated with cystic fibrosis-related diabetes.", "authors": [{"family": "Diemer", "given": "Stefanie", "initials": "S", "orcid": "0009-0006-3319-611X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b68575ebda04f75861e4c75e729e9bd.json"}}, {"family": "Chowdhury", "given": "Sounak", "initials": "S"}, {"family": "Sahl", "given": "Cecilia", "initials": "C"}, {"family": "Happonen", "given": "Lotta", "initials": "L"}, {"family": "P\u00e5hlman", "given": "Lisa I", "initials": "LI", "orcid": "0000-0001-6366-2309", "researcher": {"href": "https://publications.scilifelab.se/researcher/f58db990776f4e228707df2502d44728.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "ERJ Open Res", "issn": "2312-0541", "volume": "11", "issue": "6", "issn-l": "2312-0541"}, "abstract": "Cystic fibrosis (CF)-related diabetes (CFRD) is the most common extrapulmonary complication in CF. CFRD is associated with low lung function, but the underlying mechanisms are poorly understood. The aim of the present study was to compare airway inflammation and the airway proteome in people with CF (pwCF) with and without CFRD.\n\nSputum samples from pwCF were analysed for neutrophil elastase (NE) activity with a chromogenic assay, inflammatory cytokines using Meso Scale and bacterial load via quantitative PCR of the 16S rRNA gene. The sputum proteome was characterised by liquid chromatography-mass spectrometry.\n\n33 pwCF were included in the study, of which 55% had CFRD. The CFRD group had significantly lower lung function and higher sputum levels of NE, interleukin (IL)-8 and IL-1\u03b2, whereas IL-6 levels were lower compared to pwCF without CFRD. Proteome analysis identified 27 sputum proteins linked to CFRD, mainly involved in neutrophil degranulation. Given that lung function could be a possible confounding factor, we matched pwCF with and without CFRD based on lung function. In these lung function-matched cohorts, IL-8 and IL-6 levels did not differ significantly, but IL-1\u03b2 showed a trend towards higher levels in the CFRD group. 10 CFRD-associated proteins were significantly more abundant in the CFRD group, including prothymosin \u03b1, which plays a role in diabetes and insulin release.\n\nCFRD is associated with lower lung function, increased sputum levels of NE, IL-8 and IL-1\u03b2, and specific protein profiles.", "doi": "10.1183/23120541.00290-2025", "pmid": "41220822", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12598600"}, {"db": "pii", "key": "00290-2025"}], "notes": [], "created": "2025-11-28T10:17:17.675Z", "modified": "2025-11-28T10:17:17.777Z"}, {"entity": "publication", "iuid": "4884ce0dfe5f4ceaa6bbb3db4b417f92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4884ce0dfe5f4ceaa6bbb3db4b417f92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4884ce0dfe5f4ceaa6bbb3db4b417f92"}}, "title": "Aquatic fungal diversity assessment through metagenomics is still limited to current databases", "authors": [{"family": "Sanyal", "given": "Anushree", "initials": "A", "orcid": "0000-0002-8592-2164", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dcb90d513c445008e914bb358678adf.json"}}, {"family": "Kluge", "given": "Mariana", "initials": "M"}, {"family": "Redondo", "given": "Miguel Angel", "initials": "MA"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}], "type": "journal-article", "published": "2025-11-00", "journal": {"title": "Limnol Oceanogr", "issn": "0024-3590", "volume": "70", "issue": "11", "pages": "3249-3260", "issn-l": null}, "abstract": null, "doi": "10.1002/lno.70205", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:40:31.710Z", "modified": "2025-11-28T10:40:31.816Z"}, {"entity": "publication", "iuid": "c2874ad4279747de98010159c6b2bbcc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2874ad4279747de98010159c6b2bbcc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2874ad4279747de98010159c6b2bbcc"}}, "title": "Aberrant expression of SLAMF6 constitutes a targetable immune escape mechanism in acute myeloid leukemia.", "authors": [{"family": "Sand\u00e9n", "given": "Carl", "initials": "C", "orcid": "0000-0002-8931-9565", "researcher": {"href": "https://publications.scilifelab.se/researcher/29207805704e4660b20eebc87efe5282.json"}}, {"family": "Landberg", "given": "Niklas", "initials": "N", "orcid": "0000-0001-6752-6507", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ad422be3ea44e419662d514ca40cbbe.json"}}, {"family": "Pe\u00f1a-Mart\u00ednez", "given": "Pablo", "initials": "P", "orcid": "0000-0002-0789-6431", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d675e892dfc4334bb12051e004a7711.json"}}, {"family": "Thorsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-5393-2942", "researcher": {"href": "https://publications.scilifelab.se/researcher/7667559679a64a999d508ff7fa506782.json"}}, {"family": "Daga", "given": "Shruti", "initials": "S"}, {"family": "Puente-Moncada", "given": "Noelia", "initials": "N"}, {"family": "Rodriguez-Zabala", "given": "Maria", "initials": "M"}, {"family": "von Palffy", "given": "Sofia", "initials": "S"}, {"family": "Rissler", "given": "Marianne", "initials": "M"}, {"family": "Lazarevic", "given": "Vladimir", "initials": "V", "orcid": "0000-0002-1782-4423", "researcher": {"href": "https://publications.scilifelab.se/researcher/7113f0d0569247d4ac94b73ddc6ca74e.json"}}, {"family": "Juliusson", "given": "Gunnar", "initials": "G"}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}, {"family": "Hyrenius-Wittsten", "given": "Axel", "initials": "A"}, {"family": "Orsmark-Pietras", "given": "Christina", "initials": "C", "orcid": "0000-0002-6533-0305", "researcher": {"href": "https://publications.scilifelab.se/researcher/66a38c96c9854fb18eb2420689d620e2.json"}}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H", "orcid": "0000-0001-8703-1173", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a75300e8c346858ce8dd8f64ecae85.json"}}, {"family": "\u00c5gerstam", "given": "Helena", "initials": "H"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "volume": "6", "issue": "11", "pages": "1821-1838", "issn-l": null}, "abstract": "Immunotherapy has shown limited success in acute myeloid leukemia (AML), indicating an incomplete understanding of the underlying immunoregulatory mechanisms. Here we identify an immune evasion mechanism present in 60% of AML cases, wherein primitive AML cells aberrantly express the lymphoid surface protein SLAMF6 (signaling lymphocyte activation molecule family member 6). Knockout of SLAMF6 in AML cells enables T cell activation and highly efficient killing of leukemia cells in coculture systems, demonstrating that SLAMF6 protects AML cells from recognition and elimination by the immune system in a mode analogous to the programmed cell death protein-ligand (PDL1/PD1) axis. Targeting SLAMF6 with an antibody against the SLAMF6 dimerization site inhibits the SLAMF6-SLAMF6 interaction and induces T cell activation and killing of AML cells both in vitro and in humanized in vivo models. In conclusion, we show that aberrant expression of SLAMF6 is a common and targetable immune escape mechanism that could pave the way for immunotherapy in AML.", "doi": "10.1038/s43018-025-01054-6", "pmid": "41044242", "labels": {"Clinical Genomics Lund": "Service", "Drug Discovery and Development": "Collaborative", "Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s43018-025-01054-6"}, {"db": "pmc", "key": "PMC12643940"}], "notes": [], "created": "2025-11-05T18:37:31.700Z", "modified": "2025-11-26T16:29:09.833Z"}, {"entity": "publication", "iuid": "bda196cdca4f4695a732f2967575cb00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bda196cdca4f4695a732f2967575cb00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bda196cdca4f4695a732f2967575cb00"}}, "title": "466 Cancer intrinsic protein neddylation reprograms macrophage metabolism to constrain immune checkpoint blockade therapy", "authors": [{"family": "Papakyriacou", "given": "Irineos", "initials": "I"}, {"family": "Lu", "given": "Yonglin", "initials": "Y"}, {"family": "Bedos", "given": "Marta Rubies", "initials": "MR"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Lapins", "given": "Maris", "initials": "M"}, {"family": "Puigvert", "given": "Jordi Carreras", "initials": "JC"}, {"family": "Mao", "given": "Yumeng", "initials": "Y"}], "type": "proceedings-article", "published": "2025-11-00", "journal": {"pages": "A531-A531", "issn-l": null}, "abstract": null, "doi": "10.1136/jitc-2025-sitc2025.0466", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2026-02-23T09:10:20.502Z", "modified": "2026-02-23T09:10:20.503Z"}, {"entity": "publication", "iuid": "c3cc39df288e4158b74d51e4eceda6bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3cc39df288e4158b74d51e4eceda6bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3cc39df288e4158b74d51e4eceda6bc"}}, "title": "High-resolution structure of proIAPP(1-48) fibrils suggests a mechanistic pathway for diabetes-associated IAPP fibril polymorphs.", "authors": [{"family": "Valli", "given": "Dylan", "initials": "D", "orcid": "0009-0005-6060-4169", "researcher": {"href": "https://publications.scilifelab.se/researcher/56aa1f7e1c77487a95cbe1070944dd3c.json"}}, {"family": "Maj", "given": "Micha\u0142", "initials": "M", "orcid": "0000-0003-1567-9514", "researcher": {"href": "https://publications.scilifelab.se/researcher/1be0f07d0c5f40adac62cf38f2244e79.json"}}], "type": "journal article", "published": "2025-10-31", "journal": {"title": "RSC Chem Biol", "issn": "2633-0679", "issn-l": null}, "abstract": "The human islet amyloid polypeptide (hIAPP) aggregates into amyloid fibrils that contribute to \u03b2-cell failure in type 2 diabetes. hIAPP is produced from a 67-residue precursor, proIAPP, but incomplete cleavage by prohormone convertase 2 (PC2) produces the 48-residue intermediate proIAPP(1-48), which accelerates amyloid formation in vivo. Here we show that proIAPP(1-48) assembles almost exclusively into a single fibril polymorph. Using cryo-electron microscopy we solved its structure at 3.5 \u00c5 resolution and uncovered a P-shaped, C2-symmetric dimer whose backbone and side-chain packing are nearly identical to the disease-associated TW2 polymorph propagated from pancreatic tissue, although with different helical symmetry. All eleven extra N-terminal residues remain disordered but create a weak density around His29. Based on time-averaged density derived from molecular dynamics (MD) simulations, we identified multiple hydrogen(H)-bonding interactions, which may contribute to stabilising the TW2-like fold and explain the peripheral cryo-EM density. These data establish a structural link between defective proIAPP processing and the polymorphic spectrum of islet amyloid and suggest a seeding pathway by which proIAPP(1-48) templates pathogenic architectures that fully processed hIAPP rarely adopts in vitro.", "doi": "10.1039/d5cb00228a", "pmid": "41210656", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12590159"}, {"db": "pii", "key": "d5cb00228a"}], "notes": [], "created": "2025-11-24T16:00:26.102Z", "modified": "2025-11-24T16:00:26.208Z"}, {"entity": "publication", "iuid": "19188c6729144072978d9a3d01d09133", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19188c6729144072978d9a3d01d09133.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19188c6729144072978d9a3d01d09133"}}, "title": "Genetic Analysis of Apple Autumn Canopy Senescence in a Nordic Climate.", "authors": [{"family": "Skytte Af S\u00e4tra", "given": "Jonas", "initials": "J", "orcid": "0000-0002-2827-4842", "researcher": {"href": "https://publications.scilifelab.se/researcher/00b323220517477eb3c4acda1bb64c81.json"}}], "type": "journal article", "published": "2025-10-30", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "6", "pages": "e70599", "issn-l": "0031-9317"}, "abstract": "Autumn phenology traits are likely to be essential for the adaptation of apple to boreal climate. However, the genetic control of these traits is not well understood, and, for example, growth cessation does not appear to be controlled by day length as in many other boreal tree species. Here, I combine a quantitative genetic and population genomic approach to study autumn senescence in apple. I phenotyped a diverse germplasm collection for the timing of autumn senescence, performed quantitative trait loci (QTL) mapping in a multiparental population (MPP), and investigated genomic signals of selection to identify candidate genes. The timing of 50% autumn senescence was negatively correlated with adaptation to higher (boreal) climate zones. Two QTL were found to control the timing of autumn senescence in the MPP, exhibiting both dominance and epistatic interactions. The QTL on linkage group (LG) 17 was also variable in the diversity germplasm, while the QTL on LG11 was not. Cultivars adapted to boreal climate showed weak signals of selection at two loci within the genomic region of chromosome 17 corresponding to the LG17 QTL interval, consistent with a recent expansion to northern Sweden. These loci coincide with two predicted UGT85 genes and a possible copy number variation in PHYC, respectively. Thus, this study provides valuable information for further research and breeding of apple in light of the ongoing climate change.", "doi": "10.1111/ppl.70599", "pmid": "41164927", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573221"}], "notes": [], "created": "2025-11-07T07:26:45.450Z", "modified": "2025-11-14T11:08:25.063Z"}, {"entity": "publication", "iuid": "e3a0b036f1a64129a355aafe11a904e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3a0b036f1a64129a355aafe11a904e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3a0b036f1a64129a355aafe11a904e8"}}, "title": "Disease-specific epigenetic deregulation of enhancers, transposons, and polycomb targets in acute promyelocytic leukemia.", "authors": [{"family": "Zhong", "given": "Xiangfu", "initials": "X"}, {"family": "Cordeddu", "given": "Lina", "initials": "L"}, {"family": "Gamboa-Cedeno", "given": "Angelica", "initials": "A"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2025-10-30", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "17", "issue": "1", "pages": "135", "issn-l": "1756-994X"}, "abstract": "Acute promyelocytic leukemia (APL) is a subtype of acute myeloid leukemia (AML), characterized by a fusion between the PML and RARA genes and by a block in the myeloid maturation at the promyelocytic stage.\n\nThis study investigates the epigenetic landscape of APL by integrating ChIP-seq data on eight histone modifications and RNA-seq in APL as well as non-APL AML. APL showed a distinct chromatin profile that differed from non-APL AML.\n\nWe describe APL-specific changes in H3K27ac, H3K9me3, and H3K27me3 with impact on enhancer activity, repression of transposable elements, and Polycomb regulated gene repression. The APL-specific H3K27ac pattern identifies APL-specific enhancer and super-enhancer regions, including a subset of enhancers that are bound by the PML-RARA fusion protein. While chromatin bound specifically by PML-RARA were dominantly active, APL was also characterized by gain of APL-specific heterochromatin states with significant gains of H3K9me3 enriched lamina-associated domains and the transposable elements LINE, LTR, and SINE.\n\nThese findings suggest a unique enhancer and heterochromatin profile in APL, with implications for transcription regulation and treatment response. These findings offer novel insights into the pathogenesis of APL.", "doi": "10.1186/s13073-025-01565-y", "pmid": "41168841", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573822"}, {"db": "pii", "key": "10.1186/s13073-025-01565-y"}], "notes": [], "created": "2025-11-28T10:53:15.320Z", "modified": "2025-11-28T10:53:15.323Z"}, {"entity": "publication", "iuid": "d82e4479596f49d3b60f234cdfc74eed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d82e4479596f49d3b60f234cdfc74eed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d82e4479596f49d3b60f234cdfc74eed"}}, "title": "Advancing a sensitive method for measuring mitochondrial ATP production in small muscle biopsy samples.", "authors": [{"family": "Wibom", "given": "Rolf", "initials": "R"}, {"family": "Alsina", "given": "David", "initials": "D"}, {"family": "Naess", "given": "Karin", "initials": "K"}, {"family": "Engvall", "given": "Martin", "initials": "M"}, {"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Wredenberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-10-30", "journal": {"title": "Anal. Biochem.", "issn": "1096-0309", "volume": "709", "pages": "116004", "issn-l": "0003-2697"}, "abstract": "We present an optimised luminometric method for measuring muscle mitochondrial ATP production rate (MAPR), adapted to a 96-well microplate format. The enhanced assay enables quantification of ATP production from 12 or more substrate combinations within 15 min, using only 10 \u03bcL of isolated mitochondria. The method demonstrates high accuracy and precision, with a validated measurement range of 0.3-70 nmol/min/L. To support clinical interpretation, a reference dataset was established from 92 individuals aged seven months to 79 years. All these individuals were referred for muscle biopsy but were subsequently deemed unlikely to have a mitochondrial disorder following comprehensive clinical evaluation. An overview of the current version of our assays for oxidative phosphorylation (OXPHOS) enzymes is also provided. As proof of concept, we present three patients carrying pathogenic variants in mitochondrial DNA (ATP6 and MT-TL1) and the nuclear PDHA1 gene. All exhibited decreased MAPR with one or more substrates, along with additional clinical, biochemical, and morphological features consistent with mitochondrial disease. Furthermore, we illustrate the age-dependent development of MAPR in muscle across the human lifespan, demonstrating a 60-80 % higher maximal capacity for oxidative ATP production in adults compared with young children. In contrast, MAPR supported by fatty acid-derived substrates remains unchanged over the same period. In conclusion, the improved MAPR assay offers a robust and efficient tool for assessing mitochondrial function in both clinical diagnostics and research. Its high-throughput format and reliable performance make it particularly well-suited for the investigation of suspected mitochondrial disorders.", "doi": "10.1016/j.ab.2025.116004", "pmid": "41173120", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-2697(25)00243-X"}], "notes": [], "created": "2025-11-21T09:10:30.302Z", "modified": "2025-11-21T09:10:30.307Z"}, {"entity": "publication", "iuid": "3fe1414d1f404aa7868cec9204360adb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3fe1414d1f404aa7868cec9204360adb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3fe1414d1f404aa7868cec9204360adb"}}, "title": "Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15", "authors": [{"family": "Ebenwaldner", "given": "Carmen", "initials": "C", "orcid": "0000-0002-7919-2994", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2aedf9747ff49eb904e353f28847b61.json"}}, {"family": "Garc\u00eda Saura", "given": "Antonio Gin\u00e9s", "initials": "AG"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S", "orcid": "0000-0002-7694-285X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6416b323664f4126b70067193d7b8347.json"}}, {"family": "Bernfur", "given": "Katja", "initials": "K", "orcid": "0000-0002-7927-9563", "researcher": {"href": "https://publications.scilifelab.se/researcher/4600cd5ea61b41e4ab9b85af90fb41b4.json"}}, {"family": "Moche", "given": "Martin", "initials": "M"}, {"family": "Logan", "given": "Derek T", "initials": "DT", "orcid": "0000-0002-0098-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/da2734243cdb4142be696e5a82e788ae.json"}}, {"family": "Cohen", "given": "Michael S", "initials": "MS", "orcid": "0000-0002-7636-4156", "researcher": {"href": "https://publications.scilifelab.se/researcher/352749e458584319ab9d870abec5d90f.json"}}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H", "orcid": "0000-0003-4059-3501", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49b25ddfc934f3ca41020c3f38c6bfc.json"}}], "type": "journal-article", "published": "2025-10-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": null}, "abstract": null, "doi": "10.1038/s41467-025-65315-9", "pmid": null, "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-11-27T17:26:39.850Z", "modified": "2025-11-26T16:30:32.588Z"}, {"entity": "publication", "iuid": "ea181adcfb564b289434e673fccd07a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea181adcfb564b289434e673fccd07a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea181adcfb564b289434e673fccd07a3"}}, "title": "Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years.", "authors": [{"family": "Gilardet", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-4851-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f507b07ed934c73988dfd0537254485.json"}}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J", "orcid": "0000-0001-7973-6173", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b1165126184cb980f8bc7e9b9c0fdd.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6929-4869", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d428a542d44a829e17924e94a3f6dc.json"}}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Southon", "given": "John", "initials": "J"}, {"family": "Vasiliev", "given": "Sergey K", "initials": "SK"}, {"family": "Shunkov", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-1388-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/c43a1135a5804441b6ab9680f7cbd2b3.json"}}, {"family": "Kozlikin", "given": "Maxim B", "initials": "MB", "orcid": "0000-0001-5082-3345", "researcher": {"href": "https://publications.scilifelab.se/researcher/da2a8523fc1c42178159bbd3e8b64ecc.json"}}, {"family": "Douka", "given": "Katerina", "initials": "K", "orcid": "0000-0002-0558-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a6efe4f6db44f6b85ed2653d2a3342f.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "17", "issue": "11", "issn-l": "1759-6653"}, "abstract": "Bovines have a complex yet poorly understood evolutionary history that is characterized by admixture and diversity loss during the Late Pleistocene. Unraveling this history is challenging in part because deep-time and geographically widespread genetic data are currently limited. In mid-latitude Asia, Denisova Cave, located in the Altai, Siberia, and nearby paleontological sites have yielded a large collection of remains spanning the Middle to Late Pleistocene, many of which are identifiable as bovines via morphology or paleoproteomics. In this study, we screened these bovine bones for ancient DNA and generated mitogenomes, to refine knowledge of Pleistocene bovine diversity in the region. We found that bovines carrying a yak-like mitogenome were common residents of the Altai mountains, along with bison belonging to the clade X mitochondrial lineage and, more rarely, aurochs. The yak-like mitochondrial lineage identified in this study represents a previously unknown lineage sister to present-day yak mitogenome diversity. This yak-like mitochondrial lineage, termed yak X, was identified at several sites, and survived in mid-latitude Asia across climatic transitions for around 200,000 years. Our findings suggest that all three bovine taxa harbored diversity no longer present in extant populations, thus mirroring archaic hominin findings at Denisova Cave. The Altai mountains therefore appear to have been a hotspot of both bovine and hominin diversity.", "doi": "10.1093/gbe/evaf206", "pmid": "41206445", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12628791"}, {"db": "pii", "key": "8315343"}], "notes": [], "created": "2025-11-21T17:51:54.435Z", "modified": "2025-11-21T17:51:56.168Z"}, {"entity": "publication", "iuid": "9ffabc46b92c4c76be483815e6bba9dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ffabc46b92c4c76be483815e6bba9dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ffabc46b92c4c76be483815e6bba9dc"}}, "title": "Epigenetic mediation may explain intergenerational associations between maternal obesogenic lifestyle and children's birth weight: findings from the NorthPop prospective birth cohort.", "authors": [{"family": "De Silva", "given": "Kushan", "initials": "K", "orcid": "0000-0003-0301-0805", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fb44e3f1d204c2a996e747704e2e77f.json"}}, {"family": "Lundberg-Ulfsdotter", "given": "Richard", "initials": "R"}, {"family": "Bod\u00e9n", "given": "Stina", "initials": "S", "orcid": "0000-0002-8958-975X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dcfadb86b8040499a7af3c4a744d3b2.json"}}, {"family": "Vinnars", "given": "Marie-Therese", "initials": "MT"}, {"family": "Ryden", "given": "Patrik", "initials": "P", "orcid": "0000-0002-0577-123X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65e733a3351940749605f054834eebef.json"}}, {"family": "West", "given": "Christina E", "initials": "CE", "orcid": "0000-0001-9599-2580", "researcher": {"href": "https://publications.scilifelab.se/researcher/be2972e4afa744e5aa0525a4c9d89348.json"}}, {"family": "Domell\u00f6f", "given": "Magnus", "initials": "M"}, {"family": "Harlid", "given": "Sophia", "initials": "S", "orcid": "0000-0001-8540-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a824f2687b460890ae6d9ef40d97c9.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "17", "issue": "1", "pages": "180", "issn-l": "1868-7075"}, "abstract": "Epigenetic alterations during fetal development have been proposed as key factors explaining associations between maternal lifestyle during pregnancy and later health outcomes in the offspring, pertaining to the developmental origin of health and disease hypothesis.\n\nTo assess the association of maternal lifestyle with offsprings' birth weight and underlying epigenetic mediatory mechanisms in the NorthPop prospective birth cohort.\n\nA three-step analytic pipeline was applied. In 722 mother-child pairs, overall associations between ten maternal lifestyle factors and the offspring's standardized birth weight were first evaluated by multiple linear regression. Three high-dimensional mediation methods, based on sure independence screening and penalized regression, were then applied on the beta methylation matrix to identify candidate CpG mediators in cord blood driving the significant overall associations. Finally, robust and ordinary least squares (OLS) regression-based classical mediation methods were used with candidate CpG probes to assess single- and multiple (parallel and serial)-mediator models on a low-dimensional space.\n\nGestational weight gain (GWG) (\u03b2-adj = 0.03; p = 2 \u00d7 10-5) and maternal BMI at the beginning of pregnancy (\u03b2-adj = 0.036; p = 1 \u00d7 10-4) were significantly associated with the offspring's standardized birth weight. High-dimensional mediation analyses identified pooled sets of four (cg19242268 [TCEA2]; cg08461903 [N/A]; cg14798382 [CHERP/C19orf44] and cg21516291 [SLC35C2]) and five (cg17040807 [CYGB]; cg19242268 [TCEA2]; cg26552621 [CIRBP]; cg04457572 [CDH23] and cg06457011 [PLCG1]) candidate CpG mediators related to GWG and BMI at the beginning of pregnancy, respectively. For both exposures, classical mediation analyses revealed a range of significant single- and multiple (both serial and parallel)-mediator models via both robust and OLS regression based approaches. These indicated the likely presence of individual, causally linked multiple, and causally independent multiple mediatory pathways underlying the two significant overall associations.\n\nOur findings support the hypothesis that neonatal health effects related to maternal lifestyle may be partly mediated by epigenetic alterations. Findings also suggest the possible involvement of multiple DNA methylation sites via various mediatory pathways.", "doi": "10.1186/s13148-025-02001-z", "pmid": "41163109", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12570728"}, {"db": "pii", "key": "10.1186/s13148-025-02001-z"}], "notes": [], "created": "2025-11-07T07:25:46.328Z", "modified": "2025-11-11T13:52:44.760Z"}, {"entity": "publication", "iuid": "3f18e5c79db74984ba3dfc82d76eecf3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f18e5c79db74984ba3dfc82d76eecf3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f18e5c79db74984ba3dfc82d76eecf3"}}, "title": "A pangenome and pantranscriptome of hexaploid oat.", "authors": [{"family": "Avni", "given": "Raz", "initials": "R", "orcid": "0000-0002-0801-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e818aced4e14e529c60a7dd5d396de0.json"}}, {"family": "Kamal", "given": "Nadia", "initials": "N", "orcid": "0000-0002-3258-4130", "researcher": {"href": "https://publications.scilifelab.se/researcher/da83072939d347778c03424c656d1bae.json"}}, {"family": "Bitz", "given": "Lidija", "initials": "L"}, {"family": "Jellen", "given": "Eric N", "initials": "EN", "orcid": "0000-0002-7906-4845", "researcher": {"href": "https://publications.scilifelab.se/researcher/83594761835445f9a5c92cad770ca372.json"}}, {"family": "Bekele", "given": "Wubishet A", "initials": "WA", "orcid": "0000-0002-6463-8180", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ea58d9ecc7a45c58a19fd0a36bed3ff.json"}}, {"family": "Angessa", "given": "Tefera T", "initials": "TT"}, {"family": "Auvinen", "given": "Petri", "initials": "P", "orcid": "0000-0002-3947-4778", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b998007ca8b412c8dac49230d5cea94.json"}}, {"family": "Bitz", "given": "Oliver", "initials": "O"}, {"family": "Boyle", "given": "Brian", "initials": "B", "orcid": "0000-0002-0158-1463", "researcher": {"href": "https://publications.scilifelab.se/researcher/de076e7c690542cfbc5b2da120521e29.json"}}, {"family": "Canales", "given": "Francisco J", "initials": "FJ", "orcid": "0000-0001-7911-856X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd058ce520fc48de81a2c4f2762659b4.json"}}, {"family": "Carlson", "given": "Craig H", "initials": "CH", "orcid": "0000-0003-2050-5455", "researcher": {"href": "https://publications.scilifelab.se/researcher/f856003d4ec44935812545685e22fe41.json"}}, {"family": "Chapman", "given": "Brett", "initials": "B", "orcid": "0000-0003-4484-2253", "researcher": {"href": "https://publications.scilifelab.se/researcher/4410e6ff3a7d489e84b05dc81edf53ce.json"}}, {"family": "Chawla", "given": "Harmeet Singh", "initials": "HS"}, {"family": "Chen", "given": "Yutang", "initials": "Y", "orcid": "0000-0001-8128-8728", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d3e1845423c4e0389ee86c0986a294d.json"}}, {"family": "Copetti", "given": "Dario", "initials": "D"}, {"family": "Correia de Lemos", "given": "Samara", "initials": "S", "orcid": "0000-0003-3484-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/4105d0322d0c478e8c3758d2d353c3e2.json"}}, {"family": "Dang", "given": "Viet", "initials": "V", "orcid": "0000-0001-6408-6323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dc432298db04432b1285e4530d566de.json"}}, {"family": "Eichten", "given": "Steven R", "initials": "SR", "orcid": "0000-0003-2268-395X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c014d8bcd56b4240a3b8ed3219fac6f2.json"}}, {"family": "Klos", "given": "Kathy Esvelt", "initials": "KE"}, {"family": "Fenn", "given": "Amit M", "initials": "AM", "orcid": "0000-0003-2203-3922", "researcher": {"href": "https://publications.scilifelab.se/researcher/b27d342e880f4692bc1224c520b78dae.json"}}, {"family": "Fiebig", "given": "Anne", "initials": "A", "orcid": "0000-0003-3159-3593", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af17bbf24b34f20a9f433583ff00c05.json"}}, {"family": "Fu", "given": "Yong-Bi", "initials": "YB", "orcid": "0000-0003-3106-1247", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f089f51863447cf88cdb4ec23e009bc.json"}}, {"family": "Gundlach", "given": "Heidrun", "initials": "H", "orcid": "0000-0002-6757-0943", "researcher": {"href": "https://publications.scilifelab.se/researcher/22e6d69126dd4a9a9a99827c672b5fa5.json"}}, {"family": "Gupta", "given": "Rajeev", "initials": "R", "orcid": "0000-0002-1451-215X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd2a62988238458e9ab17d4d7f60f2bb.json"}}, {"family": "Haberer", "given": "Georg", "initials": "G", "orcid": "0000-0002-6612-6939", "researcher": {"href": "https://publications.scilifelab.se/researcher/5313eb519bd24ee3b92a090746ad93a3.json"}}, {"family": "He", "given": "Tianhua", "initials": "T"}, {"family": "Herrmann", "given": "Matthias H", "initials": "MH", "orcid": "0000-0003-1760-6167", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1be02f0c5024c29aa810cb1dcc63c3f.json"}}, {"family": "Himmelbach", "given": "Axel", "initials": "A", "orcid": "0000-0001-7338-0946", "researcher": {"href": "https://publications.scilifelab.se/researcher/473928fe106248bdba303b0455faa930.json"}}, {"family": "Howarth", "given": "Catherine J", "initials": "CJ", "orcid": "0000-0001-9364-0880", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ec8235c6e6348d3a4e1f84f0759348b.json"}}, {"family": "Hu", "given": "Haifei", "initials": "H", "orcid": "0000-0003-1070-213X", "researcher": {"href": "https://publications.scilifelab.se/researcher/573e418a00344b0192db99e0c8a4707a.json"}}, {"family": "Isidro Y S\u00e1nchez", "given": "Julio", "initials": "J", "orcid": "0000-0002-9044-3221", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef581d9a44994c798decadb0531b313c.json"}}, {"family": "Itaya", "given": "Asuka", "initials": "A", "orcid": "0000-0003-4132-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfab79c8f493415e9d86932559a40663.json"}}, {"family": "Jannink", "given": "Jean-Luc", "initials": "JL", "orcid": "0000-0003-4849-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df52f0eac0e4649adf4b87e2a702abe.json"}}, {"family": "Jia", "given": "Yong", "initials": "Y", "orcid": "0000-0002-0394-3966", "researcher": {"href": "https://publications.scilifelab.se/researcher/078c829a8fc2442da58be531b08381ee.json"}}, {"family": "Kaur", "given": "Rajvinder", "initials": "R"}, {"family": "Knauft", "given": "Manuela", "initials": "M"}, {"family": "Langdon", "given": "Tim", "initials": "T"}, {"family": "Lux", "given": "Thomas", "initials": "T", "orcid": "0000-0002-5543-1911", "researcher": {"href": "https://publications.scilifelab.se/researcher/076281817e274a45819ff2f53f9047cf.json"}}, {"family": "Marmon", "given": "Sofia", "initials": "S", "orcid": "0000-0001-6929-7859", "researcher": {"href": "https://publications.scilifelab.se/researcher/0105355f5c26423f98f7e4429318bb2c.json"}}, {"family": "Marosi", "given": "Vanda", "initials": "V"}, {"family": "Mayer", "given": "Klaus F X", "initials": "KFX", "orcid": "0000-0001-6484-1077", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd32d600030146e9891b324e80708362.json"}}, {"family": "Michel", "given": "Steve", "initials": "S"}, {"family": "Nandety", "given": "Raja Sekhar", "initials": "RS", "orcid": "0000-0002-1129-0790", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6834d990f14f578a96a7b57e06dbf8.json"}}, {"family": "Nilsen", "given": "Kirby T", "initials": "KT"}, {"family": "Paczos-Grz\u0119da", "given": "Edyta", "initials": "E", "orcid": "0000-0001-6273-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a271331d534543a3907db410616d4b.json"}}, {"family": "Pasha", "given": "Asher", "initials": "A", "orcid": "0000-0002-9315-0520", "researcher": {"href": "https://publications.scilifelab.se/researcher/dea77d66f7a040f680e391da2b46ce24.json"}}, {"family": "Prats", "given": "Elena", "initials": "E"}, {"family": "Provart", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0001-5551-7232", "researcher": {"href": "https://publications.scilifelab.se/researcher/23c3f4e8ce0c44e3a74c8c0ad1aa7554.json"}}, {"family": "Ravagnani", "given": "Adriana", "initials": "A"}, {"family": "Reid", "given": "Robert W", "initials": "RW"}, {"family": "Schlueter", "given": "Jessica A", "initials": "JA"}, {"family": "Schulman", "given": "Alan H", "initials": "AH"}, {"family": "Sen", "given": "Taner Z", "initials": "TZ"}, {"family": "Singh", "given": "Jaswinder", "initials": "J", "orcid": "0000-0002-1139-9251", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e830c055e2542d6a2e6388ec3cad25c.json"}}, {"family": "Singh", "given": "Mehtab", "initials": "M", "orcid": "0000-0003-4550-9858", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2c9ff04964e42f08b8e906b51bf0b0d.json"}}, {"family": "Sirijovski", "given": "Nick", "initials": "N", "orcid": "0000-0002-6191-3845", "researcher": {"href": "https://publications.scilifelab.se/researcher/040fc49df77d4171bf2695ae420f2302.json"}}, {"family": "Stein", "given": "Nils", "initials": "N", "orcid": "0000-0003-3011-8731", "researcher": {"href": "https://publications.scilifelab.se/researcher/11ef5173e1214a9f920bcadad30afc70.json"}}, {"family": "Studer", "given": "Bruno", "initials": "B"}, {"family": "Viitala", "given": "Sirja", "initials": "S"}, {"family": "Vronces", "given": "Shauna", "initials": "S"}, {"family": "Walkowiak", "given": "Sean", "initials": "S", "orcid": "0000-0002-3866-5038", "researcher": {"href": "https://publications.scilifelab.se/researcher/6acd3a3bf11144baa35b773b921e23c9.json"}}, {"family": "Wang", "given": "Penghao", "initials": "P", "orcid": "0000-0002-3751-3921", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cd3893272754899abcdb06dabaf195e.json"}}, {"family": "Waters", "given": "Amanda J", "initials": "AJ"}, {"family": "Wight", "given": "Charlene P", "initials": "CP", "orcid": "0000-0003-1410-5631", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bffc6376bf8453da9d6ac3b962805b6.json"}}, {"family": "Yan", "given": "Weikai", "initials": "W"}, {"family": "Yao", "given": "Eric", "initials": "E"}, {"family": "Zhang", "given": "Xiao-Qi", "initials": "XQ"}, {"family": "Zhou", "given": "Gaofeng", "initials": "G"}, {"family": "Zhou", "given": "Zhou", "initials": "Z"}, {"family": "Tinker", "given": "Nicholas A", "initials": "NA", "orcid": "0000-0002-2452-4779", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef54eb854d47488f88ffc97360bfef59.json"}}, {"family": "Fiedler", "given": "Jason D", "initials": "JD", "orcid": "0000-0001-7736-4484", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e65e63fd07a4543a61a30ea653254d7.json"}}, {"family": "Li", "given": "Chengdao", "initials": "C", "orcid": "0000-0002-9653-2700", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3e4736c749c4b07b76e1ae98c4c9bbe.json"}}, {"family": "Maughan", "given": "Peter J", "initials": "PJ", "orcid": "0000-0003-3714-3411", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f53b85b82e4ccfbb9220754ae0d59a.json"}}, {"family": "Spannagl", "given": "Manuel", "initials": "M", "orcid": "0000-0003-0701-7035", "researcher": {"href": "https://publications.scilifelab.se/researcher/88a57f18a3794d1aaf7af7c579697860.json"}}, {"family": "Mascher", "given": "Martin", "initials": "M", "orcid": "0000-0001-6373-6013", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad2d033b05734d53a888db3e03edee0a.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836"}, "abstract": "Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.", "doi": "10.1038/s41586-025-09676-7", "pmid": "41162711", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-025-09676-7"}], "notes": [], "created": "2025-11-19T07:39:59.482Z", "modified": "2025-11-28T10:46:37.749Z"}, {"entity": "publication", "iuid": "20bf7f8602df4703bfd5057606fcaa7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20bf7f8602df4703bfd5057606fcaa7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20bf7f8602df4703bfd5057606fcaa7b"}}, "title": "A Novel Supergene Controls Queen Size and Colony Social Organization in the Ant Myrmica ruginodis.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Sepp\u00e4", "given": "Perttu", "initials": "P", "orcid": "0000-0001-5393-6943", "researcher": {"href": "https://publications.scilifelab.se/researcher/700fa3a2724f442884d886463b1cf95c.json"}}, {"family": "Downing", "given": "Philip A", "initials": "PA", "orcid": "0000-0002-5286-3153", "researcher": {"href": "https://publications.scilifelab.se/researcher/e004ff0660ee411cb310ab108f29c171.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Helanter\u00e4", "given": "Heikki", "initials": "H", "orcid": "0000-0002-6468-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/3947ff78ae914e6785fb081458619533.json"}}, {"family": "Viljakainen", "given": "Lumi", "initials": "L", "orcid": "0000-0002-6587-6156", "researcher": {"href": "https://publications.scilifelab.se/researcher/462f8aece21843458fa4e3f99a5c5449.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "42", "issue": "11", "issn-l": "0737-4038"}, "abstract": "Large independently evolved supergenes control colony social organization and queen reproductive strategies in several ant lineages. Their independent origins, as well as the similarities of the associated phenotypes, make ant supergenes a promising system for studying the parallel evolution of genome organization and adaptability. However, the genetic basis of differences in social organization and queen phenotypes remains unknown in many ant species, limiting the potential power of this system for comparative studies. We investigated the genetic basis of colony social organization in the queen-size dimorphic ant Myrmica ruginodis by sampling 95 queens from 31 colonies in southern Finland. Whole-genome sequencing revealed a novel 9 Mb supergene associated with both queen size and social organization. Queens homozygous for the AA haplotype were larger and found only in single-queen colonies, while queens in multiple-queen colonies were smaller and carried only AB and BB genotypes. This supergene is not homologous to previously identified supergenes in ants, suggesting it arose through a distinct evolutionary pathway.", "doi": "10.1093/molbev/msaf255", "pmid": "41077914", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12572780"}, {"db": "pii", "key": "8284624"}], "notes": [], "created": "2025-11-21T14:49:16.789Z", "modified": "2025-11-21T14:49:17.100Z"}, {"entity": "publication", "iuid": "675f9e483128451bae7b9c4ff4df7de5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/675f9e483128451bae7b9c4ff4df7de5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/675f9e483128451bae7b9c4ff4df7de5"}}, "title": "Proteolytic cleavage activates the mitochondrial isoform of TOP3A.", "authors": [{"family": "Erdinc", "given": "Direnis", "initials": "D", "orcid": "0000-0002-5830-9911", "researcher": {"href": "https://publications.scilifelab.se/researcher/84ac70e933964561a3de794818f19bb1.json"}}, {"family": "Albus", "given": "Christin A", "initials": "CA", "orcid": "0000-0002-6259-7151", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec36c816e9fe4800aeb343752a8dea67.json"}}, {"family": "Rodr\u00edguez-Luis", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3989-1317", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6d5387162594c99b66912602952861e.json"}}, {"family": "Menger", "given": "Katja E", "initials": "KE", "orcid": "0000-0002-6972-7326", "researcher": {"href": "https://publications.scilifelab.se/researcher/591cc4b1736f480a8fa737d3125be624.json"}}, {"family": "Thorsell", "given": "Annika", "initials": "A"}, {"family": "Atanassov", "given": "Ilian", "initials": "I", "orcid": "0000-0001-8259-2545", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d22eab41e44364be8966abaf693de1.json"}}, {"family": "Rov\u0161nik", "given": "Ur\u0161ka", "initials": "U", "orcid": "0000-0001-5889-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/199ce7dade164889902f7ae01e4b4577.json"}}, {"family": "Falkenberg", "given": "Maria", "initials": "M", "orcid": "0000-0001-8713-173X", "researcher": {"href": "https://publications.scilifelab.se/researcher/562109b99a5c4eb3bd8b92f30014828b.json"}}, {"family": "Gustafsson", "given": "Claes M", "initials": "CM", "orcid": "0000-0003-3531-8468", "researcher": {"href": "https://publications.scilifelab.se/researcher/2851656430d147dab7a8a32e50fee7b7.json"}}, {"family": "Nicholls", "given": "Thomas J J", "initials": "TJJ", "orcid": "0000-0002-3034-4109", "researcher": {"href": "https://publications.scilifelab.se/researcher/46e55e31c134464c8d8f71cc553ef198.json"}}], "type": "journal article", "published": "2025-10-28", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "20", "issn-l": "0305-1048"}, "abstract": "The TOP3A gene encodes two isoforms, one targeted to the nucleus and one to mitochondria. Nuclear TOP3A functions as part of the BTRR complex to resolve double Holliday junctions during homologous recombination, while the mitochondrial isoform separates hemicatenated daughter mitochondrial DNA (mtDNA) molecules following DNA replication. Here, we show that the mitochondrial isoform of TOP3A undergoes proteolytic cleavage by the mitochondrial processing peptidase, removing ~90 amino acids from the C-terminus. This cleavage enhances the enzyme's biochemical properties, increasing single-stranded DNA binding and decatenation activity. Notably, all BTRR complex subunits, except TOP3A, are absent from mitochondria, suggesting that proteolytic processing enables TOP3A to function autonomously in mtDNA maintenance. We propose that this cleavage represents a post-import maturation step that tailors TOP3A to its mitochondrial context by uncoupling it from nuclear protein interactions and enhancing its catalytic efficiency.", "doi": "10.1093/nar/gkaf1140", "pmid": "41189053", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12585908"}, {"db": "pii", "key": "8313834"}], "notes": [], "created": "2025-11-20T18:16:59.783Z", "modified": "2025-11-24T15:41:51.127Z"}, {"entity": "publication", "iuid": "ea1d7c59296941b4bb2c44e61fe0cac6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea1d7c59296941b4bb2c44e61fe0cac6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea1d7c59296941b4bb2c44e61fe0cac6"}}, "title": "Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1.", "authors": [{"family": "Hank", "given": "Emily C", "initials": "EC", "orcid": "0000-0002-3777-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3e38aa74d2c4ae0b7c77d7f1da17727.json"}}, {"family": "D'Arcy-Evans", "given": "Nicholas D", "initials": "ND"}, {"family": "Scaletti", "given": "Emma Rose", "initials": "ER"}, {"family": "Ben\u00edtez-Buelga", "given": "Carlos", "initials": "C"}, {"family": "Wallner", "given": "Olov", "initials": "O", "orcid": "0000-0002-6481-237X", "researcher": {"href": "https://publications.scilifelab.se/researcher/83eb2f7ee2f34f2cbacaae2dadcd90e9.json"}}, {"family": "Ortis", "given": "Florian", "initials": "F"}, {"family": "Zhou", "given": "Kaixin", "initials": "K"}, {"family": "Meng", "given": "Liuzhen", "initials": "L"}, {"family": "Del Prado", "given": "Alicia", "initials": "A", "orcid": "0000-0002-5480-0367", "researcher": {"href": "https://publications.scilifelab.se/researcher/39389cbfdeac46e8985c1597e00d45e1.json"}}, {"family": "Calvo", "given": "Patricia", "initials": "P"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Wiita", "given": "Elis\u00e9e", "initials": "E"}, {"family": "Nierlin", "given": "Karen", "initials": "K"}, {"family": "Ko\u0161enina", "given": "Sara", "initials": "S", "orcid": "0000-0001-7893-0249", "researcher": {"href": "https://publications.scilifelab.se/researcher/9370d4ecf19c438bb205c43c23f94f26.json"}}, {"family": "Kr\u00e4mer", "given": "Andreas", "initials": "A"}, {"family": "Eddershaw", "given": "Alice", "initials": "A"}, {"family": "Kehler", "given": "Mario", "initials": "M"}, {"family": "Long", "given": "Maeve", "initials": "M", "orcid": "0000-0001-5146-0750", "researcher": {"href": "https://publications.scilifelab.se/researcher/b68df86f81504376b77b98b0916c84c4.json"}}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS", "orcid": "0000-0002-7550-1833", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd07c6c543544af1a904e039f73ba857.json"}}, {"family": "Dawson", "given": "Holly", "initials": "H"}, {"family": "Stewart", "given": "Josephine", "initials": "J", "orcid": "0000-0002-3506-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e8f2e54f1a4f1d96d8f4ae1de97a93.json"}}, {"family": "Dickey", "given": "Adam", "initials": "A"}, {"family": "Astorga", "given": "Mikhael E", "initials": "ME"}, {"family": "Varga", "given": "Marek", "initials": "M"}, {"family": "Homan", "given": "Evert J", "initials": "EJ", "orcid": "0000-0002-9057-1848", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d6d2714b2544bfa37d383ef1357ba4.json"}}, {"family": "Scobie", "given": "Martin", "initials": "M", "orcid": "0000-0002-7073-8495", "researcher": {"href": "https://publications.scilifelab.se/researcher/87c041a8b3414f5db02873dc8013806b.json"}}, {"family": "Knapp", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5995-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4d84c40612d48f280d4ead25558d835.json"}}, {"family": "Sastre", "given": "Leandro", "initials": "L"}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "de Vega", "given": "Miguel", "initials": "M", "orcid": "0000-0003-1285-7549", "researcher": {"href": "https://publications.scilifelab.se/researcher/77e5f3b41f634728b525ff94b0496bc4.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Michel", "given": "Maurice", "initials": "M", "orcid": "0000-0003-3261-2493", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f7cb5d695254481b745f86a824ac1b5.json"}}], "type": "journal article", "published": "2025-10-28", "journal": {"title": "RSC Chem Biol", "issn": "2633-0679", "issn-l": null}, "abstract": "Bifunctional DNA glycosylases employ an active site lysine or the N-terminus to form a Schiff base with an abasic (AP) site base excision repair intermediate. For 8-oxoguanine DNA glycosylase 1 (OGG1), cleaving this reversible structure is the rate-determining step in the initiation of 8-oxoguanine (8-oxoG) repair in DNA. Evolution has led OGG1 to use a product-assisted catalysis approach, where the excised 8-oxoG acts as a Br\u00f8nsted base for cleavage of a Schiff base intermediate. However, the physicochemical properties of 8-oxoG significantly limit the inherent enzymatic turnover leading to a weak, cellularly absent, AP lyase activity. We hypothesized that chemical synthesis of purine analogues enables access to complex structures that are suitable as product-like catalysts. Herein, the nucleobase landscape is profiled for its potential to increase OGG1 Schiff base cleavage. 8-Substituted 6-thioguanines emerge as potent and selective scaffolds enabling OGG1 to cleave AP sites opposite any canonical nucleobase by \u03b2-elimination. This effectively broadens the enzymatic substrate scope of OGG1, shaping a complete, artificial AP-lyase function. In addition, a second class of compounds, 6-substituted pyrazolo-[3,4-d]-pyrimidines, stimulate OGG1 function at high pH, while thioguanines govern enzymatic control at acidic pH. This enables up to 20-fold increased enzyme turnover and a de novo OGG1 \u03b2-elimination in conditions commonly not tolerated. The tool compounds employed here are non-toxic in cells and stimulate the repair of AP sites through a natural, APE1 dependent pathway, as opposed to previously reported \u03b2,\u03b4-lyase stimulator TH10785.", "doi": "10.1039/d4cb00323c", "pmid": "41195166", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12584757"}, {"db": "pii", "key": "d4cb00323c"}], "notes": [], "created": "2025-11-25T11:35:44.104Z", "modified": "2025-11-27T13:32:01.339Z"}, {"entity": "publication", "iuid": "a4cd79754aa24d999e8958fa41246c30", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4cd79754aa24d999e8958fa41246c30.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4cd79754aa24d999e8958fa41246c30"}}, "title": "Identification of human gut bacteria that produce bioactive serotonin and promote colonic innervation.", "authors": [{"family": "Moretti", "given": "Chiara H", "initials": "CH"}, {"family": "Grasset", "given": "Estelle", "initials": "E"}, {"family": "Zhu", "given": "Jiaying", "initials": "J"}, {"family": "Yang", "given": "Gaohua", "initials": "G"}, {"family": "Olofsson", "given": "Louise E", "initials": "LE"}, {"family": "Khan", "given": "Muhammad Tanweer", "initials": "MT"}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO"}, {"family": "Oh", "given": "Jee-Hwan", "initials": "JH"}, {"family": "Lundqvist", "given": "Annika", "initials": "A"}, {"family": "van Gils", "given": "Tom", "initials": "T"}, {"family": "Kr\u00e4mer", "given": "Manuela", "initials": "M"}, {"family": "Olsson", "given": "Lisa M", "initials": "LM"}, {"family": "Patel", "given": "Piyush", "initials": "P"}, {"family": "Mitteregger", "given": "Matthias", "initials": "M"}, {"family": "Monges", "given": "Daysi Espinola", "initials": "DE"}, {"family": "Dwibedi", "given": "Chinmay", "initials": "C"}, {"family": "Krautkramer", "given": "Kimberly A", "initials": "KA"}, {"family": "Koopman", "given": "Nienke", "initials": "N"}, {"family": "Henricsson", "given": "Marcus", "initials": "M"}, {"family": "Macpherson", "given": "Andrew J", "initials": "AJ"}, {"family": "Schwartz", "given": "Thue", "initials": "T"}, {"family": "Grompone", "given": "Gianfranco", "initials": "G"}, {"family": "Pijkeren", "given": "Jan-Peter van", "initials": "JV"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Roos", "given": "Stefan", "initials": "S"}, {"family": "Simr\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2025-10-28", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "44", "issue": "10", "pages": "116434", "issn-l": null}, "abstract": "The gut microbiota regulates host intestinal serotonin synthesis, thereby promoting the development and maintenance of the enteric nervous system, which controls bowel motility. Functional bowel disorders, including irritable bowel syndrome, are associated with altered serotonin levels and gut microbiota composition. However, it is unclear if the gut microbiota can synthesize bioactive serotonin, which may affect enteric nervous system development. Here, we identify a consortium of the human gut bacteria Limosilactobacillus mucosae and Ligilactobacillus ruminis that synthesizes serotonin in vitro by decarboxylation of 5-hydroxytryptophan and elevates fecal serotonin levels, colonic neuronal density, and serotonin-immunoreactive neurons when introduced into germ-free, serotonin-deficient mice. The consortium normalizes intestinal transit time in germ-free wild-type mice, and we observe decreased fecal abundance of L. mucosae in individuals with irritable bowel syndrome. These findings suggest that specific members of the human gut microbiota synthesize bioactive serotonin that can contribute to gut health.", "doi": "10.1016/j.celrep.2025.116434", "pmid": "41118765", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(25)01205-7"}], "notes": [], "created": "2025-11-28T10:42:26.462Z", "modified": "2025-11-28T10:42:26.469Z"}, {"entity": "publication", "iuid": "1f346661593c45e2a36c93ee5a9ecf3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f346661593c45e2a36c93ee5a9ecf3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f346661593c45e2a36c93ee5a9ecf3a"}}, "title": "Extracellular ATP is an environmental cue in bacteria.", "authors": [{"family": "Tronnet", "given": "Sophie", "initials": "S"}, {"family": "Pandey", "given": "Vikash", "initials": "V"}, {"family": "Lloret-Berrocal", "given": "Miriam", "initials": "M"}, {"family": "P\u00e9rez-Del-Pozo", "given": "Mario", "initials": "M"}, {"family": "Hern\u00e1ndez-Ortego", "given": "Carlos", "initials": "C"}, {"family": "S\u00f6derholm", "given": "Niklas", "initials": "N"}, {"family": "Billker", "given": "Oliver", "initials": "O"}, {"family": "Nordstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Puhar", "given": "Andrea", "initials": "A"}], "type": "journal article", "published": "2025-10-28", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "44", "issue": "10", "pages": "116356", "issn-l": null}, "abstract": "In animals and plants, extracellular ATP (eATP) functions as a signal and regulates the immune response. During inflammation, intestinal bacteria are exposed to elevated eATP originating from the mucosa. However, whether bacteria respond to eATP is unclear. Here, we show that non-pathogenic Escherichia coli responds to eATP by modifying its transcriptional and metabolic landscapes. A genome-scale promoter library showed that the response is dependent on time, concentration, and medium and ATP specific. Second messengers and genes related to metabolism, biofilm formation, and envelope stress were regulated downstream of eATP. Metabolomics confirmed that eATP triggers enrichment of compounds with bioactive properties in the host or bacteria. Combined genome-scale modeling revealed modifications to global metabolic and biomass building blocks. Consequently, eATP altered the sensitivity to antibiotics and antimicrobial peptides. Finally, in pathogens, eATP controlled virulence factor expression. Our results indicate that eATP is an environmental cue in prokaryotes, which broadly regulates physiology, antimicrobial resistance, and virulence.", "doi": "10.1016/j.celrep.2025.116356", "pmid": "41071676", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(25)01127-1"}], "notes": [], "created": "2025-11-18T12:14:09.249Z", "modified": "2025-11-18T12:14:09.268Z"}, {"entity": "publication", "iuid": "78586428e6d44db2a96ef24198fe1489", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78586428e6d44db2a96ef24198fe1489.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78586428e6d44db2a96ef24198fe1489"}}, "title": "Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes.", "authors": [{"family": "Pold", "given": "Grace", "initials": "G", "orcid": "0000-0002-7536-3944", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a78bb0a7f6043119b6be5e226983d04.json"}}, {"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Jones", "given": "Christopher M", "initials": "CM"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal article", "published": "2025-10-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9495", "issn-l": "2041-1723"}, "abstract": "Diverse microorganisms can execute one or more steps in denitrification, during which nitrate or nitrite is successively reduced into nitric oxide, nitrous oxide, and ultimately dinitrogen. Many of the best-characterized denitrifiers are complete denitrifiers capable of executing all steps in the pathway, but their dominance in natural communities and what metabolic traits and environmental factors drive the global distribution of complete vs. partial denitrifiers are unclear. To address this, we conducted a comparative analysis of denitrification genes in 61,293 genomes, 3991 metagenomes, and 413 terrestrial and aquatic metatranscriptomes. We show that partial denitrifiers outnumber complete denitrifiers and the potential to initiate denitrification is more common than the potential to terminate it, particularly in nutrient rich environments. Our results further indicate that complete denitrifiers tend to be fast-growing organisms, favoring organic acid over sugar metabolism, and encoding the ability to oxidize and reduce a broader range of organic and inorganic compounds compared to partial denitrifiers. This suggests complete denitrifiers are metabolically flexible opportunists. Together, our results indicate an environmental footprint on the presence of denitrification genes which favors the genomic potential for partial over complete denitrification in most biomes and highlight that completion of the denitrification pathway is a community effort.", "doi": "10.1038/s41467-025-65319-5", "pmid": "41152293", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12569097"}, {"db": "pii", "key": "10.1038/s41467-025-65319-5"}], "notes": [], "created": "2025-11-28T10:46:06.036Z", "modified": "2025-11-28T10:46:06.107Z"}, {"entity": "publication", "iuid": "388fe736e91941cd9ccb66a502243168", "links": {"self": {"href": "https://publications.scilifelab.se/publication/388fe736e91941cd9ccb66a502243168.json"}, "display": {"href": "https://publications.scilifelab.se/publication/388fe736e91941cd9ccb66a502243168"}}, "title": "Intracellular Regulation of a Serotonin-Gated Ion Channel Links Receptor Trafficking to Memory", "authors": [{"family": "Cesar", "given": "Leona", "initials": "L", "orcid": "0000-0002-4480-2000", "researcher": {"href": "https://publications.scilifelab.se/researcher/18e4da37bd9c45bb998d2f1f20af2036.json"}}, {"family": "Zabeo", "given": "Davide", "initials": "D", "orcid": "0000-0002-5912-4601", "researcher": {"href": "https://publications.scilifelab.se/researcher/03943200c1ae493ab8b7d6886d0af356.json"}}, {"family": "Aspholm", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5878-0722", "researcher": {"href": "https://publications.scilifelab.se/researcher/45811e98fea84e979a0f75adac508749.json"}}, {"family": "Panagaki", "given": "Dimitra", "initials": "D"}, {"family": "H\u00f6\u00f6g", "given": "Johanna Louise", "initials": "JL", "orcid": "0000-0003-2162-3816", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1eaedff964f4060ae6e69f59cad4521.json"}}, {"family": "Morud", "given": "Julia", "initials": "J", "orcid": "0000-0003-1925-5938", "researcher": {"href": "https://publications.scilifelab.se/researcher/d41dc497590f451994c8164a67045c6c.json"}}], "type": "posted-content", "published": "2025-10-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.10.27.684756", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-12T10:07:21.362Z", "modified": "2026-01-12T10:07:21.740Z"}, {"entity": "publication", "iuid": "83a77d8160924330b81be0f9c36ddd00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83a77d8160924330b81be0f9c36ddd00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83a77d8160924330b81be0f9c36ddd00"}}, "title": "Altered DNA Methylation Pattern Contributes to Differential Epigenetic Immune Signaling in the Upper Respiratory Airway of Unvaccinated COVID-19 Patients", "authors": [{"family": "Govender", "given": "Melissa", "initials": "M", "orcid": "0000-0001-8327-5517", "researcher": {"href": "https://publications.scilifelab.se/researcher/0283324530c24dc59a856cc26f202884.json"}}, {"family": "Das", "given": "Jyotirmoy", "initials": "J", "orcid": "0000-0002-5649-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebcbc4237c1c48aeb6bdd446fd8d2c8a.json"}}, {"family": "Hopkins", "given": "Francis R", "initials": "FR"}, {"family": "Svanberg", "given": "Cecilia", "initials": "C"}, {"family": "Nordgren", "given": "Johan", "initials": "J", "orcid": "0000-0002-5349-2569", "researcher": {"href": "https://publications.scilifelab.se/researcher/81437aaae3b44d148e838a184c455f2b.json"}}, {"family": "Hagbom", "given": "Marie", "initials": "M", "orcid": "0000-0002-9770-4623", "researcher": {"href": "https://publications.scilifelab.se/researcher/0555f8ab1b2d42fc9bead5f4c0240ec9.json"}}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Nilsdotter-Augustinsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-5719-5601", "researcher": {"href": "https://publications.scilifelab.se/researcher/129ff8d1d877437fbf37f4180ea19fb4.json"}}, {"family": "Yong", "given": "Yean K", "initials": "YK"}, {"family": "Velu", "given": "Vijayakumar", "initials": "V", "orcid": "0000-0003-4238-1924", "researcher": {"href": "https://publications.scilifelab.se/researcher/61fbbd07ba5341f087bfcc958246792a.json"}}, {"family": "Raju", "given": "Sivadoss", "initials": "S"}, {"family": "Sj\u00f6wall", "given": "Johanna", "initials": "J", "orcid": "0000-0001-5622-866X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6442643a54484b3e9a6bfd586f2c27dc.json"}}, {"family": "Shankar", "given": "Esaki M", "initials": "EM", "orcid": "0000-0002-7866-9818", "researcher": {"href": "https://publications.scilifelab.se/researcher/1edec2d2bca84f3499109c5135436309.json"}}, {"family": "Nystr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0002-0145-4966", "researcher": {"href": "https://publications.scilifelab.se/researcher/93a23955db724558abca4e7ed1265067.json"}}, {"family": "Larsson", "given": "Marie", "initials": "M", "orcid": "0000-0002-4524-0177", "researcher": {"href": "https://publications.scilifelab.se/researcher/46874786a8de48668401faba73165750.json"}}], "type": "journal-article", "published": "2025-10-27", "journal": {"title": "Cells", "issn": "2073-4409", "issn-l": "2073-4409", "volume": "14", "issue": "21", "pages": "1673"}, "abstract": null, "doi": "10.3390/cells14211673", "pmid": null, "labels": {"Clinical Genomics": "Service", "Clinical Genomics Link\u00f6ping": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-30T12:39:09.525Z", "modified": "2025-10-30T12:40:16.743Z"}, {"entity": "publication", "iuid": "1938da5a9fb54644b9fd03953d33a22d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1938da5a9fb54644b9fd03953d33a22d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1938da5a9fb54644b9fd03953d33a22d"}}, "title": "Autoreactive T cells identified in patients with anti-Jo1+ antisynthetase syndrome recognise a new epitope on histidyl t-RNA synthetase.", "authors": [{"family": "Galindo-Feria", "given": "Angeles S", "initials": "AS"}, {"family": "Sharma", "given": "Ravi Kumar", "initials": "RK"}, {"family": "Dubnovitsky", "given": "Anatoly", "initials": "A"}, {"family": "Gerstner", "given": "Christina", "initials": "C"}, {"family": "Kozhukh", "given": "Genadiy", "initials": "G"}, {"family": "Van Vollenhoven", "given": "Annika", "initials": "A"}, {"family": "Boada", "given": "Juan Sebastian Diaz", "initials": "JSD"}, {"family": "Ramsk\u00f6ld", "given": "Daniel", "initials": "D", "orcid": "0000-0003-2892-673X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc367f2adb7c4379b7dc441be34e7ded.json"}}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Dastmalchi", "given": "Maryam", "initials": "M"}, {"family": "Reid", "given": "Hugh H", "initials": "HH"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Rossjohn", "given": "Jamie", "initials": "J"}, {"family": "Chemin", "given": "Karine", "initials": "K"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V", "orcid": "0000-0001-9251-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027fbf97444632a470b33e446d4d67.json"}}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}, {"family": "Horuluoglu", "given": "Begum", "initials": "B", "orcid": "0000-0003-2241-5170", "researcher": {"href": "https://publications.scilifelab.se/researcher/19120340af6c42bd8a359ce39d4a8b99.json"}}], "type": "journal article", "published": "2025-10-25", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "issn-l": "0003-4967"}, "abstract": "Anti-Jo1+ antisynthetase syndrome (ASyS) is characterised by autoantibodies targeting histidyl t-RNA synthetase (HisRS), association with HLA-DRB1*03:01 and a distinct clinical phenotype including interstitial lung disease, myositis, arthritis, and mechanic's hands. Previous studies of autoreactive HisRS-specific CD4+T cells point to yet undiscovered T cell epitopes. We aimed to identify new epitopes on HisRS to investigate the presence of autoreactive T cells and their corresponding T-cell receptor (TCR) repertoire from patients with ASyS.\n\nPeptides from HisRS N-terminal region with appropriate major histocompatibility complex (MHC) anchor residues were selected for in vitro binding assays. The peptide (HisRS41-55) with the highest HLA-DRB1*03:01 binding affinity was selected for studies with HLA-class II tetramers. Peripheral blood mononuclear cells (PBMCs) from patients with ASyS with HLA-DRB1*03:01 (n = 12) were stimulated in vitro with peptide and peptide-HLA-DRB1*03:01 tetramers were used to detect HisRS+CD4+T cells. Single TCR sequencing of captured T cells allowed analyses of the underlying TCR repertoire.\n\nWe identified a new T cell epitope on HisRS with high affinity for HLA-DRB1*03:01. Autoreactive HisRS+CD4+T cells were detected in PBMCs of patients (n = 6/12). TCR repertoire analysis of HisRS+CD4+T cells revealed shared gene V-alpha and beta usages. Moreover, HisRS+CD4+T cells persisted after treatment in 2 patients (P2 and P4) and 2 identical T cell clones were detected between the initial and follow-up time points in 1 patient (P2).\n\nAutoreactive T-cells targeting a new HisRS epitope were identified indicating T cell reactivity to diverse epitopes of the HisRS protein in patients with anti-Jo1 autoantibodies. Furthermore, we demonstrated the TCR repertoire of autoreactive HisRS+CD4+T cells in patients. Persistence of these T-cells and specific clones may be contributing to disease.", "doi": "10.1016/j.ard.2025.09.015", "pmid": "41139557", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-4967(25)04429-2"}], "notes": [], "created": "2025-10-29T10:08:57.216Z", "modified": "2025-11-11T13:53:36.238Z"}, {"entity": "publication", "iuid": "a7fed56865ca4e36b3a0de3c2580cd45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7fed56865ca4e36b3a0de3c2580cd45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7fed56865ca4e36b3a0de3c2580cd45"}}, "title": "Comparing methods collecting mucosal secretions and detecting SARS-CoV-2 spike IgA in three laboratories across three countries.", "authors": [{"family": "Bladh", "given": "Oscar", "initials": "O"}, {"family": "Aguilera", "given": "Katherina", "initials": "K"}, {"family": "Sheikh-Mohamed", "given": "Salma", "initials": "S"}, {"family": "Nardulli", "given": "Jessica", "initials": "J"}, {"family": "Bhavsar", "given": "Disha", "initials": "D"}, {"family": "Fitzgerald", "given": "Dylan", "initials": "D"}, {"family": "Singh", "given": "Gagandeep", "initials": "G"}, {"family": "Ward", "given": "Lesley A", "initials": "LA"}, {"family": "Kleiner", "given": "Giulio", "initials": "G"}, {"family": "Chao", "given": "Gary Y C", "initials": "GYC"}, {"family": "Norin", "given": "Nina Greilert", "initials": "NG"}, {"family": "Pongr\u00e1cz", "given": "Tam\u00e1s", "initials": "T"}, {"family": "Gleason", "given": "Charles", "initials": "C"}, {"family": "Berkell", "given": "Matilda", "initials": "M"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Krammer", "given": "Florian", "initials": "F"}, {"family": "Gommerman", "given": "Jennifer L", "initials": "JL"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}, {"family": "Simon", "given": "Viviana", "initials": "V"}], "type": "journal article", "published": "2025-10-24", "journal": {"title": "Vaccine", "issn": "1873-2518", "volume": "65", "pages": "127792", "issn-l": null}, "abstract": "Mucosal IgA is key in preventing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Several mucosal vaccines are in development, and consistent methodologies assessing mucosal IgA are crucial for evaluation across clinical trials.\n\nWe compared SARS-CoV-2 ancestral spike-specific IgA and secretory IgA (SIgA) in nasal secretions and saliva from 20 adults enrolled at Danderyd Hospital, Stockholm, Sweden, and 23 adults enrolled at the Icahn School of Medicine at Mount Sinai, New York, USA. Nasal secretions were collected by Nasosorption\u00ae and nasal swabs, and saliva by passive drooling, Salivette\u00ae, and saliva swabs. Antibody levels were measured in all samples using an electrochemiluminescence assay (ECL) and two enzyme-linked immunosorbent assays (ELISAs).\n\nSpike-specific IgA and SIgA levels measured by ECL correlated well with those measured by ELISA across nasal and saliva samples (range 0.42-0.94, p < 0.01), except for saliva collected by saliva swabs yielding lower IgA concentrations and weaker correlations (range - 0.21-0.27). Spike-specific IgA levels also correlated well across collection methods (range 0.7-0.9, p < 0.0001), with a weaker correlation between saliva collected by passive drooling and saliva swab (r = 0.55, p < 0.001). Although antibody levels correlated well between nasal secretions and saliva collected by passive drooling or Salivette\u00ae (range 0.64-0.86, p < 0.01), the overall levels were > 3-fold higher in nasal secretions compared to saliva (p < 0.01).\n\nThis multi-center study demonstrates an overall good comparability between spike-specific IgA and SIgA across assays and collection methods, except for saliva swabs. Our findings suggest that nasal secretions may be preferable due to higher spike-specific IgA levels compared to in saliva.", "doi": "10.1016/j.vaccine.2025.127792", "pmid": "41046839", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0264-410X(25)01089-8"}], "notes": [], "created": "2025-11-21T12:51:55.694Z", "modified": "2025-11-25T19:19:35.240Z"}, {"entity": "publication", "iuid": "26a19cda0171462a8256035830fdb484", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26a19cda0171462a8256035830fdb484.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26a19cda0171462a8256035830fdb484"}}, "title": "Targeted proteomics identifies differentially expressed proteins in Sj\u00f6gren's disease with incident lymphoma.", "authors": [{"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Fugmann", "given": "Cecilia", "initials": "C"}, {"family": "Molin", "given": "Anna-Maja", "initials": "AM"}, {"family": "Backlin", "given": "Carin", "initials": "C"}, {"family": "Johansson", "given": "Alina", "initials": "A"}, {"family": "Vranic", "given": "Milica", "initials": "M"}, {"family": "Nikkarinen", "given": "Anna", "initials": "A"}, {"family": "Autolymphoma Study Group", "given": "", "initials": ""}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Steering committee", "given": "", "initials": ""}], "type": "journal article", "published": "2025-10-23", "journal": {"title": "RMD Open", "issn": "2056-5933", "volume": "11", "issue": "4", "issn-l": "2056-5933"}, "abstract": "Patients with primary Sj\u00f6gren's disease (SjD) have an increased risk of B cell lymphoma. The aim of this study was to determine serum protein biomarkers for lymphoma development and to advance our understanding of the functional mechanisms underlying lymphomagenesis in SjD.\n\nPatients with SjD and incident, current lymphoma (n=18) with serum sampled before treatment and at 6, 12 and 24 months of follow-up, and four patients sampled 1-5 years before lymphoma diagnosis (pre-lymphoma) were included. SjD without lymphoma (n=21), SjD with historical lymphoma (n=6) and healthy blood donors (n=39) served as controls. Differentially expressed proteins between groups were analysed using the Olink Target 96 Immuno-Oncology panel applying a false discovery rate (FDR) adjusted p value of 0.05. Protein-derived interferon activation scores (pIFN scores) were calculated.\n\nWe determined 18 differentially expressed proteins in SjD with incident lymphoma compared with both SjD without lymphoma and healthy controls. Among the top upregulated proteins were TNFSF14, FGF2, IL8, CD40 and CXCL13, where CXCL13 was the only protein with decreased levels at follow-up. We also observed upregulated expression of CD40 in the SjD pre-lymphoma group compared with SjD without lymphoma and healthy controls. All SjD patient groups presented elevated pIFN scores compared with healthy controls, where SjD sampled pre-lymphoma showed the most distinct IFN activation.\n\nWe identified altered protein expression and an increased IFN system activation in SjD with incident lymphoma and pre-lymphoma. This knowledge may contribute to earlier detection of high-risk patients, identification of therapeutic targets and may ultimately improve SjD patient outcomes.", "doi": "10.1136/rmdopen-2025-005897", "pmid": "41130745", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12551502"}, {"db": "pii", "key": "rmdopen-2025-005897"}], "notes": [], "created": "2025-11-25T19:21:15.438Z", "modified": "2025-11-25T19:21:15.489Z"}, {"entity": "publication", "iuid": "da36f1345597448ca732d4ba88913d2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da36f1345597448ca732d4ba88913d2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da36f1345597448ca732d4ba88913d2d"}}, "title": "Identification and whole-genome characterization of a novel equine papillomavirus.", "authors": [{"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "Hansen", "given": "Sanni", "initials": "S"}, {"family": "Riihim\u00e4ki", "given": "Miia", "initials": "M"}], "type": "journal article", "published": "2025-10-23", "journal": {"title": "Virus Genes", "issn": "1572-994X", "issn-l": null}, "abstract": "Papillomaviruses (PVs) are small, non-enveloped viruses with double-stranded circular DNA genomes that infect a wide range of hosts, including mammals, birds, reptiles, and fish. While human papillomaviruses are extensively studied, recent advancements in high-throughput sequencing techniques have increased the detection and genetic characterization of PVs from various animal species. Here, we describe the identification and whole-genome characterization of a divergent equine papillomavirus (EcPV) detected through a viral metagenomic investigation of a horse in Denmark exhibiting neurological signs. Using Nanopore sequencing and Sanger sequencing, we assembled a complete viral genome of 7767 nucleotides. Phylogenetic analysis, based on concatenated E1, E2, L2, and L1 gene sequences, showed that the identified virus clustered within the same clade as EcPV3 (genus Dyoiotapapillomavirus) and EcPV6 (genus Dyorhopapillomavirus) but was situated on a distinct separate branch. Comparative genome analysis revealed approximately 52% nucleotide sequence similarity to EcPV3 and EcPV6, which share 66% similarity with each other. The L1 gene, commonly used for papillomavirus classification, exhibited a sequence identity to EcPV3 (58.4%) and EcPV6 (60.0%). The other viral genes displayed a 39-62% identity to the respective genes from EcPV3 and 6 further supporting the divergence of this newly identified PV. The combination of the phylogenetic analysis and the genetic divergence suggests that this newly identified papillomavirus may constitute a novel species or genus within the Papillomaviridae family. Our findings expand the known diversity of equine papillomaviruses and contribute valuable insights into their evolutionary relationships.", "doi": "10.1007/s11262-025-02190-y", "pmid": "41128801", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s11262-025-02190-y"}], "notes": [], "created": "2025-11-28T10:41:29.043Z", "modified": "2025-11-28T10:41:29.059Z"}, {"entity": "publication", "iuid": "85c5bdfdbc81457e81767eab223261e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85c5bdfdbc81457e81767eab223261e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85c5bdfdbc81457e81767eab223261e3"}}, "title": "Diagnostic and prognostic biomarkers associated with histotype in advanced epithelial ovarian cancer.", "authors": [{"family": "Ittner", "given": "Ella", "initials": "E"}, {"family": "Swenson", "given": "Hugo", "initials": "H"}, {"family": "Werner", "given": "Lucas", "initials": "L"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Mateoiu", "given": "Constantina", "initials": "C"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Dahm-K\u00e4hler", "given": "Pernilla", "initials": "P"}, {"family": "Saed", "given": "Ghassan", "initials": "G"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ", "orcid": "0000-0003-0834-5540", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d528a2bce6c40829c1a6fed69c9f9ef.json"}}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2025-10-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "37171", "issn-l": "2045-2322"}, "abstract": "Despite advances in cancer treatments, epithelial ovarian cancer (EOC) remains the leading cause of death among gynecologic cancers. EOC is stratified into five main histopathological subtypes: high-grade serous carcinoma (HGSC), low-grade serous carcinoma (LGSC), endometrioid carcinoma (EC), clear cell carcinoma (CCC), and mucinous carcinoma (MC). However, personalized treatment strategies and reliable biomarkers for all histotypes remain elusive. Building on our previous work with early-stage EOC, we aim to explore diagnostic and prognostic biomarkers in advanced-stage EOC, updated to the latest World Health Organization classification guidelines from 2020, using comprehensive transcriptomic profiling from total RNA sequencing of 146 EOCs. Differential expression analysis identified top 9 histotype-specific gene panels for HGSC, CCC, MC, and EC, including S100A1 (HGSC), ARID3A (CCC), LGALS4 (MC), and PAX9 (EC). We also identified gene candidates associated with overall survival and disease-specific survival, reflecting both favorable (e.g., OTOF, EEF1E1-BLOC1S5, and STAC3) and unfavorable (e.g., SMOC1, GDPGP1, EPRS1) clinical outcome. Additionally, enrichment analysis revealed tumor progression-related pathways unique to each histotype, offering insights into the molecular mechanisms underlying disease progression and potential therapeutic targets. These findings provide valuable insights into the molecular landscape of advanced-stage EOC, paving the way for more effective diagnostic and prognostic tools across diverse histotypes.", "doi": "10.1038/s41598-025-24938-0", "pmid": "41131133", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12550092"}, {"db": "pii", "key": "10.1038/s41598-025-24938-0"}], "notes": [], "created": "2025-11-07T07:25:02.175Z", "modified": "2025-11-28T10:47:09.805Z"}, {"entity": "publication", "iuid": "b366156200f940fc852c263ba8ebc16d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b366156200f940fc852c263ba8ebc16d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b366156200f940fc852c263ba8ebc16d"}}, "title": "The Hybrid Landscape: Materiality, Connectivity and Mobility of the last 4000 years of Hunter-Gatherers in the Southwest Maputo Province, Mozambique", "authors": [{"family": "Muianga", "given": "D\u00e9cio", "initials": "D"}], "type": null, "published": "2025-10-22", "journal": {"title": "Studies in Global Archaeology", "issn": "1651-1255", "issn-l": null, "volume": null, "issue": null, "pages": "32-296"}, "abstract": "Mozambican Stone Age and the transition into farming communities remain poorly explored compared to the rest of the southern region, and its archaeological heritage is still primarily explained in terms of better-known sequences of other southern African countries. Southern Mozambique has very few sites with archaeological evidence related to hunter-gatherers that are well described. The lithic assemblages from Daimane I and II rock shelter in Changalane Administrative Post (Namaacha District, Maputo Province), apart from the rock art, become one of the few sources of explanation of the use of the rock shelters in the area. Lithic analysis, phytoliths, ancient soil DNA, radiocarbon and OSL dating show that formal and informal tools were produced or used in the area, as part of the hunting and gathering way of life. Rock paintings that are aspects of the symbolic behaviour of early hominids and later by foragers are also present in DAIM I and II, which marked their passage and represent a unique archaeological sequence of chronological and symbolic events during the Holocene. To build an understanding of the Stone Age sequence of the area, this dissertation considers the sequence of the occupation of the sites based on the typological and chronological features recognised on the lithic and other artefacts and also other types of data. Diagnostic cultural material at DAIM I and DAIM II strongly suggests a continuity of the hunter-gatherer presence through the first millennium AD and maintenance of the Later Stone Age way of life in the Lebombo Mountain range in the Changalane Administrative Post and surrounding areas.", "doi": null, "pmid": null, "labels": {"Ancient DNA": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-23T08:12:13.562Z", "modified": "2026-01-23T08:12:13.563Z"}, {"entity": "publication", "iuid": "b35e650e9be145ab9268e43d4adecec5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b35e650e9be145ab9268e43d4adecec5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b35e650e9be145ab9268e43d4adecec5"}}, "title": "Customizing Spider Silk: Generative Models with Mechanical Property Conditioning for Protein Engineering", "authors": [{"family": "Neeru", "given": "Dubey", "initials": "D"}, {"family": "Karlsson", "given": "Elin", "initials": "E"}, {"family": "Redondo", "given": "Miguel Angel", "initials": "MA"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Rising", "given": "Anna", "initials": "A"}, {"family": "Kjellstr\u00f6m", "given": "Hedvig", "initials": "H"}], "type": null, "published": "2025-10-22", "journal": {"title": "Transactions on ML research", "issn": "2835-8856", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "The remarkable mechanical properties of spider silk, including its tensile strength and extensibility, are primarily governed by the repeat regions of the proteins that constitute the\r\nfiber, the major ampullate spidroins (MaSps). However, establishing correlations between\r\nmechanical characteristics and repeat sequences remains challenging due to the intricate sequence\u2013structure\u2013function relationships of MaSps and the limited availability of annotated\r\ndatasets. In this study, we present a novel computational framework for designing MaSp\r\nrepeat sequences with customizable mechanical properties. To achieve this, we developed\r\na lightweight GPT-based generative model by distilling the pre-trained ProtGPT2 protein\r\nlanguage model. The distilled model was subjected to multi-level fine-tuning using curated\r\nsubsets of the Spider Silkome dataset. Specifically, we adapted the model for MaSp repeat\r\ngeneration using 6,000 MaSp repeat sequences and further refined it via cross-validation\r\non 592 repeats associated with experimentally determined fiber-level mechanical properties.\r\nOur model generates biologically plausible MaSp repeat regions tailored to specific mechanical properties, while also predicting those properties for given sequences. Validation\r\nincludes sequence-level analysis, assessing physicochemical attributes, the expected distribution of key motifs, and secondary structure compositions. A correlation study using BLAST\r\non the Spider Silkome dataset and a test set of MaSp repeats with known mechanical properties further confirmed the predictive accuracy of the model. This framework advances the\r\nrational design of spider silk-inspired biomaterials, offering a versatile tool for engineering\r\nprotein sequences with tailored mechanical attributes.", "doi": null, "pmid": null, "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-28T08:24:31.991Z", "modified": "2025-11-28T08:24:31.992Z"}, {"entity": "publication", "iuid": "25f828a506934ab9b9291c1869b794f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25f828a506934ab9b9291c1869b794f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25f828a506934ab9b9291c1869b794f5"}}, "title": "A multi-omics approach uncovers causality of IL6R on endotypes of subclinical carotid atherosclerosis and the possible role of the IL6R/OSMR pathway.", "authors": [{"family": "Chen", "given": "Qiao Sen", "initials": "QS"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-9155-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d162f3de0f941e0a91387357892d656.json"}}, {"family": "Bergman", "given": "Otto", "initials": "O"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D", "orcid": "0000-0002-2766-8882", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c131cad5784434eb16cf720f7964ecb.json"}}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Gallo", "given": "Antonio", "initials": "A"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Hedin", "given": "Ulf", "initials": "U", "orcid": "0000-0001-9212-3945", "researcher": {"href": "https://publications.scilifelab.se/researcher/29a6ec281f5d4f1a8f317dedf0404cdd.json"}}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Lind", "given": "Lars", "initials": "L", "orcid": "0000-0003-2335-8542", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c517dacca7c4ec58a3e03b59ffb4044.json"}}, {"family": "Matic", "given": "Ljubica", "initials": "L", "orcid": "0000-0002-7294-9667", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee002c0f7f2c4c339a619c56c47e9ab6.json"}}, {"family": "Mulder", "given": "Douw Johannes", "initials": "DJ"}, {"family": "Pirro", "given": "Matteo", "initials": "M"}, {"family": "Savonen", "given": "Kai", "initials": "K"}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ", "orcid": "0000-0003-1617-3179", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4b5d952d50c4801aa88c0c9ae0d5813.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}], "type": "journal article", "published": "2025-10-22", "journal": {"title": "Cardiovasc. Res.", "issn": "1755-3245", "issn-l": "0008-6363"}, "abstract": "Endotypes integrate individual clinical and molecular data and can be used to formulate molecular subclassifications of diseases. We previously derived four endotypes of subclinical carotid atherosclerosis in a large European cohort, c-IMT and c-IMT Progression as Predictors of Vascular Events in a High-Risk European Population (IMPROVE), identifying individuals with a specific cardiovascular (CV) risk, ranging from low (endotype 1) to very high (endotype 4). Here, we investigate the mechanisms underlying the differences in CV risk observed across these four endotypes.\n\nWe validated the four endotypes in SCAPIS (n = 5050) and UK Biobank (n = 50 396) using carotid plaque and carotid intima-media thickness (c-IMT) as subclinical atherosclerosis measures. Endotype 4 associated with a larger number of carotid plaques and increased c-IMT measures as compared to endotype 1. We performed a meta-analysis of individual genome wide association studies in IMPROVE (n = 3711), SCAPIS and UK Biobank, and identified 12 SNPs associated with endotypes. We investigated if they regulated gene expression and circulating protein levels. We found that rs2228145A/C at Interleukin-6 Receptor (IL6R), associated with endotype 4, regulated IL6R expression and circulating levels of OncoStatin M Receptor (OSMR), Complement Factor B (CFB) and Fibrinogen Chain A (FGA). We used rs2228145A/C as an instrument in two-sample Mendelian randomization analyses and showed that a decreasing IL6R expression, associated with increasing CFB, FGA, and OSMR circulating levels. Endotype 4, IL6R, CFB, FGA, and OSMR co-localized within 250 kb surrounding rs2228145A/C. However, only OSMR was up-regulated in advanced carotid atherosclerotic plaques in the presence of the A allele and in aortic region exposed to low wall shear stress. In the UK Biobank, we observed that each additional A allele at rs2228145 increased by 1.28-times the risk of myocardial infarction (MI) in endotype 4.\n\nRs2228145A/C associated with endotype 4 clinical and molecular characteristics and amplified the MI risk in individuals assigned to endotype 4. These effects appeared to be mediated by a crosstalk with OSMR.", "doi": "10.1093/cvr/cvaf177", "pmid": "41124095", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "8296653"}], "notes": [], "created": "2025-11-25T19:21:10.519Z", "modified": "2025-11-25T19:21:10.605Z"}, {"entity": "publication", "iuid": "c34e73cd03bb4bea92a8c1741dafab9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c34e73cd03bb4bea92a8c1741dafab9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c34e73cd03bb4bea92a8c1741dafab9d"}}, "title": "Transcriptomic responses of beet to infection by beet mild yellowing virus.", "authors": [{"family": "Puthanveed", "given": "Vinitha", "initials": "V"}, {"family": "Sajeevan", "given": "Radha Sivarajan", "initials": "RS", "orcid": "0000-0002-8671-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d0cdc56cd144c628d3c90000b782581.json"}}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"family": "Alexandersson", "given": "Erik", "initials": "E", "orcid": "0000-0001-6320-2492", "researcher": {"href": "https://publications.scilifelab.se/researcher/eae8dc98de79429495f0a1727a342e9f.json"}}, {"family": "Joshi", "given": "Pratikshya", "initials": "P", "orcid": "0000-0002-6361-5059", "researcher": {"href": "https://publications.scilifelab.se/researcher/46050ddec8f64054b3bab46c5016aebf.json"}}, {"family": "Snell", "given": "Per", "initials": "P"}, {"family": "Lennefors", "given": "Britt-Louise", "initials": "BL"}, {"family": "Kvarnheden", "given": "Anders", "initials": "A", "orcid": "0000-0001-9394-7700", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf67998333e74016847b7a6d3f121e7b.json"}}], "type": "journal article", "published": "2025-10-21", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "25", "issue": "1", "pages": "1406", "issn-l": "1471-2229"}, "abstract": "Virus yellows (VY) disease of sugar beet is caused by a complex of aphid-transmitted viruses, including beet mild yellowing virus (BMYV). Neonicotinoids have been used for preventing VY through aphid management, but with the recent ban on neonicotinoids in Europe, the risks for outbreaks of VY have increased dramatically. To study the host responses to BMYV infection and identify the differentially expressed genes (DEGs), we conducted an RNAseq experiment using a resistant genotype of wild beet and a susceptible breeding line of sugar beet. The experiment contained four plant treatments: exposure to aphids with or without BMYV, only insecticide spray and untreated control. Leaves were collected for analyses at 0, 1, 4, 14, 21 and 28 days post-inoculation (DPI).\n\nFollowing BMYV inoculation, resistant plants did not show any chlorosis even at 28 DPI, whereas susceptible plants displayed typical virus symptoms. Using RT-qPCR, BMYV was detected already at 1 DPI in both genotypes. At 14, 21 and 28 DPI, the virus titre in young and inoculated leaves of the susceptible genotype was higher. RNAseq revealed more DEGs as a response to BMYV infection for the susceptible genotype. In inoculated leaves, the number of DEGs increased faster for the susceptible genotype, while in young leaves, the trend was similar for susceptible and resistant genotypes. This shows that the plant responses in inoculated leaves to virus infection appeared at a larger scale in the susceptible genotype. Seven of the significantly upregulated genes in the resistant genotype encoded proteins involved in protein processing in the ER. This could be one mechanism contributing to the absence of symptoms in this genotype.\n\nThis study offers new insights into the transcriptomic events and genetic pathways regulating the defence response to BMYV in a partially resistant genotype. We present 14 candidate genes for partial resistance to BMYV and one of the possible mechanisms contributing to reduced virus levels and absence of symptoms. The findings will be of importance for future functional studies to understand the mechanisms of resistance and susceptibility as well as for the breeding of BMYV resistance.", "doi": "10.1186/s12870-025-07514-6", "pmid": "41120973", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12538817"}, {"db": "pii", "key": "10.1186/s12870-025-07514-6"}], "notes": [], "created": "2025-11-07T07:24:57.182Z", "modified": "2025-11-14T11:08:40.919Z"}, {"entity": "publication", "iuid": "17cc8dd239614f7a9b676fd4294a07ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17cc8dd239614f7a9b676fd4294a07ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17cc8dd239614f7a9b676fd4294a07ba"}}, "title": "Exploring Helical Fraying Linked to Dynamics and Catalysis in Adenylate Kinase.", "authors": [{"family": "Mattsson", "given": "Jonna", "initials": "J"}, {"family": "Phoeurk", "given": "Chanrith", "initials": "C"}, {"family": "Schierholz", "given": "L\u00e9on", "initials": "L"}, {"family": "Mushtaq", "given": "Ameeq Ul", "initials": "AU"}, {"family": "Rodriguez Buitrago", "given": "Jhon Alexander", "initials": "JA"}, {"family": "Rogne", "given": "Per", "initials": "P", "orcid": "0000-0002-3687-9200", "researcher": {"href": "https://publications.scilifelab.se/researcher/31042ecc88a94cd6b97cef0508da93fd.json"}}, {"family": "Sauer-Eriksson", "given": "A Elisabeth", "initials": "AE", "orcid": "0000-0003-0124-0199", "researcher": {"href": "https://publications.scilifelab.se/researcher/9435049fbe2745b59e04558cc5201f95.json"}}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9098-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c6ea8f5c456428db21b1085ad541538.json"}}], "type": "journal article", "published": "2025-10-21", "journal": {"title": "Biochemistry", "issn": "1520-4995", "volume": "64", "issue": "20", "pages": "4281-4295", "issn-l": "0006-2960"}, "abstract": "Conformational dynamics is a fundamental aspect of enzymatic catalysis that, for example, can be linked to ligand binding and release, assembly of the active site, and the catalytic mechanism. The essential and metabolic enzyme adenylate kinase (AK) undergoes large-scale conformational changes in response to binding of its substrates ATP and AMP. As such, it has been intensely studied in search of linkages between dynamics and catalysis. For a complex conformational change to occur in a protein, whether it is of an induced fit or conformational selection nature, changes at several hinges are often required. Here, based on a comparative structure-function analysis of AK enzymes from E. coli and the archaea Odinarchaeota and from human AK1, we found that conformational changes in the enzymes are to a varying degree linked to bending, fraying, or unfolding/folding events of the termini of \u03b1-helices observed in various structural hot spots of the enzymes. The findings contribute with a mechanistic angle to how enzymatic dynamics and catalysis relate to the plasticity of the termini of \u03b1-helices.", "doi": "10.1021/acs.biochem.5c00306", "pmid": "41042980", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12548092"}], "notes": [], "created": "2025-11-25T19:26:48.320Z", "modified": "2025-11-25T19:26:48.339Z"}, {"entity": "publication", "iuid": "1385430ef1d340e8841c2a15aec35a0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1385430ef1d340e8841c2a15aec35a0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1385430ef1d340e8841c2a15aec35a0e"}}, "title": "Computer Vision-Assisted Data Analysis for Correlative Electron Microscopy and Secondary Ion Mass Spectrometry Imaging.", "authors": [{"family": "du Toit", "given": "Andr\u00e9", "initials": "A"}, {"family": "Lork", "given": "Alicia A", "initials": "AA"}, {"family": "Ernst", "given": "Carl", "initials": "C"}, {"family": "Phan", "given": "Nhu T N", "initials": "NTN", "orcid": "0000-0002-3576-0494", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fa50d61430943a6af068ef05736ea4a.json"}}], "type": "journal article", "published": "2025-10-21", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "97", "issue": "41", "pages": "22807-22816", "issn-l": "0003-2700"}, "abstract": "Correlative imaging is a powerful analytical approach in bioimaging, as it offers complementary information on the samples measured by different modalities. Particularly, correlative transmission electron microscopy (EM) and nanoscale secondary ion mass spectrometry (NanoSIMS) imaging enable high-resolution morphological and chemical analysis at the subcellular level. However, manual segmentation and correlation of regions of interest (ROIs) in large EM and NanoSIMS data sets are time-consuming, prone to user bias, and limited in throughput. To address this, we developed a computer vision-assisted image analysis pipeline for automatic classification and segmentation of subcellular organelles in EM images, enabling rapid and reproducible correlation with NanoSIMS ion data. Using human neuronal progenitor cells (hNPCs) and differentiated postmitotic neurons, we trained a YOLOv8 deep learning model to recognize six major organelle types. The pipeline included EM image preprocessing, segmentation via YOLOv8, morphological filtering, and image registration with NanoSIMS ion maps. Performance evaluation demonstrated a robust model accuracy. We applied the pipeline to measure 15N-leucine abundance to study protein turnover in single organelles across different cell states. Results showed distinct turnover dynamics among organelles, with slower turnover observed in differentiated neurons compared to hNPCs. The automated pipeline significantly reduced the analysis time (from hours to minutes) while maintaining consistency with manual segmentation. Our approach demonstrates how computer vision can streamline correlative imaging workflows, improve data quality, and enable deeper insights into subcellular processes such as protein turnover, making it especially valuable for SIMS users and broader bioimaging applications.", "doi": "10.1021/acs.analchem.5c04489", "pmid": "41076583", "labels": {"Integrated Microscopy Technologies Gothenburg": "Technology development", "NanoSIMS": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12547856"}], "notes": [], "created": "2026-03-09T17:41:55.015Z", "modified": "2026-03-10T14:20:43.776Z"}, {"entity": "publication", "iuid": "d858061a910a4b309c2ee7bd9f0f2385", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d858061a910a4b309c2ee7bd9f0f2385.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d858061a910a4b309c2ee7bd9f0f2385"}}, "title": "Toxicological and nutritional evaluation of plant cell cultures from scurvy grass (Cochlearia danica) and rowan (Sorbus aucuparia).", "authors": [{"family": "Cheung", "given": "Ho Lam", "initials": "HL"}, {"family": "Lo", "given": "Emily Kwun Kwan", "initials": "EKK"}, {"family": "Zhang", "given": "Fangfei", "initials": "F"}, {"family": "Leung", "given": "Hoi Kit Matthew", "initials": "HKM"}, {"family": "Ismaiah", "given": "Marsena Jasiel", "initials": "MJ"}, {"family": "Rosa-Sibakov", "given": "Natalia", "initials": "N"}, {"family": "Iannone", "given": "Valeria", "initials": "V"}, {"family": "G\u00f3mez-Gallego", "given": "Carlos", "initials": "C"}, {"family": "Kolehmainen", "given": "Marjukka", "initials": "M"}, {"family": "Rischer", "given": "Heiko", "initials": "H"}, {"family": "Nordlund", "given": "Emilia", "initials": "E"}, {"family": "El-Nezami", "given": "Hani", "initials": "H"}], "type": "journal article", "published": "2025-10-20", "journal": {"title": "Front Toxicol", "issn": "2673-3080", "volume": "7", "pages": "1655489", "issn-l": null}, "abstract": "Plant cell culture (PCC) technology is currently being developed to produce plant foods partially decoupled from traditional agriculture practices. By now, the safety of the ingredients produced by PCC technology for food or nutritional purposes has to be tested.\n\nIn this study, the oral safety and toxicity of two novel PCCs, scurvy grass (SG) (Cochlearia danica) and rowan (RW) (Sorbus aucuparia), and to characterize the macro- and micronutrient quality, including proteomic profiles, to identify potential allergens.\n\nNutritional composition analysis showed that both SG and RW PCCs profiles are comparable to other berry cell lines with a good amount of protein, dietary fibre and vitamins. Potential allergens were identified via proteomics based on structural similarity. The acute and subacute toxicity profiles of the PCC samples were evaluated based on OECD guidelines. For both PCCs, no deaths, behavioral changes, nor metabolic effects were observed at 2000 mg/kg. In the 28-day repeated oral exposure subacute toxicity study, no mortality or significant adverse clinical, hematological, or metabolic effects were observed for either SG or RW.\n\nThese findings indicate that the no-observed-adverse-effect level (NOAEL) for both PCCs exceeds 2000 mg/kg. Overall, our findings indicate that the consumption of these PCCs could be considered safe and non-toxic, although further assessments on potential allergens and phytohormone accumulation are necessary to fully ensure consumer safety. This study highlights the oral safety of PCCs for consideration as a novel food ingredient and serve as a basis for evaluating toxicological impacts of PCCs.", "doi": "10.3389/ftox.2025.1655489", "pmid": "41189876", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12580138"}, {"db": "pii", "key": "1655489"}], "notes": [], "created": "2025-11-20T18:16:58.266Z", "modified": "2025-11-20T18:16:58.339Z"}, {"entity": "publication", "iuid": "df755f6aabf14e52986ce130ba2707c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df755f6aabf14e52986ce130ba2707c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df755f6aabf14e52986ce130ba2707c6"}}, "title": "Evaluation of a diagnostic metagenomic sequencing assay: Virus detection sensitivity and background nucleic acids in three different sample materials.", "authors": [{"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Mahani", "given": "Amir Nematollahi", "initials": "AN"}, {"family": "Aralaguppe", "given": "Shambhu Ganeshappa", "initials": "SG"}, {"family": "Normark", "given": "Tanja", "initials": "T"}, {"family": "Stamouli", "given": "Sofia", "initials": "S"}, {"family": "Andersson-Li", "given": "Lili", "initials": "L"}, {"family": "Sun", "given": "Dan", "initials": "D"}, {"family": "Broddesson", "given": "Sandra", "initials": "S"}, {"family": "Wirta", "given": "Valtteri", "initials": "V"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK"}, {"family": "Albert", "given": "Jan", "initials": "J"}, {"family": "Allander", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2025-10-20", "journal": {"title": "J. Clin. Virol.", "issn": "1873-5967", "volume": "181", "pages": "105882", "issn-l": "1386-6532"}, "abstract": "Metagenomic sequencing has emerged as an attractive, general, and agnostic diagnostic method, in particular for detection of viruses. However, its application faces limitations, including reduced sensitivity due to background nucleic acid content of samples, and the search for an optimized protocol is still ongoing.\n\nWe report the development of a metagenomic sequencing protocol for diagnostic use and its performance in detecting DNA and RNA viruses in three different sample materials: serum, cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS).\n\nSensitivity was higher for RNA viruses than for DNA viruses, and also higher in CSF than in serum and lowest in NPS. We characterized the background nucleic acids and found higher DNA than RNA levels in CSF and serum and overall highest nucleic acid levels in NPS, intermediate in serum and lowest in CSF. These differences largely explained the observed variability in sensitivity between sample preparations and sample materials.\n\nOur results highlight the need to consider sample-type specific characteristics in efforts to improve the sensitivity of metagenomic assays e.g. via host depletion protocols.", "doi": "10.1016/j.jcv.2025.105882", "pmid": "41161015", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S1386-6532(25)00124-6"}], "notes": [], "created": "2025-11-18T20:46:44.915Z", "modified": "2025-11-18T20:51:03.337Z"}, {"entity": "publication", "iuid": "d39af32e394d4cf1a1835ee46edffd2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d39af32e394d4cf1a1835ee46edffd2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d39af32e394d4cf1a1835ee46edffd2d"}}, "title": "Pan-Cancer Detection Through DNA Methylation Profiling Using Enzymatic Conversion Library Preparation with Targeted Sequencing.", "authors": [{"family": "Qvick", "given": "Alvida", "initials": "A", "orcid": "0000-0001-6688-947X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4be159eaa724d22982b7b1e24e9ba79.json"}}, {"family": "Adolfsson", "given": "Emma", "initials": "E", "orcid": "0000-0002-7954-0696", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c790fe832ec4bf68608578c0c9d4552.json"}}, {"family": "Torn\u00e9us", "given": "Lina", "initials": "L"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Carlsson", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8457-7592", "researcher": {"href": "https://publications.scilifelab.se/researcher/529469b7e1fa4bccadbea444d1e9fcd4.json"}}, {"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}, {"family": "Karlsson", "given": "Christina", "initials": "C", "orcid": "0000-0002-4669-1367", "researcher": {"href": "https://publications.scilifelab.se/researcher/166381bbbbc947cd8f5178f70df9602d.json"}}, {"family": "Helenius", "given": "Gisela", "initials": "G", "orcid": "0000-0003-2317-5738", "researcher": {"href": "https://publications.scilifelab.se/researcher/2994acfdacff45ceb9c6b29aae2148c7.json"}}], "type": "journal article", "published": "2025-10-19", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "20", "issn-l": null}, "abstract": "We investigated differences in circulating cell-free DNA (cfDNA) methylation between patients with cancer and those presenting with severe, nonspecific symptoms. Plasma cfDNA from 229 patients was analyzed, of whom 37 were diagnosed with a wide spectrum of cancer types within 12 months. Samples underwent enzymatic conversion, library preparation, and enrichment using the NEBNext workflow and Twist pan-cancer methylation panel, followed by sequencing. Methylation analysis was performed with nf-core/methylseq. Differentially methylated regions (DMRs) were identified with DMRichR. Machine learning with cross-validation was used to classify cancer and controls. The classifier was applied to an external validation set of 144 controls previously unseen by the model. Cancer samples showed higher overall CpG methylation than controls (1.82% vs. 1.34%, p < 0.001). A total of 162 DMRs were detected, 95.7% being hypermethylated in cancer. Machine learning identified 20 key DMRs for classification between cancer and controls. The final model achieved an AUC of 0.88 (83.8% sensitivity, 83.8% specificity), while mean cross-validation performance reached an AUC of 0.73 (57.1% sensitivity, 77.5% specificity). The specificity of the classifier on unseen control samples was 79.2%. Distinct methylation differences and DMR-based classification support cfDNA methylation as a robust biomarker for cancer detection in patients with confounding conditions.", "doi": "10.3390/ijms262010165", "pmid": "41155454", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12564489"}, {"db": "pii", "key": "ijms262010165"}], "notes": [], "created": "2025-11-19T15:16:19.361Z", "modified": "2025-11-19T15:16:19.949Z"}, {"entity": "publication", "iuid": "a67c5743740447bcbba2abfcda523262", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a67c5743740447bcbba2abfcda523262.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a67c5743740447bcbba2abfcda523262"}}, "title": "Glycoalkaloid-Free Starch Potatoes Generated by CRISPR/Cas9-Mediated Mutations of Genes in the Glycoalkaloid Biosynthesis Pathway Enable More Sustainable Uses of By-Products From Starch Production.", "authors": [{"family": "Liu", "given": "Ying", "initials": "Y", "orcid": "0000-0001-8826-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6294480fc9c49c494776dab3f9cd0ef.json"}}, {"family": "Merino", "given": "Irene", "initials": "I", "orcid": "0000-0002-9418-7157", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cba6cd99cb542c1bb36db80b8113eed.json"}}, {"family": "Gutensohn", "given": "Mareike", "initials": "M", "orcid": "0009-0002-4706-547X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d710e21fabb4462591baa1bb0a49db51.json"}}, {"family": "Johansson", "given": "Annika I", "initials": "AI", "orcid": "0000-0001-5000-1288", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b0835b94db946929c1cb0c8f9319068.json"}}, {"family": "Johansson", "given": "Kalle", "initials": "K", "orcid": "0009-0002-3465-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/23927b98997748ec8f17599baf7dea3f.json"}}, {"family": "Andersson", "given": "Mariette", "initials": "M", "orcid": "0000-0002-9769-5288", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed10b2742ea94f43ba535ce6b424255f.json"}}, {"family": "Hofvander", "given": "Per", "initials": "P", "orcid": "0000-0003-1048-2608", "researcher": {"href": "https://publications.scilifelab.se/researcher/80db51f10c8f4179aba3c621098b65b7.json"}}, {"family": "Sitbon", "given": "Folke", "initials": "F", "orcid": "0000-0002-6852-069X", "researcher": {"href": "https://publications.scilifelab.se/researcher/15ceb60e3b0f4d97b1a167db8c090f99.json"}}], "type": "journal article", "published": "2025-10-18", "journal": {"title": "Plant Biotechnol. J.", "issn": "1467-7652", "issn-l": "1467-7644"}, "abstract": "Steroidal glycoalkaloids (SGAs) are toxic cholesterol-derived secondary metabolites present in several Solanaceae species. In potato, tuber SGA levels are for reasons of toxicity of concern in both table and starch cultivars. In the latter, SGAs bind to proteins and fibres in starch production side-streams and prevent their further uses as food and feed. To enable more sustainable uses of starch by-products, we have here reduced SGA biosynthesis in a starch potato cultivar using DNA-free CRISPR/Cas9. Six SGA genes were targeted, encoding enzymes acting either before cholesterol (SMO1-L, DWF1-L, DWF7-L), or after (16DOX, CYP88B1, TAMiso2). Editing efficiencies varied between 20% and 49%, and generated mutants were investigated under greenhouse and field conditions. Target mass-spectrometric analyses confirmed reduced SGA levels and alterations of sterol metabolism in mutated events. Plant height and tuber yield were reduced in several events, although this was not correlated to low SGA levels. Several knockout mutants had almost SGA-free leaves and tubers, the latter also under two SGA-inducing conditions. Similarly, both fibre and protein fractions isolated from side-streams in the starch production process from mutant tubers had very low SGA levels. By contrast, the corresponding wild-type SGA levels were almost 10-fold and, respectively, 40-fold higher than the recommended upper safe limit. The results demonstrate that glycoalkaloid-free mutants can be generated and grown with moderate yield reductions under both greenhouse and field conditions. This suggests a potential for sustainable production of high-value products, e.g., food-grade protein and fibre, from starch production side-streams of SGA knockout tubers.", "doi": "10.1111/pbi.70412", "pmid": "41108596", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-18T12:03:34.024Z", "modified": "2025-11-18T12:03:34.488Z"}, {"entity": "publication", "iuid": "fa1f2b26ed3949e2bdbd3c28dd0edf08", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa1f2b26ed3949e2bdbd3c28dd0edf08.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa1f2b26ed3949e2bdbd3c28dd0edf08"}}, "title": "Cryo-EM structure of CLCA1 identifies CLCA1 as a founding member of a novel metzincin family", "authors": [{"family": "Nystr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0002-6970-7894", "researcher": {"href": "https://publications.scilifelab.se/researcher/09bd302f8a1341f6a1a5aaf3bfe94a94.json"}}, {"family": "van der Post", "given": "Sjoerd", "initials": "S", "orcid": "0000-0002-7965-5311", "researcher": {"href": "https://publications.scilifelab.se/researcher/26adc68875cb4cb08bcf969868b42890.json"}}, {"family": "Barrett", "given": "Doireann Bradley", "initials": "DB"}, {"family": "Raba", "given": "Grete", "initials": "G", "orcid": "0000-0002-7764-3878", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9c5c71873aa4992bec09f9f6aabba5c.json"}}, {"family": "Pelaseyed", "given": "Thaher", "initials": "T", "orcid": "0000-0002-6434-3913", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dc0aa3d9762420caa7efaaa19c1174b.json"}}, {"family": "Oltean", "given": "Mihai", "initials": "M", "orcid": "0000-0003-3783-5207", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a46e232d2644afbe9a4f3d89316a7a.json"}}, {"family": "Luis", "given": "Ana S", "initials": "AS", "orcid": "0000-0002-5086-7353", "researcher": {"href": "https://publications.scilifelab.se/researcher/06abcf6fc3584357afbd80d6537fdd48.json"}}, {"family": "Trillo-Muyo", "given": "Sergio", "initials": "S", "orcid": "0000-0002-3135-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e6b6b830e9145a2ae3e6c10895acbee.json"}}], "type": "posted-content", "published": "2025-10-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.10.18.683246", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-12T10:07:24.335Z", "modified": "2026-01-12T10:07:24.558Z"}, {"entity": "publication", "iuid": "d2a2d6d880234ac78144a60503cbbe20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2a2d6d880234ac78144a60503cbbe20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2a2d6d880234ac78144a60503cbbe20"}}, "title": "Ultrafast, remote-controlled protonation reaction enables structural changes in a phytochrome.", "authors": [{"family": "Shankar", "given": "Madan Kumar", "initials": "MK", "orcid": "0000-0002-7944-1081", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd956823ccdf480a8f079fbc11a6815a.json"}}, {"family": "Grunewald", "given": "Lukas", "initials": "L", "orcid": "0009-0006-2976-8680", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfc954183b184d28b1de95594ab07564.json"}}, {"family": "Wahlgren", "given": "Weixiao Yuan", "initials": "WY", "orcid": "0000-0003-0413-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/18c55c12fa894dffa8f95f325affa529.json"}}, {"family": "Stucki-Buchli", "given": "Brigitte", "initials": "B", "orcid": "0000-0002-6756-0665", "researcher": {"href": "https://publications.scilifelab.se/researcher/7755ea9da8ee490fa808a0ff505406c6.json"}}, {"family": "Nimmrich", "given": "Amke", "initials": "A", "orcid": "0000-0003-0425-2101", "researcher": {"href": "https://publications.scilifelab.se/researcher/72e8a83ab0cb4d7dad20f00784045ba4.json"}}, {"family": "Kurttila", "given": "Moona", "initials": "M"}, {"family": "Fischer", "given": "Anna-Lena", "initials": "AL", "orcid": "0009-0009-3310-5021", "researcher": {"href": "https://publications.scilifelab.se/researcher/979212c2ef024d249845258e2b322f0e.json"}}, {"family": "Salvadori", "given": "Giacomo", "initials": "G", "orcid": "0000-0001-7330-6228", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f6eae0cdb9e45f99874d6bd200b81c6.json"}}, {"family": "Cellini", "given": "Andrea", "initials": "A"}, {"family": "Maj", "given": "Piotr", "initials": "P", "orcid": "0000-0002-9832-2344", "researcher": {"href": "https://publications.scilifelab.se/researcher/70b8070ad9c349aa875c84d6e101c97a.json"}}, {"family": "Anindya", "given": "Atsarina Larasati", "initials": "AL"}, {"family": "Claesson", "given": "Elin", "initials": "E", "orcid": "0000-0001-8232-7725", "researcher": {"href": "https://publications.scilifelab.se/researcher/10fe8a3b1cc3431384cd9dbe7c9e3865.json"}}, {"family": "Luo", "given": "Fangjia", "initials": "F", "orcid": "0000-0003-0631-6236", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c5507f74fe84eee866fdf2ee3a82b44.json"}}, {"family": "Malla", "given": "Tek Narsingh", "initials": "TN", "orcid": "0000-0002-1387-0801", "researcher": {"href": "https://publications.scilifelab.se/researcher/800976e6911240d080bbf9602f26ce7c.json"}}, {"family": "Pandey", "given": "Suraj", "initials": "S", "orcid": "0000-0002-7097-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d34f3408e14d3a9bd538656c3220ab.json"}}, {"family": "Tosha", "given": "Takehiko", "initials": "T", "orcid": "0000-0002-8971-0759", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1075f4e3f1d4966bee737cea1060f75.json"}}, {"family": "Nipawan", "given": "Nuemket", "initials": "N"}, {"family": "Owada", "given": "Shigeki", "initials": "S", "orcid": "0000-0002-1451-7612", "researcher": {"href": "https://publications.scilifelab.se/researcher/78948368f25e4fffba5f79203efb84d9.json"}}, {"family": "Tono", "given": "Kensuke", "initials": "K", "orcid": "0000-0003-1218-3759", "researcher": {"href": "https://publications.scilifelab.se/researcher/3afc0496078b4d719b0653069800e667.json"}}, {"family": "Tanaka", "given": "Rie", "initials": "R", "orcid": "0000-0003-1062-4792", "researcher": {"href": "https://publications.scilifelab.se/researcher/69908679d76c42d6ad9aa42264c60de0.json"}}, {"family": "Stojkovi\u0107", "given": "Emina A", "initials": "EA", "orcid": "0000-0002-4971-5213", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e203482fbc54cbbbcd4a712f6184dd9.json"}}, {"family": "Mozorov", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9524-948X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fce1c5072a0a445f918e621e23e4687b.json"}}, {"family": "Myllyperki\u00f6", "given": "Pasi", "initials": "P", "orcid": "0000-0003-1651-1676", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e10ceedb7594f5698b53af01f444a21.json"}}, {"family": "Kumpulainen", "given": "Tatu", "initials": "T", "orcid": "0000-0001-9469-9294", "researcher": {"href": "https://publications.scilifelab.se/researcher/e94b734da6774d0fb880f361b50892e9.json"}}, {"family": "Takala", "given": "Heikki", "initials": "H", "orcid": "0000-0003-2518-8583", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf65baa23c3349caa07bc0f44cb52d88.json"}}, {"family": "Schmidt", "given": "Marius", "initials": "M", "orcid": "0000-0002-0962-9468", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e24cc255b246e8a44c52d4002eb46c.json"}}, {"family": "Ihalainen", "given": "Janne A", "initials": "JA", "orcid": "0000-0002-8741-1587", "researcher": {"href": "https://publications.scilifelab.se/researcher/4730f17c203e496bb52a8812767bf37b.json"}}, {"family": "Westenhoff", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-6961-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1519bb234b43c6a13833b04e6720b8.json"}}], "type": "journal article", "published": "2025-10-17", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "42", "pages": "eady0499", "issn-l": "2375-2548"}, "abstract": "In photoactive proteins, coupling between the chromophore and protein matrix is exquisitely tuned. Proton transfer reactions can mediate this coupling, as in proton-coupled electron transfer and excited-state proton transfer. Additional mechanisms involving proton dislocations may exist but remain undiscovered. Here, we present a femtosecond crystallographic movie of the phytochrome from Deinococcus radiodurans. The structures reveal a space-conserving mechanism for rotation of the D-ring in the excited state. We observe rearrangement of a conserved hydrogen bond network within 300 fs, which precedes the isomerization reaction of the chromophore. Aided by molecular modeling and independently confirmed by femtosecond infrared spectroscopy, we attribute these changes to a protonation shift of the strictly conserved histidine-260. Although this histidine lies close to the photoexcited \u03c0-orbitals of the chromophore, it is not directly part of them. We propose that this \"remote-controlled\" proton transfer relays photoexcitation near-instantaneously to the protein matrix. This mechanism may be widely used to transduce cofactor signals to their hosting enzymes.", "doi": "10.1126/sciadv.ady0499", "pmid": "41105772", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12533598"}], "notes": [], "created": "2025-11-28T10:51:47.654Z", "modified": "2025-11-28T10:51:48.542Z"}, {"entity": "publication", "iuid": "d9c76d2925724acb9c140d062e9a55ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9c76d2925724acb9c140d062e9a55ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9c76d2925724acb9c140d062e9a55ad"}}, "title": "Symbiont Diversity of Rice-Associated Leafhoppers (Cicadellidae) in the Tropical Floodplains of the Tonle Sap Lake, Cambodia.", "authors": [{"family": "Phauk", "given": "Sophany", "initials": "S", "orcid": "0000-0002-8019-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/80bf701bd9c14bd08c081d49b0d6ecad.json"}}, {"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Sin", "given": "Sopha", "initials": "S"}, {"family": "Uk", "given": "Onnorong", "initials": "O"}, {"family": "Hap", "given": "Sophorn", "initials": "S"}, {"family": "Terenius", "given": "Olle", "initials": "O", "orcid": "0000-0002-9909-1859", "researcher": {"href": "https://publications.scilifelab.se/researcher/3042a807e20d444cafee3f760c38d5d1.json"}}], "type": "journal article", "published": "2025-10-17", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "88", "issue": "1", "pages": "109", "issn-l": "0095-3628"}, "abstract": "Rice-associated leafhoppers (Cicadellidae) play a significant role in rice agroecosystems, contributing not only to direct crop damage but also to the transmission of plant pathogens. This study investigates the symbiont diversity of seventeen leafhopper species from the tropical floodplains of Tonle Sap Lake (TSL), Cambodia. The dominant symbiont across most species was Candidatus (Ca.) Karelsulcia muelleri, an obligate primary endosymbiont essential for nutrient synthesis. The co-obligate symbiont Ca. Nasuia deltocephalinicola was also consistently detected, particularly in Deltocephalinae hosts. In addition, several secondary symbionts, including Sodalis, Arsenophonus, Diplorickettsia, Rickettsia, Wolbachia, and Ca. Lariskella, were identified, showing species-specific associations and potential roles in host fitness and pathogen transmission. Variations in symbiont diversity were observed across cicadellid species, geographic origins, and between sex-associated symbionts, with notable differences in the bacterial composition of Nephotettix virescens. While geographical differences (Battambang vs. Kampong Thom) did not strongly affect microbial composition, sex-associated variations were evident in N. virescens. Females exhibited a higher abundance of Karelsulcia and Nasuia, suggesting possible microbial adaptation related to reproduction. This study highlights the complex and dynamic nature of cicadellid hosts-symbiont interactions and suggests that microbial communities are primarily structured by host species. While geographic distance can influence these communities, this effect is not the same for every species. These findings provide critical insights into the microbial diversity of rice-associated leafhoppers and their potential for ecological roles in rice farming systems. Further studies, including functional analysis and host-symbiont interactions, are crucial to understanding the ecological roles and evolutionary dynamics of these microbial communities.", "doi": "10.1007/s00248-025-02619-9", "pmid": "41105260", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12534257"}, {"db": "pii", "key": "10.1007/s00248-025-02619-9"}], "notes": [], "created": "2025-11-07T07:26:53.717Z", "modified": "2025-11-28T10:41:02.912Z"}, {"entity": "publication", "iuid": "261b0843fccf4712a18fb2b1182b7e69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/261b0843fccf4712a18fb2b1182b7e69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/261b0843fccf4712a18fb2b1182b7e69"}}, "title": "Recommendations for bioinformatics in clinical practice.", "authors": [{"family": "Lavrichenko", "given": "Ksenia", "initials": "K"}, {"family": "Engdal", "given": "Emilie Sofie", "initials": "ES"}, {"family": "Marvig", "given": "Rasmus L", "initials": "RL"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Vignes", "given": "Jone Marius", "initials": "JM"}, {"family": "Almusa", "given": "Henrikki", "initials": "H"}, {"family": "Saether", "given": "Kristine Bilgrav", "initials": "KB"}, {"family": "Briem", "given": "Eir\u00edkur", "initials": "E"}, {"family": "Caceres", "given": "Eva", "initials": "E"}, {"family": "Elvarsd\u00f3ttir", "given": "Edda Mar\u00eda", "initials": "EM"}, {"family": "G\u00edslason", "given": "Magn\u00fas Halld\u00f3r", "initials": "MH"}, {"family": "Haanp\u00e4\u00e4", "given": "Maria K", "initials": "MK"}, {"family": "Henmyr", "given": "Viktor", "initials": "V"}, {"family": "Hotakainen", "given": "Ronja", "initials": "R"}, {"family": "Kaasinen", "given": "Eevi", "initials": "E"}, {"family": "Kanninga", "given": "Roan", "initials": "R"}, {"family": "Khan", "given": "Sofia", "initials": "S"}, {"family": "Lie-Nielsen", "given": "Mary Gertrude", "initials": "MG"}, {"family": "Madsen", "given": "Majbritt Busk", "initials": "MB"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Maqbool", "given": "Khurram", "initials": "K"}, {"family": "Neethiraj", "given": "Ramprasad", "initials": "R"}, {"family": "Nyr\u00e9n", "given": "Karl", "initials": "K"}, {"family": "Paavola", "given": "Minna", "initials": "M"}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Sheng", "given": "Ying", "initials": "Y"}, {"family": "Singh", "given": "Ashish Kumar", "initials": "AK"}, {"family": "Srivastava", "given": "Aashish", "initials": "A"}, {"family": "Stautland", "given": "Thomas K", "initials": "TK"}, {"family": "Andreasen", "given": "Daniel T", "initials": "DT"}, {"family": "de Boer", "given": "Esmee Ten Berk", "initials": "ETB"}, {"family": "Vang", "given": "S\u00f8ren", "initials": "S"}, {"family": "Wirta", "given": "Valtteri", "initials": "V"}, {"family": "Bagger", "given": "Frederik Otzen", "initials": "FO"}], "type": "journal article", "published": "2025-10-17", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "17", "issue": "1", "pages": "124", "issn-l": "1756-994X"}, "abstract": "Next-generation sequencing (NGS) is well established in clinical diagnostics, and whole-genome sequencing (WGS) is increasingly becoming the method of choice, as a result of lower prices and robust comprehensive data. While guidelines exist for variant interpretation and laboratory quality considerations, there remains a need for standardised bioinformatics practices to ensure clinical consensus, accuracy, reproducibility and comparability.\n\nThis article presents consensus recommendations developed by 13 clinical bioinformatics units participating in the Nordic Alliance for Clinical Genomics (NACG) by expert bioinformaticians working in clinical production. The recommendations are based on clinical practice and focus on analysis types, test and validation, standardisation and accreditation, as well as core competencies and technical management required for clinical bioinformatics operations.\n\nKey recommendations include adopting the hg38 genome build as reference, and a standard set of recommended analyses, including the use of multiple tools for structural variant (SV) calling and in-house data sets for filtering recurrent calls. Clinical bioinformatics in production should operate at standards similar to ISO 15189, utilising off-grid clinical-grade high-performance computing systems, standardised file formats and strict version control. Reproducibility should be ensured through containerised software environments. Pipelines must be documented and tested for accuracy and reproducibility, minimally covering unit, integration and end-to-end testing. Standard truth sets such as GIAB and SEQC2 for germline and somatic variant calling, respectively, should be supplemented by recall testing of real human samples that have been previously tested using a validated method. Data integrity must be verified using file hashing, while sample identity must be confirmed through fingerprinting and genetically inferred identification markers such as sex and relatedness. Finally, clinical bioinformatics should encompass diverse skills, including software development, data management, quality assurance and domain expertise in human genetics.\n\nThese recommendations provide a consensus framework for standardising bioinformatics practices across clinical WGS applications and can serve as a practical guide to facilities that are new to large-scale sequencing-based diagnostics, or as a reference for those who already run high-volume clinical production using NGS.", "doi": "10.1186/s13073-025-01543-4", "pmid": "41107899", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics Ume\u00e5": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12535132"}, {"db": "pii", "key": "10.1186/s13073-025-01543-4"}], "notes": [], "created": "2025-11-26T09:16:18.557Z", "modified": "2025-11-26T09:16:18.579Z"}, {"entity": "publication", "iuid": "48bf48701cf44883bb1fe87945bf952b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48bf48701cf44883bb1fe87945bf952b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48bf48701cf44883bb1fe87945bf952b"}}, "title": "Prodan-based solvatochromic probes for polarity imaging of organelles", "authors": [{"family": "Aknine", "given": "Nathan", "initials": "N"}, {"family": "Holban", "given": "Paula", "initials": "P"}, {"family": "Ragaller", "given": "Franziska", "initials": "F", "orcid": "0000-0002-4148-262X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ead87aca17f476b9febf3f020567c4b.json"}}, {"family": "Carravilla", "given": "Pablo", "initials": "P", "orcid": "0000-0001-6592-7630", "researcher": {"href": "https://publications.scilifelab.se/researcher/b791a8068a724c179b731f0446b1737a.json"}}, {"family": "Gurdap", "given": "Cenk O", "initials": "CO", "orcid": "0000-0002-5327-2523", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e3e5501e8d84f46884f1001367ab262.json"}}, {"family": "Cetinkaya", "given": "Agit", "initials": "A"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Klymchenko", "given": "Andrey S", "initials": "AS", "orcid": "0000-0002-2423-830X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e5109394fec48b4a38f382ad62d7d31.json"}}], "type": "posted-content", "published": "2025-10-17", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.10.17.683001", "pmid": null, "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2025-10-21T09:38:09.353Z", "modified": "2025-12-18T19:01:18.923Z"}, {"entity": "publication", "iuid": "3026cc0df25b4c178a58bdb7ba158810", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3026cc0df25b4c178a58bdb7ba158810.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3026cc0df25b4c178a58bdb7ba158810"}}, "title": "Reduced vascular leakage correlates with breast carcinoma T regulatory cell infiltration but not with metastatic propensity.", "authors": [{"family": "He", "given": "Liqun", "initials": "L", "orcid": "0000-0002-4743-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6e2e4c7f88845bb895842e56a7622ae.json"}}, {"family": "Testini", "given": "Chiara", "initials": "C"}, {"family": "Hekmati", "given": "Neda", "initials": "N", "orcid": "0009-0009-4814-869X", "researcher": {"href": "https://publications.scilifelab.se/researcher/59e525846f61401ab94732e578190274.json"}}, {"family": "Bonello", "given": "Altea", "initials": "A"}, {"family": "Schiza", "given": "Aglaia", "initials": "A"}, {"family": "Nwadozi", "given": "Emmanuel", "initials": "E"}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Welsh", "given": "Michael", "initials": "M", "orcid": "0000-0002-5467-9755", "researcher": {"href": "https://publications.scilifelab.se/researcher/c01673aeb9be429c80da30d5407b2725.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "issn-l": "1574-7891"}, "abstract": "The vasculature and the immune system both play roles in breast cancer progression and metastasis. In an experimental mouse model of Shb-gene deficiency in endothelial cells, breast cancer lung metastasis correlated with immune suppression rather than with vascular leakage. The present study aimed to assess underlying gene expression changes in endothelial and immune cells responsible for this phenotype and to explore their relationship to human disease. Mouse endothelial cell Shb-gene deficiency, leading to 'vessel normalization', resulted in altered expression of chemo/cytokine genes and upregulation of immune checkpoint genes in immune cells. Endothelial cells under these conditions exhibited gene expression patterns compatible with reduced angiogenesis and vascular leakage. Additionally, genes whose products relate to immune cell vascular transmigration and function were affected. In a human triple-negative breast cancer cohort, tumors with reduced vascular leakage exhibited a higher relative proportion of regulatory T cells and larger tumor size. However, these changes were not associated with increased metastasis. In conclusion, a low leakage vascular phenotype reduces tumor cell intravasation/metastasis and modifies the immune response, which in the current context becomes pro-tumoral.", "doi": "10.1002/1878-0261.70144", "pmid": "41102920", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:23:33.643Z", "modified": "2025-11-13T17:36:03.258Z"}, {"entity": "publication", "iuid": "afb960cb22864dd38a6d8ae590cc4341", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afb960cb22864dd38a6d8ae590cc4341.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afb960cb22864dd38a6d8ae590cc4341"}}, "title": "Evaluating cell-specific gene expression using single-cell and single-nuclei RNA-sequencing data from human pancreatic islets of the same donors.", "authors": [{"family": "Engstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Nilsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Ofori", "given": "Jones K", "initials": "JK", "orcid": "0000-0001-6484-1544", "researcher": {"href": "https://publications.scilifelab.se/researcher/31b7b1843fd94a99b488eaf653c6385b.json"}}, {"family": "Wierup", "given": "Nils", "initials": "N"}, {"family": "Bacos", "given": "Karl", "initials": "K", "orcid": "0000-0002-2461-9073", "researcher": {"href": "https://publications.scilifelab.se/researcher/527a271d23de48f8937b489c43e9da1b.json"}}, {"family": "Ling", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-0587-7154", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7c1ea934034c4db99f31a5a9b04691.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "36133", "issn-l": "2045-2322"}, "abstract": "Single-cell and single-nuclei RNA-sequencing (scRNA-seq and snRNA-seq) analyze cell-specific transcriptomes. However, only snRNA-seq applies to frozen biobanked samples. For human pancreatic islets, marker genes and reference-based cell type annotation methods are mainly from scRNA-seq datasets and may not be suitable for snRNA-seq. We compared human islet scRNA-seq and snRNA-seq data from the same donors (N = 4) and evaluated annotation methods by studying cell type composition and gene detection, and identified novel marker genes. We compared cell type annotations: (1) manual annotation based on identified marker genes, (2) reference-based annotation using Azimuth's scRNA-seq pancreasref dataset, or (3) Seurat's label transfer from the Human Pancreas Analysis Program (HPAP) scRNA-seq dataset. ScRNA-seq and snRNA-seq identified the same cell types, but predicted cell type proportions differed. Cell type proportion-differences between annotation methods were larger for snRNA-seq. Reference-based annotations generated higher cell type prediction and mapping scores for scRNA-seq than snRNA-seq. Manual annotation identified the novel snRNA-seq markers DOCK10, KIRREL3 (beta cells), STK32B (alpha cells), MECOM, AC007368.1 (acinar cells), LAMC2 and SLC28A3 (ductal cells), which improve snRNA-seq-based annotation. We confirmed ZNF385D as a snRNA-seq beta cell marker and ZNF385D silencing reduced insulin secretion. In conclusion, this study discovered novel snRNA-seq cell type marker genes in human pancreatic islets, and highlights the need for tailored snRNA-seq annotation strategies.", "doi": "10.1038/s41598-025-21595-1", "pmid": "41102292", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12533216"}, {"db": "pii", "key": "10.1038/s41598-025-21595-1"}], "notes": [], "created": "2025-10-30T13:58:54.553Z", "modified": "2025-11-13T17:36:11.555Z"}, {"entity": "publication", "iuid": "d575a85bd2934bef9ca095b8f3b877ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d575a85bd2934bef9ca095b8f3b877ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d575a85bd2934bef9ca095b8f3b877ec"}}, "title": "Do 6-9-Year-Old Children in Denmark Adhere to National Dietary Recommendations and Are There Sociodemographic Disparities? The Generation Healthy Kids Study", "authors": [{"family": "Holmegaard", "given": "Frederik", "initials": "F"}, {"family": "Eilersen", "given": "Anna Gro", "initials": "AG"}, {"family": "Lauritzen", "given": "Lotte", "initials": "L"}, {"family": "M\u00f8lgaard", "given": "Christian", "initials": "C"}, {"family": "Liu", "given": "Ming Rong", "initials": "MR"}, {"family": "Stark", "given": "Ken D", "initials": "KD"}, {"family": "Landberg", "given": "Rikard", "initials": "R", "orcid": "0000-0002-6399-7608", "researcher": {"href": "https://publications.scilifelab.se/researcher/4472ec17986146d1a095acdb202815e6.json"}}, {"family": "Kr\u00f8lner", "given": "Rikke Fredenslund", "initials": "RF"}, {"family": "Toft", "given": "Ulla", "initials": "U"}, {"family": "Trab", "given": "Camilla", "initials": "C"}], "type": "posted-content", "published": "2025-10-16", "journal": {"title": "res sq", "issn": "2693-5015", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.21203/rs.3.rs-7741373/v1", "pmid": null, "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-12-01T05:42:33.027Z", "modified": "2025-12-22T07:55:29.957Z"}, {"entity": "publication", "iuid": "76bc40380dd544cdaf4932e9eb027c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/76bc40380dd544cdaf4932e9eb027c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/76bc40380dd544cdaf4932e9eb027c93"}}, "title": "Distribution of photosensitive fagopyrin in buckwheat flowers and its potential biological relevance.", "authors": [{"family": "Horny\u00e1k", "given": "Marta", "initials": "M"}, {"family": "Kula-Maximenko", "given": "Monika", "initials": "M"}, {"family": "Miszalski", "given": "Zbigniew", "initials": "Z"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "G\u00f6ransson", "given": "Ulf", "initials": "U"}, {"family": "Slazak", "given": "Blazej", "initials": "B"}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "36279", "issn-l": "2045-2322"}, "abstract": "Fagopyrum esculentum (Moench) is a valuable pseudo-cereal valued for its highly nutritious, gluten-free seeds. Despite being recognized as a 21st -century superfood, buckwheat remains non-competitive in seed yield compared to common cereals. Low productivity is mainly caused by abnormalities in female gametophyte development and frequent flower and embryo abortion. Buckwheat flowers accumulate high levels of phototoxic fagopyrin (FAG), whose physiological role remains unclear. FAG and its precursor (PFAG) are light-sensitive compounds with absorbance spectra in the green-yellow range (549-593 nm, peak at 590 nm), which makes their accumulation potentially responsive to light conditions. To address this, plants were cultivated under different light spectra, and the content of FAG and PFAG was analyzed in distinct floral organs (stamen, pistil, petal, and receptacle) using LC-MS, with their spatial distribution assessed by the MALDI-MS imaging. Pistil showed statistically the highest FAG and PFAG contents, while petals contained the lowest levels. A high density of FAG surrounding the ovary indicates a potential role in the reproductive part. Moreover, negative correlations were detected between flower production and FAG levels in the receptacles and pistils under specific light treatments. These results suggest that FAG may influence flower production and female gametophyte development, linking light environment to reproductive success in buckwheat.", "doi": "10.1038/s41598-025-20116-4", "pmid": "41102249", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12533014"}, {"db": "pii", "key": "10.1038/s41598-025-20116-4"}], "notes": [], "created": "2025-11-21T09:46:16.328Z", "modified": "2025-11-21T09:46:16.332Z"}, {"entity": "publication", "iuid": "d621c8dfa56a43f7a5840112b6226276", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d621c8dfa56a43f7a5840112b6226276.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d621c8dfa56a43f7a5840112b6226276"}}, "title": "Association of estrogen receptor single nucleotide polymorphisms and perinatal depression.", "authors": [{"family": "Bj\u00f6rvang", "given": "Richelle Duque", "initials": "RD", "orcid": "0000-0002-3619-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed3a5bfc2fab4fe4a9c83f44007431e1.json"}}, {"family": "Gumbo", "given": "Lulu Francis", "initials": "LF"}, {"family": "\u00c5rdahl", "given": "Anders", "initials": "A"}, {"family": "Lager", "given": "Susanne", "initials": "S"}, {"family": "Comasco", "given": "Erika", "initials": "E", "orcid": "0000-0002-2174-2068", "researcher": {"href": "https://publications.scilifelab.se/researcher/83fe689667824167ac7cf6a058b5e150.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A", "orcid": "0000-0002-4935-7532", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d12fb448f9241b2841a8dce8cb42560.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "10", "pages": "e0334705", "issn-l": "1932-6203"}, "abstract": "Depression during pregnancy and in the postpartum period have been receiving increasing attention considering the possible complications for the mother and baby if left untreated. Genetic variations in the estrogen receptor genes (ESR) have been implicated in susceptibility to depression. However, only few studies investigated them in perinatal depression (PND) and none on its different trajectories (i.e., patterns of time of onset and persistency of depression). Here, we explored the association of single nucleotide polymorphisms (SNPs) of the ESR1 and ESR2 genes with PND among 2,973 women in Sweden. PND was defined using the Edinburgh Postnatal Depression Scale, the Depression Self-Rating Scale, use of selective serotonin reuptake inhibitor, and/or medical records. PND trajectories were identified as follows: controls (no depression at any point in the perinatal period), antepartum (depression during pregnancy and resolved postpartum), postpartum-onset (no depression during pregnancy with onset after delivery), and persistent (depression throughout the perinatal period). Multivariable logistic regression was performed. Out of 56 SNPs analyzed, one SNP in the ESR1 gene (rs2982712) was nominally significantly associated with PND (OR 0.83, 95% CI 0.71-0.98, p = 0.03) as well as with persistent depression (OR 0.77, 95% CI 0.61-0.98, p = 0.03) in the overdominant model (DD/dd vs. Dd). In addition, we also found two SNPs, namely rs1884051 (OR 0.74, 95% CI 0.56-0.98, p = 0.03) and rs2228480 (OR 0.77, 95% CI 0.60-0.99, p = 0.04) in the ESR1 gene, that were nominally significantly associated with persistent depression only. None of the ESR1 SNPs were associated with antepartum or postpartum-onset depression. None of the ESR2 SNPs, nor any haplotypes, were associated with PND or its trajectories. Our findings suggest a role of ESR1 in PND, especially its persistent trajectory.", "doi": "10.1371/journal.pone.0334705", "pmid": "41100533", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12530586"}, {"db": "pii", "key": "PONE-D-24-49872"}], "notes": [], "created": "2025-11-07T07:23:59.861Z", "modified": "2025-11-07T07:24:00.268Z"}, {"entity": "publication", "iuid": "eaf9b454889b42e98966f350d0a69e84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84"}}, "title": "A mosaic of modular variation at a single gene underpins convergent plumage coloration.", "authors": [{"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Chase", "given": "Madeline A", "initials": "MA", "orcid": "0000-0002-7916-3560", "researcher": {"href": "https://publications.scilifelab.se/researcher/3053121df4b64418bc1dcc2d7e50d87c.json"}}, {"family": "Kakhki", "given": "Niloofar Alaei", "initials": "NA"}, {"family": "Lammers", "given": "Fritjof", "initials": "F", "orcid": "0000-0002-3110-8220", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a13a19d3594543a30c5146011aaa3a.json"}}, {"family": "de Souza", "given": "Stacey G", "initials": "SG", "orcid": "0000-0001-6596-5522", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b19ded18de4742b8b0e63408500bc7.json"}}, {"family": "Ducrest", "given": "Anne-Lyse", "initials": "AL", "orcid": "0000-0001-6412-2769", "researcher": {"href": "https://publications.scilifelab.se/researcher/020a4c63ac834ff1a09234094ff552d2.json"}}, {"family": "Burri", "given": "Marta", "initials": "M"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8407f9cb79440d80f580cef8536175.json"}}, {"family": "Lukhele", "given": "Sifiso M", "initials": "SM", "orcid": "0000-0003-0638-0641", "researcher": {"href": "https://publications.scilifelab.se/researcher/67a4a265644e452898bd89600ca081d8.json"}}, {"family": "Moysi", "given": "Michaella", "initials": "M"}, {"family": "Yohannes", "given": "Elizabeth", "initials": "E"}, {"family": "Abbasov", "given": "Abdin", "initials": "A", "orcid": "0009-0002-6370-9167", "researcher": {"href": "https://publications.scilifelab.se/researcher/de8b1ae2193849cc956e9750bfc47ead.json"}}, {"family": "Albayrak", "given": "Tamer", "initials": "T", "orcid": "0000-0003-4115-3946", "researcher": {"href": "https://publications.scilifelab.se/researcher/36f1ec59f0da42d89af256efda6c7db5.json"}}, {"family": "Aliabadian", "given": "Mansour", "initials": "M", "orcid": "0000-0002-3200-4853", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf133d36d2ec42bba680538cd5e69151.json"}}, {"family": "Auchli", "given": "Nicolas", "initials": "N"}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebafa22103ec46ab87ce2b5fa878519d.json"}}, {"family": "Christoforou", "given": "Ioulios", "initials": "I"}, {"family": "Copete", "given": "Jos\u00e9 Luis", "initials": "JL", "orcid": "0000-0001-8542-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/e18b36757e804e0fb00a2f13015e79b6.json"}}, {"family": "Fulco", "given": "Egidio", "initials": "E"}, {"family": "Garcia", "given": "Jesus T", "initials": "JT"}, {"family": "Javakhishvili", "given": "Zura", "initials": "Z", "orcid": "0000-0001-7587-4974", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15c16f36f8d407d8b3c69723f6470e2.json"}}, {"family": "Kazazou", "given": "Anna", "initials": "A", "orcid": "0009-0003-6518-8833", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdef2602fe44fd98f1b36f83acde23a.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Paposhvili", "given": "Nika", "initials": "N"}, {"family": "Patchett", "given": "Robert", "initials": "R", "orcid": "0000-0003-4105-3136", "researcher": {"href": "https://publications.scilifelab.se/researcher/787404ed66114f6ca1df945d9110ca8a.json"}}, {"family": "P\u00e9ter", "given": "\u00c1ron", "initials": "\u00c1", "orcid": "0000-0003-3219-9344", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b840805e45a4e0e95ade7ce7d0bdb99.json"}}, {"family": "Ritter", "given": "Raphael", "initials": "R", "orcid": "0009-0000-3060-1622", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b0db805e7214250b7df8d01e0803641.json"}}, {"family": "S\u00e1ndor", "given": "Attila D", "initials": "AD", "orcid": "0000-0001-8852-8341", "researcher": {"href": "https://publications.scilifelab.se/researcher/6db813f6be6943cc93dfbb9222bd112f.json"}}, {"family": "Schneider", "given": "Fabian", "initials": "F"}, {"family": "Shurulinkov", "given": "Petar", "initials": "P"}, {"family": "Sklyarenko", "given": "Sergey", "initials": "S", "orcid": "0000-0002-7443-347X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0de4c8591f1b4929ae73d3ea81ca2c17.json"}}, {"family": "Stumberger", "given": "Borut", "initials": "B"}, {"family": "Tagiyev", "given": "Abulfaz", "initials": "A"}, {"family": "Uboldi", "given": "Alessia", "initials": "A", "orcid": "0009-0001-3940-3697", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c73538105e441eb6a5402ad0883799.json"}}, {"family": "Vogiatzis", "given": "Nikitas", "initials": "N", "orcid": "0009-0008-9592-923X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9be0f74759fd4d429c3cb891c51d6e83.json"}}, {"family": "Taborsak-Lines", "given": "Fanny", "initials": "F"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Yao", "given": "Liqun", "initials": "L"}, {"family": "Peichel", "given": "Catherine L", "initials": "CL", "orcid": "0000-0002-7731-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b4d7c680f69458dbde56257ff4820c5.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Gagnaire", "given": "Pierre-Alexandre", "initials": "PA", "orcid": "0000-0002-1908-3235", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f9487cea1d40938b3f9f00f72e6433.json"}}, {"family": "Kirschel", "given": "Alexander N G", "initials": "ANG", "orcid": "0000-0003-4379-7956", "researcher": {"href": "https://publications.scilifelab.se/researcher/d533e6378c094ef7bf44e570bcbb1145.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Science", "issn": "1095-9203", "volume": "390", "issue": "6770", "pages": "eado8005", "issn-l": "0036-8075"}, "abstract": "The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and their interplay with genetic architecture remain scarce. We show that convergent plumage color evolution in wheatears involves a monogenic architecture with modular variation introgressed at the agouti signaling protein (ASIP) locus. Introgression of a new transposable element insertion and linked protein-coding variation underpin a transspecific throat color polymorphism, which stable isotopes suggest is associated with alternative foraging niches. Cointrogression of linked regulatory ASIP variation resulted in mantle color convergence in one species, whereas convergent color evolution at the genus level required new variation. Our results demonstrate evolutionary trajectories from introgressed variation realized within the constraints of a monogenic architecture.", "doi": "10.1126/science.ado8005", "pmid": "41100596", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-26T14:53:27.788Z", "modified": "2026-01-26T14:53:31.469Z"}, {"entity": "publication", "iuid": "cb92a5fa72ae4cd6953839297ce2af22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb92a5fa72ae4cd6953839297ce2af22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb92a5fa72ae4cd6953839297ce2af22"}}, "title": "A generative deep learning approach to de novo antibiotic design.", "authors": [{"family": "Krishnan", "given": "Aarti", "initials": "A"}, {"family": "Anahtar", "given": "Melis N", "initials": "MN"}, {"family": "Valeri", "given": "Jacqueline A", "initials": "JA"}, {"family": "Jin", "given": "Wengong", "initials": "W"}, {"family": "Donghia", "given": "Nina M", "initials": "NM"}, {"family": "Sieben", "given": "Leif", "initials": "L"}, {"family": "Luttens", "given": "Andreas", "initials": "A"}, {"family": "Zhang", "given": "Yu", "initials": "Y"}, {"family": "Modaresi", "given": "Seyed Majed", "initials": "SM"}, {"family": "Hennes", "given": "Andrew", "initials": "A"}, {"family": "Fromer", "given": "Jenna", "initials": "J"}, {"family": "Bandyopadhyay", "given": "Parijat", "initials": "P"}, {"family": "Chen", "given": "Jonathan C", "initials": "JC"}, {"family": "Rehman", "given": "Danyal", "initials": "D"}, {"family": "Desai", "given": "Ronak", "initials": "R"}, {"family": "Edwards", "given": "Paige", "initials": "P"}, {"family": "Lach", "given": "Ryan S", "initials": "RS"}, {"family": "Aschtgen", "given": "Marie-St\u00e9phanie", "initials": "MS"}, {"family": "Gaborieau", "given": "Margaux", "initials": "M"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M"}, {"family": "Palace", "given": "Samantha G", "initials": "SG"}, {"family": "Omori", "given": "Satotaka", "initials": "S"}, {"family": "Khonde", "given": "Lutete", "initials": "L"}, {"family": "Moroz", "given": "Yurii S", "initials": "YS"}, {"family": "Blough", "given": "Bruce", "initials": "B"}, {"family": "Jin", "given": "Chunyang", "initials": "C"}, {"family": "Loh", "given": "Edmund", "initials": "E"}, {"family": "Grad", "given": "Yonatan H", "initials": "YH"}, {"family": "Saei", "given": "Amir Ata", "initials": "AA"}, {"family": "Coley", "given": "Connor W", "initials": "CW"}, {"family": "Wong", "given": "Felix", "initials": "F"}, {"family": "Collins", "given": "James J", "initials": "JJ"}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "188", "issue": "21", "pages": "5962-5979.e22", "issn-l": "0092-8674"}, "abstract": "The antimicrobial resistance crisis necessitates structurally distinct antibiotics. While deep learning approaches can identify antibacterial compounds from existing libraries, structural novelty remains limited. Here, we developed a generative artificial intelligence framework for designing de novo antibiotics through two approaches: a fragment-based method to comprehensively screen >107 chemical fragments in silico against Neisseria gonorrhoeae or Staphylococcus aureus, subsequently expanding promising fragments, and an unconstrained de novo compound generation, each using genetic algorithms and variational autoencoders. Of 24 synthesized compounds, seven demonstrated selective antibacterial activity. Two lead compounds exhibited bactericidal efficacy against multidrug-resistant isolates with distinct mechanisms of action and reduced bacterial burden in vivo in mouse models of N. gonorrhoeae vaginal infection and methicillin-resistant S. aureus skin infection. We further validated structural analogs for both compound classes as antibacterial. Our approach enables the generative deep-learning-guided design of de novo antibiotics, providing a platform for mapping uncharted regions of chemical space.", "doi": "10.1016/j.cell.2025.07.033", "pmid": "40816267", "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)00855-4"}], "notes": [], "created": "2025-11-25T16:41:24.655Z", "modified": "2025-11-25T16:41:24.698Z"}, {"entity": "publication", "iuid": "a303b58b4fa1409b9589100fef20ee82", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a303b58b4fa1409b9589100fef20ee82.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a303b58b4fa1409b9589100fef20ee82"}}, "title": "Postnatal sustentacular cells as chromaffin progenitors and tumor cells of origin in VHL-related paragangliomas.", "authors": [{"family": "Bullova", "given": "Petra", "initials": "P"}, {"family": "Cui", "given": "Peng", "initials": "P"}, {"family": "Arceo", "given": "Maria", "initials": "M"}, {"family": "Zhu", "given": "Jiacheng", "initials": "J"}, {"family": "Li", "given": "Wenyu", "initials": "W"}, {"family": "Plescher", "given": "Monika", "initials": "M"}, {"family": "Poltorachenko", "given": "Valentin", "initials": "V"}, {"family": "Stripling", "given": "Katerina", "initials": "K"}, {"family": "Santangeli", "given": "Christian", "initials": "C"}, {"family": "Mykhaylechko", "given": "Lidiya", "initials": "L"}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME"}, {"family": "Larsson", "given": "Catharina", "initials": "C"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC"}, {"family": "Mints", "given": "Michael", "initials": "M"}, {"family": "Schlisio", "given": "Susanne", "initials": "S"}], "type": "journal article", "published": "2025-10-15", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "324", "issn-l": null}, "abstract": "The cellular source of chromaffin cell regeneration after birth and its relationship to paraganglioma tumorigenesis remains incompletely defined. Here, we identify a postnatal population of SOX2/SOX10-expressing sustentacular glia-like cells in the organ of Zuckerkandl (OZ) and adrenal gland that give rise to chromaffin cells in vivo. These cells differ transcriptionally from embryonic chromaffin progenitors known as Schwann cell precursors and exhibit a unique progenitor signature. Genetic lineage tracing confirms their postnatal contribution to chromaffin cells, and SOX2+PHOX2B+ transitional cells were observed in both human and mouse OZ and adrenal tissues. Single-nuclei RNA-seq and inferCNA analysis of pheochromocytoma and paraganglioma (PPGL) revealed that while most sustentacular cells exhibit a stromal profile, a subset in VHL-mutated PPGLs harbor the hallmark 3p chromosomal loss shared with chief tumor cells, suggesting a clonal origin. In an additional PPGL, widespread SOX2 expression in PHOX2B+ tumor cells supports this hypothesis. Finally, DLK1-NOTCH signaling was predicted as a central regulator of chromaffin-sustentacular communication, suggesting DLK1 fine-tunes chromaffin regeneration via NOTCH inhibition and may represent a therapeutic target in PPGL.", "doi": "10.1038/s41698-025-01145-8", "pmid": "41093965", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12528426"}, {"db": "pii", "key": "10.1038/s41698-025-01145-8"}], "notes": [], "created": "2025-11-21T13:44:18.484Z", "modified": "2025-11-28T10:47:30.359Z"}, {"entity": "publication", "iuid": "19581b230d654071a511b9c7c910bc48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19581b230d654071a511b9c7c910bc48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19581b230d654071a511b9c7c910bc48"}}, "title": "Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem.", "authors": [{"family": "Serrana", "given": "Joeselle M", "initials": "JM", "orcid": "0000-0002-6967-5407", "researcher": {"href": "https://publications.scilifelab.se/researcher/d042aa918de14e1bb1403a00779c0160.json"}}, {"family": "Dessirier", "given": "Beno\u00eet", "initials": "B", "orcid": "0000-0002-2261-4279", "researcher": {"href": "https://publications.scilifelab.se/researcher/76223b9a5bd34863a822d5e8f8242540.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}, {"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Posselt", "given": "Malte", "initials": "M", "orcid": "0000-0001-8979-8044", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1b4854ced5246e8a3b79d6ab03cdde1.json"}}], "type": "journal article", "published": "2025-10-15", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "13", "issue": "1", "pages": "204", "issn-l": "2049-2618"}, "abstract": "The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds.\n\nKnown hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (> 10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea.\n\nUsing metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Video Abstract.", "doi": "10.1186/s40168-025-02211-w", "pmid": "41094699", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12529799"}, {"db": "pii", "key": "10.1186/s40168-025-02211-w"}], "notes": [], "created": "2025-11-28T10:53:27.712Z", "modified": "2025-11-28T10:53:27.740Z"}, {"entity": "publication", "iuid": "165f00ce0fe84f9eb4e29f6e334ae2d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/165f00ce0fe84f9eb4e29f6e334ae2d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/165f00ce0fe84f9eb4e29f6e334ae2d4"}}, "title": "Comparable area under the curve for three risk scores to detect interstitial lung disease in patients with rheumatoid arthritis: an external validation.", "authors": [{"family": "Blomberg", "given": "Elin", "initials": "E"}, {"family": "Wahlin", "given": "Bengt", "initials": "B", "orcid": "0000-0002-0893-2326", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3803ea52b234fa8a2ef8f3aef5fb3b7.json"}}, {"family": "S\u00f6dergren", "given": "Anna", "initials": "A", "orcid": "0000-0002-7436-7900", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d220b832fb45889249c243b179540f.json"}}], "type": "journal article", "published": "2025-10-15", "journal": {"title": "Rheumatol. Int.", "issn": "1437-160X", "volume": "45", "issue": "11", "pages": "252", "issn-l": "0172-8172"}, "abstract": "Rheumatoid Arthritis associated Interstitial Lung Disease (RA-ILD) is an extraarticular manifestation of rheumatoid arthritis (RA) associated with increased morbidity and mortality. Several risk factors for RA-ILD have been identified, one is the promotor variant of mucin 5 B gene (MUC5B). Juge et al., Wheeler et al. and Koduri et al. have developed risk scores for identifying patients with RA at risk of RA-ILD. We aimed to externally validate the three risk scores and further investigate the frequency of MUC5B promotor variant and its association with subclinical lung changes in patients with RA in northern Sweden. Our cohort consisted of 54 patients with RA. The risk score variables were evaluated in binary logistic regression and validated using area under the receiver operating characteristics curve (AUC ROC). The genetic material was purified and genotyped for MUC5B. The Juge et al. risk score performed an AUC ROC of 0.71 (95% CI 0.57;0.86), the Wheeler et al. risk score an AUC ROC of 0.75 (95% CI 0.59;0.90) and Koduri et al. risk score an AUC ROC of 0.70 ((95% CI 0.55;0.85) in our cohort. The differences in AUC were not statistically significant. The MUC5B promotor variant frequency was 26% (n = 14). In our cohort, MUC5B was not significantly associated with subclinical lung changes. The three externally validated risk scores for RA-ILD performed well in this cohort and could be used clinically. In patients with RA in northern Sweden, MUC5B was not found to be independently associated with subclinical RA-ILD.", "doi": "10.1007/s00296-025-06005-z", "pmid": "41091209", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12528251"}, {"db": "pii", "key": "10.1007/s00296-025-06005-z"}], "notes": [], "created": "2025-11-26T09:18:48.425Z", "modified": "2025-11-26T09:18:48.540Z"}, {"entity": "publication", "iuid": "73fee7c76bfd49a6944ca090feb04ef1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73fee7c76bfd49a6944ca090feb04ef1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73fee7c76bfd49a6944ca090feb04ef1"}}, "title": "Structure of the central Staphylococcus aureus AAA+ protease MecA/ClpC/ClpP.", "authors": [{"family": "Azinas", "given": "Stavros", "initials": "S", "orcid": "0000-0002-3744-9229", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ec0cb5b5df4b4f89780ce3a08efc89.json"}}, {"family": "Wallden", "given": "Karin", "initials": "K"}, {"family": "Katikaridis", "given": "Panagiotis", "initials": "P"}, {"family": "Jenne", "given": "Timo", "initials": "T", "orcid": "0009-0001-2033-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a27284b457b4d84b7104cfc0a3d989c.json"}}, {"family": "Schahl", "given": "Adrien", "initials": "A", "orcid": "0000-0001-5839-7715", "researcher": {"href": "https://publications.scilifelab.se/researcher/91c1503f32d64435a8df615d167a5c6f.json"}}, {"family": "Mogk", "given": "Axel", "initials": "A", "orcid": "0000-0003-3674-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/56a1d7fc519743029c9ae615086d8093.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}], "type": "journal article", "published": "2025-10-14", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "1467", "issn-l": "2399-3642"}, "abstract": "Bacterial AAA+ proteases are composed of a AAA+ partner (e.g., ClpC) and an associated peptidase (e.g., ClpP). They represent ATP-fuelled and self-compartmentalized proteolytic machines that are crucial for stress resistance and virulence. ClpC requires cooperation with adaptor proteins such as MecA for activation and complex formation with ClpP. Here, we present the cryo-EM structure of the MecA/ClpC/ClpP complex from the major pathogen Staphylococcus aureus. MecA forms a dynamic crown on top of the ClpC/ClpP complex with its substrate-binding domain positioned near the ClpC pore site, likely facilitating substrate transfer. ClpC/ClpP complex formation involves ClpC P-loops and ClpP N-terminal \u03b2-hairpins, which insert into the central ClpC threading channel and contact sites next to the ClpC ATPase center. ClpC and ClpP interactions are asymmetric and dictated by the activity states of ClpC ATPase subunits. ClpP binding increases ClpC ATPase and threading activities in a \u03b2-hairpin dependent manner, illuminating an allosteric pathway in the cooperation of ATPase and peptidase components in bacterial AAA+ proteases.", "doi": "10.1038/s42003-025-08908-w", "pmid": "41087538", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12521514"}, {"db": "pii", "key": "10.1038/s42003-025-08908-w"}], "notes": [], "created": "2025-10-25T10:21:15.566Z", "modified": "2025-10-25T10:21:15.656Z"}, {"entity": "publication", "iuid": "62196b2aeaf64cffbdc15583c03cd12a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62196b2aeaf64cffbdc15583c03cd12a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62196b2aeaf64cffbdc15583c03cd12a"}}, "title": "Deciphering the determinants of recombinant protein expression across the human secretome.", "authors": [{"family": "Masson", "given": "Helen O", "initials": "HO"}, {"family": "Di Giusto", "given": "Pablo", "initials": "P", "orcid": "0000-0003-1024-1222", "researcher": {"href": "https://publications.scilifelab.se/researcher/443c70edc8054e5c972eea27e8e71883.json"}}, {"family": "Kuo", "given": "Chih-Chung", "initials": "CC"}, {"family": "Malm", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-1763-9073", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c4c6c276dd64fe2abe27da888cd0925.json"}}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Sievertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Grassi", "given": "Luigi", "initials": "L", "orcid": "0000-0002-6308-7540", "researcher": {"href": "https://publications.scilifelab.se/researcher/c006b891dedd483e8f01756f73fd6fb0.json"}}, {"family": "Robasky", "given": "Kimberly", "initials": "K", "orcid": "0000-0002-0090-8698", "researcher": {"href": "https://publications.scilifelab.se/researcher/16439af864534d3bb025acbb1edb933b.json"}}, {"family": "Hsieh", "given": "Chen-Lin", "initials": "CL", "orcid": "0009-0000-9239-8711", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7175e63f7d84a99ac3a2f0b1c49cf88.json"}}, {"family": "Hatton", "given": "Diane", "initials": "D", "orcid": "0000-0002-6600-021X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a947736bdbe4177a909782cea719df8.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ad1d3b1313460583a16329a0143a1d.json"}}, {"family": "Lewis", "given": "Nathan E", "initials": "NE", "orcid": "0000-0001-7700-3654", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8b8fb6dee874a178dd5c9d10d280982.json"}}], "type": "journal article", "published": "2025-10-14", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "41", "pages": "e2506036122", "issn-l": "0027-8424"}, "abstract": "Protein secretion is an essential process of mammalian cells. In biomanufacturing, this process can be optimized to enhance production yields and biotherapeutic quality. While cell line engineering and bioprocess optimization have yielded high protein titers for some recombinant proteins, many remain difficult to express. Here, we investigated factors influencing protein expression in Chinese hamster ovary (CHO) cells, expressing 2,135 Human Secretome Project proteins. While the abundance of mRNA from recombinant proteins explained less than 1% of observed variation in secretion titers, analysis of 218 biochemical and biophysical descriptors uncovered intrinsic protein features that account for ~15% of secretion variability, pinpointing key drivers such as molecular weight, cysteine content, and N-linked glycosylation, and establishing a roadmap for rational design of difficult-to-express proteins. We subsequently analyzed RNA-Seq data from 95 CHO cell cultures, each expressing a distinct recombinant protein, spanning a wide range of titers. Host cell transcriptomic signatures showed strong correlations with titer, thereby providing insights into cellular processes that covary with expression. Cells failing to produce proteins exhibited increased ubiquitin-mediated proteasomal degradation, including ER-associated degradation; whereas high-producing cells demonstrated enhanced lipid metabolism and a stronger response to oxidative stress, suggesting these factors may support successful recombinant protein productions. Together, using this resource, we quantified the contributions of various protein and cellular factors that correlate with the expression of diverse recombinant human proteins in a heterologous host, thereby providing insights for next-generation CHO cell engineering.", "doi": "10.1073/pnas.2506036122", "pmid": "41055974", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2109099"}, {"db": "pmc", "key": "PMC12541331"}], "notes": [], "created": "2025-11-21T09:55:14.036Z", "modified": "2025-11-21T09:55:15.142Z"}, {"entity": "publication", "iuid": "9d8e02af163b4c1abdc334d1ce8fb886", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d8e02af163b4c1abdc334d1ce8fb886.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d8e02af163b4c1abdc334d1ce8fb886"}}, "title": "Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity.", "authors": [{"family": "Henriques-Oliveira", "given": "Lu\u00eds", "initials": "L"}, {"family": "Altman", "given": "Abigail R", "initials": "AR"}, {"family": "Kurochkin", "given": "Ilia", "initials": "I"}, {"family": "Ascic", "given": "Ervin", "initials": "E"}, {"family": "Halitzki", "given": "Evelyn", "initials": "E"}, {"family": "Matei", "given": "Andreea-Medeea", "initials": "AM"}, {"family": "P\u00e9rtiga-Cabral", "given": "Diogo", "initials": "D"}, {"family": "Ulmert", "given": "Isabel", "initials": "I"}, {"family": "Holst", "given": "Signe", "initials": "S"}, {"family": "Nair", "given": "Malavika Sreekumar", "initials": "MS"}, {"family": "Cunha", "given": "Pedro P", "initials": "PP"}, {"family": "Park", "given": "Sun-Mi", "initials": "SM"}, {"family": "Vergani", "given": "Stefano", "initials": "S"}, {"family": "Kharas", "given": "Michael G", "initials": "MG"}, {"family": "Yuan", "given": "Joan", "initials": "J"}, {"family": "Lahl", "given": "Katharina", "initials": "K"}, {"family": "Rosa", "given": "F\u00e1bio F", "initials": "FF"}, {"family": "Pires", "given": "Cristiana F", "initials": "CF"}, {"family": "Pereira", "given": "Carlos-Filipe", "initials": "CF"}], "type": "journal article", "published": "2025-10-14", "journal": {"title": "Immunity", "issn": "1097-4180", "volume": "58", "issue": "10", "pages": "2419-2438.e13", "issn-l": "1074-7613"}, "abstract": "Transcription factor cooperation is essential for specifying the heterogeneous dendritic cell (DC) lineages that orchestrate adaptive immunity, yet how it drives subset diversification remains poorly understood. Here, we employed a sequential anchored screen of 70 transcription factors using direct cellular reprogramming to identify regulators that specify type 2 conventional DCs (cDC2s) and plasmacytoid DCs (pDCs). We identified PU.1, IRF4, and PRDM1 as inducers of a pro-inflammatory cDC2B-like fate and SPIB, IRF8, and IKZF2 as mediators of an immature lymphoid DC program. Transcriptomic profiling linked these triads to lineage-specific signatures and demonstrated their requirement for subset identity. Mechanistically, lineage divergence was driven by chromatin co-engagement at subset-specific sites early in reprogramming. Functionally, reprogrammed DCs employed distinct immune mechanisms to elicit orthogonal anti-tumor responses in different tumor models. Collectively, our findings uncover transcriptional circuits that control DC diversification and pave the way to generate patient-tailored DC subsets for cancer immunotherapy.", "doi": "10.1016/j.immuni.2025.08.001", "pmid": "40885192", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(25)00335-8"}], "notes": [], "created": "2025-11-17T07:37:31.694Z", "modified": "2025-11-17T07:37:31.699Z"}, {"entity": "publication", "iuid": "4df4dd95abb74e42ae0ea7f5cb9438d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4df4dd95abb74e42ae0ea7f5cb9438d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4df4dd95abb74e42ae0ea7f5cb9438d1"}}, "title": "Tick-borne encephalitis virus associated with foetal death in a bitch, a case report.", "authors": [{"family": "Holst", "given": "Bodil Str\u00f6m", "initials": "BS"}, {"family": "Bonnevie", "given": "Anna", "initials": "A"}, {"family": "Spens", "given": "Jennifer", "initials": "J"}, {"family": "Lindahl", "given": "Johanna F", "initials": "JF"}, {"family": "Huupponen", "given": "Anna", "initials": "A"}, {"family": "Syrj\u00e4", "given": "Pernilla", "initials": "P"}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "Virol J", "issn": "1743-422X", "volume": "22", "issue": "1", "pages": "326", "issn-l": "1743-422X"}, "abstract": "For the first time, a case of vertical transmission of TBEV in a dog associated with foetal death is described.\n\nA six-year-old beagle bitch experienced foetal death from day 49 in pregnancy. A caesarean section was performed on day 56, and one live and three dead pups in different stages of resorption were delivered. Black mucoid, non-smelling foetal membranes surrounded the dead foetuses. The live-born foetus died despite efforts to save it and was sent for autopsy together with the placenta. Autopsy demonstrated lung atelectasis and no malformations. A mild acute necrotizing placentitis was diagnosed on histopathology. Selective bacteriological cultures for Brucella canis from blood, vagina and the foetus were all negative, as was PCR for canine herpes virus (CHV). Viral metagenomics analysis identified the presence of tick-borne encephalitis virus (TBEV) in the placental tissue and in situ hybridization revealed TBEV in the trophoblasts. The bitch had antibodies to TBEV. One year later, the bitch had a normal pregnancy and whelping.\n\nWith the spread of both ticks and TBEV, infection with TBEV should be given further consideration as a potential differential diagnosis in cases of foetal death in dogs.", "doi": "10.1186/s12985-025-02965-7", "pmid": "41083999", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12519796"}, {"db": "pii", "key": "10.1186/s12985-025-02965-7"}], "notes": [], "created": "2025-11-28T10:52:55.106Z", "modified": "2025-11-28T10:52:55.115Z"}, {"entity": "publication", "iuid": "355af91bf856401ab8f7a654af8b92ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/355af91bf856401ab8f7a654af8b92ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/355af91bf856401ab8f7a654af8b92ad"}}, "title": "Multi-layered dosage compensation of the avian Z chromosome by increased transcriptional burst frequency and elevated translational rates.", "authors": [{"family": "Papanicolaou", "given": "Natali", "initials": "N", "orcid": "0000-0002-2931-3241", "researcher": {"href": "https://publications.scilifelab.se/researcher/439a0a25106742c893178f4151d71291.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications.scilifelab.se/researcher/e282901d24c64b16a540eff0d57776f4.json"}}, {"family": "Wettersten", "given": "Sebastian", "initials": "S"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Kr\u00fcger", "given": "Annika", "initials": "A", "orcid": "0000-0002-2482-0316", "researcher": {"href": "https://publications.scilifelab.se/researcher/74e46d93b561473189588abecdb96f93.json"}}, {"family": "Zhang", "given": "Jilin", "initials": "J", "orcid": "0000-0002-9976-1605", "researcher": {"href": "https://publications.scilifelab.se/researcher/b595931cc9c045dbbeb2dba7f3913d05.json"}}, {"family": "Coucoravas", "given": "Christos", "initials": "C"}, {"family": "Petrosian", "given": "Ioannis", "initials": "I"}, {"family": "Xin", "given": "Xian", "initials": "X", "orcid": "0000-0003-1460-5978", "researcher": {"href": "https://publications.scilifelab.se/researcher/612e837e68e44339b8a9a110beb38125.json"}}, {"family": "Ceyhan", "given": "Ilhan", "initials": "I", "orcid": "0009-0001-9504-6647", "researcher": {"href": "https://publications.scilifelab.se/researcher/c79c334d1b6747159586eca778e2f2df.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb82c502293d424cb266e1c4e405485f.json"}}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9088", "issn-l": "2041-1723"}, "abstract": "Sex-chromosome dosage poses a challenge for heterogametic species in maintaining the proper balance of gene products across chromosomes in each sex. While therian mammals (XX/XY system) achieve near-perfect balance of X-chromosome mRNAs through X-upregulation and X-inactivation, birds (ZW/ZZ system) have been found to lack efficient compensation at RNA level, challenging the necessity of resolving major gene-dosage asymmetries in avian cells. Through comprehensive allele-resolved multiome analyses, we examine dosage compensation in female (ZW), male (ZZ), and rare intersex (ZZW) chicken. Our data reveal that females upregulate their single Z chromosome through increased transcriptional burst frequency, mirroring mammalian X upregulation. Z-protein levels are further balanced in females through enhanced translation efficiency. Additionally, we present a global analysis of promoter elements regulating transcriptional burst kinetics in birds, revealing evolutionary conservation of the genomic encoding of burst kinetics between birds and mammals. Our study provides insights into the regulation of avian dosage compensation, and when considering all regulatory layers collectively, an unexpected similarity between avian and mammalian dosage compensation becomes apparent.", "doi": "10.1038/s41467-025-64817-w", "pmid": "41083481", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12518621"}, {"db": "pii", "key": "10.1038/s41467-025-64817-w"}], "notes": [], "created": "2025-12-08T12:39:47.612Z", "modified": "2025-12-08T12:39:48.467Z"}, {"entity": "publication", "iuid": "2fb54591262748e1980ea7e5b944dc9a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fb54591262748e1980ea7e5b944dc9a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fb54591262748e1980ea7e5b944dc9a"}}, "title": "Green Biorefinery Side Stream as a Source of Chlorophyll Pigments, Lignin, and Cellulose for Textile Fibers", "authors": [{"family": "Cid Gomes", "given": "Leandro", "initials": "L", "orcid": "0000-0001-6996-4105", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef128e0d47bd452ab1687fd4776a24f6.json"}}, {"family": "da Rosa Garcia", "given": "Andrieli", "initials": "A"}, {"family": "Raeisi", "given": "Ferdows", "initials": "F"}, {"family": "de Oliveira Barbosa", "given": "L\u00edvia Cristina", "initials": "LC"}, {"family": "Wasalabandara", "given": "Devsara", "initials": "D"}, {"family": "Panakkal Manuel", "given": "Anju", "initials": "A"}, {"family": "Skovborg", "given": "Nanna Lindgaard", "initials": "NL"}, {"family": "Hostrup", "given": "Emma Thonesen", "initials": "ET", "orcid": "0009-0004-9667-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/564536c3b87b47f9b539aa1f943de1a5.json"}}, {"family": "Wojtasz", "given": "Joanna", "initials": "J"}, {"family": "Gunnarsson", "given": "Maria", "initials": "M"}, {"family": "Ambye-Jensen", "given": "Morten", "initials": "M"}, {"family": "Bernin", "given": "Diana", "initials": "D", "orcid": "0000-0002-9611-2263", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad134b1d8ab41b8a8a3318801d92e10.json"}}], "type": "journal-article", "published": "2025-10-13", "journal": {"title": "ACS Sustainable Chem. Eng.", "issn": "2168-0485", "volume": "13", "issue": "40", "pages": "16946-16957", "issn-l": "2168-0485"}, "abstract": null, "doi": "10.1021/acssuschemeng.5c06653", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:06:29.752Z", "modified": "2025-11-27T08:06:29.971Z"}, {"entity": "publication", "iuid": "e79753171cfe4a2a9fd9b888316e8540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e79753171cfe4a2a9fd9b888316e8540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e79753171cfe4a2a9fd9b888316e8540"}}, "title": "Exposure to marine contaminant mixtures with different toxicity drivers reduces microzooplankton diversity.", "authors": [{"family": "J\u00f6nander", "given": "Christina", "initials": "C"}, {"family": "Egardt", "given": "Jenny", "initials": "J"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Spilsbury", "given": "Francis", "initials": "F"}, {"family": "Carmona", "given": "Eric", "initials": "E"}, {"family": "Inostroza", "given": "Pedro A", "initials": "PA"}, {"family": "Brack", "given": "Werner", "initials": "W"}, {"family": "Dahll\u00f6f", "given": "Ingela", "initials": "I", "orcid": "0000-0002-0777-5971", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c6230703491493eb35a7610d0299d8d.json"}}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "101", "issue": "11", "issn-l": "0168-6496"}, "abstract": "Marine surface waters contain complex mixtures of chemicals that can adversely affect microzooplankton. There is a lack of toxicity data for this organism group, and we used two different methodologies to fill this gap. We tested the toxicity of three chemical mixtures of polar organic chemicals extracted from marine surface water, using a component-based and a whole-mixture approach. The component-based approach estimates cumulative toxic units for each mixture based on concentrations of individual compounds. The observed hazard data for zooplankton was supplemented with ECOSAR-generated QSAR daphnid LC50s when observed data was missing. ECOSAR performance was evaluated for zooplankton, where 65% of the observed hazard data for zooplankton was predicted within a factor of 10. This approach suggested that none of the mixtures should be toxic to zooplankton at their respective measured environmental concentrations. We found contrasting results using the whole-mixture approach with a reduction in ciliates and dinoflagellates, and change in microzooplankton diversity, at the measured environmental concentrations. We suggest an assessment factor of at least 1000 when using additive toxic units in a component-based risk assessment approach to cover for the extrapolation from acute to chronic toxicity data and for the range of sensitivities among microzooplankton species.", "doi": "10.1093/femsec/fiaf102", "pmid": "41070938", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12551639"}, {"db": "pii", "key": "8280373"}], "notes": [], "created": "2025-11-28T10:48:55.458Z", "modified": "2025-12-05T12:21:44.926Z"}, {"entity": "publication", "iuid": "2df9d60e4f3b4842ab27975ddc213a7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2df9d60e4f3b4842ab27975ddc213a7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2df9d60e4f3b4842ab27975ddc213a7e"}}, "title": "Evolution of female ornamentation in dance flies: valuable gifts are worth dressing up for.", "authors": [{"family": "P\u00e4rssinen", "given": "Varpu", "initials": "V", "orcid": "0000-0002-9189-9765", "researcher": {"href": "https://publications.scilifelab.se/researcher/84abea496e734734a215964cf9e27782.json"}}, {"family": "Bussi\u00e8re", "given": "Luc F", "initials": "LF"}, {"family": "Wiberg", "given": "R Axel W", "initials": "RAW"}, {"family": "Wahlberg", "given": "Emma", "initials": "E"}, {"family": "LeBas", "given": "Natasha R", "initials": "NR"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Kvarnemo", "given": "Charlotta", "initials": "C", "orcid": "0000-0001-8983-2900", "researcher": {"href": "https://publications.scilifelab.se/researcher/914d1337967942d8a3790e47e5b5d86b.json"}}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "Evolution", "issn": "1558-5646", "issn-l": "0014-3820"}, "abstract": "Elaborate female ornaments are rare in nature. One explanation for this is that female investment in ornamentation may take away crucial resources from other costly life history traits, such as fecundity, for which there is likely to be a higher fitness return. However, this trade-off between ornaments and fecundity may be less severe in species where the males offer the female an edible nuptial gift during mating. The nutrition gained from mating may make attracting mates with elaborate ornaments more cost-effective for the female. We investigated this link in dance flies in which there is large variation in nuptial gifts, as well as female ornaments. Our phylogenetic analysis showed that nuptial gift value is positively associated with the evolution of female ornaments. We found that species which lack nuptial gifts have no ornaments, and high levels of female ornamentation has evolved most frequently in species with a reliable access to an edible nuptial gift with each mating. Our results also suggest that female ornaments have most likely evolved following the evolution of nuptial gifts. We argue that the added benefits from each mating have helped the females to overcome the costs associated with the development and maintenance of ornaments.", "doi": "10.1093/evolut/qpaf212", "pmid": "41081749", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "8284989"}], "notes": [], "created": "2025-12-05T11:34:02.049Z", "modified": "2025-12-05T11:34:02.317Z"}, {"entity": "publication", "iuid": "4b541203774f4f0f904e27c77dfb6ad1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b541203774f4f0f904e27c77dfb6ad1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b541203774f4f0f904e27c77dfb6ad1"}}, "title": "Association between pro-inflammatory proteins and neurofilament in plasma from persons with epilepsy.", "authors": [{"family": "Sarangdhar", "given": "Mayuresh", "initials": "M"}, {"family": "Akel", "given": "Sarah", "initials": "S"}, {"family": "Hosseini Ashtiani", "given": "Saman", "initials": "S"}, {"family": "Axelsson", "given": "Markus", "initials": "M"}, {"family": "Zelano", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "BMC Med", "issn": "1741-7015", "issn-l": "1741-7015", "volume": "23", "issue": "1", "pages": "554"}, "abstract": "Inflammation and neurodegeneration are emerging as pathophysiological processes of interest in epilepsy. Seizures can both arise from and induce inflammation and difficult-to-treat epilepsy is linked to brain atrophy. However, the interplay between inflammation and neurodegeneration remains poorly understood in epilepsy. This study investigates the association between inflammatory proteins and plasma neurofilament light chain (NEFL or NfL), a known marker of neurodegeneration, particularly in relation to active epilepsy.\r\n\r\nWe performed Olink proteomics on plasma from 176 epilepsy patients aged between 18 and 50 years. To assess systemic inflammation, a composite pro-inflammatory score was derived from the expression of 12 pro-inflammatory proteins. Patients were stratified based on pro-inflammatory score and NEFL and correlation between them was analyzed. Seizure frequency and drug resistance were assessed across patient subgroups.\r\n\r\nPro-inflammatory score and NEFL showed weak positive correlation (r = 0.1); not all patients with high levels of inflammation had high levels of NEFL. In the small proportion of patients (11%, n = 19) with high inflammation and elevated NEFL, seizures (Kruskal-Wallis test H = 9.68, p = 0.02) and drug-resistant epilepsy (\u03c72 = 13.47, p = 0.036, df = 6) were more common, whereas patients with low inflammation and normal NEFL (31.8%, n = 56) tended to have well-controlled epilepsy. Moreover, patients with high inflammation and abnormal NEFL showed protein changes suggestive of potential blood-brain barrier disruption and leukocyte migration.\r\n\r\nInflammation and neurodegeneration are not necessarily linked in all epilepsy patients, but both are more likely to exist in the subset of cases with many seizures. Conversely, absence of both processes indicates well-controlled epilepsy. The combination of plasma NEFL with inflammatory markers could improve seizure prediction and provide novel insights for personalized epilepsy management.", "doi": "10.1186/s12916-025-04425-z", "pmid": "41083978", "labels": {"Affinity Proteomics Uppsala": "Service", "National Genomics Infrastructure": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12519617"}, {"db": "pii", "key": "10.1186/s12916-025-04425-z"}], "notes": [], "created": "2025-11-25T19:19:03.981Z", "modified": "2025-11-26T11:05:31.642Z"}, {"entity": "publication", "iuid": "27c01ae4cb064dd1a4a287d1e3d822aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27c01ae4cb064dd1a4a287d1e3d822aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27c01ae4cb064dd1a4a287d1e3d822aa"}}, "title": "Integrated biological and chemical wastewater surveillance reveals local changes in dynamics of human-associated virus, bacteria and chemicals", "authors": [{"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}, {"family": "Mukhedkar", "given": "Dhananjay", "initials": "D"}, {"family": "Dillner", "given": "Joakim", "initials": "J", "orcid": "0000-0001-8588-6506", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b5c258635ad412f9e79994dcee4e323.json"}}, {"family": "Pimenoff", "given": "Ville N", "initials": "VN", "orcid": "0000-0002-0813-7031", "researcher": {"href": "https://publications.scilifelab.se/researcher/96cbbc36d7214b94a798b4c63eeb6a3a.json"}}], "type": "posted-content", "published": "2025-10-09", "journal": {"title": "medrxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.10.08.25337484", "pmid": null, "labels": {"Exposomics": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-19T13:51:04.751Z", "modified": "2026-05-12T13:10:18.629Z"}, {"entity": "publication", "iuid": "20400326c0944ebda6e786a24f339e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26"}}, "title": "A human pan-disease blood atlas of the circulating proteome.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/648c9ed3483a4eb8a1d228cf7e59f6a7.json"}}, {"family": "Kenrick", "given": "Josefin", "initials": "J", "orcid": "0000-0002-0110-5192", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83beb37b7bc4e0aa84106bea7c6e0d0.json"}}, {"family": "Johansson", "given": "Emil", "initials": "E", "orcid": "0009-0003-1250-0678", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d953dd65ab24e8ab08aee7e7f101702.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Akyildiz", "given": "Murat", "initials": "M", "orcid": "0000-0002-2080-7528", "researcher": {"href": "https://publications.scilifelab.se/researcher/439d9835321449e4811478ad27c82a99.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Sk\u00f6ld", "given": "Hilda", "initials": "H", "orcid": "0009-0004-0961-4006", "researcher": {"href": "https://publications.scilifelab.se/researcher/bef5a1edbcab4c3286df2e2652d6f931.json"}}, {"family": "Antonopoulos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0003-2781-3872", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfd9fba645e64087a41f3bc7c3d35239.json"}}, {"family": "Apostolakis", "given": "Emmanouil", "initials": "E", "orcid": "0009-0003-6873-174X", "researcher": {"href": "https://publications.scilifelab.se/researcher/419cb52646134fe2bde5d6d700845708.json"}}, {"family": "Balcioglu", "given": "Yasin Hasan", "initials": "YH", "orcid": "0000-0002-1336-1724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4e7f3fd813e432b9a3e604a2cc26832.json"}}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0002-7981-6314", "researcher": {"href": "https://publications.scilifelab.se/researcher/70d058e4d5bc49d7a3c958950c9d4e6d.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S"}, {"family": "Brage", "given": "Suzanne Egyhazi", "initials": "SE"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Butler", "given": "Lynn", "initials": "L", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications.scilifelab.se/researcher/069263856386498c8262acf10587177c.json"}}, {"family": "Cajander", "given": "Sara", "initials": "S", "orcid": "0000-0003-3921-4244", "researcher": {"href": "https://publications.scilifelab.se/researcher/43cda9fcbe7141c9aa28d349176d21c8.json"}}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "Dayangac", "given": "Murat", "initials": "M", "orcid": "0000-0002-1240-7233", "researcher": {"href": "https://publications.scilifelab.se/researcher/a72ffcb2d31744c3ac1c4e5f2221be09.json"}}, {"family": "Dinler-Doganay", "given": "Gizem", "initials": "G", "orcid": "0000-0002-3586-1287", "researcher": {"href": "https://publications.scilifelab.se/researcher/d505e0932953412683b2e511a503d489.json"}}, {"family": "Do\u011fanay", "given": "Levent", "initials": "L"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Enblad", "given": "Malin", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Falck-Jones", "given": "Sara", "initials": "S"}, {"family": "F\u00e4rnert", "given": "Anna", "initials": "A", "orcid": "0000-0001-7583-282X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0543fb8f425844bcaf599f48292132a7.json"}}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Gunnarsson", "given": "Karin", "initials": "K", "orcid": "0000-0001-9986-8341", "researcher": {"href": "https://publications.scilifelab.se/researcher/943c35b7307848fbbf7ab5312aa0a432.json"}}, {"family": "Gunnarsson", "given": "Iva", "initials": "I", "orcid": "0000-0002-4514-7706", "researcher": {"href": "https://publications.scilifelab.se/researcher/90121ddba7fe4f928c1b121b162c2509.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": 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"0000-0002-9248-3294", "researcher": {"href": "https://publications.scilifelab.se/researcher/befeb12cfba142eb9dadf81497d6c419.json"}}, {"family": "Zeybel", "given": "Mujdat", "initials": "M", "orcid": "0000-0001-5440-4623", "researcher": {"href": "https://publications.scilifelab.se/researcher/0559b83985134a0a9283ea39601a95a7.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2025-10-09", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": null, "issue": null, "pages": "eadx2678"}, "abstract": "The human blood proteome provides a holistic readout of health states through the assessment of thousands of circulating proteins. Here, we present a pan-disease resource to enable the study of diverse disease phenotypes within a harmonized proteomics dataset. By profiling protein concentrations across 59 diseases and healthy cohorts, we identified proteins associated with age, sex, and BMI, as well as disease-specific signatures. This study highlights shared and distinct protein patterns across conditions, demonstrating the power of a unified proteomics approach to uncover biological insights. The dataset, covering 8,262 individuals and up to 5,416 proteins, serves as an online resource for exploring disease-specific protein profiles and advancing precision medicine research.", "doi": "10.1126/science.adx2678", "pmid": "41066540", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-10T10:37:22.942Z", "modified": "2025-11-07T07:45:07.446Z"}, {"entity": "publication", "iuid": "6d6faf7279134df68f3e4160a4981f61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61"}}, "title": "The genomic landscape of relapsed infant and childhood KMT2A-rearranged acute leukemia.", 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"given": "Varsha", "initials": "V"}, {"family": "Castor", "given": "Anders", "initials": "A", "orcid": "0009-0007-4634-0704", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed2d2dab933049f5b69cdf0ff1e1d8a1.json"}}, {"family": "Pronk", "given": "Cornelis Jan", "initials": "CJ", "orcid": "0000-0002-0073-9660", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e42ba48d824aa0b42e871e9f11b00a.json"}}, {"family": "Marquart", "given": "Hanne Vibeke", "initials": "HV", "orcid": "0000-0001-9740-6522", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9476b7116154ea9990d7c61c675c794.json"}}, {"family": "Lausen", "given": "Birgitte", "initials": "B", "orcid": "0000-0002-5306-0774", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc5eadc48e354c4cb70d68d420bfa6fe.json"}}, {"family": "Schneider", "given": "Pauline", "initials": "P", "orcid": "0000-0003-0162-9436", "researcher": {"href": 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"researcher": {"href": "https://publications.scilifelab.se/researcher/f39ff709aa0646b8ad5e520780a0ad49.json"}}, {"family": "Menendez", "given": "Pablo", "initials": "P"}, {"family": "Pieters", "given": "Rob", "initials": "R", "orcid": "0000-0003-2997-3570", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb567d1e17e0428c843c07682decb31c.json"}}, {"family": "Zhang", "given": "Jinghui", "initials": "J", "orcid": "0000-0003-3350-9682", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe8464634149a39bc8accf6077bac4.json"}}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}, {"family": "Yang", "given": "Jun J", "initials": "JJ", "orcid": "0000-0002-0770-9659", "researcher": {"href": "https://publications.scilifelab.se/researcher/023457113ddc4e3a8309d0b4936c097e.json"}}, {"family": "Gruber", "given": "Tanja A", "initials": "TA", "orcid": "0000-0003-1072-7257", "researcher": {"href": "https://publications.scilifelab.se/researcher/c16c5b66f56f40fd93a9f398b0487a64.json"}}, {"family": "Stam", "given": "Ronald W", "initials": "RW", "orcid": "0000-0003-4986-1656", "researcher": {"href": "https://publications.scilifelab.se/researcher/f528aaa6b3ba479f85619e1496e3f395.json"}}, {"family": "Ma", "given": "Jing", "initials": "J"}, {"family": "Hagstr\u00f6m-Andersson", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-2904-1311", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc93a87c663d471ba64fc3be63212a89.json"}}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "8964", "issn-l": "2041-1723"}, "abstract": "To study the mechanisms of relapse in KMT2A-rearranged (KMT2A-r) acute lymphoblastic (ALL) and acute myeloid leukemia (AML), we performed whole-genome and exome sequencing of infants and children with relapsed ALL/AML (n = 36), and longitudinal deep-sequencing of 257 samples in 30 patients. Somatic alterations in drug-response genes, most commonly in TP53 and IKZF1 (64%), were highly enriched in early relapse ALL (79%, 9-36 months after diagnosis), but rare in very early relapse ALL (<9 months, 9%). A marked chemotherapy-exposure signature was detected for mutations in early relapse ALL but not in very early ALL or AML relapse, in line with different mechanisms of relapse. Longitudinal analyses could track residual leukemia cells, clonal drug responses, and the upcoming relapse. These results highlight that KMT2A-r ALL and AML evade therapy differently and provide insights into the mechanisms of relapse in this highly lethal form of pediatric acute leukemia.", "doi": "10.1038/s41467-025-64190-8", "pmid": "41062506", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12508131"}, {"db": "pii", "key": "10.1038/s41467-025-64190-8"}], "notes": [], "created": "2025-10-28T09:43:15.594Z", "modified": "2025-11-07T07:22:38.375Z"}, {"entity": "publication", "iuid": "1435220b47f54e8daee499c4b6e628f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1435220b47f54e8daee499c4b6e628f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1435220b47f54e8daee499c4b6e628f4"}}, "title": "LINE-1 retrotransposons mediate cis-acting transcriptional control in human pluripotent stem cells and regulate early brain development.", "authors": [{"family": "Adami", "given": "Anita", "initials": "A"}, {"family": "Garza", "given": "Raquel", "initials": "R"}, {"family": "Gerdes", "given": "Patricia", "initials": "P"}, {"family": "Johansson", "given": "Pia A", "initials": "PA"}, {"family": "Dorazehi", "given": "Fereshteh", "initials": "F"}, {"family": "Koutounidou", "given": "Symela", "initials": "S"}, {"family": "Castilla-Vallmanya", "given": "Laura", "initials": "L"}, {"family": "Atacho", "given": "Diahann A M", "initials": "DAM"}, {"family": "Sharma", "given": "Yogita", "initials": "Y"}, {"family": "Johansson", "given": "Jenny G", "initials": "JG"}, {"family": "Tam", "given": "Oliver", "initials": "O"}, {"family": "Kirkeby", "given": "Agnete", "initials": "A"}, {"family": "Barker", "given": "Roger A", "initials": "RA"}, {"family": "Hammell", "given": "Molly Gale", "initials": "MG"}, {"family": "Douse", "given": "Christopher H", "initials": "CH"}, {"family": "Jakobsson", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "5", "issue": "10", "pages": "100979", "issn-l": null}, "abstract": "Long interspersed nuclear element 1 (L1) retrotransposons represent a vast source of genetic variability. However, mechanistic analysis of whether and how L1s contribute to human developmental programs is lacking, in part due to the challenges associated with specific profiling and manipulation of human L1 expression. Here, we show that thousands of hominoid-specific L1 integrants are expressed in human induced pluripotent stem cells and cerebral organoids. The activity levels of individual L1 promoters vary widely and correlate with an active epigenetic state. Efficient on-target CRISPR interference (CRISPRi) silencing of L1s revealed nearly a hundred co-opted L1-derived chimeric transcripts, and L1 silencing resulted in changes in neural differentiation programs and reduced cerebral organoid size. Together, these data implicate L1s and L1-derived transcripts in hominoid-specific CNS developmental processes.", "doi": "10.1016/j.xgen.2025.100979", "pmid": "40848716", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pii", "key": "S2666-979X(25)00235-6"}], "notes": [], "created": "2025-11-07T15:54:07.700Z", "modified": "2025-11-10T14:12:50.177Z"}, {"entity": "publication", "iuid": "ed35b71a58134fa4a0f19ee732868ee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed35b71a58134fa4a0f19ee732868ee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed35b71a58134fa4a0f19ee732868ee7"}}, "title": "Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias.", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Goldberg", "given": "Amy", "initials": "A", "orcid": "0000-0001-9306-1539", "researcher": {"href": "https://publications.scilifelab.se/researcher/78b41470150e45288a791994d51a3e82.json"}}, {"family": "Schraiber", "given": "Joshua G", "initials": "JG"}], "type": "journal article", "published": "2025-10-08", "journal": {"issn": "2160-1836", "volume": "15", "issue": "10", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "Population genomic analyses rely on an accurate and unbiased characterization of the genetic composition of the studied population. For short-read, high-throughput sequencing data, mapping sequencing reads to a linear reference genome can bias population genetic inference due to mismatches in reads carrying non-reference alleles. In this study, we investigate the impact of mapping bias on allele frequency estimates from pseudohaploid data and genotype likelihoods, 2 approaches commonly used in ultra-low to medium coverage sequencing. To mitigate mapping bias, we propose an empirical adjustment to genotype likelihoods. Using data from the 1000 Genomes Project, we find that our new method improves allele frequency estimation. To test a downstream application, we simulate ancient DNA data with realistic post-mortem damage to compare widely used methods for estimating ancestry proportions under different scenarios, including reference genome selection, population divergence, and sequencing depth. Our findings reveal that mapping bias can lead to differences in estimated admixture proportion of up to 4% depending on the reference population. However, the choice of method has a much stronger impact, with some methods showing differences of 10%. qpAdm appears to perform best at estimating simulated ancestry proportions, but it is sensitive to mapping bias and its applicability may vary across species due to its requirement for additional populations beyond the sources and target population. Our adjusted genotype likelihood approach largely mitigates the effect of mapping bias on genome-wide ancestry estimates from genotype likelihood-based tools. However, it cannot account for the bias introduced by the method itself or the noise in individual site allele frequency estimates due to low sequencing depth. Overall, our study provides valuable insights for obtaining more precise estimates of allele frequencies and ancestry proportions in empirical studies.", "doi": "10.1093/g3journal/jkaf172", "pmid": "40737495", "labels": {"Ancient DNA": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12506655"}, {"db": "pii", "key": "8219480"}], "notes": [], "created": "2025-11-05T07:43:07.732Z", "modified": "2025-11-28T10:49:15.819Z"}, {"entity": "publication", "iuid": "e105bd630ef34bb0a01ca502b207908e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e105bd630ef34bb0a01ca502b207908e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e105bd630ef34bb0a01ca502b207908e"}}, "title": "Climate-driven deoxygenation promoted potential mercury methylators in the past Black Sea water column", "authors": [{"family": "Zhong", "given": "Meifang", "initials": "M", "orcid": "0000-0001-8995-5468", "researcher": {"href": "https://publications.scilifelab.se/researcher/db04492b3b6c4596a4b6eda2007f4dc1.json"}}, {"family": "Barrenechea Angeles", "given": "In\u00e9s", "initials": "I", "orcid": "0000-0002-8051-4110", "researcher": {"href": "https://publications.scilifelab.se/researcher/117e061371ff48088a21ac74e9321dfa.json"}}, {"family": "More", "given": "Kuldeep D", "initials": "KD", "orcid": "0000-0002-8278-8086", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b7cfdaad6614e6986ddd3a9c25434c4.json"}}, {"family": "Picard", "given": "Ma\u00eflys", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Bravo", "given": "Andrea G", "initials": "AG", "orcid": "0000-0002-8341-3462", "researcher": {"href": "https://publications.scilifelab.se/researcher/749bb106ca6b452d82603ef8cf3cbdee.json"}}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E", "orcid": "0000-0001-9570-8738", "researcher": {"href": "https://publications.scilifelab.se/researcher/d52d4c83dda84cea9e018199a8cfc304.json"}}, {"family": "Coolen", "given": "Marco J L", "initials": "MJL", "orcid": "0000-0002-0417-920X", "researcher": {"href": "https://publications.scilifelab.se/researcher/044cf58a620c40d8843b06e37942bdf4.json"}}, {"family": "Capo", "given": "Eric", "initials": "E", "orcid": "0000-0001-9143-7061", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4017e9c8167487b882ee2d045d96494.json"}}], "type": "journal-article", "published": "2025-10-08", "journal": {"title": "Nat Water", "issn": "2731-6084", "issn-l": null}, "abstract": null, "doi": "10.1038/s44221-025-00526-4", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:26:40.967Z", "modified": "2025-11-14T11:07:32.517Z"}, {"entity": "publication", "iuid": "8ed54f29f33f4ce39d346fdb35295c92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ed54f29f33f4ce39d346fdb35295c92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ed54f29f33f4ce39d346fdb35295c92"}}, "title": "Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.", "authors": [{"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S", "orcid": "0000-0001-5877-7988", "researcher": {"href": "https://publications.scilifelab.se/researcher/baea894b3ac14408a7492df2fc6c796e.json"}}, {"family": "Granstr\u00f6m", "given": "Anna L\u00f6f", "initials": "AL", "orcid": "0000-0003-2169-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c08d2119eca4e67936cd5b5d2dc47d3.json"}}, {"family": "Kiasat", "given": "Ali", "initials": "A", "orcid": "0000-0001-5568-3265", "researcher": {"href": "https://publications.scilifelab.se/researcher/f92cb577648943a2a09efe76787545c4.json"}}, {"family": "Ahlstr\u00f6m", "given": "Gustav", "initials": "G"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/6538b950bbd440e3aa32435d23c98074.json"}}, {"family": "Rautiainen", "given": "Susanne", "initials": "S", "orcid": "0000-0001-7193-6082", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb22af02cdd04e80b1a0809b163ad56e.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Andersson", "given": "Fredrik O", "initials": "FO"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications.scilifelab.se/researcher/17bed8be7a9c46b5a94147b80fd58e82.json"}}, {"family": "Gustafsson", "given": "Ulf O", "initials": "UO", "orcid": "0000-0001-9549-061X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4302890c32a24317aa1d0f6807c4458e.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "35039", "issn-l": "2045-2322"}, "abstract": "Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.", "doi": "10.1038/s41598-025-18106-7", "pmid": "41062543", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12508173"}, {"db": "pii", "key": "10.1038/s41598-025-18106-7"}], "notes": [], "created": "2025-11-07T15:05:48.239Z", "modified": "2025-11-07T15:05:53.602Z"}, {"entity": "publication", "iuid": "b9e7e13965f944baa55161e7c0cb0363", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9e7e13965f944baa55161e7c0cb0363.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9e7e13965f944baa55161e7c0cb0363"}}, "title": "Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures", "authors": [{"family": "Hawgood", "given": "Michael", "initials": "M", "orcid": "0000-0003-3886-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/bef2b485623c4421a1c8606a4d9a377b.json"}}, {"family": "Uri\u00e9n", "given": "Bruno", "initials": "B", "orcid": "0009-0006-8205-6578", "researcher": {"href": "https://publications.scilifelab.se/researcher/03de6bcb91a948d89a1cffc578dfc455.json"}}, {"family": "Agostinho", "given": "Ana", "initials": "A", "orcid": "0000-0001-6270-7384", "researcher": {"href": "https://publications.scilifelab.se/researcher/b66ed948cad14e0c9bd35e487a48d330.json"}}, {"family": "Thiagarajan", "given": "Praghadhesh", "initials": "P", "orcid": "0009-0007-6469-9243", "researcher": {"href": "https://publications.scilifelab.se/researcher/5196cd78c67a402c846717fae6dea2af.json"}}, {"family": "Giglio", "given": "Giovanni", "initials": "G"}, {"family": "Yang", "given": "Yiqiu", "initials": "Y", "orcid": "0000-0001-7099-6956", "researcher": {"href": "https://publications.scilifelab.se/researcher/c10ef02e45fa454aab36f25ca8d2ce1c.json"}}, {"family": "Zhang", "given": "Xue", "initials": "X", "orcid": "0000-0002-5616-3429", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8cbe5cf635545d88c667027762d6187.json"}}, {"family": "Quijada", "given": "Gemma", "initials": "G"}, {"family": "Fonseca", "given": "Matilde", "initials": "M", "orcid": "0000-0002-3809-7632", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ff27afd19fd4ce681d5412a02bdc51b.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J"}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "Lemmens", "given": "Bennie", "initials": "B", "orcid": "0000-0001-8051-1676", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2575a302c624ee58ea1af3cf3b0e47d.json"}}], "type": "journal-article", "published": "2025-10-07", "journal": {"title": "EMBO J.", "issn": "1460-2075", "issn-l": "0261-4189"}, "abstract": null, "doi": "10.1038/s44318-025-00574-2", "pmid": null, "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-07T11:34:33.830Z", "modified": "2025-10-07T11:34:34.247Z"}, {"entity": "publication", "iuid": "cbf0674bfb9641a5b13df8dc2fc4a132", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbf0674bfb9641a5b13df8dc2fc4a132.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbf0674bfb9641a5b13df8dc2fc4a132"}}, "title": "Long-term warming raises risks of seasonal seafloor methane release in the coastal Baltic Sea.", "authors": [{"family": "Li", "given": "Songjun", "initials": "S"}, {"family": "Ketzer", "given": "Marcelo", "initials": "M"}, {"family": "Chang", "given": "Cheng", "initials": "C"}, {"family": "Rula", "given": "Iryna", "initials": "I"}, {"family": "Seidel", "given": "Laura", "initials": "L"}, {"family": "Svendsen", "given": "Ida Krogsgaard", "initials": "IK"}, {"family": "Forsman", "given": "Anders", "initials": "A"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2025-10-07", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "16", "pages": "1636301", "issn-l": "1664-302X"}, "abstract": "Climate change driven ocean warming is a worldwide environmental issue that can impact cycling of greenhouse gases. However, how methane production in marine sediments as a potential contributor to atmospheric greenhouse gases versus its consumption at the sulfate-methane transition zone will be affected by climate change related warming is still not well constrained. In this study, sediments from two Baltic Sea bays with long-term temperature differences were collected during summer and winter. The primary difference between the two bays was that one had been heated by a nearby power plant for 50 years, resulting in a 5.1 \u00b0C increase in annual average temperature compared to an unheated control bay. The results showed that near-seafloor sediment methane concentrations were 50 times higher compared to present-day conditions. Furthermore, the sediment fluxes along with microbial community composition changes suggested that long-term warming may thin the sulfate reduction zone, such that methanotrophic archaea and sulfate reducing bacteria peaked at shallower sediment depths in the heated bay. Overall, the results from long-term warming in natural sediment environment indicated that future climate change warming may increase the risk of methane release to the water and eventually the atmosphere.", "doi": "10.3389/fmicb.2025.1636301", "pmid": "41127623", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12537722"}], "notes": [], "created": "2025-11-21T15:33:15.108Z", "modified": "2025-11-28T10:54:29.001Z"}, {"entity": "publication", "iuid": "83d4b61b754148e09946bb0b8da9c20c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83d4b61b754148e09946bb0b8da9c20c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83d4b61b754148e09946bb0b8da9c20c"}}, "title": "Characterising the Periodontal Granulation Tissue Using scRNAseq.", "authors": [{"family": "Zhu", "given": "Wentao", "initials": "W"}, {"family": "Fung", "given": "Kathy", "initials": "K"}, {"family": "Dhami", "given": "Pawan", "initials": "P"}, {"family": "Sharpe", "given": "Paul", "initials": "P"}, {"family": "Krivanek", "given": "Jan", "initials": "J"}, {"family": "Nibali", "given": "Luigi", "initials": "L", "orcid": "0000-0002-7750-5010", "researcher": {"href": "https://publications.scilifelab.se/researcher/aea99b6f369f449faae6eb967710ad95.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Neves", "given": "Vitor C M", "initials": "VCM", "orcid": "0000-0002-5111-269X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd9b74ed39e340a09892f6e48690254b.json"}}], "type": "journal article", "published": "2025-10-07", "journal": {"title": "J Clin Periodontol", "issn": "1600-051X", "issn-l": null}, "abstract": "To investigate the cellular composition and molecular mechanisms of periodontal granulation tissue formation using single-cell RNA sequencing (scRNA-seq), aiming to enhance the understanding of periodontal disease pathogenesis and identify potential targets for regenerative therapies.\n\nGranulation tissue samples were collected from patients undergoing periodontal surgery (n = 3). Fresh tissues were processed into single-cell suspensions and subjected to scRNA-seq. The data were integrated and compared with existing datasets from healthy gingiva and periodontal ligament. Computational analyses were performed and validated through immunofluorescence staining.\n\nTen distinct cell clusters were identified across the samples. Granulation tissue exhibited a higher abundance of immune cells compared to healthy tissues. A novel endothelial cell subpopulation, exclusive to granulation tissue, was discovered and characterised by NOTCH3 expression and involvement in ossification pathways. Additionally, granulation tissue fibroblast subpopulations demonstrated a progenitor-like state, characterised by extracellular matrix reorganisation and low differentiation, similar to cancer-associated fibroblasts.\n\nThis study identified a novel endothelial subpopulation offering new insights into the disease's pathogenesis and presenting potential targets for regenerative therapies. These findings will help advance the understanding of periodontal disease granulation tissue formation and provide information for the development of materials to modulate specific cellular pathways to improve periodontal disease management.", "doi": "10.1111/jcpe.70048", "pmid": "41055332", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:51:16.664Z", "modified": "2025-11-28T10:51:16.748Z"}, {"entity": "publication", "iuid": "c783ffc03b364c5c97b3c8c519bf55a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c783ffc03b364c5c97b3c8c519bf55a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c783ffc03b364c5c97b3c8c519bf55a7"}}, "title": "Autoimmunity-associated DIORA1 binds the MRCK family of serine/threonine kinases and controls cell motility.", "authors": [{"family": "Tr\u0161eli\u010d", "given": "Tilen", "initials": "T", "orcid": "0009-0006-0316-8847", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d50c0b7e88d4033b14afdc5ea254801.json"}}, {"family": "Pelo", "given": "Nathalie", "initials": "N"}, {"family": "Martin de Fremont", "given": "Gregoire", "initials": "G", "orcid": "0000-0003-3393-3969", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e1b9b6db64f4fdb9ab8b6eab5eb59ba.json"}}, {"family": "Iyer", "given": "Vaishnavi S", "initials": "VS"}, {"family": "Richardsdotter Andersson", "given": "Elina", "initials": "E", "orcid": "0009-0003-7008-529X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ff0a7a67ed4fdfb5135c2e33c429ab.json"}}, {"family": "Ottosson", "given": "Vijole", "initials": "V", "orcid": "0009-0003-6530-9033", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f0ee7dd68e3411db6975ec7aac67b16.json"}}, {"family": "Frei", "given": "David Alexander", "initials": "DA"}, {"family": "Baas", "given": "Elisa", "initials": "E", "orcid": "0009-0002-0587-7242", "researcher": {"href": "https://publications.scilifelab.se/researcher/a658fbfac5c74616ac5797b2330ae50a.json"}}, {"family": "Nyberg", "given": "William A", "initials": "WA"}, {"family": "Thorlacius", "given": "Gu\u00f0n\u00fd Ella", "initials": "GE"}, {"family": "Mentlein", "given": "Lara", "initials": "L"}, {"family": "Boddul", "given": "Sanjaykumar V", "initials": "SV", "orcid": "0000-0002-0711-1147", "researcher": {"href": "https://publications.scilifelab.se/researcher/312d8252d0c24f0583512c950504afa9.json"}}, {"family": "Sandu", "given": "Ioana", "initials": "I"}, {"family": "Velasquez Pulgarin", "given": "Diego", "initials": "D"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Gerlach", "given": "Carmen", "initials": "C", "orcid": "0000-0001-7889-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/893fad4751a6411392488c5e37c0aa13.json"}}, {"family": "Wermeling", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9633-677X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a34df8186ba24df3b14fe9743cf546b4.json"}}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Espinosa", "given": "Alexander", "initials": "A"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}], "type": "journal article", "published": "2025-10-07", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "40", "pages": "e2426917122", "issn-l": "0027-8424"}, "abstract": "Genetic association links disordered autoimmunity 1 (DIORA1) to numerous autoimmune rheumatic diseases, including systemic lupus erythematosus, Sj\u00f6gren's disease, rheumatoid arthritis, polymyositis, and systemic sclerosis. However, its cellular function has remained unknown. Here, we identify the Myotonic Dystrophy Kinase-Related Cdc42-Binding Kinases (MRCK kinases) family of serine/threonine kinases-key regulators of actomyosin contractility and cell motility-as direct interactors of DIORA1. Through interaction mapping, we show that DIORA1 binds three distinct modules of MRCK kinases, including the conserved kinase inhibitory motif, C1-PH, and citron homology domains. DIORA1 knockdown in human cells altered cellular phosphorylation patterns and reduced phosphorylation of known MRCK targets. RNA-sequencing and proteomic analyses revealed upregulation of epithelial-mesenchymal transition genes and proteins, and functional analyses confirmed increased cell invasion, following knockdown of DIORA1. Together, these findings identify the autoimmunity-associated DIORA1 protein as an interactor of MRCK kinases and a regulator of cell motility.", "doi": "10.1073/pnas.2426917122", "pmid": "41042840", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12519202"}], "notes": [], "created": "2025-11-21T17:57:08.724Z", "modified": "2025-11-21T17:57:09.957Z"}, {"entity": "publication", "iuid": "2e917c797feb476e8c34b4c4e6e2a631", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e917c797feb476e8c34b4c4e6e2a631.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e917c797feb476e8c34b4c4e6e2a631"}}, "title": "The CHCHD2-CHCHD10 protein complex is modulated by mitochondrial dysfunction and alters lipid homeostasis in the mouse brain.", "authors": [{"family": "Gerlach", "given": "Jule", "initials": "J"}, {"family": "Pireddu", "given": "Paola", "initials": "P"}, {"family": "Zhang", "given": "Xiaoqun", "initials": "X"}, {"family": "Wetzel", "given": "Simon", "initials": "S", "orcid": "0000-0003-1831-0376", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddd21b38f82f4624a40679559339c845.json"}}, {"family": "Mennuni", "given": "Mara", "initials": "M", "orcid": "0000-0001-6199-6233", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d3b8d76aacd4f47ae62d0de66e9222a.json"}}, {"family": "Milenkovic", "given": "Dusanka", "initials": "D", "orcid": "0000-0003-0151-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/7667a08efad244b88892a772f51ccf50.json"}}, {"family": "Nolte", "given": "Hendrik", "initials": "H"}, {"family": "da Silva Rodrigues", "given": "Fernanda", "initials": "F"}, {"family": "Branzell", "given": "Niclas", "initials": "N", "orcid": "0009-0009-3472-6903", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bde4ad10f0146379233871ea29ea918.json"}}, {"family": "Kaya", "given": "Ibrahim", "initials": "I", "orcid": "0000-0003-3345-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/99a00a900df8419f96fafa97344e56ea.json"}}, {"family": "Villegas", "given": "Rodolfo Garcia", "initials": "RG"}, {"family": "Rubalcava-Gracia", "given": "Diana", "initials": "D", "orcid": "0000-0002-4615-7375", "researcher": {"href": "https://publications.scilifelab.se/researcher/99b075c43c2244ee9a26fae7b09d523a.json"}}, {"family": "Alsina", "given": "David", "initials": "D"}, {"family": "Feederle", "given": "Regina", "initials": "R", "orcid": "0000-0002-3981-367X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c19111a0c7af42d4a22b7221e4426909.json"}}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}, {"family": "Langer", "given": "Thomas", "initials": "T"}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}, {"family": "Filograna", "given": "Roberta", "initials": "R", "orcid": "0000-0002-6581-9426", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d215cffe2dc48a18d051a2229c8ce9f.json"}}], "type": "journal article", "published": "2025-10-06", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "16", "issue": "1", "pages": "693", "issn-l": "2041-4889"}, "abstract": "The highly conserved CHCHD2 and CHCHD10 are small mitochondrial proteins residing in the intermembrane space. Recently, mutations in the genes encoding these proteins have been linked to severe disorders, including Parkinson's disease and amyotrophic lateral sclerosis. In cultured cells, a small fraction of CHCHD2 and CHCHD10 oligomerize to form a high molecular weight complex of unknown function. Here, we generated a whole-body Chchd2 knockout mouse to investigate the in vivo role of CHCHD2 and its protein complex. We show that CHCHD2 is crucial for sustaining full motor capacity, normal striatal dopamine levels, and lipid homeostasis in the brain of adult male mice. We also demonstrate that in mouse tissues, CHCHD2 and CHCHD10 exist exclusively as a high molecular weight complex, whose levels are finely tuned under physiological conditions. In response to mitochondrial dysfunction, the abundance and size of the CHCHD2-CHCHD10 complex increase, a mechanism conserved across different tissues. Although the loss of CHCHD2 does not abolish CHCHD10 oligomerization, it enhances cell vulnerability to mitochondrial stress, suggesting that CHCHD2 is protective against mitochondrial damage. Our findings uncover the role of CHCHD2 in preserving tissue homeostasis and provide important insights into the involvement of the CHCHD2-CHCHD10 complex in human diseases.", "doi": "10.1038/s41419-025-08030-z", "pmid": "41053020", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12501252"}, {"db": "pii", "key": "10.1038/s41419-025-08030-z"}], "notes": [], "created": "2025-11-21T09:46:18.171Z", "modified": "2025-11-27T13:31:05.879Z"}, {"entity": "publication", "iuid": "bf983717ca75466d9efd3cd55e1b5670", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf983717ca75466d9efd3cd55e1b5670.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf983717ca75466d9efd3cd55e1b5670"}}, "title": "Characterizing 13C Spectral Assignments and Substituent Distributions of Hydroxypropylmethylcellulose Acetyl Succinate Using Dynamic Nuclear Polarization Nuclear Magnetic Resonance Spectroscopy", "authors": [{"family": "Cosquer", "given": "Ronan P", "initials": "RP"}, {"family": "Pinon", "given": "Arthur C", "initials": "AC"}, {"family": "\u0160olt\u00e9sov\u00e1", "given": "M\u00e1ria", "initials": "M"}, {"family": "Hawarden", "given": "Lucy E", "initials": "LE"}, {"family": "Abraham", "given": "Anuji", "initials": "A"}, {"family": "Tobyn", "given": "Mike", "initials": "M"}, {"family": "Blanc", "given": "Fr\u00e9d\u00e9ric", "initials": "F", "orcid": "0000-0001-9171-1454", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf1f62cdf31456a870d2e8ec6a6c22d.json"}}], "type": "journal-article", "published": "2025-10-06", "journal": {"title": "Mol. Pharmaceutics", "issn": "1543-8384", "volume": "22", "issue": "10", "pages": "5870-5878", "issn-l": "1543-8384"}, "abstract": null, "doi": "10.1021/acs.molpharmaceut.5c00359", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:02:47.089Z", "modified": "2025-11-27T08:02:47.174Z"}, {"entity": "publication", "iuid": "379697221e864158b23905f98efc1f8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/379697221e864158b23905f98efc1f8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/379697221e864158b23905f98efc1f8a"}}, "title": "Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.", "authors": [{"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A"}, {"family": "Pacheco-Valenciana", "given": "Armando", "initials": "A"}, {"family": "Milke", "given": "Felix", "initials": "F"}, {"family": "Dharamshi", "given": "Jennah E", "initials": "JE"}, {"family": "Hampel", "given": "Justyna J", "initials": "JJ"}, {"family": "Damashek", "given": "Julian", "initials": "J"}, {"family": "Wienhausen", "given": "Gerrit", "initials": "G"}, {"family": "Rodriguez-R", "given": "Luis Miguel", "initials": "LM"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "34482", "issn-l": "2045-2322"}, "abstract": "Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.", "doi": "10.1038/s41598-025-22383-7", "pmid": "41044404", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12495000"}, {"db": "pii", "key": "10.1038/s41598-025-22383-7"}], "notes": [], "created": "2025-11-19T07:34:55.667Z", "modified": "2025-11-28T10:47:04.484Z"}, {"entity": "publication", "iuid": "5030ff3ac322493db0bee8969ebf9d14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5030ff3ac322493db0bee8969ebf9d14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5030ff3ac322493db0bee8969ebf9d14"}}, "title": "Reliable on-treatment prognostication and target identification with a customized assay for circulating tumor DNA in patients with newly diagnosed pancreatic cancer.", "authors": [{"family": "Petersson", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-5574-9217", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f02e97bd25493c993d1a2568935885.json"}}, {"family": "Svensson", "given": "Maja", "initials": "M"}, {"family": "Hau", "given": "Sofie Olsson", "initials": "SO"}, {"family": "Bergstr\u00f6m", "given": "Rebecka", "initials": "R", "orcid": "0000-0001-7609-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c52bb8b2ae249049f0da222bcdfe932.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3610-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/1369ca149def47a8abb8abb90b23ca66.json"}}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Chattopadhyay", "given": "Subhayan", "initials": "S", "orcid": "0000-0002-8599-2971", "researcher": {"href": "https://publications.scilifelab.se/researcher/78358668578b4661bed1f6a37365fae4.json"}}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}, {"family": "Heidenblad", "given": "Markus", "initials": "M", "orcid": "0000-0002-0668-2263", "researcher": {"href": "https://publications.scilifelab.se/researcher/b49a0816fc794c27a25b34731e8ca7bf.json"}}, {"family": "Leandersson", "given": "Karin", "initials": "K", "orcid": "0000-0001-8254-3137", "researcher": {"href": "https://publications.scilifelab.se/researcher/4736923f382845c2990efb251340bfb4.json"}}, {"family": "Gisselsson", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3653582762b14f9a9ad2fe6aba511115.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K", "orcid": "0000-0003-2257-5000", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b7c5c8216d943d2b344d9de5622770b.json"}}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "34481", "issn-l": "2045-2322"}, "abstract": "The vast majority of patients with pancreatic cancer present with unresectable disease and precision medicine is lagging behind. Circulating tumor DNA (ctDNA) has emerged as a promising tool, both as a proxy for tumor burden and for capturing tumor heterogeneity, but optimal gene panels and prognostic cutoffs remain to be determined. Herein, we applied ultra-deep ctDNA sequencing using a customized panel targeting 23 genes and six frequently altered chromosomes on plasma samples obtained before, during and after chemotherapy from 60 patients enrolled in a prospective clinical study. At baseline, positive versus negative ctDNA was not prognostic, neither in the adjuvant nor in the palliative setting, but in palliative patients, an independent prognostic cutoff could be calculated from the absolute number of mutated DNA molecules. Median overall survival was 3.7 months in the ctDNAhigh compared to 11.9 months in the ctDNAlow group (p < 0.0001), and the cutoff remained prognostic at one and three months. Moreover, relevant genetic alterations were highly concordant in ctDNA and paired tumor tissue. These findings demonstrate the potential clinical utility of a customized and focused gene panel for prognostication and target identification over time in patients with newly diagnosed pancreatic cancer, in particular in the palliative setting.ClinicalTrials.gov number: NCT03724994.", "doi": "10.1038/s41598-025-22369-5", "pmid": "41044171", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Clinical Genomics Lund": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12494785"}, {"db": "pii", "key": "10.1038/s41598-025-22369-5"}, {"db": "ClinicalTrials.gov", "key": "NCT03724994"}], "notes": [], "created": "2025-10-16T17:14:10.829Z", "modified": "2025-11-18T20:46:37.775Z"}, {"entity": "publication", "iuid": "486383c9deab4e7ebdff990f1767aee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/486383c9deab4e7ebdff990f1767aee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/486383c9deab4e7ebdff990f1767aee7"}}, "title": "Quantitative temporal analysis of pancreatic islet T lymphocyte and macrophage infiltration heralded by serum IgE in congenic BioBreeding (BB) Gimap5-/- rats at risk for insulitis and acute onset diabetes.", "authors": [{"family": "J\u00f6nsson", "given": "Josefine", "initials": "J", "orcid": "0000-0003-0709-2828", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4b2eb9eef5496eb27e76fc9fca120a.json"}}, {"family": "Faxius", "given": "Linda", "initials": "L"}, {"family": "T\u00e5ngrot", "given": "Jeanette", "initials": "J"}, {"family": "Vance", "given": "Krysten", "initials": "K", "orcid": "0000-0001-5647-1504", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ed382328ed4627b4d1eed3e125fdfb.json"}}, {"family": "Jerman", "given": "Stephanie", "initials": "S"}, {"family": "Bowman", "given": "Doug", "initials": "D"}, {"family": "Bogdani", "given": "Marika", "initials": "M"}, {"family": "Ericsson", "given": "Peter", "initials": "P"}, {"family": "Bennet", "given": "Rasmus", "initials": "R"}, {"family": "Ramelius", "given": "Anita", "initials": "A", "orcid": "0000-0003-2407-7785", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb1bdf74e09d4101a0aea80b7d79559d.json"}}, {"family": "Lernmark", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0003-1735-0499", "researcher": {"href": "https://publications.scilifelab.se/researcher/87c2498b4a66469d9fe7c21f56e2eddd.json"}}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Inflamm Res", "issn": "1420-908X", "volume": "74", "issue": "1", "pages": "134", "issn-l": null}, "abstract": "The objective was to determine the association between serum IgE levels and the infiltration order of T lymphocytes and macrophages in pancreatic islets in relation to the loss of insulin and glucagon cells in presymptomatic congenic BB Gimap5-DP (Diabetes Prone) rats.\n\nCongenic prediabetes BB Gimap5-DP and control Gimap5-DR (Diabetes Resistant) rats were followed every other day from 29 to 32 days of age until peak serum IgE (\u2264 55 days of age).\n\nSerum IgE was measured using ELISA. The HALO\u2122 platform facilitated quantitative image analysis of infiltrating T lymphocytes, macrophages, and target organ insulin and glucagon cells. Whole genome sequencing (WGS) was employed to identify candidate type 1 diabetes genes.\n\nSerum IgE levels increased with age in normoglycemic BB Gimap5-DP rats. Quantification of infiltrating cells per mm2 in and around the islets indicated that T lymphocytes are the initial infiltrators, followed by macrophages. Elevated serum IgE levels inversely correlated with beta-cell mass (total mg insulin/mg pancreas). WGS refined the risk segment for islet inflammation to 1.02 Mbp, leaving 10 candidate genes, including Gimap4 and Gimap5.\n\nElevated IgE levels herald T lymphocyte and macrophage infiltration. Pancreatic islet inflammation was linked to Gimap4, Gimap5, and other potential candidate genes on rat chromosome 4.", "doi": "10.1007/s00011-025-02101-9", "pmid": "41042382", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12494634"}, {"db": "pii", "key": "10.1007/s00011-025-02101-9"}], "notes": [], "created": "2025-11-17T15:46:13.623Z", "modified": "2025-11-28T10:40:57.524Z"}, {"entity": "publication", "iuid": "56df74106c0b479f8e63165182c08c10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56df74106c0b479f8e63165182c08c10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56df74106c0b479f8e63165182c08c10"}}, "title": "Proteomic analysis of nemaline myopathy in infants reveals distinct common dysregulated proteins and cellular pathways.", "authors": [{"family": "Hedberg-Oldfors", "given": "Carola", "initials": "C", "orcid": "0000-0002-7141-4185", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc67028bf0c04f1b9a73bac5e72f9897.json"}}, {"family": "Bedir", "given": "Ali Zeki", "initials": "AZ"}, {"family": "Visuttijai", "given": "Kittichate", "initials": "K", "orcid": "0000-0002-4800-8533", "researcher": {"href": "https://publications.scilifelab.se/researcher/f41f59ad2b0a4e1c95b0cc9cf109f6fa.json"}}, {"family": "Michael", "given": "Eva", "initials": "E"}, {"family": "Oldfors", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Front Neurol", "issn": "1664-2295", "volume": "16", "pages": "1661747", "issn-l": "1664-2295"}, "abstract": "Nemaline myopathy is a rare congenital muscle disorder characterized by the presence of nemaline rods, protein aggregates, in muscle fibers. Pathogenic variants in several genes, most commonly NEB and ACTA1, which encode thin filament proteins of the sarcomere, have been implicated in its etiology. Currently, there is no cure for nemaline myopathy, underscoring the need to identify disease-modifying targets for therapeutic development.\n\nIn this study, we employed quantitative nanoscale liquid chromatography-tandem mass spectrometry (LC-MS3) with labeled protein analysis on muscle tissue from five normal controls and seven infants diagnosed with nemaline myopathy due to NEB or ACTA1 pathogenic variants.\n\nWe identified and quantified 4,846 proteins across all samples, with 183 proteins showing significant dysregulation. Protein-protein interaction analysis revealed nine upregulated, muscle-specific proteins: NRAP, FBXO40, TRIM63, TRIM54, ALPK3, XIRP1, ANKRD2, LMOD2, and CSRP3. Further pathway analysis indicated upregulation of protein synthesis and proteasomal degradation processes, alongside downregulation of glycolysis. Notably, the dysregulated proteins and pathways were consistent across both genetic subtypes, suggesting shared molecular mechanisms underlying the disease.\n\nThis proteomic profiling study has identified key dysregulated proteins and pathways in infantile nemaline myopathy. These findings advance our understanding of the disease's molecular basis and highlight candidate targets for future therapeutic intervention.", "doi": "10.3389/fneur.2025.1661747", "pmid": "41111967", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12531377"}], "notes": [], "created": "2025-10-23T12:58:04.991Z", "modified": "2025-11-04T09:44:38.692Z"}, {"entity": "publication", "iuid": "4ae85c467a6b4088b7f92151b66e932d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ae85c467a6b4088b7f92151b66e932d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ae85c467a6b4088b7f92151b66e932d"}}, "title": "Latent plasticity of the human pancreas across development, health, and disease.", "authors": [{"family": "Mereu", "given": "Elisabetta", "initials": "E", "orcid": "0000-0001-6101-8472", "researcher": {"href": "https://publications.scilifelab.se/researcher/d263fd3d305145959169d1e1f3e76c75.json"}}, {"family": "Balboa", "given": "Diego", "initials": "D", "orcid": "0000-0002-4784-5452", "researcher": {"href": "https://publications.scilifelab.se/researcher/647a7c312e2a4307aa43a10c7d142545.json"}}, {"family": "Liebig", "given": "Johannes", "initials": "J", "orcid": "0000-0002-9188-036X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce625220e3f645eeab019e87e73b5470.json"}}, {"family": "Gonzalez-Herrero", "given": "Aitor", "initials": "A", "orcid": "0000-0002-2644-8028", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e96783efb9b45ad90ed8c1c0fa6dd11.json"}}, {"family": "Martinez-Casals", "given": "Anna", "initials": "A", "orcid": "0000-0003-2722-1965", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa27c4c76374453ba3ffe7eafff4b9a.json"}}, {"family": "Mardamshina", "given": "Mariya", "initials": "M"}, {"family": "Mollandin", "given": "Fanny", "initials": "F"}, {"family": "Schicktanz", "given": "Felix", "initials": "F"}, {"family": "Tosti", "given": "Luca", "initials": "L"}, {"family": "Vandenbempt", "given": "Valerie", "initials": "V"}, {"family": "Avrahami", "given": "Dana", "initials": "D"}, {"family": "Bernardo", "given": "Edgar", "initials": "E"}, {"family": "Bj\u00f6rklund", "given": "Frida", "initials": "F"}, {"family": "Chua", "given": "Robert Lorenz", "initials": "RL"}, {"family": "Engelse", "given": "Marten", "initials": "M"}, {"family": "Garc\u00eda-Hurtado", "given": "Javier", "initials": "J"}, {"family": "Groen", "given": "Nathalie", "initials": "N"}, {"family": "Hanegraaf", "given": "Maaike", "initials": "M"}, {"family": "Ia\u00f1ez", "given": "Pablo", "initials": "P"}, {"family": "Jechow", "given": "Katharina", "initials": "K"}, {"family": "Konukiewitz", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lawerenz", "given": "Christian", "initials": "C"}, {"family": "Marchese", "given": "Domenica", "initials": "D"}, {"family": "Muraro", "given": "Mauro J", "initials": "MJ"}, {"family": "Pellegrini", "given": "Silvia", "initials": "S"}, {"family": "Sordi", "given": "Valeria", "initials": "V"}, {"family": "Sudy", "given": "Alexander", "initials": "A"}, {"family": "Taron", "given": "Ulrike", "initials": "U"}, {"family": "Ten", "given": "Foo Wei", "initials": "FW"}, {"family": "Trefzer", "given": "Timo", "initials": "T"}, {"family": "Twardziok", "given": "Sven", "initials": "S"}, {"family": "van Agen", "given": "Maarten", "initials": "M"}, {"family": "Carlotti", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "de Koning", "given": "Eelco", "initials": "E"}, {"family": "Ferrer", "given": "Jorge", "initials": "J"}, {"family": "Glaser", "given": "Benjamin", "initials": "B"}, {"family": "Heyn", "given": "Holger", "initials": "H"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Piemonti", "given": "Lorenzo", "initials": "L"}, {"family": "Steiger", "given": "Katja", "initials": "K"}, {"family": "van Oudenaarden", "given": "Alexander", "initials": "A"}, {"family": "Weichert", "given": "Wilko", "initials": "W"}, {"family": "Conrad", "given": "Christian", "initials": "C", "orcid": "0000-0001-7036-342X", "researcher": {"href": "https://publications.scilifelab.se/researcher/64b5e1b25f354b879fb0ce43e0aba260.json"}}, {"family": "Eils", "given": "Roland", "initials": "R", "orcid": "0000-0002-0034-4036", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9ad57aa98c5431189bbd69aadc541d2.json"}}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The pancreas plays a central role in major human diseases, yet our understanding of its cellular diversity and plasticity remains incomplete. Here, we present a single-cell multiomics atlas of the human pancreas, profiling over four million cells and nuclei from 57 donors across fetal development, adult homeostasis, and type 2 diabetes (T2D). Integrating sc/snRNA-seq, snATAC-seq, VASA-seq, spatial transcriptomics (Xenium), and multiplexed proteomics (CODEX), we resolve gene expression, chromatin accessibility, and spatial organization at high resolution. We identify transcriptionally plastic centroacinar-like cells (pCACs) in adults with fetal-like features, delineate endocrine and exocrine lineage trajectories during development, and uncover HNF1A-defined beta cell epigenetic states. In T2D, we observe shifts in beta cell subtypes and altered regulatory programs. Glucose perturbation of healthy islets reveals cell-type-specific adaptation and stress responses. This atlas provides a foundational framework to understand pancreas biology and the role of cellular plasticity in regeneration and disease.", "doi": "10.1101/2025.10.01.679230", "pmid": "41256699", "labels": {"Spatial Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12622017"}, {"db": "pii", "key": "2025.10.01.679230"}], "notes": [], "created": "2025-12-02T13:50:54.585Z", "modified": "2025-12-02T13:50:55.922Z"}, {"entity": "publication", "iuid": "107c7b3b512c45f686868f13aff2dfd8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/107c7b3b512c45f686868f13aff2dfd8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/107c7b3b512c45f686868f13aff2dfd8"}}, "title": "Innate immune cell subsets are enriched in synovial fluid of ACPA-negative rheumatoid arthritis and characterized by distinct type I IFN gene signatures.", "authors": [{"family": "Argyriou", "given": "Alexandra", "initials": "A"}, {"family": "Wadsworth", "given": "Marc H", "initials": "MH"}, {"family": "Fienman", "given": "Joshua", "initials": "J"}, {"family": "Gonzalez-Sanchez", "given": "Ana Cristina", "initials": "AC"}, {"family": "Ghannoum", "given": "Salim", "initials": "S"}, {"family": "Krishna", "given": "Chirag", "initials": "C"}, {"family": "Gerstner", "given": "Christina", "initials": "C"}, {"family": "Horuluoglu", "given": "Begum", "initials": "B"}, {"family": "Sijbranda", "given": "Merel", "initials": "M"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Hensvold", "given": "Aase", "initials": "A"}, {"family": "Turcinov", "given": "Sara", "initials": "S"}, {"family": "Winkler", "given": "Aaron", "initials": "A"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}, {"family": "Chemin", "given": "Karine", "initials": "K"}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "issn-l": "0003-4967"}, "abstract": "Around 30% of patients with rheumatoid arthritis (RA) lack rheumatoid factor and anti-citrullinated protein antibodies (ACPA) complicating diagnosis and potentially delaying treatment. We hypothesised that innate immune mechanisms might be more prominent in ACPA- RA.\n\nWe performed single-cell RNA sequencing of mononuclear cells from peripheral blood (PBMC) and synovial fluid (SFMC) of patients with ACPA- and ACPA+ RA (n = 4 per group: discovery cohort; n = 8 per group: validation cohort). Dendritic cells and proinflammatory cytokine production were analysed by flow cytometry on SFMC from patients with ACPA- RA, ACPA+ RA, and psoriatic arthritis. Interferon (IFN) levels in synovial fluid (SF) and serum were measured in these groups.\n\nSeveral macrophage subsets and cDC2 were enriched in ACPA- RA SF whereas the frequency of Tph and B cells was increased in ACPA+ RA SF. Type I IFN-stimulated genes were detected in SFMC, but not PBMC, of patients with ACPA- RA. A type I IFN signature was also observed in synovial tissue from two patients with ACPA- RA in an independent dataset. IFN levels were higher in SF than serum but IFN-\u03b1/\u03b2 production did not differ between ACPA+ and ACPA- RA.\n\nThis study identifies a distinct innate cell composition and type I IFN gene response in synovial joints, but not in peripheral blood, of patients with ACPA- RA. Similar IFN levels across groups suggest the IFN signature may have been primed before the cells entered the joints. These findings provide a foundation for future research on type I IFN responses in ACPA- RA.", "doi": "10.1016/j.ard.2025.07.029", "pmid": "41046204", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-4967(25)04299-2"}], "notes": [], "created": "2025-11-19T07:45:45.847Z", "modified": "2025-11-19T07:45:45.871Z"}, {"entity": "publication", "iuid": "c739e888429e49b782d4ec4455e72f97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c739e888429e49b782d4ec4455e72f97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c739e888429e49b782d4ec4455e72f97"}}, "title": "Correlation of autoantibody profiles with clinical parameters in exfoliative glaucoma patients.", "authors": [{"family": "Potter", "given": "Ryan", "initials": "R"}, {"family": "Ayala", "given": "Marcelo", "initials": "M"}, {"family": "Tilevik", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Int Ophthalmol", "issn": "1573-2630", "volume": "45", "issue": "1", "pages": "404", "issn-l": null}, "abstract": "Exfoliative glaucoma (XFG) is characterized by elevated intraocular pressure (IOP) caused by fibrous deposits obstructing aqueous humor drainage, traditionally emphasizing mechanical factors. In this study, we aim to investigate the relationships between clinical parameters and autoimmune activity in exfoliative glaucoma (XFG) patients, and identify patterns of autoantibody reactivity among patient subgroups with differing levels of overall autoimmune activity.\n\nWe analyzed serum autoantibody profiles against 92 antigens in 116 XFG patients using an xMAP suspension bead array. Spearman correlation analysis and PERMANOVA were applied to evaluate relationships between autoantibody reactivity and clinical parameters in glaucoma management. Hierarchical clustering was used to identify clusters of patients based on overall autoantibody reactivity levels, and network analysis using shortest path mapping was utilized to explore potential connections among the proteins associated with the antigens used in this study and other proteins not targeted in this study.\n\nSignificant positive correlations were found between the clinical parameter SE and autoantibodies targeting the proteins LOXL3, CYP39A1, and HYOU1. Clustering analysis revealed distinct subgroups of patients with differing overall autoantibody reactivity levels, notably showing significant negative correlations between broad autoantibody profiles and CCT exclusively within the subgroup characterized by higher autoimmune activity. Network analysis identified CTNNB1 as a prominent multi-path intermediary connecting disparate proteins, highlighting potential common regulatory pathways.\n\nThis study identifies novel correlations between clinical parameters and autoimmune activity in XFG, suggesting refractive changes and corneal structural characteristics may be influenced by specific immune mechanisms. These findings underscore the value of integrating immunological profiling with clinical glaucoma assessments, potentially enhancing patient stratification and identifying possible therapeutic targets.", "doi": "10.1007/s10792-025-03783-0", "pmid": "41042282", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12494623"}, {"db": "pii", "key": "10.1007/s10792-025-03783-0"}], "notes": [], "created": "2025-10-24T09:38:37.892Z", "modified": "2025-10-24T09:38:37.921Z"}, {"entity": "publication", "iuid": "7e76ffce8f844e768925d3f1ccdc1ad3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e76ffce8f844e768925d3f1ccdc1ad3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e76ffce8f844e768925d3f1ccdc1ad3"}}, "title": "Prematurity and genetic liability for autism spectrum disorder.", "authors": [{"family": "Zhang", "given": "Yali", "initials": "Y"}, {"family": "Yahia", "given": "Ashraf", "initials": "A"}, {"family": "Sandin", "given": "Sven", "initials": "S"}, {"family": "\u00c5den", "given": "Ulrika", "initials": "U"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K"}], "type": "journal article", "published": "2025-10-02", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "17", "issue": "1", "pages": "108", "issn-l": "1756-994X"}, "abstract": "Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by diverse presentations and a strong genetic component. Environmental factors, such as prematurity, have also been linked to increased liability for ASD, though the interaction between genetic predisposition and prematurity remains unclear. This study aims to investigate the impact of genetic liability and preterm birth on ASD conditions.\n\nWe analyzed phenotype and genetic data from two large ASD cohorts, the Simons Foundation Powering Autism Research for Knowledge (SPARK) and Simons Simplex Collection (SSC), encompassing 78,559 individuals for phenotype analysis, 12,519 individuals with genome sequencing data, and 8104 individuals with exome sequencing data. Statistical significance of differences in clinical measures was evaluated between individuals with different ASD and preterm status. We assessed the rare variants burden using generalized estimating equations (GEE) models and polygenic load using the ASD-associated polygenic risk score (PRS). Furthermore, we developed a machine learning model to predict ASD in preterm children using phenotype and genetic features available at birth.\n\nIndividuals with both preterm birth and ASD exhibit more severe phenotypic outcomes despite similar levels of genetic liability for ASD across the term and preterm groups. Notably, preterm-ASD individuals showed an elevated rate of de novo variants identified in exome sequencing (GEE model, p = 0.005) in comparison to non-ASD-preterm group. Additionally, a GEE model showed that a higher ASD PRS, preterm birth, and male sex were positively associated with a higher predicted probability for ASD in SPARK, reaching a probability close to 90%. Lastly, we developed a machine learning model using phenotype and genetic features available at birth with limited predictive power (AUROC = 0.65).\n\nPreterm birth may exacerbate multimorbidity present in ASD, which was not due to ASD-associated genetic variants. However, increased ASD-associated rare variants may elevate the likelihood of a preterm child being diagnosed with ASD. Additionally, a polygenic load of ASD-associated variants had an additive role with preterm birth in the predicted probability for ASD, especially for boys. Future integration of genetic and phenotypic data in larger preterm or population-based cohorts will be crucial for advancing early ASD identification in preterm subgroup.", "doi": "10.1186/s13073-025-01552-3", "pmid": "41039503", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12490119"}, {"db": "pii", "key": "10.1186/s13073-025-01552-3"}], "notes": [], "created": "2025-11-28T10:53:10.261Z", "modified": "2025-11-28T10:53:10.272Z"}, {"entity": "publication", "iuid": "c9f9c04bc10d4b55b21162f79fb3dd5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9f9c04bc10d4b55b21162f79fb3dd5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9f9c04bc10d4b55b21162f79fb3dd5e"}}, "title": "The circadian clock of Populus affects physiological, transcriptional and metabolomic responses to osmotic and ionic components of salt stress", "authors": [{"family": "Ib\u00e1\u00f1ez", "given": "Cristian", "initials": "C"}, {"family": "Vergara", "given": "Alexander", "initials": "A"}, {"family": "Castro", "given": "David", "initials": "D"}, {"family": "Bascunan-Godoy", "given": "Luisa", "initials": "L"}, {"family": "Sj\u00f6lander", "given": "Johan", "initials": "J"}, {"family": "Jurca", "given": "Manuela", "initials": "M"}, {"family": "Pin", "given": "Pierre A", "initials": "PA"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Eriksson", "given": "Maria E", "initials": "ME"}], "type": "journal-article", "published": "2025-10-01", "journal": {"title": "npj Biol Timing Sleep", "issn": "2948-281X", "volume": "2", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1038/s44323-025-00052-2", "pmid": null, "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-19T10:50:37.823Z", "modified": "2025-11-19T10:50:37.851Z"}, {"entity": "publication", "iuid": "cd69deb28cb34a7ba0f06bcbdcde1b23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd69deb28cb34a7ba0f06bcbdcde1b23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd69deb28cb34a7ba0f06bcbdcde1b23"}}, "title": "Role of GDH and PARP inhibitors as novel treatments for SDHB-deficient PPGLs.", "authors": [{"family": "Tabebi", "given": "Mouna", "initials": "M", "orcid": "0000-0002-2873-161X", "researcher": {"href": "https://publications.scilifelab.se/researcher/285705c043f34b55826e7f33ab36a875.json"}}, {"family": "Abdallah", "given": "Sallam", "initials": "S"}, {"family": "El-Serafi", "given": "Ahmed", "initials": "A"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P", "orcid": "0000-0001-9867-8706", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1fc163b9a08421180f7f235af3897f4.json"}}, {"family": "Gimm", "given": "Oliver", "initials": "O", "orcid": "0000-0002-0054-664X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9879641fb40042ae90ff034f4912a16d.json"}}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "Endocr. Relat. Cancer", "issn": "1479-6821", "issn-l": "1351-0088", "volume": "32", "issue": "10", "pages": null}, "abstract": "SDHB, one of the four genes encoding the subunits of the Krebs cycle enzyme succinate dehydrogenase (SDH), acts as a tumor suppressor in several human cancers, including pheochromocytomas/paragangliomas. Mutations in SDHB lead to a reduction or complete loss of enzymatic activity, linking SDHB to paraganglioma malignancy. Given the difficulty in curing metastatic paragangliomas and the limited value of surgery, new treatments are needed. Glutamine dehydrogenase 1 (GDH1), a key regulator of glutathione metabolism, and poly (ADP-ribose) polymerase (PARP), essential for repairing single- or double-stranded DNA breaks, are crucial in cancer initiation and progression. We treated the human pheochromocytoma cell line (hPheo1) with knocked-down SDHB using radiation, the GDH inhibitor 'R162', and the PARP inhibitor 'olaparib'. Combining R162 with radiation enhances anticancer effectiveness, reduces cell proliferation, and causes G2/M phase arrest in the wild-type and KD-SDHB hPheo1 cell line. KD-SDHB hPheo1 cells treated with olaparib alone were more resistant than wild-type cells but were more sensitive in combination with radiation, activated repair mechanisms, and halted cell cycle progression at the G2/M phase. These results suggest that enhancing radiation-induced DNA damage could be a potential treatment strategy for metastatic pheochromocytomas/paragangliomas. Inhibiting GDH1 and PARP activities, with radiation, may represent promising strategies for the treatment of SDHB-deficient pheochromocytoma/paraganglioma; however, their effects do not appear to be specific to SDHB-deficient cells and require further validation.", "doi": "10.1530/ERC-25-0173", "pmid": "40990469", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics Link\u00f6ping": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ERC-25-0173"}], "notes": [], "created": "2025-10-09T06:57:26.582Z", "modified": "2025-11-04T09:44:51.833Z"}, {"entity": "publication", "iuid": "aeb92fd9030f40e5b001042ea6594c76", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aeb92fd9030f40e5b001042ea6594c76.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aeb92fd9030f40e5b001042ea6594c76"}}, "title": "Developmental low-dose bisphenol A exposure leads to extensive transcriptome female masculinization and male feminization later in life.", "authors": [{"family": "Lind", "given": "Thomas", "initials": "T", "orcid": "0000-0003-2791-688X", "researcher": {"href": "https://publications.scilifelab.se/researcher/343532f8d9b44c848895493afbf32289.json"}}, {"family": "Dunder", "given": "Linda", "initials": "L"}, {"family": "Lejonklou", "given": "Margareta H", "initials": "MH"}, {"family": "Lind", "given": "P Monica", "initials": "PM"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Lind", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "410", "issn-l": null}, "abstract": "Bisphenol A (BPA) is an endocrine disruptor, and exposure to low doses in utero has been associated with the development of metabolic diseases. Previous studies have suggested that bone marrow (BM) may be particularly susceptible to BPA exposure.\n\nHere, we investigate how developmental exposure to low levels of BPA affects the BM transcriptome and the blood metabolic profile in Fischer 344 rats later in life. We compare these effects to those observed in human metabolic syndrome (MetS) using a population-based cohort.\n\nThe results show an unexpectedly extensive sex-biased effect on the BM transcriptome from a BPA dose approximately eight times lower than the recent temporary European Food Safety Authority (EFSA) human tolerable daily intake (TDI) and a higher dose considered safe in 2015. BPA exposure induces sex-specific changes in gene expression, progressing toward a hypometabolic cancer-like state in females and a hypermetabolic autoimmunity-like state in males, with a blood metabolic profile that significantly overlaps with human MetS in a cross-sectional study.\n\nWe conclude that developmental low-dose BPA exposure might induce metabolic syndrome specifically in males, possibly by affecting T cell activity in a sex-specific manner. Our study provides biologically plausible and convincing evidence for significant effects from low-dose BPA exposure, supporting the substantial lowering of the human BPA TDI by EFSA based on its critical effects on T cells.", "doi": "10.1038/s43856-025-01119-8", "pmid": "41034487", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Swedish Metabolomics Centre": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12488919"}, {"db": "pii", "key": "10.1038/s43856-025-01119-8"}], "notes": [], "created": "2025-11-17T15:52:20.678Z", "modified": "2025-11-27T08:05:30.935Z"}, {"entity": "publication", "iuid": "85de2289fd19407dad34e21e261cb987", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85de2289fd19407dad34e21e261cb987.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85de2289fd19407dad34e21e261cb987"}}, "title": "Detection and characterisation of ligand-induced conformational changes in acetylcholine binding proteins using biosensors and X-ray crystallography.", "authors": [{"family": "FitzGerald", "given": "Edward A", "initials": "EA", "orcid": "0000-0002-0603-1241", "researcher": {"href": "https://publications.scilifelab.se/researcher/66338852ec3d475380ba5bf6d50be1b7.json"}}, {"family": "Cederfelt", "given": "Daniela", "initials": "D"}, {"family": "Kovryzhenko", "given": "Daria", "initials": "D"}, {"family": "Boronat", "given": "Pierre", "initials": "P"}, {"family": "Lund", "given": "Bjarte Aarmo", "initials": "BA", "orcid": "0000-0001-9141-0555", "researcher": {"href": "https://publications.scilifelab.se/researcher/941bad0f031c47cea46b35bc049d778a.json"}}, {"family": "Dobritzsch", "given": "Doreen", "initials": "D"}, {"family": "Hennig", "given": "Sven", "initials": "S", "orcid": "0000-0002-8297-6845", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a64c0c8bf0e457d8251a98f54fc79df.json"}}, {"family": "Paseiro", "given": "Pablo Porragas", "initials": "PP"}, {"family": "de Esch", "given": "Iwan J P", "initials": "IJP"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "RSC Chem Biol", "issn": "2633-0679", "volume": "6", "issue": "10", "pages": "1625-1639", "issn-l": null}, "abstract": "Analysis of ligand-induced structural changes in proteins is challenging due to the lack of experimental methods suited for detection and characterisation of both ligand binding and induced structural changes. We have explored biosensors with different detection principles to study interactions between ligands and acetylcholine binding proteins (AChBPs), soluble homologues of Cys-loop ligand gated ion channels (LGICs) that undergo similar structural changes as LGICs upon ligand binding. X-ray crystallography was used to identify binding sites and establish if the detected conformational changes involved small changes in loop C or major structural changes in the pentamer associated with ion channel opening. Experiments were initially focused on ligands exhibiting complex surface plasmon resonance (SPR) biosensor sensorgrams or detected by second harmonic generation (SHG) biosensor analysis. Surface acoustic wave (SAW) and SHG biosensors confirmed that complexities in SPR data were indeed due to ligand-induced conformational changes. Grating coupled interferometry (GCI) biosensor sensorgrams were less complex, despite similar detection principles. switchSENSE biosensor analysis revealed that ligands resulted in either a compaction or expansion of the protein structure. X-ray crystallography of the protein-ligand complexes was only successful for 7 out of 12 ligands, despite nM-\u03bcM affinities. Crystals were not obtained for the two compounds shown by SHG analysis to induce large structural changes, while electron densities were not seen in the structures for some ligands. The work presented herein shows that several biosensor technologies have a unique capability to detect and discriminate binding and ligand induced conformational changes in proteins, also when interactions are rapid, weak and structural changes are small. However, they are complementary and provide different information.", "doi": "10.1039/d5cb00041f", "pmid": "40896114", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12394895"}, {"db": "pii", "key": "d5cb00041f"}], "notes": [], "created": "2025-11-18T22:03:28.805Z", "modified": "2025-11-18T22:03:29.261Z"}, {"entity": "publication", "iuid": "dda4cd13d28c4f27989bed1cf9560b63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dda4cd13d28c4f27989bed1cf9560b63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dda4cd13d28c4f27989bed1cf9560b63"}}, "title": "Decoding the genetic drivers of marine bacterial blooms through comparative genomics.", "authors": [{"family": "Rey-Velasco", "given": "Xavier", "initials": "X"}, {"family": "Auladell", "given": "Adri\u00e0", "initials": "A"}, {"family": "Deulofeu-Capo", "given": "Ona", "initials": "O"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Ferrera", "given": "Isabel", "initials": "I"}, {"family": "S\u00e1nchez", "given": "Olga", "initials": "O"}, {"family": "Gasol", "given": "Josep M", "initials": "JM"}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "13", "issue": "1", "pages": "198", "issn-l": "2049-2618"}, "abstract": "While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as \"bloomers,\" have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms.\n\nWe tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle.\n\nIn this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans. Video Abstract.", "doi": "10.1186/s40168-025-02182-y", "pmid": "41029845", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12487129"}, {"db": "pii", "key": "10.1186/s40168-025-02182-y"}], "notes": [], "created": "2025-11-21T13:50:47.554Z", "modified": "2025-11-21T13:53:54.255Z"}, {"entity": "publication", "iuid": "04e9d7eb6fd041648cef2ac003bdaae7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04e9d7eb6fd041648cef2ac003bdaae7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04e9d7eb6fd041648cef2ac003bdaae7"}}, "title": "Chromosome-level assembly of the club-legged grasshopper (Gomphocerus sibiricus) genome.", "authors": [{"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Varma", "given": "Mahendra", "initials": "M"}, {"family": "Cheng", "given": "Xinyi", "initials": "X"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "MB"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836"}, "abstract": "Grasshoppers represent true outliers in genome sizes, both within insects and within animals in general. Their genomes are large and generally variable in sizes and feature a high abundance of repetitive DNA sequences. This has hampered the assembly of grasshopper genomes to chromosome level. Here we present a chromosome-level reference genome for the club-legged grasshopper (Gomphocerus sibiricus, Acrididae: Gomphocerinae) using PacBio HiFi long-read and Hi-C sequencing technologies. In male haploid cells, the species has a chromosome set of n = 9 with an X0 sex-determination system, characterized by an absence of a Y chromosome. Our assembly spans 9.57 Gb in total, with 8.87 Gb organized into nine chromosomes-eight autosomes and the X chromosome. The final assembly has a scaffold N50 value of 1.58 Gb, covers 96.7% single copy Insecta orthologs, and contains 42,665 predicted protein-coding genes and 43,385 mRNA transcripts. We compiled a curated, non-redundant, species-specific repeat library and used it to annotate repetitive DNA, covering 81.69% of the genome, mostly DNA transposons, LINE and LTR retrotransposons. The genome of the club-legged grasshopper shows high degree of synteny with the locusts Schistocerca gregaria and Locusta migratoria, and the analysis strongly indicates three autosome-autosome centric fusions in Gomphocerinae. The genome offers a valuable resource for grasshopper genomics and for exploring the genetic basis of a transspecies color polymorphism.", "doi": "10.1093/g3journal/jkaf231", "pmid": "41029998", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "8269502"}], "notes": [], "created": "2025-10-03T08:05:05.113Z", "modified": "2025-11-14T11:07:48.365Z"}, {"entity": "publication", "iuid": "3ab0bc13f5cc43e99b0e24ac58f29f78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ab0bc13f5cc43e99b0e24ac58f29f78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ab0bc13f5cc43e99b0e24ac58f29f78"}}, "title": "Bioinspired mycobacterial lipid coating of porous particles for enhanced antimicrobial efficacy.", "authors": [{"family": "Campos Pacheco", "given": "Jes\u00fas E", "initials": "JE"}, {"family": "Davids", "given": "Camilla", "initials": "C"}, {"family": "Yalovenko", "given": "Tetiana", "initials": "T"}, {"family": "N\u00e4sstr\u00f6m", "given": "Elin", "initials": "E"}, {"family": "Ahnlund", "given": "Maria", "initials": "M"}, {"family": "Godaly", "given": "Gabriela", "initials": "G"}, {"family": "Valetti", "given": "Sabrina", "initials": "S"}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "Eur J Pharm Sci", "issn": "1879-0720", "volume": "213", "pages": "107225", "issn-l": "0928-0987"}, "abstract": "The study aimed to investigate the unique lipid composition of Mycobacterium bovis BCG and its potential to enhance antimicrobial efficacy of lipid-coated mesoporous silica particles (MSPs). The bacterial lipids (BL) were extracted with petroleum ether and analyzed via LC-MS, revealing a complex mixture of phospholipids, including cardiolipin, phosphatidylcholine, phosphatidylethanolamine, and triacylglycerols. Lipid coating (using bacterial lipids and lung surfactant DPPC as the main component) was performed on MSPs via vesicle fusion approach and confirmed with ATR-FTIR spectroscopy. MSPs were loaded with clofazimine (CLZ), as a drug model for tuberculosis. The obtained BL-DPPC-coated CLZ-MSPs were more effective in inhibiting mycobacterial growth and killing intracellular mycobacteria compared to uncoated and DPPC-coated CLZ-MSPs. The bacterial lipids showed a good safety profile on M1-like and M2-like human primary macrophages without inducing a strong immune response or formation of foam cells. These findings suggest that the obtained bacterial lipid coatings can improve antimicrobial efficacy in treating both extracellular and intracellular mycobacteria infections directly in the lungs.", "doi": "10.1016/j.ejps.2025.107225", "pmid": "40780537", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0928-0987(25)00224-6"}], "notes": [], "created": "2025-11-18T12:03:29.035Z", "modified": "2025-11-18T12:03:29.055Z"}, {"entity": "publication", "iuid": "25dfec9e03fc41aeb351f41e6acf76d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25dfec9e03fc41aeb351f41e6acf76d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25dfec9e03fc41aeb351f41e6acf76d8"}}, "title": "Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr.", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K", "orcid": "0000-0002-9852-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba96d1e78654b6992ef1c25035e93da.json"}}, {"family": "Fedi", "given": "Mariano Olivera", "initials": "MO"}, {"family": "Baker", "given": "Kendall", "initials": "K"}, {"family": "Barker", "given": "Tom", "initials": "T"}, {"family": "Catchpole", "given": "Leah", "initials": "L"}, {"family": "Ciofi", "given": "Claudio", "initials": "C", "orcid": "0000-0001-8537-8659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15012e62daf4c28b3c101550f460d35.json"}}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Collins", "given": "Joanna", "initials": "J"}, {"family": "Diedericks", "given": "Genevieve", "initials": "G"}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA"}, {"family": "Durrant", "given": "Alex", "initials": "A"}, {"family": "Hindar", "given": "Kjetil", "initials": "K", "orcid": "0000-0002-2769-2284", "researcher": {"href": "https://publications.scilifelab.se/researcher/0093cfa9f60e4e7db25d898de5c194b9.json"}}, {"family": "Iannucci", "given": "Alessio", "initials": "A", "orcid": "0000-0001-7729-4412", "researcher": {"href": "https://publications.scilifelab.se/researcher/da461c1ddb4649928a998aa9802a5ea3.json"}}, {"family": "Irish", "given": "Naomi", "initials": "N"}, {"family": "Knitlhoffer", "given": "Vanda", "initials": "V"}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG"}, {"family": "Lucchini", "given": "Sacha", "initials": "S"}, {"family": "McTaggart", "given": "Seanna", "initials": "S"}, {"family": "P\u00e1lsson", "given": "Arnar", "initials": "A", "orcid": "0000-0002-6525-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbe0e0cea2254ede8a1149cc2b917b6a.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Snorrason", "given": "Sigur\u00f0ur S", "initials": "SS"}, {"family": "Svardal", "given": "Hannes", "initials": "H"}, {"family": "Swarbreck", "given": "David", "initials": "D"}, {"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Watkins", "given": "Christopher", "initials": "C"}, {"family": "Wood", "given": "Jonathan M D", "initials": "JMD", "orcid": "0000-0002-7545-2162", "researcher": {"href": "https://publications.scilifelab.se/researcher/c255ed6ec2f246028326f9fece911f74.json"}}, {"family": "Xiao", "given": "Han", "initials": "H", "orcid": "0009-0000-4699-5590", "researcher": {"href": "https://publications.scilifelab.se/researcher/12a89016ae0d41788407e0b5a342d933.json"}}, {"family": "Gharbi", "given": "Karim", "initials": "K"}, {"family": "J\u00f3nsson", "given": "Zophon\u00edas O", "initials": "ZO", "orcid": "0000-0001-5798-9647", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dabaeca1ef54eb289cc48aab86ae2aa.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e70085", "volume": "34", "issue": "19", "issn-l": "0962-1083"}, "abstract": "Salmonids have a remarkable ability to form sympatric morphs after postglacial colonisation of freshwater lakes. These morphs often differ in morphology, feeding and spawning behaviour. Here, we explored the genetic basis of morph differentiation in Arctic charr (n = 283) by first establishing a high-quality reference genome and then using this in whole genome sequencing of distinct morphs present in two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions were found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. Our findings are consistent with a highly polygenic basis of morph differentiation with population-specific selection on alleles linked to the development of similar morph phenotypes. The results support a model where morph differentiation is first established through phenotypic plasticity, leading to niche expansion and separation. This may be followed by gradual development of reproductive isolation, locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence.", "doi": "10.1111/mec.70085", "pmid": "40856096", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12456120"}], "notes": [], "created": "2025-09-08T06:59:34.138Z", "modified": "2025-11-28T10:51:42.317Z"}, {"entity": "publication", "iuid": "c9fda46a5deb4048a04ccbe376a95bed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9fda46a5deb4048a04ccbe376a95bed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9fda46a5deb4048a04ccbe376a95bed"}}, "title": "Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals.", "authors": [{"family": "More", "given": "Kuldeep D", "initials": "KD", "orcid": "0000-0002-8278-8086", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b7cfdaad6614e6986ddd3a9c25434c4.json"}}, {"family": "Lebrasseur", "given": "Oph\u00e9lie", "initials": "O", "orcid": "0000-0003-0687-8538", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f100bd635446739f54bcabbf1840bc.json"}}, {"family": "Garrido", "given": "Jaime Lira", "initials": "JL", "orcid": "0000-0002-0702-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/03c72a8c91e04eb5bd580f999435809e.json"}}, {"family": "Seguin-Orlando", "given": "Andaine", "initials": "A", "orcid": "0000-0002-8265-3229", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f62251e48e34acdb3bea43f1f88c415.json"}}, {"family": "Discamps", "given": "Emmanuel", "initials": "E", "orcid": "0000-0002-2464-0761", "researcher": {"href": "https://publications.scilifelab.se/researcher/d53686becfbd4e919aac22195bbc80c0.json"}}, {"family": "Estrada", "given": "Oscar", "initials": "O"}, {"family": "Tonasso-Calvi\u00e8re", "given": "Laure", "initials": "L"}, {"family": "Chauvey", "given": "Lorele\u00ef", "initials": "L"}, {"family": "Tressi\u00e8res", "given": "Ga\u00ebtan", "initials": "G"}, {"family": "Schiavinato", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Gibert", "given": "Morgane", "initials": "M"}, {"family": "Padula", "given": "Horacio", "initials": "H"}, {"family": "Chiavazza", "given": "Horacio", "initials": "H"}, {"family": "Fern\u00e1ndez", "given": "Pablo M", "initials": "PM"}, {"family": "Guardia", "given": "Nicol\u00e1s M", "initials": "NM"}, {"family": "Borges", "given": "Caroline", "initials": "C"}, {"family": "Bertani", "given": "St\u00e9phane", "initials": "S", "orcid": "0000-0002-0398-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3e67c04c53c4dc49da8cfb7d77d1492.json"}}, {"family": "Contreras-Mancilla", "given": "Juan", "initials": "J"}, {"family": "Allccarima-Cris\u00f3stomo", "given": "Diana", "initials": "D"}, {"family": "Fhon", "given": "Miguel", "initials": "M"}, {"family": "Barrey", "given": "Eric", "initials": "E", "orcid": "0000-0001-7691-8705", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fc1e75ebc848bd855bab192930fc5d.json"}}, {"family": "Charliquart", "given": "L\u00e9a", "initials": "L"}, {"family": "Robbe", "given": "Emilie", "initials": "E"}, {"family": "de Noblet", "given": "Thibault", "initials": "T"}, {"family": "Zhumatayev", "given": "Rinat", "initials": "R"}, {"family": "Shakenov", "given": "Samat", "initials": "S"}, {"family": "Vila", "given": "Emmanuelle", "initials": "E", "orcid": "0000-0002-2238-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb48894d055d4413a26c6f196f35497e.json"}}, {"family": "Berthon", "given": "R\u00e9mi", "initials": "R"}, {"family": "Mashkour", "given": "Marjan", "initials": "M", "orcid": "0000-0003-3630-9459", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d45bd37c43f4f7fba2c62c9a26e18c7.json"}}, {"family": "Khazaeli", "given": "Roya", "initials": "R"}, {"family": "Nikgoftar", "given": "Ahmad", "initials": "A"}, {"family": "Vahdati", "given": "Ali A", "initials": "AA"}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Houle", "given": "Jean-Luc", "initials": "JL", "orcid": "0000-0001-6711-3104", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4700112eee4f10b7175311f42e5f6b.json"}}, {"family": "Bayarsaikhan", "given": "Jamsranjav", "initials": "J"}, {"family": "Wilczynski", "given": "Jaroslaw", "initials": "J"}, {"family": "Moskal-Del Hoyo", "given": "Magdalena", "initials": "M"}, {"family": "Nowak", "given": "Marek", "initials": "M"}, {"family": "Taylor", "given": "William", "initials": "W"}, {"family": "B\u0103l\u0103\u0219escu", "given": "Adrian", "initials": "A"}, {"family": "Dobrescu", "given": "Roxana", "initials": "R"}, {"family": "Benecke", "given": "Norbert", "initials": "N"}, {"family": "Arbuckle", "given": "Benjamin", "initials": "B"}, {"family": "Steadman", "given": "Sharon", "initials": "S"}, {"family": "McMahon", "given": "Gregory", "initials": "G"}, {"family": "\u0160ikanji\u0107", "given": "Petra Raji\u0107", "initials": "PR"}, {"family": "Buric", "given": "Marcel", "initials": "M"}, {"family": "Vuki\u010devi\u0107", "given": "Tajana Trbojevi\u0107", "initials": "TT"}, {"family": "Alvarez", "given": "Nadir", "initials": "N", "orcid": "0000-0002-0729-166X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0b080976b224f75a61355bdefebe911.json"}}, {"family": "Castel", "given": "Jean-Christophe", "initials": "JC", "orcid": "0000-0002-2366-5596", "researcher": {"href": "https://publications.scilifelab.se/researcher/a75c23a0ef934486b6fa1d7015445d55.json"}}, {"family": "Boudadi-Maligne", "given": "Myriam", "initials": "M", "orcid": "0000-0003-0583-7419", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9a675a1af44c3481db66d66656f472.json"}}, {"family": "Star", "given": "Bastiaan", "initials": "B", "orcid": "0000-0003-0235-9810", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4edcdfadd284a8e9b6b474ff34fd424.json"}}, {"family": "Post-Melbye", "given": "Julian Robert", "initials": "JR"}, {"family": "R\u00f8dsrud", "given": "Christian L\u00f8chsen", "initials": "CL"}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Charlton", "given": "Sophy", "initials": "S", "orcid": "0000-0001-7487-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/32089b9969b243e8b197a9f37ffd63a3.json"}}, {"family": "Mullin", "given": "Victoria E", "initials": "VE"}, {"family": "Daly", "given": "Kevin G", "initials": "KG", "orcid": "0000-0002-5579-6144", "researcher": {"href": "https://publications.scilifelab.se/researcher/7853932330d3450d892199f99cddc921.json"}}, {"family": "Burgos", "given": "Nohemi Sala", "initials": "NS"}, {"family": "Pablos", "given": "Adrian", "initials": "A"}, {"family": "Dalen", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Bradley", "given": "Daniel G", "initials": "DG", "orcid": "0000-0001-7335-7092", "researcher": {"href": "https://publications.scilifelab.se/researcher/9598208f97ac4a76816859659695e1e3.json"}}, {"family": "Frantz", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b1179f8ee34ebbbdd466fb977f3ce7.json"}}, {"family": "Larson", "given": "Greger", "initials": "G", "orcid": "0000-0002-4092-0392", "researcher": {"href": "https://publications.scilifelab.se/researcher/8313c5d2d5a148349ad14e51deca8ab5.json"}}, {"family": "Orlando", "given": "Ludovic", "initials": "L", "orcid": "0000-0003-3936-1850", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca463500fb034711b6200d5b611e4c1d.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "25", "issue": "7", "pages": "e14112", "issn-l": "1755-098X"}, "abstract": "In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.", "doi": "10.1111/1755-0998.14112", "pmid": "40202701", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12415940"}], "notes": [], "created": "2026-02-26T11:49:10.191Z", "modified": "2026-02-26T11:49:11.976Z"}, {"entity": "publication", "iuid": "276f9dc9c9074208b65c0d97631c4af2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/276f9dc9c9074208b65c0d97631c4af2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/276f9dc9c9074208b65c0d97631c4af2"}}, "title": "Toward a Species Search Engine: KISSE Offers a Rigorous Statistical Framework for Bone Collagen Tandem Mass Spectrometry Data.", "authors": [{"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85179acfa7e4916ad40ae478d6dcc0a.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Chernobrovkin", "given": "Alexey L", "initials": "AL"}, {"family": "Lundstrom", "given": "Susanna L", "initials": "SL"}, {"family": "Lyu", "given": "Hezheng", "initials": "H", "orcid": "0009-0008-7995-6473", "researcher": {"href": "https://publications.scilifelab.se/researcher/de932cbcb2c341f7a6544104026c7b1c.json"}}, {"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b3f220ebf947779d4b2638d2ccef1c.json"}}, {"family": "Vegvari", "given": "Akos", "initials": "A", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Gaetani", "given": "Massimilliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "12", "issue": "40", "pages": "e03963", "issn-l": null}, "abstract": "DNA and bone collagen are two key sources of resilient molecular markers used to identify species from their remains. Collagen is more stable than DNA, and thus it is preferred for ancient and degraded samples. Current mass spectrometry-based collagen sequencing approaches are empirical and lack a rigorous statistical framework. Based on the well-developed approaches to protein identification in shotgun proteomics, a first approximation of the species search engine (SSE) is introduced. SSE named KISSE is based on a species-specific library of collagenous peptides that uses both peptide sequences and their relative abundances. The developed statistical model can identify the species and the probability of correct identification, as well as determine the likelihood of the analyzed species not being in the library. The advantages and limitations of the proposed approach, and the possibility of extending it to other tissues is discussed.", "doi": "10.1002/advs.202503963", "pmid": "40787835", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12561455"}], "notes": [], "created": "2025-11-25T16:41:57.206Z", "modified": "2025-11-25T16:41:57.260Z"}, {"entity": "publication", "iuid": "e851d932ff224ce9a80844e9e4e5cd2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e851d932ff224ce9a80844e9e4e5cd2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e851d932ff224ce9a80844e9e4e5cd2c"}}, "title": "The transcription factor LHX2 mediates and enhances oncogenic BMP signaling in medulloblastoma.", "authors": [{"family": "Ohata", "given": "Yae", "initials": "Y"}, {"family": "Ali", "given": "Mohamad M", "initials": "MM", "orcid": "0000-0002-4902-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/780c944670ff4d7489410895569ac257.json"}}, {"family": "Tsubakihara", "given": "Yutaro", "initials": "Y"}, {"family": "Itoh", "given": "Yuka", "initials": "Y"}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G"}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Mor\u00e9n", "given": "Anita", "initials": "A"}, {"family": "Gol\u00e1n-Cancela", "given": "Irene", "initials": "I"}, {"family": "Nakada", "given": "Ayana", "initials": "A"}, {"family": "Voytyuk", "given": "Oleksandr", "initials": "O"}, {"family": "Tsuchiya", "given": "Maiko", "initials": "M"}, {"family": "Fukui", "given": "Rei", "initials": "R"}, {"family": "Yamamoto", "given": "Kouhei", "initials": "K"}, {"family": "Mart\u00edn-Rubio", "given": "Paula", "initials": "P", "orcid": "0000-0002-2702-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71065b5619e414bb6401638b76b2160.json"}}, {"family": "Sancho", "given": "Patricia", "initials": "P"}, {"family": "Strell", "given": "Carina", "initials": "C"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Wechsler-Reya", "given": "Robert J", "initials": "RJ"}, {"family": "Hashizume", "given": "Yoshinobu", "initials": "Y"}, {"family": "Miyazono", "given": "Kohei", "initials": "K", "orcid": "0000-0001-7341-0172", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a14a58f628d435a94ad9540478117cb.json"}}, {"family": "Caja", "given": "Laia", "initials": "L", "orcid": "0000-0002-8786-8763", "researcher": {"href": "https://publications.scilifelab.se/researcher/62d8ae2bdac54a6584afeac2b766f628.json"}}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH", "orcid": "0000-0002-9508-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f705f7c509904a1db721ace2267ca48f.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Cell Death Differ.", "issn": "1476-5403", "volume": "32", "issue": "10", "pages": "1915-1929", "issn-l": "1350-9047"}, "abstract": "Oncogenic events perturb cerebellar development leading to medulloblastoma, a common childhood brain malignancy. Molecular analyses classify medulloblastoma into the WNT, SHH, Group 3 and Group 4 subgroups. Bone morphogenetic protein (BMP) pathways control cerebellar development and have been linked to the progression of medulloblastoma disease, with major remaining gaps in their mechanistic and clinically-relevant roles. We therefore aimed at exploring BMP mechanisms of action in medulloblastoma. Patient-derived tumors from different subgroups were analyzed in mouse xenografts, complemented by independent tumor immunohistochemical analysis. Cell-based assays analyzed signaling mechanisms. Medulloblastoma cell orthotopic xenografts analyzed tumor growth and metastasis in vivo. Active BMP signaling, detected as nuclear and phosphorylated SMAD1/5, characterized several medulloblastoma subgroups, with enrichment in Group 4, SHH and Group 3 tumors. Spatial transcriptomics in tumor areas, complemented by transcriptomic analysis of multiple cell models, identified BMP-dependent transcriptional induction of the LIM-homeobox gene 2 (LHX2). BMP signaling via SMADs induced LHX2 expression and LHX2 transcriptionally induced BMP type I receptor (ACVR1) expression by association with the proximal promoter region of the ACVR1 gene. BMP signaling and LHX2 gain-of-function expression led to enriched stemness and associated chemoresistance in medulloblastoma cultures. In-mouse orthotopic transplantation of paired primary/recurrent Group 4 medulloblastoma cell populations, correspondingly expressing LHX2-low/BMP-low signaling and LHX2-high/BMP-high signaling, ascribed to the latter (high) group more efficient tumor propagation and spinal cord metastatic potential. Depletion of LHX2 in these recurrent tumor cells suppressed both BMP signaling and tumor propagation in vivo. Thus, LHX2 cooperates with, and enhances, oncogenic BMP signaling in medulloblastoma tumors. The molecular pathway that couples LHX2 function to BMP signaling in medulloblastoma deepens our understanding this malignancy.", "doi": "10.1038/s41418-025-01488-6", "pmid": "40148468", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12501261"}, {"db": "pii", "key": "10.1038/s41418-025-01488-6"}], "notes": [], "created": "2025-09-08T06:54:49.956Z", "modified": "2025-11-28T10:45:02.518Z"}, {"entity": "publication", "iuid": "cba3159ec5424a728069f17f7d0bdd59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cba3159ec5424a728069f17f7d0bdd59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cba3159ec5424a728069f17f7d0bdd59"}}, "title": "The barramundi (Lates calcarifer) mucus glycome is conserved across oral, skin and gill tissues but varies between individuals.", "authors": [{"family": "Thomsson", "given": "Kristina A", "initials": "KA"}, {"family": "Benktander", "given": "John", "initials": "J"}, {"family": "Erhardsson", "given": "Mattias", "initials": "M"}, {"family": "Wynne", "given": "James W", "initials": "JW"}, {"family": "Taylor", "given": "Richard S", "initials": "RS"}, {"family": "Lind\u00e9n", "given": "Sara K", "initials": "SK"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Fish Shellfish Immunol.", "issn": "1095-9947", "volume": "165", "pages": "110515", "issn-l": "1050-4648"}, "abstract": "Infections cause recurring setbacks in aquaculture and the mucus covering the fish surfaces is the first barrier pathogens encounter. The mucus is made up by highly glycosylated mucin glycoproteins. The glycan part of the mucins confers many of the mucus properties and pathogen regulating activities of the mucins, but these glycans remain largely uncharacterised in a range of aquacultured fish species. Barramundi (Lates calcarifer), also called Asian Sea Bass, is cultured in southeast Asia, Australia, USA, UK, Netherlands and Israel. Here we identified 74 O-glycans and three N-glycans in mucus from the oral cavity, skin, gills and intestine using liquid chromatography mass spectrometry. O-glycans from the oral cavity, skin and gill mucus were highly acidic and similar between these epithelia. The barramundi O-glycome displayed a relatively large inter-individual variation, which lead to that glycan features differing between oral cavity, skin and gills were not clearly distinguishable, although the intestinal glycan profiles clearly differed from the other epithelial sites. Barramundi intestinal glycans contained large glycans consisting of up to 14 monosaccharides, often including core 2 glycans with diHexNAc epitopes. This glycan library can serve as a platform for other studies, for example aiming for characterising host-microbe interactions, diagnostic purposes or disease intervention therapies. Furthermore, identification of novel glycans adds to the total glycan library available, leading to that artificial intelligence driven glycomics will become more accurate, allowing the glycomics field to move from a manual and time-consuming activity performed by specialists to automatic data analysis, more similar to other omics.", "doi": "10.1016/j.fsi.2025.110515", "pmid": "40578586", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1050-4648(25)00404-8"}], "notes": [], "created": "2025-11-20T18:08:59.622Z", "modified": "2025-11-20T18:08:59.628Z"}, {"entity": "publication", "iuid": "f790d37b3e404a3cb7752afc90ae9af5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f790d37b3e404a3cb7752afc90ae9af5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f790d37b3e404a3cb7752afc90ae9af5"}}, "title": "Systemic inflammatory biomarkers in relation to lung function and exercise-induced bronchoconstriction in adolescents.", "authors": [{"family": "Ersson", "given": "Karin", "initials": "K", "orcid": "0000-0003-3185-3316", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5f1f5fe2980458f9dd5dff19d5bc371.json"}}, {"family": "Alving", "given": "Kjell", "initials": "K"}, {"family": "Emtner", "given": "Margareta", "initials": "M"}, {"family": "Janson", "given": "Christer", "initials": "C"}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Malinovschi", "given": "Andrei", "initials": "A", "orcid": "0000-0002-4098-7765", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c246a24a09a4e67836f7ca6f1282610.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Pediatr Allergy Immunol", "issn": "1399-3038", "volume": "36", "issue": "10", "pages": "e70231", "issn-l": "0905-6157"}, "abstract": "The forced oscillation technique (FOT) complements spirometry in assessing lung function, with higher sensitivity to small airway dysfunction. Systemic inflammation is thought to influence lung development and exercise-induced bronchoconstriction (EIB), but its relationship to circulating inflammatory proteins in adolescents is unclear.\n\nTo investigate associations between systemic inflammatory biomarkers and baseline lung function and post-exercise airway responses in adolescents.\n\nIn 143 adolescents (13-15 years) from a population-based cohort, baseline spirometry, FOT, and baseline blood samples were obtained. Participants completed an exercise challenge to assess EIB via changes in forced expiratory volume in 1 s (FEV1), resistance at 5 Hz (R5), and reactance at 5 Hz (X5). Plasma protein levels were measured using the proximity extension assay technique (Olink Target Inflammation and Immune Response panels). Associations with lung function (FEV1% predicted, R5, and X5 z-scores) and post-exercise responses (\u2206FEV1, \u2206R5, \u2206X5) were analyzed using linear regression with false discovery rate correction. Interaction with atopy was also examined.\n\nHigher plasma levels of C-C motif chemokine 19 (CCL19) were significantly associated with lower FEV1% predicted and lower X5 z-scores at baseline, indicating reduced lung function and impaired small airway function. No proteins were associated with post-exercise airway responses after correction. Five proteins showed significant interactions with atopy in relation to EIB.\n\nElevated CCL19 may reflect systemic inflammatory processes contributing to impaired lung function in early adolescence. The observed atopy-related interactions suggest the need to consider atopy in studies of systemic inflammation and airway physiology.", "doi": "10.1111/pai.70231", "pmid": "41132128", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12550650"}], "notes": [], "created": "2025-11-25T19:21:13.160Z", "modified": "2025-11-25T19:21:13.273Z"}, {"entity": "publication", "iuid": "becf664053ca48debb8b2b1fb5214a6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/becf664053ca48debb8b2b1fb5214a6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/becf664053ca48debb8b2b1fb5214a6a"}}, "title": "State-of-the-Art and Future Directions in Structural Proteomics.", "authors": [{"family": "Happonen", "given": "Lotta J", "initials": "LJ"}, {"family": "Varjosalo", "given": "Markku", "initials": "M"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Mol. Cell Proteomics", "issn": "1535-9484", "issn-l": "1535-9476", "volume": "24", "issue": "10", "pages": "101065"}, "abstract": "Structural proteomics has undergone a profound transformation, driven by the convergence of advanced experimental methodologies and computational innovations. Cutting-edge mass spectrometry (MS)-based approaches, including cross-linking MS (XL-MS), hydrogen-deuterium exchange MS (HDX-MS), and limited proteolysis MS (LiP-MS), now enable unprecedented insights into protein topology, conformational dynamics, and protein-protein interactions. These methods, complemented by affinity purification (AP), co-immunoprecipitation (co-IP), proximity labeling (PL), and spatial proteomics techniques, have expanded our ability to characterize the structural proteome at a systems-wide scale. Integration with electron cryo-microscopy (cryo-EM), cryo-electron tomography (cryo-ET), nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, and small-angle X-ray/neutron scattering (SAXS/SANS) methods has further driven the field of integrative structural biology. These methods, in conjunction with AI-driven predictive models such as AlphaFold and RoseTTAFold, enable the high-resolution modeling of protein complexes and dynamic assemblies, bridging the gap between static structures and real-time conformational changes. This review explores the current state-of-the-art in structural proteomics, with a focus on methodological advances and the integration of XL-MS, HDX-MS, and LiP-MS with methods in structural biology. We further discuss the application of structural proteomics in deciphering disease mechanisms, identifying therapeutic targets, and guiding drug discovery, with these techniques poised to revolutionize precision medicine. Future directions emphasize fully integrative, multimodal approaches that unify experimental and computational paradigms, fostering a holistic understanding of the human proteome.", "doi": "10.1016/j.mcpro.2025.101065", "pmid": "40912403", "labels": {"Structural Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12546877"}, {"db": "pii", "key": "S1535-9476(25)00164-1"}], "notes": [], "created": "2025-11-27T15:00:10.314Z", "modified": "2025-11-27T15:01:19.675Z"}, {"entity": "publication", "iuid": "6ecf241cbd074ff794e16d5e6386bd62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ecf241cbd074ff794e16d5e6386bd62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ecf241cbd074ff794e16d5e6386bd62"}}, "title": "Spatial transcriptomics exploration of the primary neuroblastoma microenvironment in archived FFPE samples unveils novel paracrine interactions.", "authors": [{"family": "Siaw", "given": "Joachim T", "initials": "JT", "orcid": "0000-0002-1286-4485", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a4ce00b5a4b4ebb9ee746de59e2e943.json"}}, {"family": "Merseburger", "given": "Peter", "initials": "P", "orcid": "0000-0002-5154-8696", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad0a5677b41b4ffcb46c4e2ce9303e72.json"}}, {"family": "Boren\u00e4s", "given": "Marcus", "initials": "M", "orcid": "0009-0007-6326-5224", "researcher": {"href": "https://publications.scilifelab.se/researcher/9157baf8e62947f8995c484d3cfb93f1.json"}}, {"family": "Jansson", "given": "Caroline", "initials": "C", "orcid": "0009-0001-4115-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d696fca9d64a9f841c0ad59d454156.json"}}, {"family": "Karlsson", "given": "Jenny", "initials": "J", "orcid": "0000-0001-7681-0059", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e2ccecaff1d41bfa863dde6616eeadd.json"}}, {"family": "Claeys", "given": "Arne", "initials": "A", "orcid": "0000-0001-6990-1569", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3e7d3acc40b47bd8c5bc8313499dd61.json"}}, {"family": "Jennische", "given": "Eva", "initials": "E", "orcid": "0000-0002-2147-8412", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bc34c602c73456585a2a5815637ebb3.json"}}, {"family": "Lind", "given": "Dan E", "initials": "DE", "orcid": "0000-0002-8299-5659", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ba0b43eeb64fc28393a871fb507ca2.json"}}, {"family": "Gisselsson Nord", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3653582762b14f9a9ad2fe6aba511115.json"}}, {"family": "Palmer", "given": "Ruth H", "initials": "RH", "orcid": "0000-0002-2735-8470", "researcher": {"href": "https://publications.scilifelab.se/researcher/808281ecc2634b66a274895e58a122bd.json"}}, {"family": "Van den Eynden", "given": "Jimmy", "initials": "J", "orcid": "0000-0003-0002-5614", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b20f02703024987bc9791df1dc80e51.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "J. Pathol.", "issn": "1096-9896", "volume": "267", "issue": "2", "pages": "181-195", "issn-l": "0022-3417"}, "abstract": "High-risk neuroblastomas exhibit a high degree of intratumoral heterogeneity. Single-cell RNA sequencing has greatly improved our understanding of these tumors, but the method lacks cellular tissue context and spatial information about local signaling dynamics. To address this, we profiled untreated and chemotherapy-treated high-risk neuroblastomas from archived, formalin-fixed, paraffin-embedded (FFPE) tissues from two patients using spatial transcriptomics. We confirmed the transcriptional and cellular heterogeneous nature of the neuroblastoma microenvironment and identified several unique spatial niches and patterns. In one of the treated tumors, a spatially constrained cluster of undifferentiated and 11p-gained cancer cells was identified, surrounded by a rim of macrophages. A signaling interaction between the chemokine CCL18 and its receptor PITPNM3 was predicted between these cells. In the other tumor, we identified a stromal cluster with high transcriptional similarity to the adrenal cortex. These adrenocortical-like cells expressed several oncogenic ligand-encoding genes (e.g. ALKAL2 and NRTN), which were predicted to communicate with neighboring cancer cells that expressed the corresponding receptors (e.g. ALK, RET). Several of these interactions were further validated experimentally and were shown to be clinically relevant. Collectively, our spatial analysis identifies multiple previously unrecognized signaling axes that may offer novel therapeutic options in neuroblastoma. \u00a9 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.", "doi": "10.1002/path.6457", "pmid": "40778592", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12438011"}], "notes": [], "created": "2025-08-29T10:01:28.113Z", "modified": "2025-11-28T10:40:36.891Z"}, {"entity": "publication", "iuid": "1c9408722a544c9399742b1a4fbcdfd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c9408722a544c9399742b1a4fbcdfd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c9408722a544c9399742b1a4fbcdfd2"}}, "title": "Sleep health associations with serum metabolites in healthy adults.", "authors": [{"family": "S\u00f8rensen", "given": "Charlotte", "initials": "C"}, {"family": "Dudka", "given": "Ilona", "initials": "I"}, {"family": "Virel", "given": "Ana", "initials": "A"}, {"family": "K\u00e5reholt", "given": "Ingemar", "initials": "I"}, {"family": "Balter", "given": "Leonie Jt", "initials": "LJ"}, {"family": "Axelsson", "given": "John", "initials": "J"}, {"family": "Kalpouzos", "given": "Gr\u00e9goria", "initials": "G"}, {"family": "Sindi", "given": "Shireen", "initials": "S"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Brain Behav Immun Health", "issn": "2666-3546", "volume": "48", "pages": "101050", "issn-l": null}, "abstract": "Short and long sleep duration as well as poor sleep quality have been linked to higher prevalence of metabolic disorders. However, it is still unclear how diverse sleep variables relate to different metabolic pathways. This study examines how different features of sleep health relate to serum metabolites.\n\nThe study used data from 197 healthy individuals aged 20-79 (Females n = 103) from the IronAge study performed at Karolinska Institutet in Sweden. Sleep variables were assessed with the Karolinska Sleep Questionnaire, where the following variables were computed: sleep duration, sleep debt, midpoint, social jetlag (i.e., the discrepancy between midpoint on free and workdays), napping frequency and sleep quality. Morning fasting blood samples were collected and 1H NMR spectroscopy was utilized for metabolomic analysis. The metabolites were categorized according to their major metabolic pathways: amino acid, lipid, carbohydrate, energy and gut microbiota. Linear regressions were performed to examine the relationship between each sleep variable and metabolite.\n\nSleep duration, midpoint of sleep on free days, social jetlag and chronotype associated with eight metabolites at a significance level of p<0.01. Notably, midpoint associated with most metabolites spanning multiple pathways. A later midpoint was associated with higher levels of metabolites in the lipid pathway, and lower levels in the amino acid and energy pathway.\n\nThese observations indicate that sleep timing features, midpoint and social jetlag, have a stronger relationship with morning metabolism than other sleep health dimensions. Following replication in larger samples, these complex relationships may hold potential for health promotion.", "doi": "10.1016/j.bbih.2025.101050", "pmid": "40697974", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12281066"}, {"db": "pii", "key": "S2666-3546(25)00108-5"}], "notes": [], "created": "2025-09-10T14:26:50.336Z", "modified": "2025-10-17T13:03:52.184Z"}, {"entity": "publication", "iuid": "ee2e0ed6e5fc4e969acfc7bd207dfefe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee2e0ed6e5fc4e969acfc7bd207dfefe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee2e0ed6e5fc4e969acfc7bd207dfefe"}}, "title": "Progenitor exhausted PD-1+ T cells are cellular targets of immune checkpoint inhibition in atherosclerosis.", "authors": [{"family": "Mulholland", "given": "Megan", "initials": "M", "orcid": "0000-0002-3352-0403", "researcher": {"href": "https://publications.scilifelab.se/researcher/332a484487504958849ef563550cd8a0.json"}}, {"family": "Chalou", "given": "Anthi", "initials": "A", "orcid": "0009-0008-4969-3262", "researcher": {"href": "https://publications.scilifelab.se/researcher/5294de2282b44506977b10f1f8da6f47.json"}}, {"family": "Andersson", "given": "Samuel H A", "initials": "SHA", "orcid": "0009-0009-7497-9403", "researcher": {"href": "https://publications.scilifelab.se/researcher/863588877fc848ca96ba6b2e66c9086a.json"}}, {"family": "Depuydt", "given": "Marie A C", "initials": "MAC", "orcid": "0000-0002-7174-1952", "researcher": {"href": "https://publications.scilifelab.se/researcher/1725c990029e403fb7b0c228b112f418.json"}}, {"family": "Yu", "given": "Yinda", "initials": "Y"}, {"family": "Lin", "given": "Shiying", "initials": "S"}, {"family": "Tallb\u00e4ck", "given": "Klara", "initials": "K", "orcid": "0009-0009-4506-6330", "researcher": {"href": "https://publications.scilifelab.se/researcher/1210f8d35a2d480d839300492143a8bc.json"}}, {"family": "Ericsson", "given": "Astrid", "initials": "A"}, {"family": "Jakobsson", "given": "Gabriel", "initials": "G", "orcid": "0000-0001-5071-9505", "researcher": {"href": "https://publications.scilifelab.se/researcher/99f0995b89884f6eb8d33e0e51c33800.json"}}, {"family": "de Mol", "given": "Jill", "initials": "J", "orcid": "0000-0003-3541-9912", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c34c673397547b4bcecf3994d44882a.json"}}, {"family": "Kryvokhyzha", "given": "Dmytro", "initials": "D"}, {"family": "Lichtman", "given": "Andrew H", "initials": "AH", "orcid": "0000-0002-3546-058X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c22011616511413b8c9f22be31a1f951.json"}}, {"family": "Foks", "given": "Amanda C", "initials": "AC", "orcid": "0000-0002-9747-3458", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6713b7fbb8942bea6789bc4e07d575c.json"}}, {"family": "Schiopu", "given": "Alexandru", "initials": "A", "orcid": "0000-0002-7587-5050", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7d2edf9030a445583f692dc4d884b7f.json"}}, {"family": "Bj\u00f6rkbacka", "given": "Harry", "initials": "H", "orcid": "0000-0003-3918-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f4c07bc840f491d843f67a9932d5f3a.json"}}, {"family": "Sl\u00fctter", "given": "Bram", "initials": "B", "orcid": "0000-0003-3996-0503", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa4acafdcb714986a064c0c0369bd4f8.json"}}, {"family": "Gister\u00e5", "given": "Anton", "initials": "A", "orcid": "0000-0002-4614-8030", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e2beec3559745a6ba1859252df4a547.json"}}, {"family": "Engelbertsen", "given": "Daniel", "initials": "D", "orcid": "0000-0002-0289-5210", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc4f0e42f9444337adb276360c27c5cc.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Nat Cardiovasc Res", "issn": "2731-0590", "volume": "4", "issue": "10", "pages": "1311-1328", "issn-l": null}, "abstract": "Immune checkpoint inhibitors (ICIs), targeting checkpoint receptors such as programmed cell death protein 1 (PD-1), are associated with increased risk of cardiovascular events, but the underlying mechanisms remain poorly understood. Here we show that PD-1+ T cells from murine atherosclerotic aortas mainly display a progenitor exhausted phenotype (PD-1intSlamf6+Tim3-), produce IFN\u03b3 in vivo, exhibit signs of recent proliferation and maintain polyfunctionality. PD-1 blockade induced marked changes in plaque immune phenotype, with increased PD-1high T cell accumulation, IFN\u03b3 production, formation of lymphocyte foci and neutrophil recruitment. Depletion of PD-1high T cells prior to PD-1 blockade did not impede T cell recruitment, suggesting a role for progenitor exhausted PD-1int T cells in ICI-driven T cell plaque accumulation. Human circulating PD-1+ T cells produced IFN\u03b3 and were associated with subclinical coronary atherosclerosis. Our studies highlight IFN\u03b3-producing PD-1+ T cells as a potential key immune cell population mediating increased cardiovascular risk in patients with cancer receiving ICI.", "doi": "10.1038/s44161-025-00713-2", "pmid": "41057609", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12520982"}, {"db": "pii", "key": "10.1038/s44161-025-00713-2"}], "notes": [], "created": "2025-11-06T09:28:37.756Z", "modified": "2025-11-06T09:28:38.934Z"}, {"entity": "publication", "iuid": "ae53f79971b5422e8d7b0c5ef5626fe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae53f79971b5422e8d7b0c5ef5626fe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae53f79971b5422e8d7b0c5ef5626fe0"}}, "title": "Primary and Secondary Symbionts of Cambodian Cicadellidae and the Role of Parasitisation.", "authors": [{"family": "Phauk", "given": "Sophany", "initials": "S", "orcid": "0000-0002-8019-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/80bf701bd9c14bd08c081d49b0d6ecad.json"}}, {"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Meas", "given": "Seanghun", "initials": "S", "orcid": "0009-0003-8813-8839", "researcher": {"href": "https://publications.scilifelab.se/researcher/829ed324071b46cc8720d6ffcf68b701.json"}}, {"family": "Terenius", "given": "Olle", "initials": "O", "orcid": "0000-0002-9909-1859", "researcher": {"href": "https://publications.scilifelab.se/researcher/3042a807e20d444cafee3f760c38d5d1.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "17", "issue": "5", "pages": "e70196", "issn-l": "1758-2229"}, "abstract": "Leafhoppers (Hemiptera: Cicadellidae) are important vectors of plant pathogens in agricultural systems. Biological control via parasitisation is a key management strategy, but little is known about how microbial symbionts mediate host-parasitoid interactions. Here, we characterise the bacterial communities of six Cambodian leafhopper species (Cofana spectra, Exitianus sp., Goniagnathus punctifer, Maiestas dorsalis, Nephotettix virescens, and Stirellus sp.) and their parasitoids from the families Dryinidae (Hymenoptera) and Halictophagidae (Strepsiptera). We found that the bacterial symbiont Sulcia dominates cicadellid microbiotas, often coexisting with secondary symbionts. For example, Nasuia is present alongside Sulcia in Nephotettix, while Wolbachia is prevalent in Exitianus and Goniagnathus. Parasitoids exhibited distinct microbiotas with greater diversity; Rhodobacteraceae and Comamonadaceae were in dryinids, while Wolbachia was common in Halictophagidae. We analysed the microbiota of individual pairs of host-parasitoid and although parasitism did not significantly alter cicadellid overall microbiotas, some secondary symbionts (e.g., Arsenophonus, Wolbachia, Rickettsia, and Sodalis) were detected in both hosts and parasitoids, suggesting possible microbial transmission that warrants further investigation. These findings improve our understanding of host-parasitoid microbial interactions and highlight the relationship between primary and secondary symbiont communities.", "doi": "10.1111/1758-2229.70196", "pmid": "40957832", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12440678"}], "notes": [], "created": "2025-11-07T07:26:49.751Z", "modified": "2025-11-28T10:50:56.250Z"}, {"entity": "publication", "iuid": "de6969e0378342fcbb7457fa20c1eaaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de6969e0378342fcbb7457fa20c1eaaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de6969e0378342fcbb7457fa20c1eaaa"}}, "title": "Morphology and molecular mobility of plasticized lignins studied with polarization transfer solid-state NMR and SAXS", "authors": [{"family": "Henrik-Klemens", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0009-0007-1976-3285", "researcher": {"href": "https://publications.scilifelab.se/researcher/5941ad6feeb64db18edc253eeb47d016.json"}}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Bj\u00f6rn", "given": "Linnea", "initials": "L"}, {"family": "Matic", "given": "Aleksandar", "initials": "A", "orcid": "0000-0003-4414-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/74e8b2a137594fec8ac65918ccfbab94.json"}}, {"family": "Larsson", "given": "Anette", "initials": "A"}], "type": "journal-article", "published": "2025-10-00", "journal": {"title": "Polymer Testing", "issn": "0142-9418", "issn-l": null, "volume": "151", "issue": null, "pages": "108942"}, "abstract": null, "doi": "10.1016/j.polymertesting.2025.108942", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-09-10T14:22:08.316Z", "modified": "2025-10-17T13:03:52.202Z"}, {"entity": "publication", "iuid": "6566d93fe33a4568a9009b47056369d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6566d93fe33a4568a9009b47056369d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6566d93fe33a4568a9009b47056369d1"}}, "title": "Microbiota modulates compound-specific toxicity of environmental chemicals: A multi-omics analysis in zebrafish embryos.", "authors": [{"family": "Gugescu", "given": "Lydia", "initials": "L"}, {"family": "Yang", "given": "Ying", "initials": "Y"}, {"family": "Kool", "given": "Judy Fabienne", "initials": "JF"}, {"family": "Fyhrquist", "given": "Nanna", "initials": "N"}, {"family": "Wincent", "given": "Emma", "initials": "E"}, {"family": "Alenius", "given": "Harri", "initials": "H"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Environ Int", "issn": "1873-6750", "volume": "204", "pages": "109828", "issn-l": "0160-4120"}, "abstract": "Interactions between gut microbiota and environmental chemicals critically influence toxicological outcomes, yet mechanistic insights remain limited. Here, we combine developmental toxicity with full-length 16S rRNA gene sequencing, transcriptomic, and metabolomic analyses in germ-free (GF) and conventionally colonized wild-type (WT) zebrafish embryos to elucidate the microbiota's role in modulating chemical toxicity. Using representative compounds from major classes of environmental contaminants, we show that microbial presence significantly alters toxicity profiles in a compound-specific manner. The perfluorinated contaminant PFOS (perfluorooctanesulfonic acid) induced the strongest microbiota-dependent effects, with a greater number of differentially expressed genes in WT embryos and pronounced changes in immune and stress-related pathways. The pesticide boscalid and bisphenol F elicited distinct microbiota-modulated transcriptional and metabolic responses. Gene network analysis identified baseline microbial regulation of immune and metabolic programs, while metabolomics showed PFOS-dependent changes in L-tryptophan and its microbe-associated metabolites, including inosine, indoxyl sulfate and indole acetaldehyde, exclusively in WT embryos. These findings establish a mechanistically grounded framework for microbiota-chemical interactions and highlight the importance of integrating microbiome context into environmental health assessments.", "doi": "10.1016/j.envint.2025.109828", "pmid": "41043219", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S0160-4120(25)00579-3"}], "notes": [], "created": "2025-11-18T12:07:43.093Z", "modified": "2025-11-18T12:07:43.096Z"}, {"entity": "publication", "iuid": "3c388bd21b3d422ab656f4d2a33baa85", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c388bd21b3d422ab656f4d2a33baa85.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c388bd21b3d422ab656f4d2a33baa85"}}, "title": "Metaaltijden (vol. 12). Bijdragen in de studie van de metaaltijden", "authors": [], "type": "edited-book", "published": "2025-10-00", "journal": {"title": "ISBN: 9789464264180", "issn": "ISBN: 9789464264180", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "The Eurasian elk (Alces alces), the largest extant deer species in Europe, was once an impressive fixture of the Dutch ecosystem. Archaeological evidence has shown that it was not until the Middle Ages that the elk was extirpated in the Netherlands and many other European countries, due to overhunting, deforestation, and wetland redevelopment (Jensen et al. 2020; Schm\u00f6lcke & Zachos 2005; Walch 2000a). Despite being an indigenous animal, not much is known about the elk\u2019s existence in the Netherlands nor its relationship with humans. The last study on elk stems from over 20 years ago (Walch 2000a; 2000b). Since then, there has been an exponential increase in excavations in the Netherlands, yielding rich faunal records. While few in absolute terms, elk remains are relatively common in the Dutch archaeological record. Moreover, the discovery of three young elk skeletons deposited in a Bronze Age well, a unique find for Dutch \u2013 and possibly northern European \u2013 archaeology, provides an opportune starting point to explore past human-elk relationships.\r\nIn this article, we investigate the role of elk in the Dutch Bronze Age (2000-800 BCE). We focus on this period not only due to this unique deposition but also because this period has yielded the most elk finds. This makes it an intriguing period for the study of human-elk relationships. Furthermore, wild animals are often neglected in the study of farming societies, with the emphasis being instead on domesticates. This research is part of a broader project on elk in the Dutch Holocene.", "doi": "10.59641/nn278qz", "pmid": null, "labels": {"Ancient DNA": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-03T13:24:43.550Z", "modified": "2025-12-18T20:58:08.435Z"}, {"entity": "publication", "iuid": "89dc7c83508f4e3090b61c3c703047f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89dc7c83508f4e3090b61c3c703047f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89dc7c83508f4e3090b61c3c703047f1"}}, "title": "In Atlantic salmon skin infested with salmon lice, elevated seawater temperatures change gene expression and mucus glycosylation, which promotes pathogen binding.", "authors": [{"family": "Thomsson", "given": "Kristina A", "initials": "KA"}, {"family": "Sveen", "given": "Lene", "initials": "L"}, {"family": "Benktander", "given": "John", "initials": "J"}, {"family": "Dagnachew", "given": "Binyam S", "initials": "BS"}, {"family": "Quintana-Hayashi", "given": "Macarena P", "initials": "MP"}, {"family": "Johansen", "given": "Lill-Heidi", "initials": "LH"}, {"family": "Breiland", "given": "Mette W", "initials": "MW"}, {"family": "Jacq", "given": "Celeste", "initials": "C"}, {"family": "Ytteborg", "given": "Elisabeth", "initials": "E"}, {"family": "Linden", "given": "Sara K", "initials": "SK"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Fish Shellfish Immunol.", "issn": "1095-9947", "volume": "165", "pages": "110557", "issn-l": "1050-4648"}, "abstract": "Skin barrier function is paramount for fish health and is likely affected by the predicted increases in seawater temperature. Salmonid skin produces a mucus layer mainly composed of mucins. Mucin glycans regulate interactions with pathogens, including binding to host cells, quorum sensing and regulation of virulence genes. In this work, the objective was to elucidate the Atlantic salmon (Salmo salar) skin mucosal responses to temperature in the presence of salmon lice (Lepeophtheirus salmonis) to mimic salmon louse pressure at sea. A simultaneous louse and temperature challenge trial was performed, at low (5 \u00b0C), medium (10 \u00b0C), and high (17 \u00b0C) temperatures, using a protocol resulting in lice at the same development stage and density in all groups. Temperature affected skin morphology, with a thinner outer epidermal layer with fewer mucous cells at 17 \u00b0C than at 5 \u00b0C. Liquid chromatography-mass spectrometry demonstrated that the skin mucin O-glycome changed with temperature: the most pronounced glycan changes were a decrease of the disaccharide Sialyl-Tn and an increase of the tetrasaccharide NeuAc\u03b12-3Gal\u03b21-3[NeuAc\u03b12-6]GalNAcol and sulfated glycans at 17 \u00b0C. Principal component analysis of gene expression data clustered samples according to temperature treatments, and changes in expression of homologues of human sialyl-, core 1-, Gal, and GalNAc transferase genes were proposed to be linked to the glycan changes observed by mass spectrometry. Finally, Aeromonas salmonicida had a higher ability to bind mucins from fish kept at 17 \u00b0C than at 5 \u00b0C, demonstrating effects of temperature related glycosylation changes on host-pathogen interactions.", "doi": "10.1016/j.fsi.2025.110557", "pmid": "40639705", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1050-4648(25)00446-2"}], "notes": [], "created": "2025-11-20T18:09:00.842Z", "modified": "2025-11-20T18:09:00.847Z"}, {"entity": "publication", "iuid": "108b93c501e4463db30a9f3ede2b5468", "links": {"self": {"href": "https://publications.scilifelab.se/publication/108b93c501e4463db30a9f3ede2b5468.json"}, "display": {"href": "https://publications.scilifelab.se/publication/108b93c501e4463db30a9f3ede2b5468"}}, "title": "Impact of systemic SARS-CoV-2 vaccination on mucosal IgA responses to subsequent breakthrough infection.", "authors": [{"family": "Marking", "given": "Ulrika", "initials": "U"}, {"family": "Bladh", "given": "Oscar", "initials": "O"}, {"family": "Aguilera", "given": "Katherina", "initials": "K"}, {"family": "Pongracz", "given": "Tamas", "initials": "T"}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Greilert-Norin", "given": "Nina", "initials": "N"}, {"family": "Blom", "given": "Kim", "initials": "K"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "120", "pages": "105912", "issn-l": "2352-3964"}, "abstract": "Mucosal IgA responses are central to protection against SARS-CoV-2 infection and viral transmission. While systemic immunity following SARS-CoV-2 infection and vaccination is thoroughly investigated, we have limited understanding of factors affecting the generation and boosting of mucosal IgA.\n\nIn this cohort study, we investigated factors influencing mucosal SARS-CoV-2 IgA responses among 879 healthcare workers enrolled in the longitudinal COMMUNITY study. Blood samples and clinical data were collected from all participants every four months since April 2020. SARS-CoV-2 immune histories are well characterized through national vaccine and infection registries along with regular monitoring of seroconversion of spike and/or nucleocapsid antigen. Regression models were developed to assess the influence of vaccinations and prior infections on the magnitude of SARS-CoV-2 spike-specific IgA in nasal secretions collected from the cohort in October 2022.\n\nMucosal SARS-CoV-2 spike-specific IgA was detected in 81% of participants, with a positive association with number of prior infections, indicating a booster effect by reinfection. The increased odds ratio of detectable mucosal IgA remained for at least 22 months post infection. There was a strong association between repeated systemic vaccinations and a lower magnitude of mucosal IgA responses. Moreover, the temporal sequence of infection and vaccination influenced mucosal IgA responses, with higher levels among participants with infection prior to systemic vaccination as compared to those with breakthrough infection as the first viral encounter.\n\nThe observation that repeated mucosal exposures elicit enhanced and long-lasting mucosal IgA responses strengthens the rationale for developing effective mucosal vaccines. While systemic vaccination remains essential for preventing severe disease, our findings suggest that it may influence subsequent generation of mucosal IgA trough a reduction of viral load and inflammation in the mucosa. This is highly relevant for both understanding the development of population immunity and for optimizing the timing of a sequential systemic and mucosal vaccination approach.\n\nThis study was supported by grants from Region Stockholm, and SciLifeLab and the Knut and Alice Wallenberg Foundation, SSMF and European Research Council. We thank the Public Health Agency of Sweden for support.", "doi": "10.1016/j.ebiom.2025.105912", "pmid": "40961508", "labels": {"Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12466159"}, {"db": "pii", "key": "S2352-3964(25)00356-1"}], "notes": [], "created": "2025-11-25T19:16:29.573Z", "modified": "2025-11-25T19:19:37.215Z"}, {"entity": "publication", "iuid": "e9e5f0d76e26448ea903e68b1e56373e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9e5f0d76e26448ea903e68b1e56373e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9e5f0d76e26448ea903e68b1e56373e"}}, "title": "Heat-affected zone cracking in new 718-type superalloy VDM alloy 780: Effect of solution heat treatments and comparison with alloy 718", "authors": [{"family": "Ariaseta", "given": "Achmad", "initials": "A", "orcid": "0000-0002-9520-0456", "researcher": {"href": "https://publications.scilifelab.se/researcher/c51dbaf873644924be646d70c5d2f45f.json"}}, {"family": "Andersson", "given": "Joel", "initials": "J", "orcid": "0000-0001-9065-0741", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb14103bdd9b4df994ba97e3d17fb1c3.json"}}, {"family": "Ojo", "given": "Olanrewaju", "initials": "O"}], "type": "journal-article", "published": "2025-10-00", "journal": {"title": "Materials &amp; Design", "issn": "0264-1275", "volume": "258", "pages": "114733", "issn-l": null}, "abstract": null, "doi": "10.1016/j.matdes.2025.114733", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "NanoSIMS": "Service"}, "xrefs": [], "notes": [], "created": "2026-03-10T07:24:05.465Z", "modified": "2026-03-10T14:20:39.630Z"}, {"entity": "publication", "iuid": "b3ff74796a8d45b9ab091761be90b9a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b3ff74796a8d45b9ab091761be90b9a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b3ff74796a8d45b9ab091761be90b9a6"}}, "title": "Harmonizing human plasma metabolite annotation with Plasma Benchmark.", "authors": [{"family": "Koistinen", "given": "Ville", "initials": "V"}, {"family": "Meuronen", "given": "Topi", "initials": "T", "orcid": "0000-0002-8856-0680", "researcher": {"href": "https://publications.scilifelab.se/researcher/476315a03da040cd9c58f89a283f419a.json"}}, {"family": "Keski-Rahkonen", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9437-3040", "researcher": {"href": "https://publications.scilifelab.se/researcher/c240e626e40d4559b989cea840cc3877.json"}}, {"family": "Salek", "given": "Reza", "initials": "R", "orcid": "0000-0001-8604-1732", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b52e18b22e44da188a8ad1145cc957b.json"}}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Ahmed", "given": "Hany", "initials": "H", "orcid": "0000-0002-5876-3970", "researcher": {"href": "https://publications.scilifelab.se/researcher/92fdd5c32a3a4c62bdb4818a24f61313.json"}}, {"family": "Brunius", "given": "Carl", "initials": "C", "orcid": "0000-0003-3957-870X", "researcher": {"href": "https://publications.scilifelab.se/researcher/560a5d14ee83421680058b00df2ac9e2.json"}}, {"family": "Landberg", "given": "Rikard", "initials": "R", "orcid": "0000-0002-6399-7608", "researcher": {"href": "https://publications.scilifelab.se/researcher/4472ec17986146d1a095acdb202815e6.json"}}, {"family": "Lehtonen", "given": "Marko", "initials": "M"}, {"family": "Auriola", "given": "Seppo", "initials": "S"}, {"family": "Scalbert", "given": "Augustin", "initials": "A"}, {"family": "Hanhineva", "given": "Kati", "initials": "K", "orcid": "0000-0001-6834-7375", "researcher": {"href": "https://publications.scilifelab.se/researcher/a68564c3565940d78d96db2bd63042b9.json"}}], "type": "letter", "published": "2025-10-00", "journal": {"title": "Nat Metab", "issn": "2522-5812", "volume": "7", "issue": "10", "pages": "1955-1957", "issn-l": "2522-5812"}, "abstract": null, "doi": "10.1038/s42255-025-01376-w", "pmid": "40935890", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s42255-025-01376-w"}], "notes": [], "created": "2025-11-27T11:24:28.657Z", "modified": "2025-11-27T11:24:29.135Z"}, {"entity": "publication", "iuid": "80e99fbd84564cf4ac30476f23324ecb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80e99fbd84564cf4ac30476f23324ecb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80e99fbd84564cf4ac30476f23324ecb"}}, "title": "Frequent longitudinal blood microsampling and proteome monitoring identify disease markers and enable timely intervention in a mouse model of type 1 diabetes.", "authors": [{"family": "Parajuli", "given": "Anirudra", "initials": "A", "orcid": "0000-0001-6886-0566", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fe93f2ebd614b8aad9655bbde6b4561.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "Byvald", "given": "Fabian", "initials": "F", "orcid": "0000-0003-0516-5448", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f5e5ac109d4efaa0878ff7b21e07e2.json"}}, {"family": "Stone", "given": "Virginia M", "initials": "VM", "orcid": "0000-0003-3091-2142", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7c201c6440e42419ca79d35c2b7dbcc.json"}}, {"family": "Ringqvist", "given": "Emma E", "initials": "EE", "orcid": "0000-0001-6303-6076", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfad17442063471cb570d5be1c4dbc48.json"}}, {"family": "Butrym", "given": "Marta", "initials": "M", "orcid": "0000-0002-9285-7276", "researcher": {"href": "https://publications.scilifelab.se/researcher/81afcc509ade4f959e996f2ce8775fbc.json"}}, {"family": "Angelis", "given": "Emmanouil", "initials": "E"}, {"family": "Kipper", "given": "Sophie", "initials": "S", "orcid": "0009-0004-8075-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1d4e2b9a8984cad89430969277a9f73.json"}}, {"family": "Bauer", "given": "Stefan", "initials": "S", "orcid": "0000-0003-1712-060X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cc1926b89e545f4973968445a4fead0.json"}}, {"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Flodstr\u00f6m-Tullberg", "given": "Malin", "initials": "M", "orcid": "0000-0003-2685-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6d04afbe8141c2b9297854de64dab8.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Diabetologia", "issn": "1432-0428", "volume": "68", "issue": "10", "pages": "2277-2289", "issn-l": "0012-186X"}, "abstract": "Type 1 diabetes manifests after irreversible beta cell damage, highlighting the crucial need for markers of the presymptomatic phase to enable early and effective interventions. Current efforts to identify molecular markers of disease-triggering events lack resolution and convenience. Analysing frequently self-collected dried blood spots (DBS) could enable the detection of early disease-predictive markers and facilitate tailored interventions. Here, we present a novel strategy for monitoring transient molecular changes induced by environmental triggers that enable timely disease interception.\n\nWhole blood (10 \u03bcl) was sampled regularly (every 1-5 days) from adult NOD mice infected with Coxsackievirus B3 (CVB3) or treated with vehicle alone. Blood samples (5 \u03bcl) were dried on filter discs. DBS samples were analysed by proximity extension assay. Generalised additive models were used to assess linear and non-linear relationships between protein levels and the number of days post infection (p.i.). A multi-layer perceptron (MLP) classifier was developed to predict infection status. CVB3-infected SOCS-1-transgenic (tg) mice were treated with immune- or non-immune sera on days 2 and 3 p.i., followed by monitoring of diabetes development.\n\nFrequent blood sampling and longitudinal measurement of the blood proteome revealed transient molecular changes in virus-infected animals that would have been missed with less frequent sampling. The MLP classifier predicted infection status after day 2 p.i. with over 90% accuracy. Treatment with immune sera on day 2 p.i. prevented diabetes development in all (100%) of CVB3-infected SOCS-1-tg NOD mice while five out of eight (62.5%) of the CVB3-infected controls treated with non-immune sera developed diabetes.\n\nOur study demonstrates the utility of frequently collected DBS samples to monitor dynamic proteome changes induced by an environmental trigger during the presymptomatic phase of type 1 diabetes. This approach enables disease interception and can be translated into human initiatives, offering a new method for early detection and intervention in type 1 diabetes.\n\nAdditional data available at https://doi.org/10.17044/scilifelab.27368322 . Additional visualisations are presented in the Shiny app interface https://mouse-dbs-profiling.serve.scilifelab.se/ .", "doi": "10.1007/s00125-025-06502-7", "pmid": "40760251", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12423192"}, {"db": "pii", "key": "10.1007/s00125-025-06502-7"}], "notes": [], "created": "2025-09-19T16:31:14.024Z", "modified": "2025-09-19T16:31:15.201Z"}, {"entity": "publication", "iuid": "118f758d51d0462c8f73929b8a44a96a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/118f758d51d0462c8f73929b8a44a96a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/118f758d51d0462c8f73929b8a44a96a"}}, "title": "Effects of rainfall exclusion on soil fungi in a boreal forest landscape", "authors": [{"family": "Koelemeijer", "given": "Irena A", "initials": "IA", "orcid": "0000-0003-4298-5066", "researcher": {"href": "https://publications.scilifelab.se/researcher/599ff1ffee81411fa1de7d7eb09d05d7.json"}}, {"family": "Casta\u00f1o", "given": "Carles", "initials": "C", "orcid": "0000-0002-2403-7006", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7bfa857714f425886c4484c15eb59a5.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Ehrl\u00e9n", "given": "Johan", "initials": "J"}, {"family": "De Frenne", "given": "Pieter", "initials": "P"}, {"family": "J\u00f6nsson", "given": "Mari", "initials": "M"}, {"family": "Hylander", "given": "Kristoffer", "initials": "K"}], "type": "journal-article", "published": "2025-10-00", "journal": {"title": "Fungal Ecology", "issn": "1754-5048", "volume": "77", "pages": "101452", "issn-l": "1878-0083"}, "abstract": null, "doi": "10.1016/j.funeco.2025.101452", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-08-19T13:54:10.578Z", "modified": "2025-09-18T07:35:23.289Z"}, {"entity": "publication", "iuid": "dc2d123aa12840a1b57b3bc44298ff8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc2d123aa12840a1b57b3bc44298ff8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc2d123aa12840a1b57b3bc44298ff8e"}}, "title": "Dynamics of SARS-CoV-2 variants and mutations in Central Sweden between 2023 and 2024 and their potential implications on monoclonal antibodies pemivibart and sipavibart as PrEP in the region.", "authors": [{"family": "Haars", "given": "Jonathan", "initials": "J"}, {"family": "Wallin", "given": "Frans", "initials": "F"}, {"family": "Elfving", "given": "Karin", "initials": "K"}, {"family": "Jonsson", "given": "Anna-Karin", "initials": "AK"}, {"family": "Ellstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Lindh", "given": "Johan", "initials": "J"}, {"family": "Yin", "given": "Hong", "initials": "H"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "Kaden", "given": "Ren\u00e9", "initials": "R"}, {"family": "Palanisamy", "given": "Navaneethan", "initials": "N"}, {"family": "Lennerstrand", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Infect Dis (Lond)", "issn": "2374-4243", "volume": "57", "issue": "10", "pages": "956-965", "issn-l": "2374-4235"}, "abstract": "Monoclonal antibodies (mAbs) are an important option against SARS-CoV-2, especially as pre-exposure prophylaxis (PrEP) for patients with immune system impairment. PrEP mAbs like sipavibart and pemivibart have been approved for limited use in several countries. Certain SARS-CoV-2 variants carry mutations in the spike (S) protein, conferring resistance to these mAbs.\n\nWe aimed to examine the relative abundance of different circulating SARS-CoV-2 variants/mutations in central Sweden between 2023 and 2024, and to predict the effectiveness of sipavibart and pemivibart.\n\nAn amplicon-based Nanopore sequencing method was used for sequencing SARS-CoV-2 samples. Coronapp was used to identify mutations in these sequences. Using the published in vitro resistance data for sipavibart and pemivibart, the effectiveness of these mAbs was inferred.\n\nWe have observed that the relative abundance of the KP.3.1.1 variant and the Q493E mutation started to increase in the later part of 2024 in the region. Also, since April 2024, the relative abundance of the F456L mutation reached 100% during many weeks until the end of the study period. The KP.3.1.1 variant is significantly resistant to pemivibart. Further, the presence of the F456L mutation in the Omicron subvariants confers high fold resistance towards sipavibart.\n\nThe use of sipavibart or pemivibart as PrEP for COVID-19 in the region may currently not be effective unless new SARS-CoV-2 variants appear not containing these resistance mutations. Further, new mAbs under development as PrEP for COVID-19 can be effectively used by routinely sequencing SARS-CoV-2 in patients to identify variants and resistance mutations.", "doi": "10.1080/23744235.2025.2509011", "pmid": "40418159", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-26T14:14:33.395Z", "modified": "2025-11-26T14:14:33.411Z"}, {"entity": "publication", "iuid": "43f2d1c1d2be4645ac8ecf2d7559b8b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43f2d1c1d2be4645ac8ecf2d7559b8b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43f2d1c1d2be4645ac8ecf2d7559b8b7"}}, "title": "Cross-Sectional and Longitudinal Immunoprofiling of Oligoarticular Juvenile Idiopathic Arthritis Reveals Different Patterns in Synovial Fluid and Plasma.", "authors": [{"family": "Qu", "given": "Heshuang", "initials": "H", "orcid": "0000-0001-6011-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/25c0b095647d4af39ccc62e357fed1c3.json"}}, {"family": "Neog", "given": "Manoj", "initials": "M"}, {"family": "Palmblad", "given": "Karin", "initials": "K"}, {"family": "Sundberg", "given": "Erik", "initials": "E"}, {"family": "L\u00f6vquist", "given": "Alexandra", "initials": "A"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}, {"family": "Aulin", "given": "Cecilia", "initials": "C"}, {"family": "Harris", "given": "Helena Erlandsson", "initials": "HE"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Scand. J. Immunol.", "issn": "1365-3083", "volume": "102", "issue": "4", "pages": "e70055", "issn-l": "0300-9475"}, "abstract": "Oligoarticular juvenile idiopathic arthritis (oligoJIA) constitutes nearly 60% of all JIA cases. The immune mechanisms involved in the pathogenesis remain incompletely understood. Few proteomic studies have been performed using synovial fluid (SF) samples. We conducted an exploratory analysis of plasma and SF samples to define inflammatory profiles, assess plasma-SF correlation and examine longitudinal variations. Using proximity extension assay (PEA), we profiled 92 immune-related proteins in plasma and Sf from 14 oligoJIA patients (untreated or NSAID-treated) and plasma from 28 age and sex-matched healthy controls. Differentially expressed proteins were analysed using gene ontology (GO) and KEGG pathways via STRING. Plasma proteomic immune profiles from oligoJIA patients were highly overlapping with immune profiles of healthy donors. Six proteins were differentially expressed between the two groups. Overall, plasma and SF protein expressions correlated (r = 0.78), mainly driven by 13 proteins including CCL25, FGF21 and KITLG. However, the differentially expressed proteins in plasma did not correlate with those in SF. Longitudinal analysis of 20 SF and 10 plasma samples from one patient revealed immunosuppressive effects of methotrexate (MTX) with distinct kinetics in plasma and SF. Paired SF samples from five patients revealed that cell chemotaxis was a key feature in early disease, distinguishing it from the persistent phase. Immunoprofiling of SF from patients with oligoJIA identified more disease-relevant characteristics than analysis of plasma samples. Several proteins, but not all, correlated between plasma and SF. Early-phase enrichment of chemotaxis suggests that targeting chemokines may offer therapeutic potential for early disease remission.", "doi": "10.1111/sji.70055", "pmid": "41013715", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12475091"}], "notes": [], "created": "2025-11-24T22:14:09.393Z", "modified": "2025-11-24T22:14:09.654Z"}, {"entity": "publication", "iuid": "327b9c8fe3af4244865e6d31c0901bb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/327b9c8fe3af4244865e6d31c0901bb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/327b9c8fe3af4244865e6d31c0901bb5"}}, "title": "Add-on probiotics for inflammatory depression - A double-blind randomized placebo-controlled trial.", "authors": [{"family": "S\u00f6derberg Veib\u00e4ck", "given": "Gustav", "initials": "G"}, {"family": "Lindahl", "given": "Jesper", "initials": "J"}, {"family": "Suneson", "given": "Klara", "initials": "K"}, {"family": "Tjernberg", "given": "Johanna", "initials": "J"}, {"family": "St\u00e5hl", "given": "Darya", "initials": "D"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Asp", "given": "Marie", "initials": "M"}, {"family": "Kjellberg", "given": "Amanda", "initials": "A"}, {"family": "Falkn\u00e4s", "given": "Fabian", "initials": "F"}, {"family": "Sj\u00f6berg", "given": "Klas", "initials": "K"}, {"family": "Lavebratt", "given": "Catharina", "initials": "C"}, {"family": "Wolkowitz", "given": "Owen M", "initials": "OM"}, {"family": "Lindqvist", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Brain, Behavior, and Immunity", "issn": "1090-2139", "volume": "129", "pages": "348-358", "issn-l": "0889-1591"}, "abstract": "Previous treatment studies have suggested an antidepressant effect of adjunctive probiotics, but more high-quality randomized controlled trials (RCTs) are needed before clinical implementation. The mechanisms underlying putative antidepressant effects of probiotics are not understood, but one possibility is that they are mediated via short-chain fatty acids (SCFAs) - neuroactive bacterial metabolites with anti-inflammatory properties. The main aim of this study was to test the adjunctive antidepressant efficacy of a Lactobacillus probiotic in depressed patients with concomitant systemic low-grade inflammation, and to test the relationship between treatment response and short-chain fatty acids (SCFAs) in blood and feces. In this 8-week double-blind RCT, patients with major depressive disorder (MDD), BMI \u2265 25 kg/m2 and high-sensitivity C-reactive protein (hs-CRP) \u2265 1 mg/L were randomized to receive either a Limosilactobacillus reuteri (L. reuteri) probiotic supplement or placebo added to their regular and stable treatment. Primary outcomes were changes in the Montgomery-\u00c5sberg Depression Rating Scale (MADRS) total score and \"inflammatory depressive symptoms\" defined as a composite score of Patient Health Questionnaire-9 items related to sleep disturbance, energy levels, and appetite disturbance. Secondary outcomes included anxiety symptoms, anhedonia, insomnia, fatigue, and gastrointestinal symptoms. SCFAs were analyzed in blood and feces pre- and post-intervention. In a modified intention-to-treat analysis including all patients with at least one post-baseline visit (n = 75), there were no significant effects of probiotics relative to placebo on any of the primary or secondary outcomes (all p > 0.25). Lower baseline levels, and a greater treatment-associated increase, of fecal formic acid was significantly associated with a decrease in MADRS score in the probiotics group (p < 0.01). While we did not observe an overall antidepressant effect of add-on L. reuteri probiotic for overweight depressed patients with systemic low-grade inflammation, we found preliminary evidence for anti-inflammatory formic acid as a biomarker, and possibly a mediator, of treatment response.", "doi": "10.1016/j.bbi.2025.06.002", "pmid": "40484149", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0889-1591(25)00209-0"}], "notes": [], "created": "2025-12-01T05:42:40.040Z", "modified": "2025-12-01T05:42:40.044Z"}, {"entity": "publication", "iuid": "0a21377a927f4c7b9dcc0f4a24c18b60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a21377a927f4c7b9dcc0f4a24c18b60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a21377a927f4c7b9dcc0f4a24c18b60"}}, "title": "Use of skeletal muscle fiber composition to assess relationship between amino acid metabolism and insulin sensitivity.", "authors": [{"family": "Magnusson", "given": "Tova Eur\u00e9n", "initials": "TE"}, {"family": "Blackwood", "given": "Sarah J", "initials": "SJ"}, {"family": "Tischer", "given": "Dominik", "initials": "D"}, {"family": "Strme\u0148", "given": "Timotej", "initials": "T"}, {"family": "Pont\u00e9n", "given": "Marjan", "initials": "M"}, {"family": "Edman", "given": "Sebastian", "initials": "S"}, {"family": "Horwath", "given": "Oscar", "initials": "O"}, {"family": "Apr\u00f3", "given": "William", "initials": "W"}, {"family": "Moberg", "given": "Marcus", "initials": "M", "orcid": "0000-0003-3747-0148", "researcher": {"href": "https://publications.scilifelab.se/researcher/c56b55e299b7409b9ad77eedc225d651.json"}}, {"family": "Chorell", "given": "Elin", "initials": "E", "orcid": "0000-0002-8057-1684", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3f7dfbecd6d4f80a9015080ec717ccc.json"}}, {"family": "Katz", "given": "Abram", "initials": "A", "orcid": "0000-0003-3402-9891", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d2257c053ec4b5099fae8114a8c80a1.json"}}], "type": "journal article", "published": "2025-09-30", "journal": {"title": "Eur. J. Endocrinol.", "issn": "1479-683X", "volume": "193", "issue": "4", "pages": "553-563", "issn-l": "0804-4643"}, "abstract": "Here we use skeletal muscle fiber composition to investigate whether defects in amino acid metabolism are involved in the early development of IR in healthy young individuals before the onset of clinical manifestations.\n\nTwo groups consisting of healthy young men and women, insulin-sensitive and insulin-resistant, were studied using a cross-sectional design.\n\nBiopsies were obtained from the vastus lateralis muscle, and an intravenous glucose tolerance test was performed. Plasma and muscle tissue were analyzed by metabolomics.\n\nSubjects in group 1 (n = 20; age 28 \u00b1 5 years; body mass index 22.3 \u00b1 2.7 kg/m2) had an expression of type I muscle fibers and whole-body insulin sensitivity of 58.8% \u00b1 5.7% and 1.8 \u00b1 0.7 units, respectively. Subjects in group 2 (n = 16; age 25 \u00b1 6 years; body mass index 22.6 \u00b1 3.0 kg/m2) had an expression of type I muscle fibers and whole-body insulin sensitivity, respectively, of 29.8% \u00b1 6.6% and 0.8 \u00b1 0.3 units (P < .001 vs group 1 for both). Anserine and \u03b2-alanine contents in muscle were significantly higher and taurine lower in group 2 vs 1, consistent with the differences in muscle fiber composition between groups. Taurine correlated well with insulin sensitivity and expression of type I muscle fibers (r = 0.63; P < .001 for both). In contrast, there were no significant differences in plasma or tissue contents of glutamine, arginine, or branched-chain amino acids between groups.\n\nThese data demonstrate that the early development of IR is not a consequence of defects in amino acid metabolism. Rather, defects in amino acid metabolism in diseased states are more likely a consequence of IR.", "doi": "10.1093/ejendo/lvaf195", "pmid": "40973635", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "8258554"}], "notes": [], "created": "2025-11-18T12:13:58.163Z", "modified": "2025-11-18T12:13:58.281Z"}, {"entity": "publication", "iuid": "4b5f96f6fc484dbfa3dc0d11b4c505e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b5f96f6fc484dbfa3dc0d11b4c505e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b5f96f6fc484dbfa3dc0d11b4c505e9"}}, "title": "Disrupting Notch signalling by a small molecule inhibiting dihydroorotate dehydrogenase activity", "authors": [{"family": "Braune", "given": "Eike Benjamin", "initials": "EB", "orcid": "0009-0003-1019-8137", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca99d2f589348cfad6c2bfc8a641558.json"}}, {"family": "Wienke", "given": "Dirk", "initials": "D"}, {"family": "Seshire", "given": "Anita", "initials": "A"}, {"family": "Heinrich", "given": "Timo", "initials": "T"}, {"family": "Haraldsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-0743-7830", "researcher": {"href": "https://publications.scilifelab.se/researcher/42031e3e48ba47f896b74bfb733cdeff.json"}}, {"family": "Lain", "given": "Sonia", "initials": "S"}, {"family": "Lendahl", "given": "Urban", "initials": "U", "orcid": "0000-0001-9543-8141", "researcher": {"href": "https://publications.scilifelab.se/researcher/c61e35bb0bfc40e2968aa758873ee27a.json"}}], "type": "posted-content", "published": "2025-09-30", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.09.29.679158", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T11:34:09.982Z", "modified": "2025-12-18T19:08:44.093Z"}, {"entity": "publication", "iuid": "56befe88ff594e78a518686fbd435d80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56befe88ff594e78a518686fbd435d80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56befe88ff594e78a518686fbd435d80"}}, "title": "Cellular Hallmarks From Volume Electron Microscopy Reveal Developmental Progression of Plasmodium Ookinetes.", "authors": [{"family": "Darif", "given": "Nedal", "initials": "N", "orcid": "0000-0001-9254-6454", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7bbe64dcc274760a36c84f0ad43a4ed.json"}}, {"family": "Rheinnecker", "given": "Marco", "initials": "M", "orcid": "0009-0009-7181-3977", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc4a591c88da4bbcb6bba65de69fb696.json"}}, {"family": "Hildenbrand", "given": "Kolja", "initials": "K", "orcid": "0000-0002-9329-9253", "researcher": {"href": "https://publications.scilifelab.se/researcher/7aa272fa9e374f8c850aaaca925108e0.json"}}, {"family": "Chookajorn", "given": "Thanat", "initials": "T"}, {"family": "Dorner", "given": "Lilian P", "initials": "LP"}, {"family": "H\u00e9rich\u00e9", "given": "Jean-Karim", "initials": "JK", "orcid": "0000-0001-6867-9425", "researcher": {"href": "https://publications.scilifelab.se/researcher/d28d2e90ab8a4d5694d25802f0ad3e61.json"}}, {"family": "Henriksson", "given": "Sara", "initials": "S"}, {"family": "Funaya", "given": "Charlotta", "initials": "C"}, {"family": "Hentzschel", "given": "Franziska", "initials": "F", "orcid": "0000-0002-9812-0128", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d77121cce034bd694bcc7d29d8f2a1a.json"}}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Billker", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1716-168X", "researcher": {"href": "https://publications.scilifelab.se/researcher/baa3de453a8047688800db0d5a14e291.json"}}, {"family": "Schwab", "given": "Yannick", "initials": "Y", "orcid": "0000-0001-8027-1836", "researcher": {"href": "https://publications.scilifelab.se/researcher/b874b87c8a8245be9b1e64adad9f7685.json"}}, {"family": "Frischknecht", "given": "Friedrich", "initials": "F", "orcid": "0000-0002-8332-6668", "researcher": {"href": "https://publications.scilifelab.se/researcher/e319b02a06bb4d0eb9f5c3c71a573b1c.json"}}], "type": "journal article", "published": "2025-09-30", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "pages": "e08250", "issn-l": null}, "abstract": "Unicellular organisms or cells of metazoans often change their morphology during development or life cycle progression to adapt to environmental changes. Malaria parasites undergo a striking range of morphological transformations as they navigate through the different environments of mammalian hosts and mosquito vectors. These developmental transitions are accompanied by changes in the subcellular organelles. Here, this work introduces an unbiased approach using volume electron microscopy (vEM) to facilitate cluster analyses of morphometric parameters during developmental transformation. Investigating the transformation of fertilized Plasmodium zygotes into the motile ookinetes with three complementary vEM techniques revealed intimate mitochondrion-nucleus interactions, different microtubule arrangements, elongated shapes of micronemes and their close interaction with the apicoplast. The presented data and approach provide an open-access subcellular atlas for ookinete development to aid mechanistic molecular insights from reverse genetic studies and a framework for the ultrastructural study of other parasite stages and developmental transitions in general.", "doi": "10.1002/advs.202508250", "pmid": "41025598", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-14T14:54:43.477Z", "modified": "2025-11-14T14:54:44.358Z"}, {"entity": "publication", "iuid": "fbe87ad7cdb14ba598144e9efea8ef01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbe87ad7cdb14ba598144e9efea8ef01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbe87ad7cdb14ba598144e9efea8ef01"}}, "title": "Plasma proteomic and metabolomic profiling of coronary and carotid atherosclerosis in the SCAPIS study-differences and similarities.", "authors": [{"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Ahlstr\u00f6m", "given": "H\u00e5kan", "initials": "H"}, {"family": "Anger\u00e5s", "given": "Oskar", "initials": "O", "orcid": "0000-0002-3474-2438", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffefb8f0aa0b4622b2eb80551a9389c5.json"}}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Brandberg", "given": "John", "initials": "J"}, {"family": "Caidahl", "given": "Kenneth", "initials": "K"}, {"family": "Chorell", "given": "Elin", "initials": "E", "orcid": "0000-0002-8057-1684", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3f7dfbecd6d4f80a9015080ec717ccc.json"}}, {"family": "Engvall", "given": "Jan Edvin", "initials": "JE"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Erlinge", "given": "David", "initials": "D"}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}, {"family": "Hjelmgren", "given": "Ola", "initials": "O"}, {"family": "Hultdin", "given": "Johan", "initials": "J"}, {"family": "Jernberg", "given": "Tomas", "initials": "T", "orcid": "0000-0003-1695-379X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbe08775f7a047ffa46bf6e065c776c9.json"}}, {"family": "Kihlberg", "given": "Johan", "initials": "J"}, {"family": "Lind", "given": "Lars", "initials": "L", "orcid": "0000-0003-2335-8542", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c517dacca7c4ec58a3e03b59ffb4044.json"}}, {"family": "Magnusson", "given": "Martin", "initials": "M"}, {"family": "Nystr\u00f6m", "given": "Fredrik Hans", "initials": "FH"}, {"family": "Pirazzi", "given": "Carlo", "initials": "C"}, {"family": "Schiopu", "given": "Alexandru", "initials": "A", "orcid": "0000-0002-7587-5050", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7d2edf9030a445583f692dc4d884b7f.json"}}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-8618-9152", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40c03613a3a46368ed855fc95b79e31.json"}}], "type": "journal article", "published": "2025-09-29", "journal": {"title": "Cardiovasc. Res.", "issn": "1755-3245", "volume": "121", "issue": "11", "pages": "1649-1652", "issn-l": "0008-6363"}, "abstract": null, "doi": "10.1093/cvr/cvaf076", "pmid": "40327543", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12477672"}, {"db": "pii", "key": "8125826"}], "notes": [], "created": "2025-11-25T19:22:38.477Z", "modified": "2025-11-25T19:23:39.737Z"}, {"entity": "publication", "iuid": "bd8ee65af385457db50b264c74fcf328", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd8ee65af385457db50b264c74fcf328.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd8ee65af385457db50b264c74fcf328"}}, "title": "Comparative analysis of commercial human primary mesangial cell, implications for experimental design.", "authors": [{"family": "Johansson", "given": "Alva", "initials": "A"}, {"family": "Narasimhan", "given": "Gayathri", "initials": "G"}, {"family": "Keuenhof", "given": "Katharina", "initials": "K"}, {"family": "Boi", "given": "Roberto", "initials": "R"}, {"family": "Ebefors", "given": "Kerstin", "initials": "K", "orcid": "0000-0002-6884-183X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d22d973dc54e28b44a3a9c1e427af3.json"}}], "type": "journal article", "published": "2025-09-29", "journal": {"title": "BMC Nephrol", "issn": "1471-2369", "volume": "26", "issue": "1", "pages": "539", "issn-l": "1471-2369"}, "abstract": "Mesangial cells (MCs) are involved in several glomerular diseases such as IgA nephropathy and diabetic kidney disease. In vitro work on human MCs is mainly conducted on primary MCs. However, cells from different donors could be significantly different, thus potentially affecting the outcome of the experiments.\n\nWe have compared commercially available primary human MCs from two different sources: HMCv1 and HMCv2. The cells were characterized using qPCR, western blot, and immunofluorescence. Response to PDGF-BB was assessed with proliferation assays, proteomics, and qPCR. Response to angiotensin II was assessed through contractility assay and response to IL-1\u03b2, diabetic milieu and TGF\u03b21 with qPCR.\n\nCells from both sources expressed mesangial markers. HMCv1, but not HMCv2, showed significant contractility in response to angiotensin II. Both HMCv1 and 2 significantly increased their proliferation rate in response to PDGF-BB. Proteomics revealed a stronger response to PDGF-BB for HMCv1 in respect to HMCv2, though similar pathways were regulated in both. IL-1\u03b2 stimulus was stronger in HMCv1 in terms of increased expression of IL6 and CCL2/MCP1 mRNA. Diabetic milieu increased expression of IL-6 for both HMCv1 and 2, but significantly higher for HMCv1. TGF\u03b21 gave similar results in terms of IL-6 expression for cells from both sources. In addition, a list of 144 potential mesangial markers was compiled, that can be used for identification of MCs in omics data.\n\nThis study shows that there are broad differences between sources of primary human MCs. The potential differences between clones of primary MCs need to be carefully considered when conducting in vitro experiments.", "doi": "10.1186/s12882-025-04444-1", "pmid": "41023975", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12482395"}, {"db": "pii", "key": "10.1186/s12882-025-04444-1"}], "notes": [], "created": "2025-11-20T18:09:54.185Z", "modified": "2025-11-20T18:09:54.282Z"}, {"entity": "publication", "iuid": "50dce12ee1534ab1828e5d094a809dca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50dce12ee1534ab1828e5d094a809dca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50dce12ee1534ab1828e5d094a809dca"}}, "title": "Allosteric control of the bacterial ClpC/ClpP protease and its hijacking by antibacterial peptides.", "authors": [{"family": "Jenne", "given": "Timo", "initials": "T", "orcid": "0009-0001-2033-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a27284b457b4d84b7104cfc0a3d989c.json"}}, {"family": "Engelhardt", "given": "Lisa", "initials": "L", "orcid": "0009-0003-7437-2130", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb7d64c7eba74479a29e9b4cf4769b81.json"}}, {"family": "Baronaite", "given": "Ieva", "initials": "I", "orcid": "0009-0006-5515-8528", "researcher": {"href": "https://publications.scilifelab.se/researcher/afecab33e8a94b218741ab24bdb13f19.json"}}, {"family": "Levy", "given": "Dorit", "initials": "D"}, {"family": "Riven", "given": "Inbal", "initials": "I"}, {"family": "Malolepszy", "given": "Maciej", "initials": "M", "orcid": "0009-0000-9501-5990", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd88f5c57b7e4a6480d1716eca601748.json"}}, {"family": "Azinas", "given": "Stavros", "initials": "S", "orcid": "0000-0002-3744-9229", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ec0cb5b5df4b4f89780ce3a08efc89.json"}}, {"family": "Sych", "given": "Taras", "initials": "T"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E"}, {"family": "Flemming", "given": "Dirk", "initials": "D", "orcid": "0000-0002-1528-5032", "researcher": {"href": "https://publications.scilifelab.se/researcher/64abbbdb3c624cd4acaf2bebdbd27e82.json"}}, {"family": "Sinning", "given": "Irmgard", "initials": "I", "orcid": "0000-0001-9127-4477", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c8d58ff4cd24b05b4f23e4f4ef471ad.json"}}, {"family": "Haran", "given": "Gilad", "initials": "G", "orcid": "0000-0003-1837-9779", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebd2c5d7c4e649dd8ed69fc4c6ac6b8d.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Mogk", "given": "Axel", "initials": "A", "orcid": "0000-0003-3674-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/56a1d7fc519743029c9ae615086d8093.json"}}], "type": "journal article", "published": "2025-09-29", "journal": {"title": "EMBO J.", "issn": "1460-2075", "issn-l": "0261-4189"}, "abstract": "The hexameric AAA+ protein ClpC, combined with peptidase ClpP, forms a critical ATP-dependent protease in bacteria, essential for virulence. ClpC is usually repressed in an inactive resting state, where two ClpC spirals interact via coiled-coil M-domains. Antibacterial peptides and partner proteins trigger ClpC activation by binding to its N-terminal domain (NTD). This study reveals that the NTD stabilizes the resting state through multiple anchoring points to M-domains and ATPase domains. The same NTD sites also serve as binding sites for adaptor proteins and substrates carrying phosphorylated arginines (pArg), disrupting resting state interactions and promoting active ClpC hexamer formation. This coupling ensures that ClpC activation aligns with substrate and partner protein availability. Toxic peptides exploit this regulatory mechanism, leading to continuous ClpC activation and harmful, uncontrolled proteolysis. These findings highlight the dual role of the NTD in maintaining resting state stability and mediating activation, emphasizing its critical role in bacterial protease regulation and its potential as a drug target.", "doi": "10.1038/s44318-025-00575-1", "pmid": "41023306", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s44318-025-00575-1"}], "notes": [], "created": "2025-10-25T10:20:13.858Z", "modified": "2025-10-25T10:20:15.032Z"}, {"entity": "publication", "iuid": "89a9d81b95104d2ead4db6caebd4990c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89a9d81b95104d2ead4db6caebd4990c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89a9d81b95104d2ead4db6caebd4990c"}}, "title": "Scalable deep learning reconstruction for accelerated multidimensional nuclear magnetic resonance spectroscopy of proteins", "authors": [{"family": "Huang", "given": "Yihui", "initials": "Y", "orcid": "0000-0002-5035-7687", "researcher": {"href": "https://publications.scilifelab.se/researcher/773bedbe71644bb3adab46fba3477c24.json"}}, {"family": "Gao", "given": "Yuncheng", "initials": "Y", "orcid": "0009-0005-8549-1789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b568fae51f86472487896e51029f0c6f.json"}}, {"family": "Tu", "given": "Zhangren", "initials": "Z", "orcid": "0000-0002-0863-2454", "researcher": {"href": "https://publications.scilifelab.se/researcher/e450c06cfb6d4ff3847e5d98dc818d2b.json"}}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Orekhov", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7892-6896", "researcher": {"href": "https://publications.scilifelab.se/researcher/77382c412de04fa08ff7c3bc7087b77e.json"}}, {"family": "Hyberts", "given": "Sven G", "initials": "SG", "orcid": "0000-0002-3169-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a0d5dc0f7b040f1b979312bf59a5daf.json"}}, {"family": "Wagner", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-2063-4401", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6dec04566246c28cfd076fb667f929.json"}}, {"family": "Lin", "given": "Yanqin", "initials": "Y", "orcid": "0000-0003-0596-0740", "researcher": {"href": "https://publications.scilifelab.se/researcher/92d8757206c6419c97d3e6699cc1a8d0.json"}}, {"family": "Chen", "given": "Zhong", "initials": "Z", "orcid": "0000-0002-1473-2224", "researcher": {"href": "https://publications.scilifelab.se/researcher/c95d3606af9b4826a6a298c5ddcdc01e.json"}}, {"family": "Guo", "given": "Di", "initials": "D", "orcid": "0000-0002-9910-5720", "researcher": {"href": "https://publications.scilifelab.se/researcher/0450ec43a296466d8a31387fa3bd9ea6.json"}}, {"family": "Qu", "given": "Xiaobo", "initials": "X", "orcid": "0000-0002-8675-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0bbb61a58d4218ac29f5ec08ed3520.json"}}], "type": "journal-article", "published": "2025-09-26", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "39", "issn-l": "2375-2548"}, "abstract": null, "doi": "10.1126/sciadv.adw8122", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:02:33.748Z", "modified": "2025-11-27T08:02:34.801Z"}, {"entity": "publication", "iuid": "02f127da3ff74424b59f25012f4991b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02f127da3ff74424b59f25012f4991b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02f127da3ff74424b59f25012f4991b9"}}, "title": "Liquid biomarkers associate with TGF-\u03b2 Type I receptor and hypoxia in kidney cancer.", "authors": [{"family": "Mallikarjuna", "given": "Pramod", "initials": "P"}, {"family": "Erdem", "given": "Cemal", "initials": "C", "orcid": "0000-0003-3663-3646", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7540b2308f548ab82104ba653ee5eb5.json"}}, {"family": "Beorlegui", "given": "Ruben Ilundain", "initials": "RI"}, {"family": "Larsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-3161-0402", "researcher": {"href": "https://publications.scilifelab.se/researcher/2276de26382b402aa384ac231f30f156.json"}}, {"family": "Ljungberg", "given": "B\u00f6rje", "initials": "B"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Landstr\u00f6m", "given": "Mar\u00e9ne", "initials": "M", "orcid": "0000-0001-6737-7230", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2f02fcfb1c1497d81a6f343bc0e6928.json"}}], "type": "letter", "published": "2025-09-26", "journal": {"title": "Signal Transduct Target Ther", "issn": "2059-3635", "volume": "10", "issue": "1", "pages": "309", "issn-l": null}, "abstract": null, "doi": "10.1038/s41392-025-02404-7", "pmid": "40998794", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12464240"}, {"db": "pii", "key": "10.1038/s41392-025-02404-7"}], "notes": [], "created": "2025-11-25T19:21:37.895Z", "modified": "2025-11-25T19:21:38.040Z"}, {"entity": "publication", "iuid": "2277209cfb104c25a0c16a2adf69d785", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2277209cfb104c25a0c16a2adf69d785.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2277209cfb104c25a0c16a2adf69d785"}}, "title": "An injury-associated lobular microniche is associated with the classical tumor cell phenotype in pancreatic cancer.", "authors": [{"family": "S\u00f6derqvist", "given": "Sara", "initials": "S"}, {"family": "Viljamaa", "given": "Annika", "initials": "A", "orcid": "0009-0002-8511-8181", "researcher": {"href": "https://publications.scilifelab.se/researcher/7db15c31004649d4b3f7bc965cd2e738.json"}}, {"family": "Geyer", "given": "Natalie", "initials": "N"}, {"family": "Keller", "given": "Anna-Lena", "initials": "A"}, {"family": "Ruksha", "given": "Kseniya", "initials": "K"}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Hekmati", "given": "Neda", "initials": "N"}, {"family": "Niculae", "given": "Alexandra", "initials": "A"}, {"family": "Engstrand", "given": "Jennie", "initials": "J", "orcid": "0000-0003-1123-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef6292473b94b3b90e78745841cdeaa.json"}}, {"family": "Sparrelid", "given": "Ernesto", "initials": "E"}, {"family": "Salm\u00e9n", "given": "Caroline", "initials": "C"}, {"family": "Costa", "given": "T\u00e2nia D F", "initials": "TDF", "orcid": "0000-0002-6296-5225", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d1862cdeabd47bcaafcafd47bff7a5c.json"}}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Str\u00f6mblad", "given": "Staffan", "initials": "S", "orcid": "0000-0002-1236-6339", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4ef16afaed741f4851f1591d3005882.json"}}, {"family": "Zacharouli", "given": "Argyro", "initials": "A"}, {"family": "Ghorbani", "given": "Poya", "initials": "P"}, {"family": "Harrizi", "given": "Sara", "initials": "S"}, {"family": "Hamidi", "given": "Yousra", "initials": "Y"}, {"family": "Khorosjutina", "given": "Olga", "initials": "O", "orcid": "0009-0001-0786-0260", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ada08b5ada04dfb8e948e0873ccf07d.json"}}, {"family": "Milanova", "given": "Stefina", "initials": "S"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Boz\u00f3ky", "given": "B\u00e9la", "initials": "B"}, {"family": "Fern\u00e1ndez Moro", "given": "Carlos", "initials": "C", "orcid": "0000-0001-6863-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/216d382919954ccfb4b47458bb3d9b08.json"}}, {"family": "Gerling", "given": "Marco", "initials": "M", "orcid": "0000-0002-1810-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f9aa5d37124e379eb160737d657bab.json"}}], "type": "journal article", "published": "2025-09-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "8307"}, "abstract": "Pancreatic cancer is an aggressive disease with a dense fibrotic stroma and is often accompanied by chronic inflammation. Peritumoral inflammation is typically viewed as a reaction to nearby tumor growth. Here, we report that the inflamed pancreatic lobules are frequently invaded by tumor cells, forming a distinct, non-fibrotic tumor niche. Using a semi-supervised machine learning approach for annotations of clinical samples and multiplex protein profiling, we show that tumor cells at the invasion front are closely associated with acinar cells undergoing damage-induced changes, and with activated fibroblasts expressing markers of injury. The invaded lobules are linked to classical tumor phenotypes, in contrast to fibrotic areas where tumor cells display a more basal profile, highlighting microenvironment-dependent tumor subtype differences. In female mice, lobular invasion similarly aligns with the classical tumor phenotype. Together, our data reveal that pancreatic tumors colonize injured lobules, creating a unique niche that shapes tumor characteristics and contributes to disease biology.", "doi": "10.1038/s41467-025-63864-7", "pmid": "41006303", "labels": {"CRISPR Functional Genomics": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12475445"}, {"db": "pii", "key": "10.1038/s41467-025-63864-7"}], "notes": [], "created": "2025-11-13T15:11:41.935Z", "modified": "2026-03-18T09:36:43.639Z"}, {"entity": "publication", "iuid": "45682d38345b42169cbcba464ca3a942", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45682d38345b42169cbcba464ca3a942.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45682d38345b42169cbcba464ca3a942"}}, "title": "Patients with systemic lupus erythematosus (SLE) have an increased bisphenol A methylation score linked to SLE risk genes and selected clinical subphenotypes.", "authors": [{"family": "Vestin", "given": "Holme", "initials": "H", "orcid": "0009-0005-6622-8897", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ab6d55e8ab4f8b92ae43b924f7453f.json"}}, {"family": "Oparina", "given": "Nina", "initials": "N"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Frodlund", "given": "Martina", "initials": "M"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}], "type": "journal article", "published": "2025-09-25", "journal": {"title": "RMD Open", "issn": "2056-5933", "volume": "11", "issue": "3", "issn-l": "2056-5933"}, "abstract": "Bisphenol A (BPA), a xenoestrogen that can alter DNA methylation status, has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). This study aimed to investigate whether methylation changes at BPA-sensitive 5'-C-phosphate-G-3' (CpG) sites are associated with SLE and clinical subphenotypes.\n\nA discovery cohort (n=747) and a replication cohort (n=388) including Swedish patients with SLE and healthy controls were investigated using the Illumina HM450k bead chip. BPA-sensitive CpG sites were selected if differentially methylated in \u22652 of 7 BPA exposure studies and supported by cell line data. A BPAAll score including 19 CpGs and a BPASLE score based on three CpG sites co-localised in the genome with SLE risk loci were calculated for each individual, analysed for associations with clinical data and then compared with publicly available transcriptomic data from BPA-treated cells.\n\nPatients with SLE had significantly higher BPASLE score than controls in the discovery (OR 1.34, p=4.6\u00d710-13), replication (OR 1.28, p=1.1\u00d710-5) and meta-analysis (OR 1.32, p=3.3\u00d710-17). Higher BPAAll score was associated with SLE in the discovery cohort (OR 1.05, p=2.3\u00d710-3) but not in the replication cohort (OR 1.04, p=0.12) with a significant difference in the meta-analysis (OR 1.05, p=7.0\u00d710-4). Both scores were associated with prednisolone treatment (p<0.001), and the BPASLE score was associated with serositis and autoantibodies (p<0.05). Transcriptomic analysis of BPA-treated cells revealed enrichment in pathways such as interferon and mitogen-activated protein kinase signalling.\n\nOur findings reveal a novel association between BPA exposure and DNA methylation changes in SLE, with potential implications for the regulation of immune-related gene expression.", "doi": "10.1136/rmdopen-2025-006021", "pmid": "40998523", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12481292"}, {"db": "pii", "key": "rmdopen-2025-006021"}], "notes": [], "created": "2025-11-07T07:30:46.128Z", "modified": "2025-11-07T07:30:46.264Z"}, {"entity": "publication", "iuid": "c93e8fb856474957a4fcdb00299da4f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c93e8fb856474957a4fcdb00299da4f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c93e8fb856474957a4fcdb00299da4f9"}}, "title": "Oral mucosal manifestations with identical mutations to the bone marrow in a patient with VEXAS syndrome", "authors": [{"family": "Vasaitis", "given": "Lilian", "initials": "L"}, {"family": "Blomstrand", "given": "Lena", "initials": "L"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Gulyas", "given": "Miklos", "initials": "M"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V", "orcid": "0009-0005-4633-2099", "researcher": {"href": "https://publications.scilifelab.se/researcher/84eb698040ca44c8830bd7f0c6bc10aa.json"}}], "type": "journal-article", "published": "2025-09-25", "journal": {"title": "Rheumatology &amp; Autoimmunity", "issn": "2767-1410", "issn-l": null}, "abstract": null, "doi": "10.1002/rai2.70025", "pmid": null, "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-26T14:13:58.897Z", "modified": "2025-11-26T14:13:58.965Z"}, {"entity": "publication", "iuid": "6d1bf375c94f4c969b3b0be66809e1db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d1bf375c94f4c969b3b0be66809e1db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d1bf375c94f4c969b3b0be66809e1db"}}, "title": "Intrinsic heterogeneity of primary cilia revealed through spatial proteomics.", "authors": [{"family": "Hansen", "given": "Jan N", "initials": "JN"}, {"family": "Sun", "given": "Huangqingbo", "initials": "H"}, {"family": "Kahnert", "given": "Konstantin", "initials": "K"}, {"family": "Westenius", "given": "Eini", "initials": "E"}, {"family": "Johannesson", "given": "Alexandra", "initials": "A"}, {"family": "Villegas", "given": "Carmela", "initials": "C"}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Tzavlaki", "given": "Kalliopi", "initials": "K"}, {"family": "Winsnes", "given": "Casper", "initials": "C"}, {"family": "Pohjanen", "given": "Emmie", "initials": "E"}, {"family": "M\u00e4kiniemi", "given": "Anna", "initials": "A"}, {"family": "Fall", "given": "Jenny", "initials": "J"}, {"family": "Ballllosera Navarro", "given": "Frederic", "initials": "F"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Johansson", "given": "Fredric", "initials": "F"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Delgado-Vega", "given": "Angelica M", "initials": "AM"}, {"family": "Martinez Casals", "given": "Anna", "initials": "A"}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Sheu", "given": "Shu-Hsien", "initials": "SH"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}], "type": "journal article", "published": "2025-09-25", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674"}, "abstract": "Primary cilia are critical organelles found on most human cells. Their dysfunction is linked to hereditary ciliopathies with a wide phenotypic spectrum. Despite their significance, the specific roles of cilia in different cell types remain poorly understood due to limitations in analyzing ciliary protein composition. We employed antibody-based spatial proteomics to expand the Human Protein Atlas to primary cilia. Our analysis identified the subciliary locations of 715 proteins across three cell lines, examining 128,156 individual cilia. We found that 69% of the ciliary proteome is cell-type specific, and 78% exhibited single-cilia heterogeneity. Our findings portray cilia as sensors tuning their proteome to effectively sense the environment and compute cellular responses. We reveal 91 cilia proteins and found a genetic candidate variant in CREB3 in one clinical case with features overlapping ciliopathy phenotypes. This open, spatial cilia atlas advances research on cilia and ciliopathies.", "doi": "10.1016/j.cell.2025.08.039", "pmid": "41005307", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)01029-3"}], "notes": [], "created": "2025-11-18T20:48:47.028Z", "modified": "2025-11-18T20:48:47.031Z"}, {"entity": "publication", "iuid": "6f47d65ab69d4679a11ed59bb80b8255", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f47d65ab69d4679a11ed59bb80b8255.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f47d65ab69d4679a11ed59bb80b8255"}}, "title": "Apoptotic bodies in phytoplankton suggest evolutionary conservation of cell death mechanisms.", "authors": [{"family": "Corredor", "given": "Luisa", "initials": "L", "orcid": "0000-0003-0274-4962", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b51b1c56fdc49fbb0596c6ca8448315.json"}}, {"family": "Vergou", "given": "Georgia Antonia", "initials": "GA", "orcid": "0009-0004-0913-7203", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe3d2255d757451a8565911e9924486c.json"}}, {"family": "Skalick\u00fd", "given": "Vladim\u00edr", "initials": "V", "orcid": "0000-0001-5369-8906", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa0883baaa234b1eb8f80b6b5dc2ac07.json"}}, {"family": "Antoniadi", "given": "Ioanna", "initials": "I", "orcid": "0000-0001-9053-2788", "researcher": {"href": "https://publications.scilifelab.se/researcher/60bcbb474ded4df08079520c92de49bf.json"}}, {"family": "Wheaton", "given": "Benjamin J", "initials": "BJ", "orcid": "0000-0003-0619-4777", "researcher": {"href": "https://publications.scilifelab.se/researcher/399d29926ef74784aeda6c6ada5cedb4.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Gorzs\u00e1s", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-2298-8844", "researcher": {"href": "https://publications.scilifelab.se/researcher/8070792ccead4c809c89943d84cf0e03.json"}}, {"family": "Funk", "given": "Christiane", "initials": "C", "orcid": "0000-0002-7897-4038", "researcher": {"href": "https://publications.scilifelab.se/researcher/5db6c5fa2a754060b1583caf37bba1b8.json"}}], "type": "journal article", "published": "2025-09-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "8427", "issn-l": "2041-1723"}, "abstract": "Programmed Cell Death (PCD) in eukaryotes is a regulated process occurring during development, cell differentiation and aging. Apoptosis is a particularly well studied morphotype of PCD, only observed in animal cells (metazoan). Its most definitive hallmark is the formation and release of membrane-enclosed extracellular vesicles called Apoptotic Bodies (ABs). Although apoptotic-like features have been described in plants, yeast, protozoa and phytoplankton, the production of ABs has been thought to be limited to multicellular animals. Here we report the production and release of extracellular ABs in a non-metazoan unicellular eukaryote, the cryptophyte alga Guillardia theta. Morphologies of G. theta cells during aging and pharmacologically-induced cell death confirm the presence of ABs and apoptosis in phytoplankton. G. theta ABs have similar composition to metazoan ABs, carrying DNA, proteins, lipids, carbohydrates, fragments of organelles and cytosol portions. Our results demonstrate that G. theta, a microalga that arose from secondary endosymbiosis, experiences apoptotic cell death in physiological conditions, similar to animal cells. Since secondary endosymbiosis occurred prior to the origin of multicellularity, our discovery questions the evolutionary origin of PCD.", "doi": "10.1038/s41467-025-63956-4", "pmid": "40998840", "labels": {"Cryo-EM": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12462507"}, {"db": "pii", "key": "10.1038/s41467-025-63956-4"}], "notes": [], "created": "2025-09-30T12:06:57.996Z", "modified": "2025-10-30T12:08:13.065Z"}, {"entity": "publication", "iuid": "0f4c20c99096436cbbe67ed86c7cdf12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f4c20c99096436cbbe67ed86c7cdf12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f4c20c99096436cbbe67ed86c7cdf12"}}, "title": "Position specific isotope analysis of diethylamine by 2H and 13C NMR - Dual nucleus analysis in forensic investigation of illegal use of chemical weapons.", "authors": [{"family": "Lindberg", "given": "Sandra", "initials": "S"}, {"family": "Sparrman", "given": "Tobias", "initials": "T"}, {"family": "Schleucher", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Norlin", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2025-09-24", "journal": {"title": "Talanta", "issn": "1873-3573", "volume": "298", "issue": "Pt A", "pages": "128912", "issn-l": null}, "abstract": "Diethylamine (DEA) is a known precursor to some of the most toxic chemical warfare agents (CWA) as both V-agents and Fourth Generation Agents (FGAs) contain the dialkylamine functionality. DEA is also a readily available commercial substance with extensive use in the chemical industry for legitimate purposes. Because of this potential dual use, it is desirable to develop methods to trace the origin of dialkylamines if they are used for illicit purposes. We herein demonstrate that it is possible to differentiate six commercial batches of DEA using position-specific isotope analysis (PSIA) by both 2H and 13C NMR. Using a high-field NMR spectrometer together with a cryogenic 2H probe, we have produced 2H-{1H} NMR data with high accuracy and precision. The PSIA by NMR results show that the intramolecular 2H ratios of all six DEAs are significantly different while two of the six DEAs have unique 13C ratios. Further, the intramolecular isotopic variations can be used to link the DEAs to different suppliers. The two nuclei separately contribute to isotopic profiles of the DEAs. However, combining the two techniques provides a higher-resolved isotopic profile that can differentiate all DEAs and thus be useful in forensic investigations of illegal use of chemical weapons.", "doi": "10.1016/j.talanta.2025.128912", "pmid": "41022010", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0039-9140(25)01403-1"}], "notes": [], "created": "2025-11-25T19:19:53.213Z", "modified": "2025-11-25T19:19:53.228Z"}, {"entity": "publication", "iuid": "e35988a7938b44638700ddc6625bc6aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e35988a7938b44638700ddc6625bc6aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e35988a7938b44638700ddc6625bc6aa"}}, "title": "Major Histocompatibility Complex modulation of Batrachochytrium dendrobatidis and Ranavirus infections in amphibians.", "authors": [{"family": "Cortazar-Chinarro", "given": "M", "initials": "M", "orcid": "0000-0003-4604-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/6eeac642337c4ca5aab0275dcae9a8b9.json"}}, {"family": "Richter-Boix", "given": "A", "initials": "A"}, {"family": "Halvarsson", "given": "P", "initials": "P"}, {"family": "Palomar", "given": "G", "initials": "G"}, {"family": "Bosch", "given": "J", "initials": "J"}], "type": "journal article", "published": "2025-09-24", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X"}, "abstract": "Genetic variation in immune genes is an important component of genetic diversity. The genes in the Major Histocompatibility Complex (MHC) provide an excellent model system for studying the mechanisms that generate and maintain genetic diversity in natural populations. While both demographic factors and pathogen-mediated selection processes contribute to the extreme diversity observed in the MHC systems, determining the relative importance of these evolutionary mechanisms has remained challenging. We investigated the role of pathogen-mediated selection in driving MHC diversity in three amphibian species: Ichthyosaura alpestris, Pleurodeles waltl and Pelophilax perezi. Our study examined the relationships between individual MHC diversity, infection status, infection intensity, and co-infection with two major amphibian pathogens: Batrachochytrium dendrobatidis (Bd) and Ranavirus sp. (Rv) in natural populations. Our research demonstrated significant differences in Bd and Rv infection intensities among individuals with varying numbers of MHC loci. However, co-infection showed no discernible influence on infection intensities. We observed stronger associations of specific MHC alleles and supertypes with infection intensity and status in I. alpestris. These findings suggest that, in the context of multi-host infections, MHC genes may provide valuable insights into the evolutionary forces shaping MHC diversity, although the specific effects of individual MHC alleles on disease dynamics are yet to be clarified.", "doi": "10.1093/jeb/voaf112", "pmid": "40990944", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "8262903"}], "notes": [], "created": "2025-11-07T07:26:58.477Z", "modified": "2025-11-07T07:26:58.555Z"}, {"entity": "publication", "iuid": "2110c851b57d4479b99eb959647a15e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2110c851b57d4479b99eb959647a15e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2110c851b57d4479b99eb959647a15e4"}}, "title": "High Cerebrospinal DOPA Decarboxylase Level Predicts Cognitive Decline in Parkinson's Disease.", "authors": [{"family": "Sturchio", "given": "Andrea", "initials": "A"}, {"family": "Paslawski", "given": "Wojciech", "initials": "W", "orcid": "0000-0003-2141-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce039c7e5e774d66a8c0331a3c990ccc.json"}}, {"family": "Khosousi", "given": "Shervin", "initials": "S"}, {"family": "Markaki", "given": "Ioanna", "initials": "I", "orcid": "0000-0003-3328-5746", "researcher": {"href": "https://publications.scilifelab.se/researcher/929b8fea137e410b96d1a6754690c447.json"}}, {"family": "Nalls", "given": "Michael A", "initials": "MA"}, {"family": "Singleton", "given": "Andrew B", "initials": "AB"}, {"family": "Iwaki", "given": "Hirotaka", "initials": "H"}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}], "type": "journal article", "published": "2025-09-24", "journal": {"title": "Mov Disord Clin Pract", "issn": "2330-1619", "issn-l": null}, "abstract": "DOPA decarboxylase (DDC) in cerebrospinal fluid (CSF) is an emerging Parkinson's disease (PD) biomarker, but its association with nonmotor symptoms is unclear.\n\nWe aimed to determine if baseline DDC was associated with future cognitive decline in PD.\n\nWe correlated baseline CSF DDC, detected using the proximity extension assay, with Montreal Cognitive Assessment (MoCA) score using longitudinal data from 3 cohorts: Biopark, PPMI, and PDBP.\n\nDDC was significantly associated with cognitive decline in both the Biopark cohort (P-value < 0.0001) and the PDBP/PPMI cohorts (P-value < 0.0001). The results were still significant after correcting for levodopa-equivalent daily dose in the Biopark cohort (P-value < 0.0001) and when the analysis was restricted to the de novo subjects, both in Biopark (P-value: 0.0065) and PPMI (P-value<0.0001) cohorts.\n\nCSF DDC is a potential biomarker for the prediction of cognitive decline in PD patients.", "doi": "10.1002/mdc3.70367", "pmid": "40990085", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-24T22:25:28.475Z", "modified": "2025-11-24T22:25:28.974Z"}, {"entity": "publication", "iuid": "c7985d3e4b4342dd8faf493f01cc6d1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7985d3e4b4342dd8faf493f01cc6d1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7985d3e4b4342dd8faf493f01cc6d1b"}}, "title": "Corrigendum to \"In vitro study of cold atmospheric plasma-induced proliferation inhibition and morphological changes in head and neck carcinoma cell lines\" [Journal of Dentistry161 (2025) 106007].", "authors": [{"family": "Maravic", "given": "Tatjana", "initials": "T"}, {"family": "Petrucci", "given": "Giulia", "initials": "G"}, {"family": "di Giacomo", "given": "Viviana", "initials": "V"}, {"family": "Mazzitelli", "given": "Claudia", "initials": "C"}, {"family": "Acharya", "given": "Tirtha Raj", "initials": "TR"}, {"family": "Kaushik", "given": "Nagendra Kumar", "initials": "NK"}, {"family": "Choi", "given": "Eun Ha", "initials": "EH"}, {"family": "Rapino", "given": "Monica", "initials": "M"}, {"family": "D'Urso", "given": "Diego", "initials": "D"}, {"family": "Josic", "given": "Uros", "initials": "U"}, {"family": "Caponio", "given": "Vito Carlo Alberto", "initials": "VCA"}, {"family": "Micaroni", "given": "Massimo", "initials": "M"}, {"family": "Mancuso", "given": "Edoardo", "initials": "E"}, {"family": "Russo", "given": "Lucio Lo", "initials": "LL"}, {"family": "Muzio", "given": "Lorenzo Lo", "initials": "LL"}, {"family": "Breschi", "given": "Lorenzo", "initials": "L"}, {"family": "Perrotti", "given": "Vittoria", "initials": "V"}], "type": "published erratum", "published": "2025-09-24", "journal": {"title": "J Dent", "issn": "1879-176X", "pages": "106098", "issn-l": null}, "abstract": null, "doi": "10.1016/j.jdent.2025.106098", "pmid": "40992958", "labels": {"Integrated Microscopy Technologies Gothenburg": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0300-5712(25)00544-5"}], "notes": [], "created": "2025-11-05T13:56:41.915Z", "modified": "2025-11-05T13:56:41.945Z"}, {"entity": "publication", "iuid": "6e26d1e012d84cf286167008cf1a09d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e26d1e012d84cf286167008cf1a09d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e26d1e012d84cf286167008cf1a09d5"}}, "title": "Tertiary lymphoid structures in Merkel cell carcinoma facilitate na\u00efve and central memory T-cell infiltration linked to immunotherapy response.", "authors": [{"family": "Srinivas", "given": "Nalini", "initials": "N"}, {"family": "Spassova", "given": "Ivelina", "initials": "I"}, {"family": "Lei", "given": "Kuan Cheok", "initials": "KC"}, {"family": "Gao", "given": "Jiwei", "initials": "J"}, {"family": "Pino", "given": "Mar\u00eda Jos\u00e9", "initials": "MJ", "orcid": "0009-0004-0516-6867", "researcher": {"href": "https://publications.scilifelab.se/researcher/eca8bbd58ba34f47be73ac29e905743c.json"}}, {"family": "Giglio", "given": "Giovanni", "initials": "G"}, {"family": "Kitanovski", "given": "Simo", "initials": "S"}, {"family": "Dalkoohi", "given": "Mazdak", "initials": "M"}, {"family": "Livingstone", "given": "Elisabeth", "initials": "E"}, {"family": "Leiter", "given": "Ulrike", "initials": "U"}, {"family": "Mohr", "given": "Peter", "initials": "P"}, {"family": "Gambichler", "given": "Thilo", "initials": "T"}, {"family": "Stoffels", "given": "Ingo", "initials": "I"}, {"family": "Ugurel", "given": "Selma", "initials": "S", "orcid": "0000-0002-9384-6704", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9566da004fc4f759d6a032c38c0800f.json"}}, {"family": "Cheung", "given": "Phyllis Fung-Yi", "initials": "PF"}, {"family": "Engblom", "given": "Camilla", "initials": "C"}, {"family": "Lui", "given": "Weng-Onn", "initials": "WO"}, {"family": "Becker", "given": "J\u00fcrgen Christian", "initials": "JC", "orcid": "0000-0001-9183-653X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a21ac93fdb54dc4b674a82ec44c7214.json"}}], "type": "journal article", "published": "2025-09-23", "journal": {"title": "J Immunother Cancer", "issn": "2051-1426", "volume": "13", "issue": "9", "issn-l": null}, "abstract": "The presence of tertiary lymphoid structures (TLS) in solid tumors, including Merkel cell carcinoma (MCC), is associated with a better prognosis and a better response to immunotherapy with immune checkpoint inhibition (ICI). The detailed mechanisms by which TLS influence antitumor immune responses are only partially understood.\n\nClinically annotated tumor tissues of 27 patients with MCC were obtained prior to ICI therapy. Tumor samples were subjected to transcriptomic and multiplex immuno-visual profiling, T-cell receptor (TCR) clonotype mapping, as well as-in selected cases-spatial transcriptomics to comprehensively characterize the tumor immune microenvironment.\n\nWeighted gene co-expression network analysis (WGCNA) of transcriptomic data in combination with topological overlap measures indicated a higher abundance of TLS in tumors of patients with MCC responding to ICI therapy. This concept was substantiated through immunomorphological analyses, revealing mature B-cell follicle-like structures characterized by high endothelial venules (HEVs). Further supporting HEVs as critical entry points for na\u00efve T cells, the presence of TLS was correlated with a pronounced infiltration of CD4+ and CD8+ T cells, exhibiting both na\u00efve and central memory phenotypes. The TCR repertoire of these infiltrates exhibited enhanced richness and diversity with a pronounced reactivity toward Merkel cell polyomavirus-derived T-cell epitopes. Spatially resolved RNA and V(D)J sequencing revealed the expression of genes associated with T-cell recruitment within TLS, alongside the presence of na\u00efve and central memory T-cell markers. Notably, individual clonally expanded TCR transcripts were detected both within TLS and among tumor-infiltrating lymphocytes. The latter were associated with low expression of memory cell markers and high expression of effector cell markers. Additionally, a spatial gradient in the expression of genes linked to immune stress in MCC cells-such as those involved in the interferon-\u03b3 response and antigen processing and presentation machinery-originated in proximity to the TLS.\n\nOur findings are consistent with a key role of TLS in shaping immune interactions within the MCC microenvironment, driving the recruitment of diverse tumor-reactive T cells. These insights hold promise for advancing immunotherapeutic strategies.", "doi": "10.1136/jitc-2025-012224", "pmid": "40992783", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12458699"}, {"db": "pii", "key": "jitc-2025-012224"}], "notes": [], "created": "2025-11-04T15:34:44.091Z", "modified": "2025-11-04T15:34:44.656Z"}, {"entity": "publication", "iuid": "467584c1e0774aef801f14804cc86726", "links": {"self": {"href": "https://publications.scilifelab.se/publication/467584c1e0774aef801f14804cc86726.json"}, "display": {"href": "https://publications.scilifelab.se/publication/467584c1e0774aef801f14804cc86726"}}, "title": "Influence of the pre-membrane and envelope proteins on structure, pathogenicity, and tropism of tick-borne encephalitis virus.", "authors": [{"family": "Rosendal", "given": "Ebba", "initials": "E", "orcid": "0000-0001-8512-0535", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda3f5ae552241eea145e011afdfad20.json"}}, {"family": "Bisikalo", "given": "Kyrylo", "initials": "K"}, {"family": "Willekens", "given": "Stefanie M A", "initials": "SMA"}, {"family": "Lindgren", "given": "Marie", "initials": "M"}, {"family": "Holoubek", "given": "Ji\u0159\u00ed", "initials": "J"}, {"family": "Svoboda", "given": "Pavel", "initials": "P"}, {"family": "Lappalainen", "given": "Amanda", "initials": "A"}, {"family": "K\u00f6nighofer", "given": "Ebba", "initials": "E"}, {"family": "Mirgorodskaya", "given": "Ekaterina", "initials": "E"}, {"family": "Nord\u00e9n", "given": "Rickard", "initials": "R"}, {"family": "Morini", "given": "Federico", "initials": "F"}, {"family": "Rosenbaum", "given": "William", "initials": "W"}, {"family": "R\u016f\u017eek", "given": "Daniel", "initials": "D"}, {"family": "Ahlgren", "given": "Ulf", "initials": "U"}, {"family": "Anastasina", "given": "Maria", "initials": "M"}, {"family": "Merits", "given": "Andres", "initials": "A", "orcid": "0000-0001-8193-0071", "researcher": {"href": "https://publications.scilifelab.se/researcher/f77e550339464de88e94f9aa9a91e324.json"}}, {"family": "Butcher", "given": "Sarah J", "initials": "SJ", "orcid": "0000-0001-7060-5871", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7076e70172b45d7ab9de4ab86775ae9.json"}}, {"family": "Nilsson", "given": "Emma", "initials": "E"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}], "type": "journal article", "published": "2025-09-23", "journal": {"title": "J. Virol.", "issn": "1098-5514", "volume": "99", "issue": "9", "pages": "e0087025", "issn-l": "0022-538X"}, "abstract": "Tick-borne encephalitis virus (TBEV) is a neurotropic flavivirus that causes thousands of human infections annually. Viral tropism in the brain is determined by the presence of necessary receptors, entry factors, and the ability of the virus to overcome host defenses. The viral structural proteins, pre-membrane (prM), and envelope (E) play an important role in receptor binding, membrane fusion, particle maturation, and antibody neutralization. To understand how these proteins influence virus distribution and tropism in the brain, we generated a chimeric virus harboring the prM and ectodomain of E from TBEV in the background of the low-pathogenic Langat virus (LGTV). We solved the atomic structures of both the chimeric virus and LGTV to compare them to the known TBEV structure. We show that this chimeric virus remains low-pathogenic, while being structurally and antigenically similar to TBEV. Using 3D optical whole brain imaging combined with immunohistochemistry, we found that both LGTV and the chimeric virus primarily infect the cerebral cortex, with no significant differences in their localization or tropism. In contrast, TBEV shows high infection of the cerebellum and a strong preference toward Purkinje cells, indicating that factors other than the prM and E proteins are important for determining TBEV tropism in the brain. Together, this provides new insights into the roles of the structural and non-structural proteins of tick-borne flaviviruses.\n\nAlthough an effective vaccine exists, there is no treatment for those infected by the tick-borne encephalitis virus (TBEV). This study aimed to better understand how the virus's surface proteins influence viral tropism and pathogenicity. We created a chimeric virus with prM and E proteins of TBEV in the genetic background of the low-pathogenic Langat virus (LGTV). The chimeric virus remained low pathogenic, similar to LGTV. Both viruses infected similar brain regions, while TBEV showed a strong preference for the cerebellum and Purkinje cells. This means that other parts of the virus, such as non-structural proteins or NCR, likely decide how the virus behaves in the brain. This study also presents the first cryogenic electron microscopy structure of LGTV, the first whole-brain imaging of TBEV infection in mouse brain, and a new model system to study surface proteins in tick-borne flaviviruses-laying groundwork for future studies on viral tropism, antibody cross-reactivity, and virus-receptor interaction.", "doi": "10.1128/jvi.00870-25", "pmid": "40827915", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative", "Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12456022"}], "notes": [], "created": "2025-10-22T19:22:15.679Z", "modified": "2025-11-13T09:31:25.575Z"}, {"entity": "publication", "iuid": "d86873f5763144d9906b64d27226fbe4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d86873f5763144d9906b64d27226fbe4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d86873f5763144d9906b64d27226fbe4"}}, "title": "FET fusion oncoproteins enrich SWI/SNF complex subtypes and interaction partners.", "authors": [{"family": "Lind\u00e9n", "given": "Malin", "initials": "M", "orcid": "0000-0002-9055-2575", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fbef56453374b4ba9533eced197b35f.json"}}, {"family": "Andersson", "given": "Lisa", "initials": "L"}, {"family": "Albatrok", "given": "Heba", "initials": "H"}, {"family": "Canfjorden", "given": "Vilma", "initials": "V"}, {"family": "Jonasson", "given": "Emma", "initials": "E"}, {"family": "Gr\u00f6nqvist", "given": "Kajsa", "initials": "K"}, {"family": "Sj\u00f6vall", "given": "Daniel", "initials": "D"}, {"family": "Jaako", "given": "Pekka", "initials": "P"}, {"family": "Crescitelli", "given": "Rossella", "initials": "R"}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "\u00c5man", "given": "Pierre", "initials": "P"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}], "type": "journal article", "published": "2025-09-23", "journal": {"title": "Cell Mol Biol Lett", "issn": "1689-1392", "volume": "30", "issue": "1", "pages": "107", "issn-l": null}, "abstract": "FET (FUS, EWSR1, and TAF15) fusion oncoproteins are characteristic for several sarcomas and leukemias, including myxoid liposarcoma and Ewing sarcoma. FET oncoproteins interact with the SWI/SNF chromatin remodeling complex subtypes cBAF, PBAF, and GBAF, but their impact on SWI/SNF compositions, interactions, and downstream epigenetic effects remains elusive.\n\nWe employ a comprehensive immunoprecipitation and quantitative mass spectrometry approach to determine the impact of FET oncoproteins on SWI/SNF composition and their interactomes. Validation of complex composition and interaction partners is performed by glycerol gradient sedimentation assays and co-immunofluorescence analysis. Furthermore, we determine the differential chromatin accessibility and gene regulation in FET sarcomas using assay for transposase-accessible chromatin sequencing and RNA sequencing, respectively.\n\nOur data show that FET sarcomas have distinct SWI/SNF complex compositions, with different subunit paralogs and subtype-specific components that utilize distinct sets of interaction partners, including specific transcription factors. We show that FET oncoproteins cause no major disruption of the SWI/SNF complex composition. Instead, FUS::DDIT3-bound SWI/SNF complexes in myxoid liposarcoma cells are enriched in PBAF and GBAF components as well as most interaction partners.\n\nThese data suggest that FET oncoproteins act together with fully assembled and functional SWI/SNF complexes and recruited interaction partners. Finally, our data reveal that the SWI/SNF compositions, interactomes, and epigenetic background contribute to the tumor type in FET sarcoma. Trial registration Clinical trial number: not applicable.", "doi": "10.1186/s11658-025-00792-w", "pmid": "40988026", "labels": {"Glycoproteomics and MS Proteomics": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12455829"}, {"db": "pii", "key": "10.1186/s11658-025-00792-w"}], "notes": [], "created": "2025-10-23T13:33:49.013Z", "modified": "2025-11-28T10:52:34.797Z"}, {"entity": "publication", "iuid": "e8e2a29927cd48e6bc32204e43189fbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8e2a29927cd48e6bc32204e43189fbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8e2a29927cd48e6bc32204e43189fbb"}}, "title": "SAG1.3-derived Frizzled-targeting small molecule compounds.", "authors": [{"family": "Gr\u00e4tz", "given": "Lukas", "initials": "L"}, {"family": "Turku", "given": "Ainoleena", "initials": "A"}, {"family": "Kozielewicz", "given": "Pawel", "initials": "P"}, {"family": "Bowin", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Scharf", "given": "Magdalena M", "initials": "MM"}, {"family": "Voss", "given": "Jan H", "initials": "JH"}, {"family": "Kinsolving", "given": "Julia", "initials": "J"}, {"family": "Shekhani", "given": "Rawan", "initials": "R"}, {"family": "Oliva-Vilarnau", "given": "Nuria", "initials": "N"}, {"family": "Koolmeister", "given": "Tobias", "initials": "T"}, {"family": "K\u00f6rber", "given": "Marlies", "initials": "M"}, {"family": "Lauschke", "given": "Volker M", "initials": "VM"}, {"family": "L\u00f6ber", "given": "Stefan", "initials": "S"}, {"family": "Gmeiner", "given": "Peter", "initials": "P"}, {"family": "Schulte", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2025-09-22", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "pages": "110751", "issn-l": "0021-9258"}, "abstract": "Exaggerated Wingless/Int1 (WNT)/Frizzled (FZD) signaling contributes to pathologies including fibrosis and different forms of cancers. Thus, targeting FZDs as WNT receptors for therapeutic purposes constitutes a promising intervention if the imminent risk of unwanted side effects caused by the involvement of WNT/FZD signaling in stem cell regulation and tissue homeostasis can be controlled. Here, we derivatize SAG1.3, which acts through FZD6 as a partial agonist. Screening of SAG1.3 derivatives identified compound 11 that competed with BODIPY-cyclopamine binding at different FZDs and inhibited WNT-induced FZD dynamics and \u03b2-catenin signaling in HEK293 cells. Furthermore, compound 11 blocked WNT-3A-induced Lgr5 gene expression in human primary hepatocyte spheroids and reduced the viability of RNF43-mutated but not RNF43-wildtype pancreatic cancer cells. Based on our data, we suggest that compound 11 acts on FZDs to limit WNT- and WNT-surrogate-induced receptor dynamics providing a valid proof-of-concept for targeting FZDs with small molecule compounds.", "doi": "10.1016/j.jbc.2025.110751", "pmid": "40992662", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0021-9258(25)02603-1"}], "notes": [], "created": "2025-10-14T15:26:07.354Z", "modified": "2025-10-17T13:04:26.480Z"}, {"entity": "publication", "iuid": "ab9d1b96921b4340bf1580058440e585", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab9d1b96921b4340bf1580058440e585.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab9d1b96921b4340bf1580058440e585"}}, "title": "Effects of Stress Coping Styles and Social Defeat on Zebrafish Behaviour and Brain Transcriptomics.", "authors": [{"family": "Huben\u00e1", "given": "Pavla", "initials": "P", "orcid": "0000-0001-6351-6395", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6289bcd5ca44998a6dfd876a82ba132.json"}}, {"family": "Benrejdal", "given": "Lisa", "initials": "L", "orcid": "0000-0002-0707-1296", "researcher": {"href": "https://publications.scilifelab.se/researcher/21a1aabfa72342179ddd1b334d403d53.json"}}, {"family": "Brodin", "given": "David", "initials": "D", "orcid": "0000-0002-1768-6761", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b8b61f55e9b49529f1bc412e07db318.json"}}, {"family": "Axling", "given": "Johanna", "initials": "J", "orcid": "0000-0001-6753-6457", "researcher": {"href": "https://publications.scilifelab.se/researcher/5857d627e160441196581f048bb800f1.json"}}, {"family": "Sarma", "given": "Oly Sen", "initials": "OS"}, {"family": "Bergman", "given": "Peter", "initials": "P", "orcid": "0000-0003-3306-3713", "researcher": {"href": "https://publications.scilifelab.se/researcher/397d11713c80456bb600b1e4c88ff843.json"}}, {"family": "Winberg", "given": "Svante", "initials": "S", "orcid": "0000-0003-4252-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3f91e307ce54a9385b84784a7c8b107.json"}}], "type": "journal article", "published": "2025-09-22", "journal": {"title": "Neurosci Bull", "issn": "1995-8218", "issn-l": null}, "abstract": "Individuals with divergent personality traits corresponding to stress coping styles have been suggested to differ in behavioural and neural plasticity. We used a model of social defeat stress to assess the coping ability of wild zebrafish selectively bred for boldness/shyness. Behavioural tests were applied to assess parameters such as boldness/exploration, aggressiveness, and displacement behaviour. Gene expression changes in the brain were assessed via RNA sequencing. The main results show a strong effect of shyness and boldness phenotype on behaviour and the brain transcriptome. Fish of the shy line displayed significant behavioural differences, while the number of differentially-expressed genes remained low. In contrast, fish of the bold line exhibited a small effect on behaviour and pronounced changes in brain gene expression. This study highlights the importance of boldness phenotype and its influence on the response to social challenges at the behavioural and transcriptomic levels.", "doi": "10.1007/s12264-025-01506-0", "pmid": "40982127", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s12264-025-01506-0"}], "notes": [], "created": "2025-11-28T10:41:34.101Z", "modified": "2025-11-28T14:59:54.531Z"}, {"entity": "publication", "iuid": "617294cc6c804df0aba2f985c3b8a7e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/617294cc6c804df0aba2f985c3b8a7e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/617294cc6c804df0aba2f985c3b8a7e8"}}, "title": "Natural Language Response Formats for Assessing Depression and Worry With Large Language Models: A Sequential Evaluation With Model Pre-Registration.", "authors": [{"family": "Gu", "given": "Zhuojun", "initials": "Z", "orcid": "0009-0000-1610-4830", "researcher": {"href": "https://publications.scilifelab.se/researcher/18420c30c5c84acd88f7ad6ce53429c3.json"}}, {"family": "Kjell", "given": "Katarina", "initials": "K"}, {"family": "Schwartz", "given": "H Andrew", "initials": "HA", "orcid": "0000-0002-6383-3339", "researcher": {"href": "https://publications.scilifelab.se/researcher/d598047e39d349d3b5242747ea553a5a.json"}}, {"family": "Kjell", "given": "Oscar", "initials": "O"}], "type": "journal article", "published": "2025-09-20", "journal": {"title": "Assessment", "issn": "1552-3489", "pages": "10731911251364022", "issn-l": null}, "abstract": "Large language models can transform individuals' mental health descriptions into scores that correlate with rating scales approaching theoretical upper limits. However, such analyses have combined word- and text responses with little known about their differences. We develop response formats ranging from closed-ended to open-ended: (a) select words from lists, write (b) descriptive words, (c) phrases, or (d) texts. Participants answered questions about their depression/worry using the response formats and related rating scales. Language responses were transformed into word embeddings and trained to rating scales. We compare the validity (concurrent, incremental, face, discriminant, and external validity) and reliability (prospective sample and test-retest reliability) of the response formats. Using the Sequential Evaluation with Model Pre-Registration design, machine-learning models were trained on a development dataset (N = 963), and then pre-registered before tested on a prospective sample (N = 145). The pre-registered models demonstrate strong validity and reliability, yielding high accuracy in the prospective sample (r = .60-.79). Additionally, the models demonstrated external validity to self-reported sick-leave/healthcare visits, where the text-format yielded the strongest correlations (being higher/equal to rating scales for 9 of 12 cases). The overall high validity and reliability across formats suggest the possibility of choosing formats according to clinical needs.", "doi": "10.1177/10731911251364022", "pmid": "40974258", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:52:29.563Z", "modified": "2025-11-28T10:52:29.714Z"}, {"entity": "publication", "iuid": "556d4edffc90459c9381cdfb5d6a1eaf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/556d4edffc90459c9381cdfb5d6a1eaf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/556d4edffc90459c9381cdfb5d6a1eaf"}}, "title": "Late Iron Age and Roman equine breeding north of the Alps: Genetic insights and cultural implications.", "authors": [{"family": "Sharif", "given": "Muhammad Bilal", "initials": "MB"}, {"family": "Mohaseb", "given": "Azadeh Fatemeh", "initials": "AF"}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "Saliari", "given": "Konstantina", "initials": "K"}, {"family": "Kunst", "given": "G\u00fcnther Karl", "initials": "GK"}, {"family": "Czeika", "given": "Sigrid", "initials": "S"}, {"family": "Mashkour", "given": "Marjan", "initials": "M"}, {"family": "Cucchi", "given": "Thomas", "initials": "T"}, {"family": "Peters", "given": "Joris", "initials": "J"}, {"family": "Trixl", "given": "Simon", "initials": "S"}, {"family": "Mohandesan", "given": "Elmira", "initials": "E"}], "type": "journal article", "published": "2025-09-19", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "28", "issue": "9", "pages": "113224", "issn-l": "2589-0042"}, "abstract": "The Roman conquest of the northern Alpine foreland in 15 BCE introduced larger-sized horses and hybrid mules to the region. To investigate their genetic profiles and influence on local breeding, we analyzed our previously generated shallow shotgun DNA data from 402 Late Iron Age and Roman equids, supplemented with mitochondrial and nuclear capture data from 40 to 31 equids from the same regions and periods. Late Iron Age and Roman horses exhibit high matrilineal diversity, with unique haplogroups in the latter indicating exogenous animals. The preferred use of male mounts in army service mentioned in historical writings is confirmed. The absence of donkey jacks in our study area and the lack of mule matrilineal lineages unique to Late Iron Age horses contradict local hybrid breeding. Alleles associated with speed, endurance, or rare coat colors have not been identified, nor has a genetic basis for the larger body size of Roman horses, although illustrated by archaeozoological and historical data.", "doi": "10.1016/j.isci.2025.113224", "pmid": "40837235", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12362026"}, {"db": "pii", "key": "S2589-0042(25)01485-3"}], "notes": [], "created": "2025-11-28T10:43:50.194Z", "modified": "2025-11-28T10:43:50.198Z"}, {"entity": "publication", "iuid": "65436332bae2406a9b356319a482d5fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65436332bae2406a9b356319a482d5fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65436332bae2406a9b356319a482d5fb"}}, "title": "Controllable properties and versatile dynamics of meron topological magnetism in van der Waals multiferroic CuCrP2S6.", "authors": [{"family": "Cui", "given": "Qirui", "initials": "Q"}, {"family": "Ge", "given": "Yuqing", "initials": "Y"}, {"family": "Bai", "given": "Xiaocheng", "initials": "X"}, {"family": "Sassa", "given": "Yasmine", "initials": "Y"}, {"family": "Delin", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-09-19", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "28", "issue": "9", "pages": "113291", "issn-l": "2589-0042"}, "abstract": "The ability to efficiently control topological magnetism is crucial for advancing technological applications and deepening our understanding of magnetic systems. Although emerging van der Waals (vdW) multiferroics present a promising frontier for energy-efficient spin manipulation, the control of topological magnetism remains challenging due to its scarcity in multiferroics. Here, we demonstrate that highly tunable merons and antimerons emerge in monolayer multiferroic (CCPS). The antiferroelectric-to-ferroelectric (AFE-FE) transition enhances exchange couplings, notably reducing meron density and increasing meron size during cooling. Merons exhibit unique dynamics, characterized by nontrivial attraction and annihilation processes, which generates distinct long-lived spin waves and reduces meron number difference between AFE and FE phases until they vanish. Importantly, ultrafast laser pulses can induce ferroelectricity-tunable merons from a uniform in-plane magnetization, re-leading to a large difference in meron density between the AFE and FE phases. These findings enhance our understanding of topological magnetism and open up exciting avenues for controlling the properties and dynamics of topological states through electrical and optical methods. CuCrP 2 S 6", "doi": "10.1016/j.isci.2025.113291", "pmid": "40894898", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12391263"}, {"db": "pii", "key": "S2589-0042(25)01552-4"}], "notes": [], "created": "2025-11-28T10:43:55.249Z", "modified": "2025-11-28T10:43:55.252Z"}, {"entity": "publication", "iuid": "3dea4d3c9bd849c3980d258e4d8074db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3dea4d3c9bd849c3980d258e4d8074db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3dea4d3c9bd849c3980d258e4d8074db"}}, "title": "Unveiling histotype-specific biomarkers in ovarian carcinoma using proteomics.", "authors": [{"family": "Werner", "given": "Lucas", "initials": "L"}, {"family": "Ittner", "given": "Ella", "initials": "E"}, {"family": "Swenson", "given": "Hugo", "initials": "H"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Mateoiu", "given": "Claudia", "initials": "C"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Dahm-K\u00e4hler", "given": "Pernilla", "initials": "P"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Thorsell", "given": "Annika", "initials": "A"}, {"family": "Rekabdar", "given": "Elham", "initials": "E"}, {"family": "Esmaeili", "given": "Parisa", "initials": "P"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E"}, {"family": "Tullberg", "given": "Axel Stenmark", "initials": "AS"}, {"family": "Saed", "given": "Ghassan", "initials": "G"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ", "orcid": "0000-0003-0834-5540", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d528a2bce6c40829c1a6fed69c9f9ef.json"}}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2025-09-18", "journal": {"title": "Mol Ther Oncol", "issn": "2950-3299", "volume": "33", "issue": "3", "pages": "201019", "issn-l": null}, "abstract": "Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy, yet clinical tools for diagnosis, prognosis, and treatment remain limited, and molecular profiling of histotypes is lacking. Here, we leverage proteomic data to further stratify four main EOC histotypes, borderline (BL) and benign (B) tumors, and identify candidate prognostic and diagnostic biomarkers. Using proteomic data from 300 patient samples, we identified differentially abundant proteins (DAPs) such as SNCG, S100A1, VWA2, AGR2, CTH, and SPINK1 and biomarker panels to stratify the tissues. Enrichment of biological processes profiled histotypes and involvement of DAPs. Survival analysis identified candidate biomarkers predicting overall- and disease-specific survival with histotype-specificity. Of these, GLYR1, RPL12, GDPGP1, and POLR2M were associated with favorable outcomes, while SDF4, PPP3CC, EIF2AK2, and STX6 were linked to unfavorable outcomes. Collectively, these findings provide histotype-specific attributes for known and EOC biomarkers that may serve as clinical tools for EOC diagnosis and treatment decisions.", "doi": "10.1016/j.omton.2025.201019", "pmid": "40778374", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12328698"}, {"db": "pii", "key": "S2950-3299(25)00088-8"}], "notes": [], "created": "2025-10-22T19:23:09.822Z", "modified": "2025-10-23T08:55:10.395Z"}, {"entity": "publication", "iuid": "f4701608c6464c3288865cdcb70e61c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4701608c6464c3288865cdcb70e61c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4701608c6464c3288865cdcb70e61c9"}}, "title": "Low-Dose Aspirin for PI3K-Altered Localized Colorectal Cancer.", "authors": [{"family": "Martling", "given": "Anna", "initials": "A", "orcid": "0000-0001-5998-4735", "researcher": {"href": "https://publications.scilifelab.se/researcher/dab7d4e9839b4cd5be9393a04b089d33.json"}}, {"family": "Hed Myrberg", "given": "Ida", "initials": "I"}, {"family": "Nilbert", "given": "Mef", "initials": "M"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Granath", "given": "Fredrik", "initials": "F"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "\u00d6resland", "given": "Tom", "initials": "T"}, {"family": "Iversen", "given": "Lene H", "initials": "LH"}, {"family": "Haapam\u00e4ki", "given": "Carola", "initials": "C"}, {"family": "Janson", "given": "Martin", "initials": "M"}, {"family": "Westberg", "given": "Karin", "initials": "K"}, {"family": "Segelman", "given": "Josefin", "initials": "J"}, {"family": "Ersson", "given": "Urban", "initials": "U"}, {"family": "Prytz", "given": "Mattias", "initials": "M"}, {"family": "Angenete", "given": "Eva", "initials": "E", "orcid": "0000-0001-9966-4904", "researcher": {"href": "https://publications.scilifelab.se/researcher/07bd63b6d277460ca830518ed23fa31e.json"}}, {"family": "Bergstr\u00f6m", "given": "Rebecka", "initials": "R", "orcid": "0000-0001-7609-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c52bb8b2ae249049f0da222bcdfe932.json"}}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Glimelius", "given": "Bengt", "initials": "B"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "ALASCCA Study Group", "given": "", "initials": ""}], "type": "clinical trial, phase iii", "published": "2025-09-18", "journal": {"title": "N. Engl. J. Med.", "issn": "1533-4406", "volume": "393", "issue": "11", "pages": "1051-1064", "issn-l": "0028-4793"}, "abstract": "Aspirin reduces the incidence of colorectal adenoma and colorectal cancer among high-risk persons. Observational studies suggest that aspirin may also improve disease-free survival after diagnosis, particularly among patients with tumors harboring somatic PIK3CA mutations. However, data from randomized trials are lacking.\n\nWe conducted a double-blind, randomized, placebo-controlled trial involving patients with stage I, II, or III rectal cancer or stage II or III colon cancer with somatic alterations in PI3K pathway genes. The patients were assigned in a 1:1 ratio to receive 160 mg of aspirin or matched placebo once daily for 3 years. Patients with prespecified PIK3CA hotspot mutations in exon 9 or 20 (group A alterations) and those with other moderate- or high-impact somatic variants in PIK3CA, PIK3R1, or PTEN (group B alterations) were eligible for randomization. The primary end point was colorectal cancer recurrence, assessed in a time-to-event analysis, in patients with group A alterations. Secondary end points included colorectal cancer recurrence in patients with group B alterations, disease-free survival, and safety.\n\nAlterations in PI3K pathway genes were detected in 1103 of 2980 patients (37.0%) with complete genomic data. Of 515 patients with group A alterations and 588 patients with group B alterations, 314 and 312, respectively, were assigned to receive aspirin or placebo. The estimated 3-year cumulative incidence of recurrence was 7.7% with aspirin and 14.1% with placebo (hazard ratio, 0.49; 95% confidence interval [CI], 0.24 to 0.98; P = 0.04) among patients with group A alterations and 7.7% and 16.8%, respectively (hazard ratio, 0.42; 95% CI, 0.21 to 0.83), among those with group B alterations. The estimated 3-year disease-free survival was 88.5% with aspirin and 81.4% with placebo (hazard ratio, 0.61; 95% CI, 0.34 to 1.08) among patients with group A alterations and 89.1% and 78.7%, respectively (hazard ratio, 0.51; 95% CI, 0.29 to 0.88), among those with group B alterations. Severe adverse events occurred in 16.8% of aspirin recipients and 11.6% of placebo recipients.\n\nAspirin led to a significantly lower incidence of colorectal cancer recurrence than placebo among patients with PIK3CA hotspot mutations in exon 9 or 20 and appeared to have a similar benefit among those with other somatic alterations in PI3K pathway genes. (Funded by the Swedish Research Council and others; ALASCCA ClinicalTrials.gov number, NCT02647099; EudraCT number, 2015-004240-19.).", "doi": "10.1056/NEJMoa2504650", "pmid": "40961426", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "ClinicalTrials.gov", "key": "NCT02647099"}, {"db": "EudraCT", "key": "2015-004240-19"}], "notes": [], "created": "2025-10-06T11:47:12.777Z", "modified": "2025-11-18T20:46:30.247Z"}, {"entity": "publication", "iuid": "f2d93ddd22d1448f94d015eade7992ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2d93ddd22d1448f94d015eade7992ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2d93ddd22d1448f94d015eade7992ac"}}, "title": "Continuous Serial Electron Diffraction for High Quality Protein Structures", "authors": [{"family": "Hofer", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-9248-6989", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcf436f51b14189b0c6668e6903afd8.json"}}, {"family": "Wang", "given": "Lei", "initials": "L", "orcid": "0000-0002-7398-1124", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd71b3e4c1b541d8b7f894e7670635f7.json"}}, {"family": "Pacoste", "given": "Laura", "initials": "L", "orcid": "0009-0005-6090-8736", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d78c5b22b984ee5b2803a2bfe8458a3.json"}}, {"family": "Hager", "given": "Paul", "initials": "P", "orcid": "0009-0008-1551-2515", "researcher": {"href": "https://publications.scilifelab.se/researcher/54a85f27eb9b47f48e8fe651912bec02.json"}}, {"family": "Fonjallaz", "given": "Alexis", "initials": "A", "orcid": "0000-0002-9390-1654", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70ff766fd004acd9088745fbefe8c0a.json"}}, {"family": "Williams", "given": "Lewis", "initials": "L", "orcid": "0009-0002-4066-3899", "researcher": {"href": "https://publications.scilifelab.se/researcher/2efd72c134204b249eaac0f870e10824.json"}}, {"family": "Scaletti Hutchinson", "given": "Emma", "initials": "E", "orcid": "0000-0002-8741-8981", "researcher": {"href": "https://publications.scilifelab.se/researcher/34a21e353ecb49eba831f7b0d68e024a.json"}}, {"family": "Di Palma", "given": "Michele", "initials": "M", "orcid": "0000-0002-0710-9389", "researcher": {"href": "https://publications.scilifelab.se/researcher/d568035c6a0345c990ee44ab38e85e01.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Worral", "given": "Jonathan", "initials": "J"}, {"family": "Steiner", "given": "Roberto A", "initials": "RA", "orcid": "0000-0001-7084-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/88121996557f4c0a884e49b720e735cb.json"}}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}], "type": "posted-content", "published": "2025-09-17", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.09.14.676192", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-26T08:59:49.401Z", "modified": "2025-12-18T19:09:08.443Z"}, {"entity": "publication", "iuid": "486aead1940949e6b3216f50ecb9404f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/486aead1940949e6b3216f50ecb9404f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/486aead1940949e6b3216f50ecb9404f"}}, "title": "Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma.", "authors": [{"family": "Wan", "given": "Hui", "initials": "H"}, {"family": "Ren", "given": "Weicheng", "initials": "W"}, {"family": "Yang", "given": "Mingyu", "initials": "M"}, {"family": "Nie", "given": "Man", "initials": "M"}, {"family": "Wasik", "given": "Agata M", "initials": "AM"}, {"family": "Du", "given": "Likun", "initials": "L"}, {"family": "de Campos-Mata", "given": "Leire", "initials": "L"}, {"family": "Sun", "given": "Rui", "initials": "R"}, {"family": "Bai", "given": "Zhiliang", "initials": "Z"}, {"family": "Enninful", "given": "Archibald", "initials": "A"}, {"family": "Wang", "given": "Yating", "initials": "Y"}, {"family": "Berglund", "given": "Mattias", "initials": "M"}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM"}, {"family": "Li", "given": "Xiaobo", "initials": "X"}, {"family": "Yang", "given": "Chunli", "initials": "C"}, {"family": "Ye", "given": "Xiaofei", "initials": "X"}, {"family": "Yang", "given": "Zhi-Zhang", "initials": "ZZ"}, {"family": "Ansell", "given": "Stephen M", "initials": "SM"}, {"family": "Liu", "given": "Dongbing", "initials": "D"}, {"family": "van der Burg", "given": "Mirjam", "initials": "M"}, {"family": "Fan", "given": "Rong", "initials": "R"}, {"family": "Wu", "given": "Kui", "initials": "K"}, {"family": "Sander", "given": "Birgitta", "initials": "B"}, {"family": "Pan-Hammarstr\u00f6m", "given": "Qiang", "initials": "Q"}], "type": "journal article", "published": "2025-09-16", "journal": {"title": "Cell Reports Medicine", "issn": "2666-3791", "volume": "6", "issue": "9", "pages": "102318", "issn-l": "2666-3791"}, "abstract": "Mantle cell lymphoma (MCL) is a rare but often aggressive type of B cell lymphoma with a high risk of relapse. To explore intratumoral clonal diversity and tumor evolution related to disease relapse, we integrate single-cell RNA and B cell receptor sequencing with whole-genome sequencing in 20 diagnosed/untreated and/or relapsed samples from 11 MCL patients. Our results reveal significant intratumor heterogeneity in MCL already at diagnosis. We further show that the evolutionary paths during disease progression for each patient are unique, where minor clones present at diagnosis may acquire different mutations and copy-number variations and/or migrate to various microenvironments. Despite significant interpatient heterogeneity, recurrent genetic and transcriptomic changes in tumor cells affecting key signaling pathways, along with alterations involved in the tumor microenvironment, are also observed during disease progression. Taken together, our findings elucidate the diverse and dynamic tumor-immune evolution processes associated with disease progression and relapse in MCL.", "doi": "10.1016/j.xcrm.2025.102318", "pmid": "40876452", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12490240"}, {"db": "pii", "key": "S2666-3791(25)00391-X"}], "notes": [], "created": "2025-11-28T10:44:46.757Z", "modified": "2025-11-28T10:44:46.762Z"}, {"entity": "publication", "iuid": "35d4093216fd4b19b04911045f02ce71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35d4093216fd4b19b04911045f02ce71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35d4093216fd4b19b04911045f02ce71"}}, "title": "Targeted ferroptosis induction enhances chemotherapy efficacy in chemoresistant neuroblastoma.", "authors": [{"family": "Ma\u00f1as", "given": "Adriana", "initials": "A"}, {"family": "Seger", "given": "Alexandra", "initials": "A"}, {"family": "Adamska", "given": "Aleksandra", "initials": "A"}, {"family": "Smyrilli", "given": "Kyriaki", "initials": "K"}, {"family": "Siaw", "given": "Joachim T", "initials": "JT"}, {"family": "Radke", "given": "Katarzyna", "initials": "K"}, {"family": "Muci\u00f1o-Olmos", "given": "Erick A", "initials": "EA"}, {"family": "Bedoya-Reina", "given": "Oscar C", "initials": "OC"}, {"family": "Esfandyari", "given": "Javanshir", "initials": "J"}, {"family": "Aaltonen", "given": "Kristina", "initials": "K"}, {"family": "Bexell", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-09-16", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "311", "issn-l": null}, "abstract": "Neuroblastoma (NB) is an aggressive pediatric solid tumor which often develops chemoresistance. Ferroptosis is a potential vulnerability in NB, but its interplay with chemoresistance and standard-of-care chemotherapy is not known. Here, we report that key antioxidant pathways are enriched in refractory NB, and that ferroptosis can be induced in NB through various mechanisms of action (MOA) in vitro and in vivo. We observed that NB standard-of-care chemotherapy can interfere with certain ferroptosis-inducing mechanisms, particularly those targeting GPX4, and that the combination of ferroptosis-inducing drugs with current clinical therapy should be based on MOA. Our work also shows that a combination of chemotherapy and the thioredoxin reductase inhibitor Auranofin counteracted some of the anti-ferroptotic effects of chemotherapy and the combination outperformed chemotherapy alone, resulting in increased survival in a chemoresistant NB patient-derived xenograft model. The combination of Auranofin and chemotherapy decreased the population of immature mesenchymal-like NB cells in vivo and exerted its effect through ferritinophagy, lysosome accumulation and iron overload. Thus, upon careful selection of the MOA, the inclusion of ferroptosis-inducing agents within a clinically relevant treatment protocol is feasible and can outperform standard-of-care chemotherapy in high-risk NB.", "doi": "10.1038/s41698-025-01090-6", "pmid": "40957885", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12441132"}, {"db": "pii", "key": "10.1038/s41698-025-01090-6"}], "notes": [], "created": "2025-11-10T13:47:49.160Z", "modified": "2025-11-10T13:47:49.165Z"}, {"entity": "publication", "iuid": "529c1d9b93b7499997f647488acac746", "links": {"self": {"href": "https://publications.scilifelab.se/publication/529c1d9b93b7499997f647488acac746.json"}, "display": {"href": "https://publications.scilifelab.se/publication/529c1d9b93b7499997f647488acac746"}}, "title": "Pronounced seasonal dynamics in transcription of vitamin B1 acquisition strategies diverge among Baltic Sea bacterioplankton.", "authors": [{"family": "P\u00e9rez-Mart\u00ednez", "given": "Clara", "initials": "C"}, {"family": "Pontiller", "given": "Benjamin", "initials": "B"}, {"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}, {"family": "Paerl", "given": "Ryan W", "initials": "RW"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2025-09-16", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "20", "issue": "1", "pages": "115", "issn-l": null}, "abstract": "Vitamin B1 (thiamin) is essential to life; yet little is known of the regulation of its availability in marine environments or how it varies seasonally. Since microbes are the key synthesizers of the vitamin in marine environments, we here used metatranscriptomics to examine the seasonal dynamics of B1 acquisition strategies (including both uptake and synthesis pathways) in Baltic Sea bacterioplankton.\n\nElevated B1-related gene expression was observed in summer, coinciding with increased temperatures and bacterial activity and decreased nutrient availability. Different bacterial taxa exhibited distinct B1 acquisition strategies. We identified filamentous Cyanobacteria of the order Nostocales as critical to sustaining B1 production during summer, potentially compensating for limited synthesis in heterotrophic bacteria, especially for 4-amino-5-hydroxymethylpyrimidine (HMP) synthesis. Also, Pelagibacterales accounted for major portions of the community transcription, primarily taking up and salvaging the B1 precursor HMP during summer. This study highlights the partitioning of B1 synthesis, salvage, and uptake among microbial taxa, underscoring that transcriptional activity was more dynamic over time than changes in the genomic potential.\n\nWe emphasize the influence of environmental conditions on microbial community dynamics and B1 cycling in general, and the potential implications of global change-induced increases in filamentous Cyanobacteria blooms on vitamin food web transfer in particular.", "doi": "10.1186/s40793-025-00780-9", "pmid": "40958120", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12442306"}, {"db": "pii", "key": "10.1186/s40793-025-00780-9"}], "notes": [], "created": "2025-11-21T13:08:52.937Z", "modified": "2025-11-21T13:08:52.943Z"}, {"entity": "publication", "iuid": "a9cc98d146944fd492f16a8e9cc30177", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9cc98d146944fd492f16a8e9cc30177.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9cc98d146944fd492f16a8e9cc30177"}}, "title": "Effects of Oligolysine-Polyethylene Glycol Coating on the Biodistribution of Wireframe DNA Origami Nanosheets in Zebrafish Embryos.", "authors": [{"family": "Kolonelou", "given": "Christina", "initials": "C", "orcid": "0000-0002-5625-5569", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f25477ca214d38a87d4998f6199bc4.json"}}, {"family": "Engstr\u00f6m", "given": "Enya", "initials": "E", "orcid": "0009-0009-6574-0652", "researcher": {"href": "https://publications.scilifelab.se/researcher/d28127bf85bb4581bb77e33e480f61a6.json"}}, {"family": "Br\u00e4utigam", "given": "Lars", "initials": "L"}, {"family": "Edwards", "given": "Steven", "initials": "S"}, {"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/82499805c5c24c46b8c2ec6427345c89.json"}}, {"family": "Spratt", "given": "Joel", "initials": "J", "orcid": "0000-0002-8720-5011", "researcher": {"href": "https://publications.scilifelab.se/researcher/7614bed2922848859b450473137f9a80.json"}}, {"family": "Karampelias", "given": "Christos", "initials": "C"}, {"family": "Rocamonde-Lago", "given": "Iris", "initials": "I"}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications.scilifelab.se/researcher/13b88210e9b64000a27d2eb914fb519c.json"}}, {"family": "Wennmalm", "given": "Stefan", "initials": "S"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Andersson", "given": "Olov", "initials": "O"}, {"family": "Teixeira", "given": "Ana I", "initials": "AI", "orcid": "0000-0001-8169-8815", "researcher": {"href": "https://publications.scilifelab.se/researcher/064f9662cf0247ef9737e7dbcfdeb885.json"}}], "type": "journal article", "published": "2025-09-16", "journal": {"title": "ACS Nano", "issn": "1936-086X", "issn-l": "1936-0851", "volume": "19", "issue": "36", "pages": "32145-32157"}, "abstract": "DNA origami-based nanotechnology is a versatile tool for exploring fundamental biological questions and holds significant promise for future biomedical applications. Here, we leverage the optical transparency of the embryonic zebrafish to analyze live embryos injected intravenously with fluorescently labeled wireframe DNA origami nanosheets. Our approach integrated long-term, high-resolution imaging of transgenic live zebrafish embryos with single-cell RNA sequencing to elucidate the effects of oligolysine-polyethylene glycol copolymer (K-PEG) coating on the biodistribution of fluorescence signal in embryos injected with wireframe DNA origami nanosheets. We observed rapid accumulation of fluorescence signal in the caudal hematopoietic tissue (CHT). K-PEG coating mitigated the accumulation of fluorescence signal in CHT, enabling increased detection of signal in other tissues. Our findings highlighted the pivotal role of scavenger endothelial cells in DNA origami clearance, with K-PEG enabling the prolonged detection of fluorescence signal at the CHT. Furthermore, using a transgenic zebrafish line designed for targeted macrophage ablation, we found that macrophages contribute to the clearance of fluorescence signal in embryos injected with the noncoated but not with K-PEG-coated nanosheets. This study introduces a framework for the analyses of the biodistribution and clearance of DNA origami nanostructures in vivo with single-cell resolution in zebrafish models.", "doi": "10.1021/acsnano.5c05801", "pmid": "40900000", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12444974"}], "notes": [], "created": "2025-09-08T07:33:12.059Z", "modified": "2025-11-13T14:06:13.263Z"}, {"entity": "publication", "iuid": "14fae7f53f414c66aa6903c0f026d037", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14fae7f53f414c66aa6903c0f026d037.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14fae7f53f414c66aa6903c0f026d037"}}, "title": "Circulating soluble LOX-1 and patient prognosis after an acute coronary syndrome.", "authors": [{"family": "Schiopu", "given": "Alexandru", "initials": "A", "orcid": "0000-0002-7587-5050", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7d2edf9030a445583f692dc4d884b7f.json"}}, {"family": "Svedlund", "given": "Sara", "initials": "S"}, {"family": "Narasimhan", "given": "Gayathri", "initials": "G"}, {"family": "Juin Loong", "given": "Bi", "initials": "B"}, {"family": "Yndigegn", "given": "Troels", "initials": "T", "orcid": "0000-0002-8960-2125", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c5f5069c767413eaa653581f7f0bfe9.json"}}, {"family": "Varma", "given": "Vijayalakshmi", "initials": "V"}, {"family": "Ongstad", "given": "Emily L", "initials": "EL"}, {"family": "Goncalves", "given": "Isabel", "initials": "I"}, {"family": "Coll\u00e9n", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Jan", "initials": "J"}, {"family": "Gan", "given": "Li-Ming", "initials": "LM"}], "type": "journal article", "published": "2025-09-16", "journal": {"title": "Heart", "issn": "1468-201X", "issn-l": "1355-6037"}, "abstract": "The lectin-like oxidised low-density lipoprotein receptor-1 (LOX-1) mediates atherosclerotic plaque inflammation and vulnerability. On activation, LOX-1 sheds its extracellular domain into the circulation as soluble LOX-1 (sLOX-1). sLOX-1 is markedly elevated in patients with acute coronary syndrome (ACS).\n\nWe prospectively assessed the associations between plasma sLOX-1 and the development of heart failure (HF), major adverse cardiovascular events (MACE) and coronary and left ventricular (LV) dysfunction in two cohorts of patients with ACS. The first cohort comprised 524 patients recruited during the acute index event at the coronary care unit of Sk\u00e5ne University Hospital, Malm\u00f6, Sweden. The second cohort included 363 patients with ACS treated with acute percutaneous intervention at Sahlgrenska University Hospital, Gothenburg, Sweden. Additionally, we examined the anti-inflammatory effects of LOX-1 blockade in vitro using human umbilical vein endothelial cells (HUVECs).\n\nIn the first cohort, acute-phase sLOX-1 was associated with incident HF and MACE independently of cardiovascular risk factors, revascularisation and medication (HR per 1-SD sLOX-1 increase: 1.57 (95% CI: 1.10 to 2.23; p=0.012) for HF and 1.36 (1.08 to 1.71; p=0.009) for MACE). Elevated sLOX-1 was also associated with lower LV ejection fraction and accelerated remodelling, as measured by echocardiography at 1-year post-ACS. In the second cohort, sLOX-1 was negatively associated with left anterior descending coronary artery flow reserve and LV systolic function, and positively correlated with soluble markers of systemic inflammation and cardiac overload at 4 and 16 weeks post-ACS. In vitro, antibody-mediated LOX-1 blockade prevented oxidised low-density lipoprotein-induced HUVEC activation.\n\nElevated plasma sLOX-1 at baseline and during follow-up is associated with incident HF and MACE, as well as cardiac and coronary dysfunction in patients with ACS. As plasma sLOX-1 levels may reflect the intensity of LOX-1 expression on vascular and immune cells, these findings support LOX-1 as a potentially important therapeutic target to improve prognosis in patients with ACS.", "doi": "10.1136/heartjnl-2025-326315", "pmid": "40957671", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "heartjnl-2025-326315"}], "notes": [], "created": "2025-11-25T19:20:38.823Z", "modified": "2025-11-25T19:20:38.894Z"}, {"entity": "publication", "iuid": "90b2d9da448b4ce6a2cfd431c81f5002", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90b2d9da448b4ce6a2cfd431c81f5002.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90b2d9da448b4ce6a2cfd431c81f5002"}}, "title": "Protocol for genomic surveillance of Plasmodium falciparum antigens using amplicon-based PacBio long-read sequencing.", "authors": [{"family": "Plaza", "given": "David Fernando", "initials": "DF"}], "type": "journal article", "published": "2025-09-15", "journal": {"title": "STAR Protoc", "issn": "2666-1667", "volume": "6", "issue": "4", "pages": "104093", "issn-l": null}, "abstract": "Here, we present a protocol that identifies and classifies structurally diverse variants of msp1, msp2, glurp, and csp in Plasmodium falciparum using an amplicon-based long-read sequencing platform. We describe steps for PCR barcoding, PacBio circular consensus sequencing (CCS), in silico PCR-based size variant calling, and advanced data analysis in Galaxy. By resolving full-length sequences for each antigenic clone, this approach measures infection complexity, constructs isolate phylogenies, and supports vaccine design. For complete details on the use and execution of this protocol, please refer to Plaza et al.1.", "doi": "10.1016/j.xpro.2025.104093", "pmid": "40956667", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12464706"}, {"db": "pii", "key": "S2666-1667(25)00499-X"}], "notes": [], "created": "2025-11-03T09:58:50.283Z", "modified": "2025-11-03T09:58:50.291Z"}, {"entity": "publication", "iuid": "3b3186c13ec643ad9e563c8f99446d2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b3186c13ec643ad9e563c8f99446d2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b3186c13ec643ad9e563c8f99446d2d"}}, "title": "Method development and validation for quantitative determination of urinary biomarkers of food intake for multiple foods.", "authors": [{"family": "Hassenberg", "given": "Christoph", "initials": "C"}, {"family": "Soukup", "given": "Sebastian T", "initials": "ST"}, {"family": "Armeni", "given": "Marina", "initials": "M"}, {"family": "Bub", "given": "Achim", "initials": "A"}, {"family": "Cannas", "given": "Jil V", "initials": "JV"}, {"family": "Fuentes", "given": "David", "initials": "D"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Seifert", "given": "Stephanie", "initials": "S"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Kulling", "given": "Sabine E", "initials": "SE"}, {"family": "Mack", "given": "Carina I", "initials": "CI"}], "type": "journal article", "published": "2025-09-15", "journal": {"title": "Journal of Chromatography B", "issn": "1873-376X", "volume": "1268", "pages": "124793", "issn-l": "1570-0232"}, "abstract": "Biomarkers of food intake (BFIs) have emerged as a promising objective tool to complement traditional self-reported dietary assessment in nutritional research, with the potential to reduce systematic errors and improve accuracy. The development of comprehensive and robust quantification methods for BFIs is essential for widespread application. However, existing methods typically cover only a moderate number of BFIs per method, hindering their wide application in the field. In this study, we present the development and validation of a method for simultaneous quantification of 80 BFIs in urine reflecting 27 foods. The method utilizes a simple sample preparation procedure, followed by separation using both high-performance liquid chromatography (HPLC) on a C18 column and a hydrophilic interaction chromatography (HILIC) column, combined with tandem mass spectrometry in positive and negative mode (HPLC-MS/MS) (individual runs: 6 min). The working range for each analyte was determined in urine samples from a non-randomized, non-blinded nutritional intervention study. The method was validated with respect to selectivity, linearity, robustness, matrix effects, recovery, accuracy, and precision. In total, 44 BFIs could be absolutely quantified without or with only limitations at low concentrations, while 36 BFIs could only be measured semi-quantitatively, including 16 BFIs with limited validation data due to uncertainties. The 80 BFIs represent 27 foods (6 semi-quantitative) frequently consumed in European diets, including 24 plant-derived and 3 animal-derived items. The future implementation of this large-scale BFI quantification method in nutritional studies is expected to demonstrate the benefits of routinely measuring BFIs to improve the accuracy of dietary assessment.", "doi": "10.1016/j.jchromb.2025.124793", "pmid": "41175511", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1570-0232(25)00347-2"}], "notes": [], "created": "2025-11-27T11:24:31.552Z", "modified": "2025-11-27T11:24:31.563Z"}, {"entity": "publication", "iuid": "7b2118e734d34424950d390248954deb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b2118e734d34424950d390248954deb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b2118e734d34424950d390248954deb"}}, "title": "Insights into the Metabolic Adaptations of a Carbapenem-Resistant Klebsiella pneumoniae Strain on Exposure to Sublethal Concentrations of Ertapenem.", "authors": [{"family": "Ja\u00e9n-Luchoro", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5988-6227", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a821a703a144b5aa5a783e7f8043d86.json"}}, {"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F", "orcid": "0000-0003-0173-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d15be15c484e6a99f22b466bf99166.json"}}, {"family": "Pi\u00f1eiro-Iglesias", "given": "Beatriz", "initials": "B", "orcid": "0000-0003-3125-0822", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f4f8871d0ce48149f88b24b6fb42c6c.json"}}, {"family": "Marathe", "given": "Nachiket", "initials": "N", "orcid": "0000-0003-2955-3402", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b806ecb68c246beacbf04550e422714.json"}}, {"family": "Moore", "given": "Edward R B", "initials": "ERB", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1c68436094391bfefd7de22757aba.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}], "type": "journal article", "published": "2025-09-15", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "18", "issn-l": null}, "abstract": "Klebsiella pneumoniae strains that are resistant to carbapenems are of great concern. Exposure to low concentrations of antibiotics may influence tolerance to antibiotics. Novel antibiotics and treatment options are thus needed, and this need is exacerbated by the rapid and global spread of antibiotic resistance. In this study, we determined the global proteome changes in a K. pneumoniae strain (CCUG 70747) carrying carbapenem resistance genes when exposed to low concentrations of ertapenem. Quantitative proteomics was achieved by the tandem mass tag labeling of peptides generated by trypsin proteolysis and mass spectrometry analysis. Bioinformatics analyses were used to observe changes in protein abundance, as well as the gene ontology (GO) terms and pathways associated with the differentially expressed proteins. The number of proteins detected with significant differential abundance were 87 at the highest concentration applied and 61 in the lowest concentration, all compared with the strain cultured without any antibiotics present. Several of these proteins, as well as the GO terms and pathways associated with the proteins, were linked to mechanisms of antibiotic resistance. However, this strain encodes a carbapenemase and other beta-lactamases, and thus, as expected, presented a reasonably modest adaptation in the global proteome upon exposure to the low concentrations of ertapenem applied. Nevertheless, our study identifies pathways that may lead to adaptation under sublethal concentrations of antibiotics leading to strains with higher tolerance.", "doi": "10.3390/ijms26188988", "pmid": "41009554", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12470040"}, {"db": "pii", "key": "ijms26188988"}], "notes": [], "created": "2025-10-23T12:42:51.224Z", "modified": "2025-10-23T12:42:51.506Z"}, {"entity": "publication", "iuid": "fb76f18dd39f4a29abe21cc711f27555", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb76f18dd39f4a29abe21cc711f27555.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb76f18dd39f4a29abe21cc711f27555"}}, "title": "Temporal control of human DNA replication licensing by CDK4/6-RB signalling and chemical genetics.", "authors": [{"family": "Sosenko Piscitello", "given": "Anastasia", "initials": "A"}, {"family": "Nilsson", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Hawgood", "given": "Michael", "initials": "M", "orcid": "0000-0003-3886-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/bef2b485623c4421a1c8606a4d9a377b.json"}}, {"family": "Sayyid", "given": "Abid H", "initials": "AH", "orcid": "0009-0001-7956-8947", "researcher": {"href": "https://publications.scilifelab.se/researcher/f24975c6e3ba47a78118c4b546fc0005.json"}}, {"family": "Dionellis", "given": "Vasilis S", "initials": "VS"}, {"family": "Giglio", "given": "Giovanni", "initials": "G", "orcid": "0009-0009-0349-3756", "researcher": {"href": "https://publications.scilifelab.se/researcher/897b67515f6c4c6ea7737f97cd324bfd.json"}}, {"family": "Uri\u00e9n", "given": "Bruno", "initials": "B", "orcid": "0009-0006-8205-6578", "researcher": {"href": "https://publications.scilifelab.se/researcher/03de6bcb91a948d89a1cffc578dfc455.json"}}, {"family": "Bajgain", "given": "Pratikiran", "initials": "P", "orcid": "0009-0003-0686-3253", "researcher": {"href": "https://publications.scilifelab.se/researcher/1936aaa66d5844b29336ddb30b6b2a8d.json"}}, {"family": "Ntallis", "given": "Sotirios G", "initials": "SG", "orcid": "0000-0002-6093-8979", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd3c7c3b90144587812ecf4f623f8be1.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J", "orcid": "0000-0003-2013-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0d4d98261f41268c76dd91345a1857.json"}}, {"family": "Halazonetis", "given": "Thanos D", "initials": "TD", "orcid": "0000-0001-8384-5030", "researcher": {"href": "https://publications.scilifelab.se/researcher/015df5789e4c4723bcde2a5e3a3ff87c.json"}}, {"family": "Lemmens", "given": "Bennie", "initials": "B", "orcid": "0000-0001-8051-1676", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2575a302c624ee58ea1af3cf3b0e47d.json"}}], "type": "journal article", "published": "2025-09-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "8268", "issn-l": "2041-1723"}, "abstract": "Cyclin-dependent kinases (CDKs) coordinate DNA replication and cell division, and play key roles in tissue homeostasis, genome stability and cancer development. The first step in replication is origin licensing, when minichromosome maintenance (MCM) helicases are loaded onto DNA by CDC6, CDT1 and the origin recognition complex (ORC). In yeast, origin licensing starts when CDK activity plummets in G1 phase, reinforcing the view that CDKs inhibit licensing. Here we show that, in human cells, CDK4/6 activity promotes origin licensing. By combining rapid protein degradation and time-resolved EdU-sequencing, we find that CDK4/6 activity acts epistatically to CDC6 and CDT1 in G1 phase and counteracts RB pocket proteins to promote origin licensing. Therapeutic CDK4/6 inhibitors block MCM and ORC6 loading, which we exploit to trigger mitosis with unreplicated DNA in p53-deficient cells. The CDK4/6-RB axis thus links replication licensing to proliferation, which has implications for human cell fate control and cancer therapy design.", "doi": "10.1038/s41467-025-63669-8", "pmid": "40940326", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-63669-8"}, {"db": "pmc", "key": "PMC12432183"}], "notes": [], "created": "2025-09-15T10:02:40.183Z", "modified": "2025-09-15T10:02:41.130Z"}, {"entity": "publication", "iuid": "1e91a38573084e70b528d25e8d48af33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e91a38573084e70b528d25e8d48af33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e91a38573084e70b528d25e8d48af33"}}, "title": "Genome sequences of six clinical isolates of Candida parapsilosis exhibiting different degrees and temporal regulation of biofilm formation.", "authors": [{"family": "Shafeeq", "given": "Sulman", "initials": "S", "orcid": "0000-0003-1152-526X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e86a079677ae47dc9a6bc423dba02515.json"}}, {"family": "Pannanusorn", "given": "Srisuda", "initials": "S"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Dadvar", "given": "Ali", "initials": "A", "orcid": "0009-0001-0938-5125", "researcher": {"href": "https://publications.scilifelab.se/researcher/86139f3c58d14385a92dbabad382a0ca.json"}}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U", "orcid": "0000-0003-3812-6621", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a59ac735d61485aa43ee7a2ae3a526d.json"}}], "type": "journal article", "published": "2025-09-11", "journal": {"title": "Microbiol Resour Announc", "issn": "2576-098X", "issn-l": "2576-098X", "volume": "14", "issue": "9", "pages": "e0130024"}, "abstract": "Candida parapsilosis is a major pathogen causing central venous catheter-associated bloodstream infections with biofilm formation as virulence factor. We sequenced the genomes of six C. parapsilosis isolates from bloodstream infections displaying no, low, and high biofilm under conditions mimicking the clinical setting.", "doi": "10.1128/mra.01300-24", "pmid": "40788144", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12424353"}], "notes": [], "created": "2025-11-03T08:33:51.246Z", "modified": "2025-11-17T16:31:31.430Z"}, {"entity": "publication", "iuid": "71ccdbd2e86142819f626395f6e88614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71ccdbd2e86142819f626395f6e88614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71ccdbd2e86142819f626395f6e88614"}}, "title": "Personality and repeated social defeat affect health condition and gene expression in the skin and intestines in zebrafish.", "authors": [{"family": "Benrejdal", "given": "Lisa", "initials": "L"}, {"family": "Huben\u00e1", "given": "Pavla", "initials": "P"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Morales Castro", "given": "Rodrigo A", "initials": "RA"}, {"family": "Rekha", "given": "Rokeya Sultana", "initials": "RS"}, {"family": "Winberg", "given": "Svante", "initials": "S"}, {"family": "Bergman", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "Prog. Neuropsychopharmacol. Biol. Psychiatry", "issn": "1878-4216", "pages": "111487", "issn-l": "0278-5846"}, "abstract": "Personality traits and acquired experience affect the capacity of an individual to cope with environmental and social changes. Behavioural adaptation and physiological alterations are important to prepare the body for these potential challenges. Whether inherited traits or acquired social rank (reflecting stress levels) are more important and how different personality-social rank combinations affect an individual's health is not well understood. One important aspect of health status is the function of biological barriers, as they represent the first line of defence of an organism. In the current study, we used a model of social defeat stress applied to a bold and a shy line of zebrafish. The Fulton's condition factor was determined, and gene expression analysis was performed on skin and intestines. The differences between lines explained a major part of the transcriptional changes observed as compared to differences in social rank. Additionally, shy fish that experienced repeated social defeat presented a poor body condition, accompanied by changes in gene expression suggesting inflammation in the gut. In the skin, shy fish showed a transcriptional enrichment of pathways related to cell division as well as increased expression of the stress response-associated gene crh2r. Together, these results complement our previous work and show that shy loser fish experience important changes not only in behaviour but also in their biological barriers, potentially putting their overall health at higher risk.", "doi": "10.1016/j.pnpbp.2025.111487", "pmid": "40935229", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0278-5846(25)00241-6"}], "notes": [], "created": "2025-09-30T13:55:16.843Z", "modified": "2025-09-30T13:55:16.858Z"}, {"entity": "publication", "iuid": "39cafd188c9e4072bfd89e2955794ce5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39cafd188c9e4072bfd89e2955794ce5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39cafd188c9e4072bfd89e2955794ce5"}}, "title": "Immunogenicity and innate immunity to high-dose and repeated vaccination of modified mRNA versus unmodified mRNA.", "authors": [{"family": "Engstrand", "given": "Olivia", "initials": "O"}, {"family": "Joas", "given": "Gustav", "initials": "G"}, {"family": "Miranda", "given": "Marcos C", "initials": "MC"}, {"family": "Yan", "given": "Xianglei", "initials": "X"}, {"family": "Lenart", "given": "Klara", "initials": "K"}, {"family": "Cerveira", "given": "Rodrigo Arcoverde", "initials": "RA"}, {"family": "Reinhardt", "given": "Annika", "initials": "A"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "Mol Ther Nucleic Acids", "issn": "2162-2531", "volume": "36", "issue": "3", "pages": "102588", "issn-l": "2162-2531"}, "abstract": "mRNA vaccines represent a new era with several novel constructs underway. We compared the responses of high doses and multiple repetitive immunizations of a nucleoside-modified mRNA construct to a sequence-codon-optimized unmodified mRNA construct encoding the identical model antigen (HIV-1 gag). Rhesus macaques were immunized five times at 2-week intervals, with a final boost 20 weeks later. At 24 h post-vaccination, both unmodified (160 \u03bcg) and modified (400 \u03bcg and 800 \u03bcg) mRNA constructs elicited clear but transient increase of plasmacytoid dendritic cells, intermediate CD14+ CD16+ monocytes, and neutrophils along with secretion of type I interferon (IFN)-related and inflammatory cytokines. Unmodified mRNA induced higher interleukin-7 (IL-7) and IFN-\u03b1 levels, whereas modified mRNA induced higher IL-6 levels. Transcriptomic profiling showed significant upregulation of genes related to type I IFN signaling, antigen presentation, and innate immune activation induced by both mRNA constructs. The high-dose modified mRNA induced a higher number of differentially expressed genes at prime, which further increased after the fifth immunization. These differences in innate immune activation nonetheless led to similar levels and kinetics of gag-specific antibody and T cell responses. These findings offer insights into the immunogenic and reactogenic potential of different mRNA vaccine modalities, guiding future vaccine and therapy development.", "doi": "10.1016/j.omtn.2025.102588", "pmid": "40612710", "labels": {"Affinity Proteomics Stockholm": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12221724"}, {"db": "pii", "key": "S2162-2531(25)00142-8"}], "notes": [], "created": "2025-09-19T14:41:12.463Z", "modified": "2025-11-28T14:59:07.787Z"}, {"entity": "publication", "iuid": "70f7e8042eb044dea68e5464e92ef637", "links": {"self": {"href": "https://publications.scilifelab.se/publication/70f7e8042eb044dea68e5464e92ef637.json"}, "display": {"href": "https://publications.scilifelab.se/publication/70f7e8042eb044dea68e5464e92ef637"}}, "title": "Genetic heterogeneity in childhood leukemia/lymphoma: a Turkish cohort with strong predisposition.", "authors": [{"family": "Onder", "given": "Gizem", "initials": "G"}, {"family": "Ozdemir", "given": "Ozkan", "initials": "O"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Canpolat", "given": "Cengiz", "initials": "C"}, {"family": "Yalcin", "given": "Koray", "initials": "K"}, {"family": "Erbey", "given": "Fatih", "initials": "F"}, {"family": "Sozmen", "given": "Banu Oflaz", "initials": "BO"}, {"family": "Asarcikli", "given": "Fikret", "initials": "F"}, {"family": "Bayhan", "given": "Turan", "initials": "T"}, {"family": "Akcabelen", "given": "Yunus Murat", "initials": "YM"}, {"family": "Yarali", "given": "Nese", "initials": "N"}, {"family": "Ozbek", "given": "Namik Yasar", "initials": "NY"}, {"family": "Bozkaya", "given": "Ikbal Ok", "initials": "IO"}, {"family": "Kacar", "given": "Dilek", "initials": "D"}, {"family": "Ergun", "given": "Berk", "initials": "B"}, {"family": "Akkus", "given": "Alper", "initials": "A"}, {"family": "Albayrak", "given": "Davut", "initials": "D"}, {"family": "Ince", "given": "Elif", "initials": "E"}, {"family": "Demirsoy", "given": "Ugur", "initials": "U"}, {"family": "Ozdemir", "given": "Gul Nihal", "initials": "GN"}, {"family": "Dogru", "given": "Omer", "initials": "O"}, {"family": "Aras", "given": "Seda", "initials": "S"}, {"family": "Aydin", "given": "Eylul", "initials": "E"}, {"family": "Unal", "given": "Busra", "initials": "B"}, {"family": "Amanvermez", "given": "Ufuk", "initials": "U"}, {"family": "Dogan", "given": "Ozlem Akgun", "initials": "OA"}, {"family": "Akyoney", "given": "Sezer", "initials": "S"}, {"family": "Sayitoglu", "given": "Muge", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Bugra Agaoglu", "given": "Nihat", "initials": "N"}, {"family": "Ozbek", "given": "Ugur", "initials": "U"}, {"family": "Ng", "given": "Ozden Hatirnaz", "initials": "OH"}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "Front Genet", "issn": "1664-8021", "volume": "16", "pages": "1624306", "issn-l": "1664-8021"}, "abstract": "Leukemia is the most common cancer in children, and 10%-15% of patients with leukemia/lymphoma carry pathogenic germline cancer-predisposing variants. Identifying these variants is critical for understanding the genetic predisposition and optimizing clinical management.\n\nWe performed germline short-read sequencing in 36 individuals from 20 families with suspected leukemia/lymphoma predisposition, including 20 index cases, 9 affected relatives, and 7 unaffected members.\n\nWe identified 13 clinically relevant germline variants in known cancer predisposition genes including TP53, ETV6, MSH6, MLH1, and BRCA1. Notably, we uncovered novel candidate variants in ATR, TNFRSF9, ETAA1, and KSR1, which was supported by segregation analysis, consanguinity patterns, and secondary malignancy phenotypes. Several index cases exhibited striking familial cancer syndromes involving both hematologic and solid tumors, with progression from ALL to AML or glioma. Deep clinical-genomic correlation enabled reclassification of variants and refined diagnostic and therapeutic decision-making in multiple cases. The patients were referred to genetic counseling for surveillance of carriers and risk assessment for various family members.\n\nThese findings emphasize the clinical utility of germline testing in pediatric hematologic cancers by providing novel insights into the predisposition to leukemia/lymphoma and contributing to treatment regimens, donor selection, and diagnostic refinement, particularly in populations with high consanguinity.", "doi": "10.3389/fgene.2025.1624306", "pmid": "40995433", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12454056"}, {"db": "pii", "key": "1624306"}], "notes": [], "created": "2025-11-20T20:36:39.190Z", "modified": "2025-11-20T20:36:39.197Z"}, {"entity": "publication", "iuid": "1da67eaf49c14bdab8a4d24096830778", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1da67eaf49c14bdab8a4d24096830778.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1da67eaf49c14bdab8a4d24096830778"}}, "title": "Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data.", "authors": [{"family": "Li", "given": "Tianyi", "initials": "T"}, {"family": "Yang", "given": "Qiao", "initials": "Q"}, {"family": "Acs", "given": "Balazs", "initials": "B"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Engblom", "given": "Camilla", "initials": "C"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Lin", "given": "Qirong", "initials": "Q"}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Sun", "given": "Wenwen", "initials": "W"}, {"family": "Boyaci", "given": "Ceren", "initials": "C"}, {"family": "Steen", "given": "Sanna", "initials": "S"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Chen", "given": "Xinsong", "initials": "X"}, {"family": "Hartman", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "310", "issn-l": null}, "abstract": "Breast cancer is a highly heterogeneous disease with diverse outcomes, and intra-tumoral heterogeneity plays a significant role in both diagnosis and treatment. Despite its importance, the spatial distribution of intra-tumoral heterogeneity is not fully elucidated. Spatial transcriptomics has emerged as a promising tool to study the molecular mechanisms behind many diseases. It offers accurate measurements of RNA abundance, providing powerful tools to correlate the morphologies of cellular neighborhoods with localized gene expression patterns. However, the spot-based spatial transcriptomic tools, including the most widely used platform, Visium, do not achieve single-cell resolution readouts, which hinders data interpretability. In this study, we present a computational pathology image analysis pipeline (i.e., computational tissue annotation, CTA) that utilizes machine learning algorithms to accurately map tumor, stroma, and immune compartments within Visium-assayed tumor sections. Using a cohort of 23 breast tumor sections from four patients, we demonstrate that CTA can provide high-resolution annotations on the hematoxylin-and-eosin-stained images alongside the paired sequencing data, support the evaluation of deconvolution methods, deepen insights into intra-tumoral heterogeneity by increasing data analysis resolution, assist with spatially resolved intrinsic subtyping, and enhance the visualization of lymphocyte clones at single-cell resolution. The proposed pipeline provides valuable insights into the complex spatial architecture of breast cancer, contributing to more personalized diagnostics and treatment strategies.", "doi": "10.1038/s41698-025-01104-3", "pmid": "40925915", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12420830"}, {"db": "pii", "key": "10.1038/s41698-025-01104-3"}], "notes": [], "created": "2025-11-19T08:43:31.550Z", "modified": "2025-11-28T10:47:25.200Z"}, {"entity": "publication", "iuid": "e4627393b013442f8e99034335510387", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4627393b013442f8e99034335510387.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4627393b013442f8e99034335510387"}}, "title": "Avenanthramides and avenacosides as biomarkers of oat intake: a pharmacokinetic study of solid and liquid oat consumption under single and repeated dose conditions.", "authors": [{"family": "Armeni", "given": "Marina", "initials": "M"}, {"family": "Cardilin", "given": "Tim", "initials": "T"}, {"family": "Fristedt", "given": "Rikard", "initials": "R"}, {"family": "Karlsson", "given": "Therese", "initials": "T"}, {"family": "Jenkins", "given": "Caroline Orfila", "initials": "CO"}, {"family": "Nordin", "given": "Elise", "initials": "E"}, {"family": "Qin", "given": "Panpan", "initials": "P"}, {"family": "Jirstrand", "given": "Mats", "initials": "M"}, {"family": "Kristiansen", "given": "Karsten", "initials": "K"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "Nutr J", "issn": "1475-2891", "volume": "24", "issue": "1", "pages": "136", "issn-l": "1475-2891"}, "abstract": "Avenanthramides (AVAs) and Avenacosides (AVEs) are unique to oats (Avena Sativa) and may serve as biomarkers of oat intake. However, information regarding their validity as food intake biomarkers is missing. We aimed to investigate critical validation parameters such as half-lives, dose-response, matrix effects, relative bioavailability under single dose, and in relation to the abundance of Feacalibacterium prausnitzii, and under repeated dosing, to understand the potential applications of AVAs and AVEs as biomarkers of oat intake.\n\nTwenty-one healthy participants consumed two oat products (solid and liquid) in a non-blinded randomized crossover study for the pharmacokinetics (PK) assessment of multiple AVAs (2p, 2c,2f, 2fd and 2pd) and AVEs (A and B). At phase I, postprandial data were collected after a single dose of either product. At phase II, fasting sample was drawn after a 4-days repeated dose setup. The postprandial data were used in a compartmental PK model and the PK parameters were consequently utilized to predict individual plasma concentrations, which were compared with the data of the second phase of the study.\n\nTmax values were shorter in liquid compared to solid form for AVAs (0.7-1.6 h and 1.1-2.3 h, respectively). In liquid, T1/2 were 1.3 h (AVA 2p and AVA 2fd), 3.2 h (AVA 2f, AVE A) and 2.5 h (AVA 2pd, AVE B). In solid form, T1/2 were shorter for AVAs (1.4-2.6 h) compared to AVEs (3.3-3.8 h). The normalized area under the curve (AUCnorm) was greater for liquid than solid form for AVA2p, 2f and AVE-A [0.7-27 nM\u2219h (liquid), 0.4-20.1 (solid)] while for AVE-B AUCnorm were comparable [1.8 \u00b1 0.2 nM\u2219h (liquid),2.1 \u00b1 0.3 nM\u2219h (solid)]. A pharmakcokinetic prediction model described 75% of the experimental plasma-concentration data from phase II, with good agreement (bias: -0.145 nM).\n\nAVAs are promising candidates as compliance biomarkers of oat intake in intervention studies regardless of the tested food matrices. However, due to their short elimination half-lives, their applicability in nutritional epidemiology where long-term habitual intake is of main interest, seems restricted.\n\nThis study was registered at clinicaltrials.gov with the clinical trial number: NCT05511077, on August 22nd, 2022.", "doi": "10.1186/s12937-025-01204-7", "pmid": "40926245", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12418703"}, {"db": "pii", "key": "10.1186/s12937-025-01204-7"}, {"db": "ClinicalTrials.gov", "key": "NCT05511077"}], "notes": [], "created": "2025-11-27T11:24:07.631Z", "modified": "2025-11-27T11:24:07.646Z"}, {"entity": "publication", "iuid": "59aa3bfaa17d4c5f88c7b8cdf0f1a206", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59aa3bfaa17d4c5f88c7b8cdf0f1a206.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59aa3bfaa17d4c5f88c7b8cdf0f1a206"}}, "title": "Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity.", "authors": [{"family": "Xu", "given": "Yunyun", "initials": "Y"}, {"family": "Lou", "given": "Daohua", "initials": "D"}, {"family": "Chen", "given": "Ping", "initials": "P"}, {"family": "Li", "given": "Gang", "initials": "G"}, {"family": "Usoskin", "given": "Dimtry", "initials": "D"}, {"family": "Pan", "given": "Jian", "initials": "J"}, {"family": "Li", "given": "Fang", "initials": "F"}, {"family": "Huang", "given": "Shungen", "initials": "S"}, {"family": "Hess", "given": "Caroline", "initials": "C"}, {"family": "Tang", "given": "Ruze", "initials": "R"}, {"family": "Hu", "given": "Xiaohan", "initials": "X"}, {"family": "Yu", "given": "Juanjuan", "initials": "J"}, {"family": "Arceo", "given": "Maria", "initials": "M"}, {"family": "de Krijger", "given": "Ronald R", "initials": "RR"}, {"family": "Tischler", "given": "Arthur S", "initials": "AS"}, {"family": "Schlisio", "given": "Susanne", "initials": "S"}, {"family": "Ernfors", "given": "Patrik", "initials": "P"}, {"family": "Hu", "given": "Yizhou", "initials": "Y"}, {"family": "Wang", "given": "Jian", "initials": "J"}], "type": "journal article", "published": "2025-09-08", "journal": {"title": "Dev. Cell", "issn": "1878-1551", "issn-l": "1534-5807", "volume": "60", "issue": "17", "pages": "2248-2263.e11"}, "abstract": "Neuroblastoma, the most prevalent extracranial pediatric solid tumor, arises from neural crest progeny cells. It exhibits substantial developmental plasticity and intratumoral heterogeneity, leading to survival rates below 50% in high-risk cases. The regulatory mechanisms underlying this plasticity remain largely elusive. In this integrative study, we used single-cell MultiOmics from a mouse spontaneous tumor model and spatial transcriptomics from human patient samples to dissect the transcriptional and epigenetic landscapes that govern developmental states in neuroblastoma. We identified developmental intermediate states in high-risk neuroblastomas critical for malignant transitions and uncovered extensive epigenetic priming with latent capacity for diverse state transitions. Furthermore, we mapped enhancer gene regulatory networks (eGRNs) and tumor microenvironments sustaining these aggressive states. State transitions and malignancy could be interfered with by targeting transcription factors controlling the eGRNs.", "doi": "10.1016/j.devcel.2025.04.013", "pmid": "40347947", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1534-5807(25)00251-5"}], "notes": [], "created": "2025-05-26T07:50:11.913Z", "modified": "2025-11-14T11:05:58.511Z"}, {"entity": "publication", "iuid": "f99abb60556e417282a30affe3cdf0a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f99abb60556e417282a30affe3cdf0a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f99abb60556e417282a30affe3cdf0a1"}}, "title": "Polygenic scores in Familial breast cancer cases with and without pathogenic variants and the risk of contralateral breast cancer.", "authors": [{"family": "Kvist", "given": "Anders", "initials": "A"}, {"family": "K\u00e4mpe", "given": "Anders", "initials": "A"}, {"family": "T\u00f6rngren", "given": "Therese", "initials": "T"}, {"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P"}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Eriksson", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-09-08", "journal": {"title": "Breast Cancer Res.", "issn": "1465-542X", "volume": "27", "issue": "1", "pages": "160", "issn-l": "1465-5411"}, "abstract": "Polygenic risk scores (PRS) are not yet standard in clinical risk assessments for familial breast cancer in Sweden. This study evaluated the distribution and impact of an established PRS (PRS313) in women undergoing clinical sequencing for hereditary breast cancer.\n\nWe integrated PRS313 into a hereditary breast cancer gene panel used in clinical practice and calculated scores for 262 women. Comparisons were made between women with unilateral and contralateral breast cancer, as well as those with and without pathogenic variants in breast cancer susceptibility genes. PRS313 was significantly higher in women with contralateral breast cancer (median + 1.3 SD, n = 33, P = 8e-9) compared to those with unilateral disease (median + 0.66 SD, n = 197, P = 5e-10). Elevated PRS313 was also observed in women with pathogenic variants, including those in high-penetrance genes (+ 0.65 SD) and moderate-penetrance genes (+ 0.93 SD), compared to population controls. Incorporating PRS313 into a clinical risk model (BOADICEA), shifted 20%-27% of women with moderate-penetrance variants and 23%-32% of women without pathogenic variants into different risk categories according to NCCN and NICE guidelines.\n\nWomen with familial breast cancer showed elevated PRS313, including those with pathogenic variants, contributing to the observed high risk in these families. Integrating PRS into risk assessment and genetic counselling has the potential to refine risk predictions, even among women with breast cancer attributed to monogenic variants.", "doi": "10.1186/s13058-025-02107-5", "pmid": "40922009", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12418628"}, {"db": "pii", "key": "10.1186/s13058-025-02107-5"}], "notes": [], "created": "2025-11-26T14:14:01.393Z", "modified": "2025-11-28T10:53:05.161Z"}, {"entity": "publication", "iuid": "cdb29234ff42469f8e1910f10359d71c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cdb29234ff42469f8e1910f10359d71c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cdb29234ff42469f8e1910f10359d71c"}}, "title": "Proteome integral solubility alteration assay for monitoring antibody-antigen cell interactions", "authors": [{"family": "Lu", "given": "Weiqi", "initials": "W"}, {"family": "Lundstrom", "given": "Susanna L", "initials": "SL", "orcid": "0000-0003-2363-4287", "researcher": {"href": "https://publications.scilifelab.se/researcher/916e190e150e465c9e6afc11911bae04.json"}}, {"family": "Hou", "given": "Yaolin", "initials": "Y", "orcid": "0000-0002-2750-4167", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c659cd3e4674b409d4d140adcd6a7dc.json"}}, {"family": "Mukherjee", "given": "Sourav", "initials": "S"}, {"family": "Haeggstr\u00f6m", "given": "Jesper Z", "initials": "JZ", "orcid": "0000-0002-1823-5153", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee1e25240017456f80599973397b4bd6.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "posted-content", "published": "2025-09-06", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.09.04.673944", "pmid": null, "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2025-11-25T16:24:40.307Z", "modified": "2025-12-18T19:09:30.114Z"}, {"entity": "publication", "iuid": "322034029b43432995b1728787b2cbba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/322034029b43432995b1728787b2cbba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/322034029b43432995b1728787b2cbba"}}, "title": "Mass Spectrometry-Based Analysis of Surface Proteins in Staphylococcus aureus Clinical Strains: Identification of Promising k-mer Targets for Diagnostics.", "authors": [{"family": "Svetlicic", "given": "Ema", "initials": "E", "orcid": "0009-0001-5062-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3d7fa745d34006ba08ceed4ff2c452.json"}}, {"family": "Alarcon", "given": "Leonarda A", "initials": "LA"}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}, {"family": "Jers", "given": "Carsten", "initials": "C"}, {"family": "Mijakovic", "given": "Ivan", "initials": "I", "orcid": "0000-0002-8860-6853", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0e5dfcc215b494a860ca6d9254b0b56.json"}}], "type": "journal article", "published": "2025-09-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "24", "issue": "9", "pages": "4575-4585", "issn-l": "1535-3893"}, "abstract": "Surface proteins of Gram-positive bacteria are critical for adherence to host tissues, evasion of the immune system, and interaction with the environment. They can be utilized as biomarkers in diagnostics, for vaccine development, and as therapeutic targets due to their accessibility and role in pathogenicity. If utilized as diagnostic targets, surface biomarkers should be highly conserved across different strains of the pathogen, unique to the species to avoid cross-reactivity, abundantly expressed on the bacterial surface, and accessible to antibodies or detection reagents. Mass spectrometry-based proteomics methods have advanced the studies of surface proteins, often in combination with selective enrichment strategies such as tryptic \"shaving\". In this study, 11 clinical strains of Staphylococcus aureus underwent tryptic shaving to identify common surface proteins. Further bioinformatics analysis confirmed that these proteins are encoded in the core genome of S. aureus strains and contain species-specific peptides. In silico analysis identified 26 k-mer peptides in 15 surface proteins with structural accessibility to detection agents, making them the ideal targets for molecular diagnostics or as linear epitope targets for vaccine development or therapeutics. Among the identified candidates were known virulence-associated proteins such as PbpA, Sbi, and Asp23\u2500previously studied in the context of vaccines\u2500as well as uncharacterized proteins encoded by the gene loci SAUSA300_1904 and SAUSA300_1685, whose unique and surface-exposed features suggest unexplored diagnostic potential.", "doi": "10.1021/acs.jproteome.5c00321", "pmid": "40772958", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12418492"}], "notes": [], "created": "2025-10-23T16:02:13.534Z", "modified": "2025-10-23T16:02:15.152Z"}, {"entity": "publication", "iuid": "7dde054c9c0243a18bbb34e6abd3167f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7dde054c9c0243a18bbb34e6abd3167f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7dde054c9c0243a18bbb34e6abd3167f"}}, "title": "CRISPR-Cas9 targeting of G-Quadruplex DNA in ADH1 promoter highlights its role in transcriptome and metabolome regulation.", "authors": [{"family": "Obi", "given": "Ikenna", "initials": "I", "orcid": "0000-0003-0364-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/e46c65e7b0e540b0a7c225d54c1502d7.json"}}, {"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}], "type": "journal article", "published": "2025-09-05", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "17", "issn-l": "0305-1048"}, "abstract": "G-quadruplex (G4) structures are critical regulators of gene expression, yet the role of an individual G4 within its native chromatin remains underexplored, especially outside human systems. Here, we used CRISPR-Cas9 to introduce guanine-to-thymine mutations at a G4-forming motif within the adh1+ promoter in yeast Schizosaccharomyces pombe, creating two mutant strains: one with G4-only mutations and another with both G4 and TATA-box mutations. Chromatin immunoprecipitation using BG4 antibody confirmed reduced G4 enrichment in both mutants, validating G4 structure formation in the wild-type chromatin. Detailed characterizations demonstrated that the G4 mutations alter its dynamics without fully preventing its formation. These mutations significantly reduce adh1 transcript levels, with G4 TATA-box mutant causing the strongest transcriptional suppression. This indicates a positive regulatory role for the G4 structure in transcription. Furthermore, both mutants displayed altered transcriptomic profiles, particularly impacting the oxidoreductase pathway. Metabolomic analyses by mass spectrometry further highlighted substantial disruptions in NAD+/NADH metabolism, a key energy reservoir for metabolic regulation. These results highlight that tuning G4 dynamics, without abolishing the structure, can still profoundly affect gene expression and metabolism, unlike prior studies on the human MYC promoter that disrupted G4 formation. This represents the first such finding in yeast.", "doi": "10.1093/nar/gkaf853", "pmid": "40966507", "labels": {"Swedish Metabolomics Centre": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12448892"}, {"db": "pii", "key": "8252031"}], "notes": [], "created": "2025-11-18T12:14:00.787Z", "modified": "2025-11-27T12:55:10.572Z"}, {"entity": "publication", "iuid": "df68d30a60804dbab4be6450c496ca2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df68d30a60804dbab4be6450c496ca2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df68d30a60804dbab4be6450c496ca2e"}}, "title": "Subtelomeric elements provide stability to short telomeres in telomerase-negative cells of the budding yeast Naumovozyma castellii.", "authors": [{"family": "Jaiswal", "given": "Rishi K", "initials": "RK"}, {"family": "Garibo Domingo", "given": "Teresa", "initials": "T"}, {"family": "Grunchec", "given": "H\u00e9lo\u00efse", "initials": "H"}, {"family": "Singh", "given": "Komudi", "initials": "K"}, {"family": "Pirooznia", "given": "Mehdi", "initials": "M", "orcid": "0000-0002-4210-6458", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b65f2a816224c6f91b136a2a6e0ecc0.json"}}, {"family": "Elhaik", "given": "Eran", "initials": "E"}, {"family": "Cohn", "given": "Marita", "initials": "M", "orcid": "0000-0002-3370-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f6375da7f964ac49517c2e41de8c074.json"}}], "type": "journal article", "published": "2025-09-03", "journal": {"title": "Curr Genet", "issn": "1432-0983", "issn-l": null, "volume": "71", "issue": "1", "pages": "19"}, "abstract": "Telomerase plays an important role in sustaining eukaryotic linear chromosomes, as elongation of telomeres is needed to counterbalance the shortening occurring in each replication round. Nevertheless, in telomerase-deficient cells, Alternative Lengthening of Telomeres (ALT) pathways can maintain telomeres by employing recombination-based mechanisms. In the budding yeast Naumovozyma castellii, effective activation of the ALT pathway leads to bypass of senescence and supports long-term growth. We found that telomere structures in N. castellii ALT cells are stably maintained at a shortened uniform length over extensive numbers of generations. This is correlated to the spreading of a subtelomeric sequence, TelKO element, to all telomeres. Genome sequencing of the wild-type strain revealed variants of the TelKO element, differing in their lengths, and separate ALT strains are maintained by spreading of distinct TelKO element variants. Although short uniform telomere structures are predominant, sporadic telomere lengthening events occur by addition of long repeated arrays of TelKO elements. The telomere-binding protein Rap1 can bind to TelKO sequences in vitro, indicating a functional role of TelKO elements in providing stability to shortened ALT telomeres. Our results suggest that stable maintenance and telomere functionality may be achieved by incorporating the distal subtelomeric TelKO sequences into the telomeric chromatin cap.", "doi": "10.1007/s00294-025-01325-w", "pmid": "40900359", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12408736"}, {"db": "pii", "key": "10.1007/s00294-025-01325-w"}], "notes": [], "created": "2025-11-04T10:56:32.978Z", "modified": "2025-11-28T10:41:08.037Z"}, {"entity": "publication", "iuid": "30c686df62fe461f86a6429840e60bef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30c686df62fe461f86a6429840e60bef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30c686df62fe461f86a6429840e60bef"}}, "title": "Next-Generation Sequencing in the Diagnostic Workup of Neonatal Dried Blood Spot Screening in Sweden 2015-2023.", "authors": [{"family": "S\u00f6rensen", "given": "Lene", "initials": "L", "orcid": "0000-0002-0309-4247", "researcher": {"href": "https://publications.scilifelab.se/researcher/81e4acdb19cc45558e9414b39d518d62.json"}}, {"family": "Asin-Cayuela", "given": "Jorge", "initials": "J", "orcid": "0000-0003-0609-5760", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8a9fb9921c54276b2212b64db43606e.json"}}, {"family": "Barbaro", "given": "Michela", "initials": "M", "orcid": "0000-0002-7598-9330", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6b9b246e0d4187be04071f5a53574f.json"}}, {"family": "Bruhn", "given": "Helene", "initials": "H", "orcid": "0009-0007-4449-5382", "researcher": {"href": "https://publications.scilifelab.se/researcher/789656ba85444c398bd2ebc03283f992.json"}}, {"family": "Engvall", "given": "Martin", "initials": "M", "orcid": "0000-0002-8339-3545", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb742d63d69d42849f0cd842ecad88c8.json"}}, {"family": "Lesko", "given": "Nicole", "initials": "N", "orcid": "0000-0001-8770-1878", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b2ed29329e449bbe832174668d1d82.json"}}, {"family": "Naess", "given": "Karin", "initials": "K", "orcid": "0000-0003-4310-7927", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cf2472011ec46bf841260c7515fbbfc.json"}}, {"family": "Oscarson", "given": "Mikael", "initials": "M", "orcid": "0000-0002-8407-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a8412f43ec94b34ad350aa2d65bbd89.json"}}, {"family": "Shen", "given": "Yan", "initials": "Y"}, {"family": "Uebersch\u00e4r", "given": "Malin", "initials": "M", "orcid": "0000-0001-8377-5896", "researcher": {"href": "https://publications.scilifelab.se/researcher/21a63829fb8e4442bf6556cbdcf97142.json"}}, {"family": "Wredenberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-2500-6121", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ea9ee7305424cdb8c238ef569e5be03.json"}}, {"family": "Sterky", "given": "Fredrik H", "initials": "FH", "orcid": "0000-0001-8881-0523", "researcher": {"href": "https://publications.scilifelab.se/researcher/c882670f832e4412869ab7667b115a81.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A", "orcid": "0000-0002-2612-6301", "researcher": {"href": "https://publications.scilifelab.se/researcher/15f660ec95994b6a83d540e48c9b7610.json"}}, {"family": "Zetterstr\u00f6m", "given": "Rolf H", "initials": "RH", "orcid": "0000-0002-3016-0019", "researcher": {"href": "https://publications.scilifelab.se/researcher/5357002f410245c7a8d1e84dfed6a2a9.json"}}], "type": "journal article", "published": "2025-09-03", "journal": {"title": "Int J Neonatal Screen", "issn": "2409-515X", "volume": "11", "issue": "3", "issn-l": null}, "abstract": "Sweden has one neonatal screening laboratory and two centers conducting diagnostic workup for inborn errors of metabolism (IEM). Next-generation sequencing (NGS) has been gradually introduced as a confirmatory diagnostic test in the Swedish newborn screening program. Here, we describe the use of NGS in the diagnostic workup of IEM in screening-detected babies in Sweden between 2015 and 2023. During this period, 1,023,344 newborn children were screened, and 81 of 290 IEM cases were genetically confirmed using NGS. Planned improvements to the program are to perform genetic validation directly on the initial dried blood spot (DBS). As whole-genome sequencing (WGS) is superior in detecting causative genetic variants compared to Sanger sequencing, targeted NGS, and whole-exome sequencing (WES), it will likely become the method of choice more broadly in the future. A strong focus is to consolidate the nationally coordinated DBS newborn screening program, with all its individual components, including screening, targeted diagnostics, individualized treatment, and follow-up. This challenges the current regionalized organization of Swedish healthcare, which hinders close national collaboration between experts and sharing of data, as well as equal access to advanced treatments for identified patients, regardless of their place of birth.", "doi": "10.3390/ijns11030073", "pmid": "40981303", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12452496"}, {"db": "pii", "key": "ijns11030073"}], "notes": [], "created": "2025-11-21T09:09:56.459Z", "modified": "2025-11-21T09:09:58.049Z"}, {"entity": "publication", "iuid": "36d41f27cba2473e9498ad1733f0a1ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36d41f27cba2473e9498ad1733f0a1ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36d41f27cba2473e9498ad1733f0a1ad"}}, "title": "Metabolite Biomarkers Linking a High-Fiber Rye Intervention with Cardiometabolic Risk Factors: The RyeWeight Study.", "authors": [{"family": "Uni\u00f3n Caballero", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5500-9019", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef06c4ba2cd471c97c402af62b34385.json"}}, {"family": "Mero\u00f1o", "given": "Tom\u00e1s", "initials": "T", "orcid": "0000-0002-2673-3494", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a887d04cc84fe394befeee1c5e6cc1.json"}}, {"family": "\u00c5berg", "given": "Sebastian", "initials": "S"}, {"family": "Nordin", "given": "Elise", "initials": "E"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "S\u00e1nchez-Pla", "given": "Alex", "initials": "A"}, {"family": "Cubedo", "given": "Marta", "initials": "M"}, {"family": "Carmona-Pontaque", "given": "Francisco", "initials": "F"}, {"family": "Iversen", "given": "Kia No\u0337hr", "initials": "KN"}, {"family": "Mart\u00ednez-Hu\u00e9lamo", "given": "Miriam", "initials": "M"}, {"family": "Guadall", "given": "Anna", "initials": "A"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Andr\u00e9s-Lacueva", "given": "Cristina", "initials": "C", "orcid": "0000-0002-8494-4978", "researcher": {"href": "https://publications.scilifelab.se/researcher/5374c25bdb4845ddaf5afc498ff68222.json"}}], "type": "journal article", "published": "2025-09-03", "journal": {"title": "J. Agric. Food Chem.", "issn": "1520-5118", "volume": "73", "issue": "35", "pages": "21869-21879", "issn-l": "0021-8561"}, "abstract": "Wholegrain rye, considered one of the cereals with the highest content of dietary fiber and bioactive compounds, has been linked with reduced risk of cardiometabolic diseases. Thus, biomarkers reflecting its intake and/or the metabolic effect after consumption are essential to better elucidate its health effects. Our aim was to identify plasma metabolite biomarkers associated with a high-fiber rye intervention and to assess the associations between these metabolites, gut microbiota composition, and cardiometabolic risk factors in a 12-week randomized controlled trial comparing a hypocaloric diet with high-fiber rye (n = 108) or refined wheat (n = 99) in participants with obesity. Rye intervention increased plasma concentrations of benzoxazinoids (DIBOA-S) and phenylacetamides (2-HPA-S and 2-HHPA-S), gut microbial metabolites (indolepropionic acid, 2-aminophenol, enterolactone sulfate, and enterolactone glucuronide), betainized compounds (pipecolic-betaine), phenolic acids (2,6-DHBA and gallic acid-4-sulfate), and diverse endogenous metabolites. Microbiota composition changes were increased Eubacterium xylanophilum and Agathobacter and decreased Ruminococcus torques and Romboutsia. Moreover, the intervention effect was mostly captured by changes in metabolites and gut microbiota compared to clinical variables. Gallic acid-4-sulfate and phenylacetamides were associated with reductions in weight, fat mass, BMI, or fasting insulin levels even after adjusting for plasma alkylresorcinols, used as markers for rye intake compliance. Altogether, these metabolites may constitute biomarkers of wholegrain rye cardiometabolic effects.", "doi": "10.1021/acs.jafc.5c01415", "pmid": "40838659", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12412176"}], "notes": [], "created": "2025-12-01T05:42:35.304Z", "modified": "2025-12-01T05:42:35.625Z"}, {"entity": "publication", "iuid": "ebe4355205e54bc3b50d10a1a62fb6e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ebe4355205e54bc3b50d10a1a62fb6e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ebe4355205e54bc3b50d10a1a62fb6e8"}}, "title": "Genetic Adaptation to Brackish Water and Spawning Season in European Cisco.", "authors": [{"family": "Deng", "given": "Qiaoling", "initials": "Q", "orcid": "0000-0002-3776-1132", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdfda2d3f64742e8a09bbded5f322f96.json"}}, {"family": "Goodall", "given": "Jake", "initials": "J", "orcid": "0000-0003-0960-4241", "researcher": {"href": "https://publications.scilifelab.se/researcher/457d1a2733cc4a569ffeb70750999199.json"}}, {"family": "Bergenius Nord", "given": "Mikaela", "initials": "M"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Delling", "given": "Bo", "initials": "B", "orcid": "0000-0001-9148-9574", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c1c3f7ddf0945d18660ecbaa85303b0.json"}}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "Palm", "given": "Stefan", "initials": "S", "orcid": "0000-0002-9890-8265", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ebffe35bae646eb8a15163b0cb0820f.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59d0c98de64ac1a62234792258ee62.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2025-09-03", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": null, "issue": null, "pages": "e70094"}, "abstract": "How species adapt to diverse environmental conditions is essential for understanding evolution and the maintenance of biodiversity. The European cisco (Coregonus albula) is a salmonid that occurs in both fresh and brackish water, and this together with the presence of sympatric spring- and autumn-spawning lacustrine populations provides an opportunity for studying the genetics of adaptation in relation to salinity and timing of reproduction. Here, we present a high-quality reference genome of the European cisco based on PacBio HiFi long read sequencing and HiC-directed scaffolding. We generated low-coverage whole-genome sequencing data from 336 individuals across 12 population samples to explore population structure and genetics of ecological adaptation. We found a major subdivision between two groups of populations most likely reflecting colonisation from different glacial refugia. Within the two major groups, we detected further genetic differentiation between spring- and autumn-spawning populations and between populations from freshwater lakes, rivers and brackish water (Bothnian Bay). A genome-wide screen for genetic differentiation among populations identified a set of outlier SNPs strongly correlated with spawning timing and salinity. Several of the genes associated with spawning time, including BHLHE40, TIMELESS and CPT1A, have previously been shown to have a role in circadian rhythm biology. As many as 17 loci were associated with genetic differentiation between populations reproducing in fresh and brackish water. This study provides insights into the genomic basis of ecological adaptation in European cisco with implications for sustainable fishery management.", "doi": "10.1111/mec.70094", "pmid": "40903929", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": null, "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-09-08T14:16:37.667Z", "modified": "2025-11-21T12:48:41.202Z"}, {"entity": "publication", "iuid": "948b1d732d0f46f49ce4462a16405462", "links": {"self": {"href": "https://publications.scilifelab.se/publication/948b1d732d0f46f49ce4462a16405462.json"}, "display": {"href": "https://publications.scilifelab.se/publication/948b1d732d0f46f49ce4462a16405462"}}, "title": "Tissue Architecture Modulates Compositional and Structural Properties of Corneal Myofibroblast-Derived Matrix.", "authors": [{"family": "Giannopoulos", "given": "Antonios", "initials": "A"}, {"family": "Backman", "given": "Ludvig J", "initials": "LJ"}, {"family": "Danielson", "given": "Patrik", "initials": "P"}], "type": "journal article", "published": "2025-09-02", "journal": {"title": "Transl Vis Sci Technol", "issn": "2164-2591", "volume": "14", "issue": "9", "pages": "9", "issn-l": null}, "abstract": "To develop an in vitro model that mimics aspects of corneal healing in humans for uncovering key mechanisms involved in the mechanisms involved in the healing and scarring processes.\n\nAs part of the healing matrix, TGF-\u03b21-induced and corneal-derived myofibroblasts were cultured in fibrin hydrogels with configurations that recapitulate the healthy (aligned) and wounded (random) microenvironment of the cornea.\n\nEvaluation of cellular alpha smooth muscle actin (\u03b1-SMA) and collagen hybridizing peptide (CHP) showed cell and matrix alignment, respectively. The aligned compared to the random constructs demonstrated an increased ability to synthesize total soluble proteins, including collagen type V, but collagen type I levels were reduced. This finding reveals a differential pattern for these proteins. Additionally, the collagen fibril diameters were larger in the aligned tissue constructs compared to the random constructs. Fibronectin and CHP colocalization patterns did not differ between groups; however, fibronectin and decorin were increased in the aligned group in contrast to tenascin C, which showed no difference.\n\nThese findings suggest that the alignment of the healing microenvironment plays a crucial role in modulating the structural properties of the extracellular matrix (ECM) and regulates the synthesis of key proteins that are closely involved in fibrillogenesis and are indicative of the quality of the deposited ECM.\n\nWe developed a three-dimensional in vitro model that closely mimics in vivo conditions to investigate the role of corneal myofibroblasts in healing and regeneration. Ultimately, this model can help develop targeted antifibrotic therapies to prevent corneal scarring.", "doi": "10.1167/tvst.14.9.9", "pmid": "40905747", "labels": {"Cryo-EM": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12416519"}, {"db": "pii", "key": "2810780"}], "notes": [], "created": "2025-11-17T12:51:51.283Z", "modified": "2025-11-17T12:51:51.360Z"}, {"entity": "publication", "iuid": "1aaa12b892a3412c8c4670979e8eb459", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1aaa12b892a3412c8c4670979e8eb459.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1aaa12b892a3412c8c4670979e8eb459"}}, "title": "SPNS1 variants cause multiorgan disease and implicate lysophospholipid transport as critical for mTOR-regulated lipid homeostasis.", "authors": [{"family": "He", "given": "Menglan", "initials": "M"}, {"family": "Ding", "given": "Mei", "initials": "M"}, {"family": "Chocholouskova", "given": "Michaela", "initials": "M"}, {"family": "Chin", "given": "Cheen Fei", "initials": "CF"}, {"family": "Engvall", "given": "Martin", "initials": "M"}, {"family": "Malmgren", "given": "Helena", "initials": "H"}, {"family": "Wagner", "given": "Matias", "initials": "M"}, {"family": "Lauffer", "given": "Marlen C", "initials": "MC"}, {"family": "Heisinger", "given": "Jacob", "initials": "J"}, {"family": "Malicdan", "given": "May Christine V", "initials": "MCV"}, {"family": "Allamand", "given": "Valerie", "initials": "V"}, {"family": "Durbeej", "given": "Madeleine", "initials": "M"}, {"family": "Delgado Vega", "given": "Angelica", "initials": "A"}, {"family": "Sejersen", "given": "Thomas", "initials": "T"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Torta", "given": "Federico", "initials": "F"}, {"family": "Silver", "given": "David L", "initials": "DL"}], "type": "journal article", "published": "2025-09-02", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "135", "issue": "17", "issn-l": "0021-9738"}, "abstract": "SPNS1 is a lysosomal transporter that mediates the salvage of lysoglycerophospholipids, the degradative products of lysosomal phospholipid catabolism. However, an understanding of the role of lysolipid transport and salvage in regulating cellular lipid homeostasis and in disease is lacking. Here, we identified members of 2 families with biallelic SPNS1 loss-of-function variants, who presented primarily with progressive liver and striated muscle injury. Patients' fibroblasts accumulated lysophospholipids including lysoplasmalogens and cholesterol in lysosomes with reduced cellular plasmalogens. Notably, SPNS1 deficiency resulted in reduced biogenesis of cytosolic lipid droplets containing triglycerides and cholesteryl esters. Mechanistically, we found that lysophospholipids transported by SPNS1 into the cytosol quantitatively contributed to triglyceride synthesis, whereas lysosomal buildup of lyso-ether-phospholipid inhibited lysosomal cholesterol egress, effects that were enhanced with inhibition of mTOR. These findings support a gene-disease association and reveal connectivity between lysosomal transport of lysophospholipids and storage of reserve cellular energy as triglycerides and the regulation of cholesterol homeostasis, processes that become important under nutrient limitation.", "doi": "10.1172/JCI193099", "pmid": "40608416", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12404768"}, {"db": "pii", "key": "193099"}], "notes": [], "created": "2025-11-28T18:04:12.720Z", "modified": "2025-11-28T18:04:12.725Z"}, {"entity": "publication", "iuid": "f2c25c4dfd474273b0524f9b366d3a5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2c25c4dfd474273b0524f9b366d3a5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2c25c4dfd474273b0524f9b366d3a5c"}}, "title": "Limited resource use overlaps among small pelagic fish species in the central Baltic Sea", "authors": [{"family": "Jan", "given": "Kinlan M G", "initials": "KMG", "orcid": "0000-0002-5579-0017", "researcher": {"href": "https://publications.scilifelab.se/researcher/503d30c9c45541db8a9bd9d37220775b.json"}}, {"family": "Hentati-Sundberg", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3201-9262", "researcher": {"href": "https://publications.scilifelab.se/researcher/584f21d647fc4806b3173e0a83770038.json"}}, {"family": "Larson", "given": "Niklas", "initials": "N", "orcid": "0000-0001-6296-8410", "researcher": {"href": "https://publications.scilifelab.se/researcher/78216d19926a40fe85c65d5615a93a17.json"}}, {"family": "Winder", "given": "Monika", "initials": "M", "orcid": "0000-0001-9467-3035", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b09dfb6b68445249b8a93c655433189.json"}}], "type": "journal-article", "published": "2025-09-02", "journal": {"issn": "1054-3139", "volume": "82", "issue": "9", "issn-l": null}, "abstract": null, "doi": "10.1093/icesjms/fsaf122", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:49:26.367Z", "modified": "2025-11-28T10:49:26.595Z"}, {"entity": "publication", "iuid": "203d08d6d1304755a054814170303345", "links": {"self": {"href": "https://publications.scilifelab.se/publication/203d08d6d1304755a054814170303345.json"}, "display": {"href": "https://publications.scilifelab.se/publication/203d08d6d1304755a054814170303345"}}, "title": "Plasma membrane labelling efficiency, internalization and partitioning of functionalized fluorescent lipids as a function of lipid structure.", "authors": [{"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}], "type": "journal article", "published": "2025-09-01", "journal": {"title": "RSC Chem Biol", "issn": "2633-0679", "issn-l": null}, "abstract": "Labeling the plasma membrane for advanced imaging remains a significant challenge. For time-lapse live cell imaging, probe internalization and photobleaching are major limitations affecting most membrane-specific dyes. In fixed or permeabilized cells, many membrane probes either lose signal after fixation or fail to remain localized to the plasma membrane. Thus, improved probes are critically needed for applications in spatial biology. In this study, we systematically compared a range of custom-synthesized and commercially available lipid-based probes for their efficiency in labeling the plasma membrane in live, fixed, and permeabilized cells. We identified a superior probe, which outperformed others due to its lipid structure. This comparison provides insights into ideal lipid probes for visualizing the plasma membrane using advanced imaging techniques.", "doi": "10.1039/d5cb00116a", "pmid": "40927427", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12415625"}, {"db": "pii", "key": "d5cb00116a"}], "notes": [], "created": "2025-09-13T11:07:39.964Z", "modified": "2025-09-15T10:04:02.296Z"}, {"entity": "publication", "iuid": "d1f8810655e14e5896912d1b996ed6a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1f8810655e14e5896912d1b996ed6a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1f8810655e14e5896912d1b996ed6a7"}}, "title": "Immune-coagulation dynamics in severe COVID-19 revealed by autoantibody profiling and multi-omics integration.", "authors": [{"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Cederholm", "given": "Axel", "initials": "A", "orcid": "0009-0006-5973-9637", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2dffb2fd8e446d6a72c765602b97291.json"}}, {"family": "Rezene", "given": "Sefanit", "initials": "S"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M", "orcid": "0000-0003-0050-704X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65dc88b917274bc595daed855b63abab.json"}}, {"family": "Nordqvist", "given": "Hampus", "initials": "H"}, {"family": "Treutiger", "given": "Carl Johan", "initials": "CJ"}, {"family": "Lira-Junior", "given": "Ronaldo", "initials": "R"}, {"family": "Landegren", "given": "Nils", "initials": "N", "orcid": "0000-0002-6163-9540", "researcher": {"href": "https://publications.scilifelab.se/researcher/13ceacb17b7448709f9bfcd593bec1e2.json"}}, {"family": "Gupta", "given": "Soham", "initials": "S", "orcid": "0000-0003-1136-3010", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bbd430437164ba38676d7b94e2189ab.json"}}], "type": "journal article", "published": "2025-09-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "32149", "issn-l": "2045-2322"}, "abstract": "Severe COVID-19 is characterized by immune-coagulation dysregulation, yet the contribution of related autoantibodies remains poorly understood. We investigated relationships between plasma autoantibody reactivities, whole-blood transcriptomics, plasma proteomics, and clinical laboratory parameters in a cohort of hospitalized COVID-19 patients. Transcriptomic analysis revealed that 42 curated coagulation and complement cascade genes were upregulated in severe cases compared to healthy controls, with 15 genes, including CR1L, ELANE, ITGA2B, ITGB3, VWF, TFPI, PROS1, MMRN1, and SELP (> 1.2 log2 fold-change), also significantly different from mild cases. Autoantibody profiling against eight coagulation-related proteins (ADAMTS13, Factor V, Protein S, SERPINC1, Apo-H, PROC1, Prothrombin, and PF4) showed reactivities below positivity thresholds across all groups. Using an exploratory approach, in severe cases, subthreshold autoantibody candidates (FDR < 0.25) showed negative correlation trends with select gene expressions and inflammatory markers (Factor V with IL-6 and CXCL10), suggesting potential disease-specific immunomodulatory associations. In contrast, while mild cases exhibited stronger gene-protein correlations, they showed limited associations with antigen reactivities or clinical laboratory parameters. Additionally, no correlations were observed between autoantibodies and platelet-counts or Fibrin-D-dimer levels. Age-associated increases in antigen reactivities were noted in severe disease, implying a role for immunosenescence. These findings support further investigation into the role of subthreshold autoantibody candidates in thromboinflammatory COVID-19 pathogenesis.", "doi": "10.1038/s41598-025-17054-6", "pmid": "40890263", "labels": {"Autoimmunity and Serology Profiling": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12402181"}, {"db": "pii", "key": "10.1038/s41598-025-17054-6"}], "notes": [], "created": "2025-09-10T08:19:37.842Z", "modified": "2025-11-25T19:21:42.478Z"}, {"entity": "publication", "iuid": "6668bbc3d5d9465089cd9823657f2d8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6668bbc3d5d9465089cd9823657f2d8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6668bbc3d5d9465089cd9823657f2d8c"}}, "title": "Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland.", "authors": [{"family": "Wiley", "given": "Mandi M", "initials": "MM"}, {"family": "Radziszewski", "given": "Marcin", "initials": "M"}, {"family": "Khatri", "given": "Bhuwan", "initials": "B"}, {"family": "Joachims", "given": "Michelle L", "initials": "ML"}, {"family": "Tessneer", "given": "Kandice L", "initials": "KL"}, {"family": "Stolarczyk", "given": "Anna M", "initials": "AM"}, {"family": "Yao", "given": "Songyuan", "initials": "S"}, {"family": "Li", "given": "James", "initials": "J"}, {"family": "Pritchett-Frazee", "given": "Cherilyn", "initials": "C"}, {"family": "Johnston", "given": "Audrey A", "initials": "AA"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Anaya", "given": "Juan-Manuel", "initials": "JM"}, {"family": "Aqrawi", "given": "Lara A", "initials": "LA"}, {"family": "Bae", "given": "Sang-Cheol", "initials": "SC"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Bj\u00f6rk", "given": "Albin", "initials": "A"}, {"family": "Brun", "given": "Johan G", "initials": "JG"}, {"family": "Bucher", "given": "Sara Magnusson", "initials": "SM"}, {"family": "Dand", "given": "Nick", "initials": "N"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Engelke", "given": "Fiona", "initials": "F"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Fugmann", "given": "Cecilia", "initials": "C"}, {"family": "Glenn", "given": "Stuart B", "initials": "SB"}, {"family": "Gong", "given": "Chen", "initials": "C"}, {"family": "Gottenberg", "given": "Jacques-Eric", "initials": "JE"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Jensen", "given": "Janicke Liaaen", "initials": "JL"}, {"family": "Johnsen", "given": "Svein Joar Augl\u00e6nd", "initials": "SJA"}, {"family": "Jonsson", "given": "Malin V", "initials": "MV"}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Khanam", "given": "Sharmily", "initials": "S"}, {"family": "Kim", "given": "Kwangwoo", "initials": "K"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Mart\u00edn", "given": "Javier", "initials": "J"}, {"family": "Morris", "given": "David L", "initials": "DL"}, {"family": "Nocturne", "given": "Gaetane", "initials": "G"}, {"family": "Norheim", "given": "Katrine Br\u00e6kke", "initials": "KB"}, {"family": "Olsson", "given": "Peter", "initials": "P"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Pers", "given": "Jacques-Olivier", "initials": "JO"}, {"family": "Rhodus", "given": "Nelson L", "initials": "NL"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Skarstein", "given": "Kathrine", "initials": "K"}, {"family": "Taylor", "given": "Kimberly E", "initials": "KE"}, {"family": "Tombleson", "given": "Phil", "initials": "P"}, {"family": "Thorlacius", "given": "Gudny Ella", "initials": "GE"}, {"family": "Venuturupalli", "given": "Swamy R", "initials": "SR"}, {"family": "Vital", "given": "Edward M", "initials": "EM"}, {"family": "Wallace", "given": "Daniel J", "initials": "DJ"}, {"family": "Radfar", "given": "Lida", "initials": "L"}, {"family": "Brennan", "given": "Michael T", "initials": "MT"}, {"family": "James", "given": "Judith A", "initials": "JA"}, {"family": "Scofield", "given": "R Hal", "initials": "RH"}, {"family": "Gaffney", "given": "Patrick M", "initials": "PM"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Appel", "given": "Silke", "initials": "S"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Bowman", "given": "Simon J", "initials": "SJ"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Warner", "given": "Blake M", "initials": "BM"}, {"family": "Rischmueller", "given": "Maureen", "initials": "M"}, {"family": "Witte", "given": "Torsten", "initials": "T"}, {"family": "Farris", "given": "A Darise", "initials": "AD"}, {"family": "Mariette", "given": "Xavier", "initials": "X"}, {"family": "Shiboski", "given": "Caroline H", "initials": "CH"}, {"family": "Sj\u00f6gren\u2019s International Collaborative Clinical Alliance (SICCA)", "given": "", "initials": ""}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta E", "initials": "ME"}, {"family": "PRECISESADS Clinical Consortium", "given": "", "initials": ""}, {"family": "Ng", "given": "Wan-Fai", "initials": "WF"}, {"family": "UK Primary Sj\u00f6gren\u2019s Syndrome Registry", "given": "", "initials": ""}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}, {"family": "Guthridge", "given": "Joel M", "initials": "JM"}, {"family": "Adrianto", "given": "Indra", "initials": "I"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}, {"family": "Tsao", "given": "Betty P", "initials": "BP"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Lessard", "given": "Christopher J", "initials": "CJ"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "volume": "84", "issue": "9", "pages": "1512-1527", "issn-l": "0003-4967"}, "abstract": "Sj\u00f6gren's disease (SjD) and systemic lupus erythematosus (SLE) share genetic risk at the DDX6-CXCR5 locus (11q23.3). Identifying and functionally characterising shared SNPs spanning this locus can provide new insights into common genetic mechanisms of autoimmunity.\n\nTransdisease meta-analyses, fine-mapping, and bioinformatic analyses prioritised shared likely functional single nucleotide polymorphisms (SNPs) for allele-specific and cell type-specific functional interrogation using electromobility shift, luciferase reporter, and quantitative chromatin conformation capture assays and clustered regularly interspaced short palindromic repeat (CRISPR) gene regulation.\n\nFive shared SNPs were identified as likely functional in primary human immune cells, salivary gland and kidney tissues: rs57494551, rs4936443, rs4938572, rs7117261, and rs4938573. All 5 SNPs exhibited cell type-specific and allele-specific effects on nuclear protein binding affinity and enhancer/promoter regulatory activity in immune, salivary gland epithelial, and kidney epithelial cell models. Mapping of chromatin-chromatin interactions revealed a chromatin regulatory network that expanded beyond DDX6 and CXCR5 to include PHLDB1, lnc-PHLDB1-1, BCL9L, TRAPPC4, among others. Coalescence of functional assays and multiomic data analyses indicated that these SNPs likely modulate the activity of 3 regulatory regions: intronic rs57494551 regulatory region, intergenic SNP haplotype (rs4938572, rs4936443, and rs7117261) regulatory region, and rs4938573 regulatory region upstream of the CXCR5 promoter.\n\nShared genetic susceptibly at the DDX6-CXCR5 locus in SjD and SLE likely alters common mechanisms of autoimmunity, including interferon signalling (DDX6), autophagy (TRAPPC4), and lymphocytic infiltration of disease-target tissues (CXCR5). Further, using multiomic data from patients with SjD, combined with bioinformatic and in vitro functional studies, can provide mechanistic insights into how genetic risk influences the biological pathways that drive complex autoimmunity.", "doi": "10.1016/j.ard.2025.04.023", "pmid": "40447495", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2086461"}, {"db": "pmc", "key": "PMC12236377"}, {"db": "pii", "key": "S0003-4967(25)00949-5"}], "notes": [], "created": "2025-11-07T07:33:24.582Z", "modified": "2025-11-07T07:33:24.589Z"}, {"entity": "publication", "iuid": "a3100db488e742d697ed58d6ab55c467", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3100db488e742d697ed58d6ab55c467.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3100db488e742d697ed58d6ab55c467"}}, "title": "Systematic profiling of cancer-fibroblast interactions reveals drug combinations in ovarian cancer.", "authors": [{"family": "Gudoityte", "given": "Greta", "initials": "G", "orcid": "0000-0003-1963-7856", "researcher": {"href": "https://publications.scilifelab.se/researcher/a853b5ae2279410aab1b89ad437e4d82.json"}}, {"family": "Sharma", "given": "Osheen", "initials": "O"}, {"family": "Leuenberger", "given": "Laura", "initials": "L"}, {"family": "Wallin", "given": "Emelie", "initials": "E"}, {"family": "Fernebro", "given": "Josefin", "initials": "J"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bergstr\u00f6m", "given": "Rebecka", "initials": "R", "orcid": "0000-0001-7609-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c52bb8b2ae249049f0da222bcdfe932.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Joneborg", "given": "Ulrika", "initials": "U"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "19", "issue": "9", "pages": "2574-2593", "issn-l": "1574-7891"}, "abstract": "Ovarian cancer (OC) is a leading cause of death of gynecological cancers in women. Poor patient response to treatment highlights the need to better understand how the tumor microenvironment affects OC progression. Growing evidence indicates the crucial role of non-cancerous components, such as cancer-associated fibroblasts, in establishing a complex network of cellular and molecular interactions, influencing cancer progression and response to treatment. Therefore, in this study, we sought to characterize the impact of fibroblasts on OC cell behavior and drug response. Using both direct and indirect cell co-culture systems, we observed distinct changes in cancer cell proliferation, morphology, and secretome in the presence of fibroblasts. Furthermore, an imaging-based high-throughput drug screen of 528 oncology compounds revealed multiple drugs that showed altered efficacy in the co-culture conditions, demonstrating the role of fibroblasts in driving cancer cell resistance to treatment. Most importantly, our data identified the two drug combinations of Birinapant or Vorinostat with Carboplatin as promising treatments, exploiting the altered cancer cell phenotype in co-cultures. These findings were supported by the increased sensitivity of ex vivo cultures to these combinations.", "doi": "10.1002/1878-0261.70051", "pmid": "40411295", "labels": {"Affinity Proteomics Stockholm": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12420376"}], "notes": [], "created": "2025-11-07T13:36:45.741Z", "modified": "2025-11-18T20:45:51.242Z"}, {"entity": "publication", "iuid": "0c35ae7c18b94e239d19318c61b04c7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c35ae7c18b94e239d19318c61b04c7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c35ae7c18b94e239d19318c61b04c7a"}}, "title": "Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring.", "authors": [{"family": "L\u00f3pez Clinton", "given": "Samantha", "initials": "S", "orcid": "0000-0003-1364-9135", "researcher": {"href": "https://publications.scilifelab.se/researcher/46b97ad0ac8541dc807e570724e58c69.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Miraldo", "given": "Andreia", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Goodsell", "given": "Robert", "initials": "R"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "15", "issue": "9", "pages": "e72163"}, "abstract": "Obtaining genome-wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenomic sequencing to 40 arthropod bulk samples collected with Malaise traps across Sweden and compared results with metabarcoding of the same material. Using a custom genome database, we achieved genus-level classification largely consistent with metabarcoding. While metagenomics detected all genera identified by metabarcoding, conservative filtering thresholds designed to minimise false positives also excluded some true signals, particularly for low-abundance taxa. Taxonomic overlap between methods was further constrained by limited reference database representation. Beyond taxonomic assignment, metagenomic sequencing yielded genome-level information: we inferred haplotype diversity, heterozygosity and geographic population structure for several abundant species, including variable degrees of hybrid origin in red wood ants and the genetic distinctiveness of Gotland bumblebees. Finally, by-catch plant DNA present in the bulk samples revealed plausible arthropod-plant interactions, several of which align with known ecological associations. Together, these results demonstrate the potential of metagenomics for biodiversity monitoring and population genomics, while underscoring the importance of filtering criteria and comprehensive reference databases.", "doi": "10.1002/ece3.72163", "pmid": "40964625", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12440566"}, {"db": "pii", "key": "ECE372163"}], "notes": [], "created": "2025-11-19T08:12:39.732Z", "modified": "2025-11-28T10:40:00.285Z"}, {"entity": "publication", "iuid": "a321ba70d5a8449193a0b042ea632cc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a321ba70d5a8449193a0b042ea632cc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a321ba70d5a8449193a0b042ea632cc6"}}, "title": "Sex Dependent and Sj\u00f6gren Disease Like Immune Responses Against Phosphoantigens in Balb/C Mice.", "authors": [{"family": "Czwakiel", "given": "Paulina", "initials": "P"}, {"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Eghbali", "given": "Atiyeh", "initials": "A"}, {"family": "Dircksen", "given": "Heinrich", "initials": "H"}, {"family": "Kamal", "given": "Kahkashan", "initials": "K", "orcid": "0000-0003-0968-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/56449fc911fd48b98b207c394d635507.json"}}, {"family": "Payandeh", "given": "Zahra", "initials": "Z"}, {"family": "Ozata", "given": "Deniz", "initials": "D", "orcid": "0000-0001-5215-8684", "researcher": {"href": "https://publications.scilifelab.se/researcher/933850bed34c4517b01e915cf8831686.json"}}, {"family": "Troye-Blomberg", "given": "Marita", "initials": "M"}, {"family": "Faye", "given": "Ingrid", "initials": "I", "orcid": "0000-0003-4382-7238", "researcher": {"href": "https://publications.scilifelab.se/researcher/28e762d6a5a845e79a7a107f700a82b5.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Scand. J. Immunol.", "issn": "1365-3083", "volume": "102", "issue": "3", "pages": "e70052", "issn-l": "0300-9475"}, "abstract": "The initial aim of this study on Balb/C mice was to investigate the putative effects on feeding and appetite of isopentenyl pyrophosphate (IPP) and E-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), also known as phosphoantigens (pAgs). HMBPP was recently shown to increase blood meal appetite in malaria mosquitoes. Both IPP and HMBPP are metabolites produced by the normal gut microbiota and apicomplexan parasites such as Plasmodium. To explore potential effects on appetite, male and female mice were treated by gavage with these metabolites, and body mass and gene expression were monitored in brain, stomach and small intestine at 3 h and 7 weeks. Body mass gain did not clearly differ between pAg-treated and water control mice. However, beginning between 4 and 7 weeks, the salivary glands of IPP-treated males began to swell. With the autoimmune Sj\u00f6gren disease (SjD) in mind, we subsequently investigated the salivary glands after 1, 4 and 7 weeks of IPP treatment. Fast gene set enrichment analysis (FGSEA) of marginal zone B-cell (MZB) transcripts from salivary glands, together with B-cell infiltration in both sexes at 4 weeks, suggested similarities to SjD pathology. Using ELISA, we measured serum autoantibodies against Ro52, Ro60 and La. Multivariate analysis at 7 weeks showed treatment-associated trends: levels of anti-Ro52 and anti-La tended to increase in IPP-treated males, but not in females. Notably, IL-6 serum levels displayed a sex-dependent pattern, and PCA analyses of transcriptomic data from brain, stomach and small intestine-though with some exceptions-also indicated differential responses to pAgs between males and females.", "doi": "10.1111/sji.70052", "pmid": "40898584", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12405675"}], "notes": [], "created": "2025-09-10T08:38:36.714Z", "modified": "2025-11-07T07:24:59.576Z"}, {"entity": "publication", "iuid": "e679aca133c2422599ac1891a96c1a05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05"}}, "title": "Resistance and resilience of co-occurring nitrifying microbial guilds to drying-rewetting stress in soil", "authors": [{"family": "M\u00fcller", "given": "Laura J", "initials": "LJ", "orcid": "0009-0009-5747-2432", "researcher": {"href": "https://publications.scilifelab.se/researcher/11dad561c7e24e68b9ed71a015aa2263.json"}}, {"family": "Alicke", "given": "Mara", "initials": "M", "orcid": "0009-0000-0244-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5d4c9a20fc04322a8babeaded66302f.json"}}, {"family": "Romdhane", "given": "Sana", "initials": "S", "orcid": "0000-0003-0295-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/494ad3e37974440988db1f7b377bae76.json"}}, {"family": "Pold", "given": "Grace", "initials": "G", "orcid": "0000-0002-7536-3944", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a78bb0a7f6043119b6be5e226983d04.json"}}, {"family": "Jones", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-2723-6019", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c04ad1e78da45ee8b383fb09fc5d44a.json"}}, {"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal-article", "published": "2025-09-00", "journal": {"title": "Soil Biology and Biochemistry", "issn": "0038-0717", "volume": "208", "pages": "109846", "issn-l": null}, "abstract": null, "doi": "10.1016/j.soilbio.2025.109846", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:13:11.714Z", "modified": "2025-09-08T07:13:12.028Z"}, {"entity": "publication", "iuid": "a55ef8049c1b4f12854e114a58705dd7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a55ef8049c1b4f12854e114a58705dd7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a55ef8049c1b4f12854e114a58705dd7"}}, "title": "Proteomic biomarkers and pathway analysis for progression to heart failure in three epidemiological representative cohorts.", "authors": [{"family": "Dieden", "given": "Anna", "initials": "A", "orcid": "0000-0002-1041-937X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e96e4a0acde4458493f95f1b4d42d9c2.json"}}, {"family": "Girerd", "given": "Nicolas", "initials": "N"}, {"family": "Ottosson", "given": "Filip", "initials": "F"}, {"family": "Molvin", "given": "John", "initials": "J"}, {"family": "Pareek", "given": "Manan", "initials": "M"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Bachus", "given": "Erasmus", "initials": "E"}, {"family": "R\u00e5stam", "given": "Lennart", "initials": "L"}, {"family": "Lindblad", "given": "Ulf", "initials": "U"}, {"family": "Daka", "given": "Bledar", "initials": "B"}, {"family": "Le\u00f3sd\u00f3ttir", "given": "Margr\u00e9t", "initials": "M"}, {"family": "Nilsson", "given": "Peter M", "initials": "PM"}, {"family": "Olsen", "given": "Michael H", "initials": "MH"}, {"family": "Clark", "given": "Andrew L", "initials": "AL"}, {"family": "Cleland", "given": "John G F", "initials": "JGF"}, {"family": "Delles", "given": "Christian", "initials": "C"}, {"family": "Gonz\u00e1lez", "given": "Arantxa", "initials": "A"}, {"family": "Lamiral", "given": "Zohra", "initials": "Z"}, {"family": "Duarte", "given": "Kevin", "initials": "K"}, {"family": "Rossignol", "given": "Patrick", "initials": "P"}, {"family": "Zannad", "given": "Faiez", "initials": "F"}, {"family": "Gudmundsson", "given": "Petri", "initials": "P"}, {"family": "Juji\u0107", "given": "Amra", "initials": "A"}, {"family": "Magnusson", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Eur. J. Heart Fail.", "issn": "1879-0844", "volume": "27", "issue": "9", "pages": "1764-1774", "issn-l": "1388-9842"}, "abstract": "Biomarkers associated with asymptomatic ventricular dysfunction might improve risk stratification and identify pathways leading to heart failure (HF). We explored the association between proteomic biomarkers and left ventricular hypertrophy (LVH), diastolic dysfunction (DD) and incident HF in three population-based cohorts.\n\nA chip was used to measure 92 protein biomarkers in blood samples from >1500 Malm\u00f6 Preventive Project (MPP) participants, of whom 514 had LVH (34%), 462 had DD (32.4%) and, over a median follow-up of 13 (11-14) years, 130 developed HF (7.7%). Findings were confirmed in the STANISLAS (n > 1500, 238 participants with LVH, 76 with DD) and HOMAGE case-control (562 cases of incident HF, 871 controls) cohorts. In multivariable logistic or Cox regression analyses adjusted for age, sex and cardiovascular risk factors, N-terminal pro-B-type natriuretic peptide (NT-proBNP) was associated with LVH, DD and incident HF in all cohorts: MPP (LVH odds ratio [OR] [95% confidence interval] 1.48 [1.28-1.71]; DD OR 1.71 [1.53-1.92]; HF HR 1.98 [1.66-2.36]); STANISLAS (LVH OR 1.20 [1.02-1.41]; DD OR 1.46 [1.12-1.90]); HOMAGE (HF HR 1.85 [1.62-2.12]). Galectin-4, growth differentiation factor 15 and suppression of tumorigenicity-2 were associated with incident HF in MPP and HOMAGE. A pathway enrichment analysis suggested that inflammation and viral infection were related to incident HF.\n\nIn conclusion, our study reinforces the role of NT-proBNP as a key biomarker for asymptomatic cardiac dysfunction and incident HF, consistent with its established use in clinical practice. This underscores the value of NT-proBNP for identifying patients at high risk for HF, and provides insights into pathways leading to HF and potential therapeutic targets.", "doi": "10.1002/ejhf.3502", "pmid": "39466935", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12502458"}], "notes": [], "created": "2025-11-25T19:20:33.978Z", "modified": "2025-11-25T19:20:34.042Z"}, {"entity": "publication", "iuid": "b5df9eacc566429a92e2fec363fc008e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5df9eacc566429a92e2fec363fc008e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5df9eacc566429a92e2fec363fc008e"}}, "title": "Pericytes change function depending on glioblastoma vicinity: emphasis on immune regulation.", "authors": [{"family": "Buizza", "given": "Carolina", "initials": "C"}, {"family": "Carlsson", "given": "Robert", "initials": "R"}, {"family": "Gamper", "given": "Coralie", "initials": "C"}, {"family": "Chitale", "given": "Gayatri", "initials": "G"}, {"family": "Bengzon", "given": "Johan", "initials": "J"}, {"family": "Paul", "given": "Gesine", "initials": "G", "orcid": "0000-0002-6806-2254", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbbb29ff13af4e28afddbf78764cad29.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "19", "issue": "9", "pages": "2491-2514", "issn-l": "1574-7891"}, "abstract": "Glioblastoma (GBM), the most aggressive brain tumor in adults, is characterized by its infiltrative growth along the perivascular space. Mural cells (MCs), encompassing pericytes and smooth muscle cells, are multifunctional perivascular cells implicated in GBM progression. MCs not only facilitate vascular co-option but have also been suggested to contribute to the immunosuppressive tumor microenvironment, promoting tumor growth and migration. However, whether MC interactions with immune cells differ based on their proximity to the tumor remains unclear. Using single-cell RNA sequencing, we analyzed MC transcriptome profiles across distinct regions relative to the tumor mass in mouse and human GBM samples. Tumor-residing MCs exhibited profound phenotypic changes, showing upregulated gene expression and enhanced signaling activity toward immune cells, with region-specific ligand-receptor interactions. Conversely, border-residing MCs, despite their abundance, showed reduced activation and lacked distinct transcriptional profiles. These findings reveal spatially defined transcriptional heterogeneity in MCs within the GBM microenvironment, underscoring their dynamic role in the GBM microenvironment. This study provides novel insights into MC responses in GBM, identifying potential avenues for targeting MC-immune-cell interactions in therapeutic interventions.", "doi": "10.1002/1878-0261.70095", "pmid": "40674254", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12420362"}], "notes": [], "created": "2025-11-28T10:39:43.920Z", "modified": "2025-11-28T10:39:44.007Z"}, {"entity": "publication", "iuid": "0b4241ad42b14fed843bccebe6ab11be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b4241ad42b14fed843bccebe6ab11be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b4241ad42b14fed843bccebe6ab11be"}}, "title": "Oral contraceptive use increases bone density and reduces the risk of osteoporosis.", "authors": [{"family": "Ivansson", "given": "Emma L", "initials": "EL"}, {"family": "Johansson", "given": "Therese", "initials": "T"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Eur. J. Epidemiol.", "issn": "1573-7284", "volume": "40", "issue": "9", "pages": "1123-1131", "issn-l": "0393-2990"}, "abstract": "Osteoporotic fractures, largely resulting from reduced estrogen levels after menopause and subsequent bone loss, are a leading cause of disability among older women. Although oral contraceptive pills (OCPs) contain estrogen, their long-term impact on bone health and osteoporosis risk remain uncertain. Here, we assessed the effect of OCP use on bone mineral density (BMD) and osteoporosis using data from 257,185 women from the UK Biobank, born 1936-1970. Time-dependent Cox regression was used to estimate adjusted hazard ratios (HRs) and 95% confidence intervals (CI) for osteoporosis, while multivariable linear regression was used to assess the effect of OCP use on BMD, measured as T-scores in standard deviation units based on quantitative ultrasound of the calcaneus. By the end of follow-up in 2020, 7.6% of the participants had received an osteoporosis diagnosis. The rate of osteoporosis was lower among ever OCP users (HR = 0.86; 95% CI 0.83-0.89; P = 2.8 \u00d7 10-17). OCP use was also associated with a higher BMD T-score (0.052; 0.038-0.067; P = 2.1 \u00d7 10-12) with an increasing effect with longer use. Use of OCPs for 0-1 years had no significant effect on BMD (P = 0.081). However, longer durations were associated with increased BMD T-scores compared to never users: 2-5 years (0.046; 0.027-0.065, P = 2.2 \u00d7 10-6), 6-10 years (0.062; 0.043-0.080; P = 3.5 \u00d7 10-12), 11-15 years (0.062; 0.042-0.081; P = 3.2 \u00d7 10-12) and 16 + years (0.064; 0.044-0.083; P = 1.2 \u00d7 10-10). We found prior OCP use to be associated with higher BMD and a reduced risk of osteoporosis, potentially offering long-term benefits and suggesting that OCP use could reduce osteoporotic complications in older women.", "doi": "10.1007/s10654-025-01273-2", "pmid": "40632378", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12537589"}, {"db": "pii", "key": "10.1007/s10654-025-01273-2"}], "notes": [], "created": "2025-11-28T10:41:18.514Z", "modified": "2025-11-28T10:41:18.557Z"}, {"entity": "publication", "iuid": "96e40f0e3f1e469e8f39ed47c75492f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96e40f0e3f1e469e8f39ed47c75492f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96e40f0e3f1e469e8f39ed47c75492f7"}}, "title": "Ontogeny-specific induction of the KMT2A::AFF1-fusion drives development of a distinct CD24 positive pre-leukemic state.", "authors": [{"family": "Calder\u00f3n", "given": "Ariana S", "initials": "AS", "orcid": "0000-0001-6271-6256", "researcher": {"href": "https://publications.scilifelab.se/researcher/67a972ca632a414f8d82013f69af6d15.json"}}, {"family": "Ghazanfari", "given": "Roshanak", "initials": "R"}, {"family": "Masoumi", "given": "Zahra", "initials": "Z"}, {"family": "Kharazi", "given": "Shabnam", "initials": "S"}, {"family": "Palo", "given": "Sara", "initials": "S"}, {"family": "Lang", "given": "Stefan", "initials": "S", "orcid": "0000-0002-0854-2328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eed2cc9c00a7404d9cd4821a7d0cd92d.json"}}, {"family": "\u017demaitis", "given": "Kristijonas", "initials": "K"}, {"family": "Eldeeb", "given": "Mohamed", "initials": "M", "orcid": "0000-0002-8636-2189", "researcher": {"href": "https://publications.scilifelab.se/researcher/00a89e30b4ba4216ae5a9ca189fd8da0.json"}}, {"family": "Subramaniam", "given": "Agatheeswaran", "initials": "A", "orcid": "0000-0003-3966-3875", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb1e6798b84f128c3143c8da8bd35a.json"}}, {"family": "Soneji", "given": "Shamit", "initials": "S"}, {"family": "Stam", "given": "Ronald W", "initials": "RW", "orcid": "0000-0003-4986-1656", "researcher": {"href": "https://publications.scilifelab.se/researcher/f528aaa6b3ba479f85619e1496e3f395.json"}}, {"family": "Bryder", "given": "David", "initials": "D", "orcid": "0000-0002-8761-4237", "researcher": {"href": "https://publications.scilifelab.se/researcher/30133810251344cb9fa3e42f0e2fd511.json"}}, {"family": "B\u00f6iers", "given": "Charlotta", "initials": "C", "orcid": "0000-0002-4876-1218", "researcher": {"href": "https://publications.scilifelab.se/researcher/e33b5ec83be045c693675ab6bda2e9d0.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "volume": "39", "issue": "9", "pages": "2099-2111", "issn-l": "0887-6924"}, "abstract": "Infant Acute Lymphoblastic Leukemia (ALL) driven by the KMT2A::AFF1 onco-fusion is an aggressive, poor prognosis disease with few co-operative mutations. The fusion originates in utero, yet the embryonic initiating steps of disease development remain poorly understood. Here, we present a novel murine KMT2A::AFF1 model, that provides key insights into KMT2A::AFF1 pre-leukemia, relevant to human disease. The model enables precise oncogene induction, and upon targeting hematopoietic stem and progenitor cells (HSPCs) a selective negative impact on proliferation of hematopoietic stem cells (HSCs) was observed, regardless of developmental state during induction. However, a unique CD24+PreProB subset expanded exclusively within the KMT2A::AFF1 embryonic context. This population was absent when targeting lymphoid progenitors, highlighting the importance of the cell of origin for leukemic development. The CD24+PreProB subset displayed key features of pre-leukemic stem cells, including lineage plasticity and aberrant engraftment ability. In line with their pre-malignant phenotype, single-cell transcriptomics revealed a signature consistent with stemness, and notable, up-regulation of Hmga2, a regulator of self-renewal. The signature was critically transferable to human KMT2A::AFF1 patients. Furthermore, given that CD24 is a potential therapeutic target, our findings uncover a distinct embryonic pre-leukemic state with direct relevance to human disease.", "doi": "10.1038/s41375-025-02665-9", "pmid": "40646135", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12380613"}, {"db": "pii", "key": "10.1038/s41375-025-02665-9"}], "notes": [], "created": "2025-11-05T18:41:18.358Z", "modified": "2025-11-10T14:06:52.558Z"}, {"entity": "publication", "iuid": "c027601d1dfd4b72a6c77d6aada03e78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c027601d1dfd4b72a6c77d6aada03e78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c027601d1dfd4b72a6c77d6aada03e78"}}, "title": "Multilayered Epigenetic Analysis Identifies a Molecular Portrait for Psychological Resilience in Patients With Breast Cancer.", "authors": [{"family": "Richter", "given": "Corinna", "initials": "C"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Lundberg", "given": "Kristina", "initials": "K"}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L"}, {"family": "Johnsson", "given": "Per", "initials": "P"}, {"family": "Ringdahl", "given": "Ulrika", "initials": "U"}, {"family": "Hallberg", "given": "Ingalill Rahm", "initials": "IR"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CAK"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Biol Psychiatry Glob Open Sci", "issn": "2667-1743", "volume": "5", "issue": "5", "pages": "100545", "issn-l": null}, "abstract": "Psychological resilience refers to a person's positive adaptation when faced with adversities, such as a breast cancer (BC) diagnosis. Highly resilient patients are more likely to regain stability and be protected from health conditions such as depression, anxiety, and posttraumatic stress disorder. We aimed to identify epigenetic markers that distinguish high- and low-resilient patients in a BC cohort at time of diagnosis.\n\nGenome-wide DNA methylation was determined in participants selected from a prospectively collected cohort of 1040 newly diagnosed BC patients with known resilience status. DNA methylation of those displaying the highest and lowest scores (n = 425), as measured by the Connor-Davidson Resilience Scale, was analyzed in whole blood, using a multilayered bioinformatic approach. Sample subsets were created to identify differentially methylated probes (DMPs) and differentially methylated regions (DMRs), and fold change and area size were used to estimate the strength of methylation differences. The key regions associated with psychological resilience allowed us to build a classifier, using a random forest model, which was validated using an independent cohort (n = 80).\n\nDMPs and DMRs that consistently distinguished samples derived from high- and low-resilient patients were identified, and methylation differences followed a dose-response pattern related to resilience levels. DMRs included LY6G5C, ZFP57, CDH9, ZNF727, and C8orf31, where LY6G5C was found to be the most consistent DMR. Psychological resilience status could be predicted in the independent cohort with an area under the curve of 0.74 and a sensitivity and specificity of 0.67 and 0.72, respectively.\n\nLY6G5C was identified as a novel marker for psychological resilience, paving the way for a more conceptual and comprehensive molecular understanding.", "doi": "10.1016/j.bpsgos.2025.100545", "pmid": "40697488", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12281357"}, {"db": "pii", "key": "S2667-1743(25)00099-0"}], "notes": [], "created": "2025-11-17T10:18:22.349Z", "modified": "2025-11-17T10:18:22.358Z"}, {"entity": "publication", "iuid": "e662b245c1b54ff9af9f7b916a2ea5b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e662b245c1b54ff9af9f7b916a2ea5b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e662b245c1b54ff9af9f7b916a2ea5b9"}}, "title": "Metabolic analysis of sarcopenic muscle identifies positive modulators of longevity and healthspan in C. elegans.", "authors": [{"family": "Jonk", "given": "Steffi M", "initials": "SM"}, {"family": "Nicol", "given": "Alan", "initials": "A"}, {"family": "Chrysostomou", "given": "Vicki", "initials": "V"}, {"family": "Lardner", "given": "Emma", "initials": "E"}, {"family": "Yu", "given": "Shu-Che", "initials": "SC"}, {"family": "St\u00e5lhammar", "given": "Gustav", "initials": "G"}, {"family": "Crowston", "given": "Jonathan G", "initials": "JG"}, {"family": "Tribble", "given": "James R", "initials": "JR"}, {"family": "Swoboda", "given": "Peter", "initials": "P"}, {"family": "Williams", "given": "Pete A", "initials": "PA"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Redox Biol", "issn": "2213-2317", "volume": "85", "pages": "103732", "issn-l": null}, "abstract": "Sarcopenia is the age-related degeneration of skeletal muscle, resulting in loss of skeletal muscle tone, mass, and quality. Skeletal muscle is a source of systemic metabolites and macromolecules important for neuronal health, function, and healthy neuronal aging. Age-related loss of skeletal muscle might result in decreased metabolite and macromolecule availability, resulting in reduced neuronal function or increased susceptibility to unhealthy aging and neurodegenerative diseases. We aimed to identify muscle metabolite candidates that regulate healthy aging. C57BL/6J mice were aged to young adult (4 months) and old age (25 months) and skeletal muscle was collected. Age-related muscle loss was confirmed by reduced muscle mass, muscle fiber degeneration, reduced myosin intensity, in addition to a metabolic shift and increased DNA damage in skeletal muscle. Using a low molecular weight enriched metabolomics protocol, we assessed the metabolic profile of skeletal muscle from young adult and old age mice and identified 20 metabolites that were significantly changed in aged muscle. These metabolite candidates were tested in C. elegans assays of lifespan, healthspan, muscle, and mitochondrial morphology under normal and stressed conditions. We identified four metabolite candidates (beta-alanine, 4-guanidinobutanoic acid, 4-hydroxyproline, pantothenic acid) that, when supplemented in C. elegans provided robust gero- and mitochondrial protection. These candidates also affected life-, and health- span in C. elegans models of amyotrophic lateral sclerosis (ALS) and Duchenne muscular dystrophy (DMD). Our findings support that aging muscle can be used to identify novel metabolite modulators of lifespan and health and may show promise for future treatments of neurodegenerative and neuromuscular disorders.", "doi": "10.1016/j.redox.2025.103732", "pmid": "40544604", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12226095"}, {"db": "pii", "key": "S2213-2317(25)00245-9"}], "notes": [], "created": "2025-11-18T12:13:51.391Z", "modified": "2025-11-18T12:13:51.395Z"}, {"entity": "publication", "iuid": "df60b381dc4943cdbbccf12206421777", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df60b381dc4943cdbbccf12206421777.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df60b381dc4943cdbbccf12206421777"}}, "title": "Lineage-specific targets of positive selection in three leaf beetles correspond with defence capacity against their shared parasitoid wasp.", "authors": [{"family": "Yang", "given": "Xuyue", "initials": "X"}, {"family": "Tunstr\u00f6m", "given": "Kalle", "initials": "K", "orcid": "0000-0002-5285-1531", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd0ddb97d724542b6e7c46f782f3bbd.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-6362-6199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddfc67c7c774583861a5ea3774eaa1a.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "134", "issue": "9", "pages": "567-575", "issn-l": "0018-067X"}, "abstract": "Parasitoid wasps are major causes of mortality of many species, making host immune defences a common target of adaptive evolution, though such targets outside model species are poorly understood. In this study, we used two tests of positive selection to compare across three closely related Galerucella leaf beetles that show substantial differences in their phenotypic response to the shared parasitoid wasp Asecodes parviclava, their main natural enemy. Using a codon-based test, which detects excess amino acid fixations per locus along each species' lineage, we found more evidence of positive selection on parasitoid-relevant immune genes in the species with the strongest immunocompetence (G. pusilla) compared with the species having weaker immunocompetence (G. tenella and G. calmariensis). Moreover, genes coding for the early phases in the immune response cascade were predominantly among the positively selected immune genes, providing targets for future functional genomic study to pin-point connections between genotypic and phenotypic differences in defences towards a parasitoid wasp. In contrast, genome-wide analyses of the haplotype frequency spectrum, which quantify selection over recent evolutionary time scales, revealed similar signatures of positive selection on immune genes across species. These results advance the field of host-parasitoid dynamics by providing novel insights into the tempo and mode of insect host evolutionary dynamics, and offering a framework for making genotype to phenotype connections for immunocompetence phenotypes.", "doi": "10.1038/s41437-025-00794-6", "pmid": "40921792", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12457636"}, {"db": "pii", "key": "10.1038/s41437-025-00794-6"}], "notes": [], "created": "2025-09-29T07:36:03.222Z", "modified": "2025-11-21T09:22:48.226Z"}, {"entity": "publication", "iuid": "a85db0b07abe4009bca2bcadb5b9d3f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a85db0b07abe4009bca2bcadb5b9d3f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a85db0b07abe4009bca2bcadb5b9d3f5"}}, "title": "LIGHT/TNFSF14 Levels in Carotid Plaques Are Associated With Symptomatic Cerebrovascular Disease.", "authors": [{"family": "Gon\u00e7alves", "given": "Isabel", "initials": "I"}, {"family": "Sun", "given": "Jiangming", "initials": "J"}, {"family": "Singh", "given": "Pratibha", "initials": "P"}, {"family": "Pan", "given": "Mengyu", "initials": "M"}, {"family": "Gialeli", "given": "Chrysostomi", "initials": "C"}, {"family": "Bengtsson", "given": "Eva", "initials": "E"}, {"family": "Nilsson", "given": "Jan", "initials": "J"}, {"family": "Lutgens", "given": "Esther", "initials": "E"}, {"family": "Edsfeldt", "given": "Andreas", "initials": "A"}, {"family": "Shami", "given": "Annelie", "initials": "A"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "J Stroke", "issn": "2287-6391", "volume": "27", "issue": "3", "pages": "381-389", "issn-l": null}, "abstract": "Plaque rupture is the underlying cause of most cardiovascular events, such as stroke and myocardial infarction. The co-stimulatory molecule LIGHT (tumor necrosis factor superfamily member 14, TNFSF14) has been detected in foam cell-rich regions of atherosclerotic plaques, but whether it has a role in plaque stability is not known. This study investigates the association between intraplaque LIGHT levels and plaque vulnerability.\n\nLIGHT levels were measured in homogenates of carotid endarterectomy samples by proximity extension assay (n=202) and through bulk RNA sequencing and spatial transcriptomics (Visium) of plaques from patients included in the Carotid Plaque Imaging Project. Homogenates were further examined by multiplex analyses and enzyme-linked immunosorbent assay, and plaque sections by immunohistochemistry.\n\nPlaque levels of LIGHT were associated with occurrence of preoperative cerebrovascular symptoms, including stroke. LIGHT levels correlated with a histological plaque vulnerability index, necrotic core size, and inflammatory cytokine levels. Additionally, expression of extracellular matrix turnover machinery components, including the collagen cross-linking proteoglycan fibromodulin and matrix metalloproteinases 1, 2, 9, and 10, was associated with plaque LIGHT levels.\n\nExpression of LIGHT in atherosclerotic plaques not only correlates with markers of plaque destabilization, but is also significantly elevated in plaques from symptomatic compared to those from asymptomatic patients. These results associate LIGHT content with a rupture-prone plaque phenotype, potentially upregulated as part of a reparative response, warranting further studies.", "doi": "10.5853/jos.2025.00703", "pmid": "41084292", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12527579"}, {"db": "pii", "key": "jos.2025.00703"}], "notes": [], "created": "2025-11-25T19:21:19.769Z", "modified": "2025-11-25T19:21:19.802Z"}, {"entity": "publication", "iuid": "c57d8ac1a6904e40856c4f78a2d6803b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c57d8ac1a6904e40856c4f78a2d6803b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c57d8ac1a6904e40856c4f78a2d6803b"}}, "title": "Induced somatic mutation accumulation during skeletal muscle regeneration reduces muscle strength.", "authors": [{"family": "Vrta\u010dnik", "given": "Peter", "initials": "P"}, {"family": "Merino", "given": "Lara G", "initials": "LG", "orcid": "0000-0002-7208-953X", "researcher": {"href": "https://publications.scilifelab.se/researcher/afebb85c860744dc8ad5840caa6f06c0.json"}}, {"family": "Subhash", "given": "Santhilal", "initials": "S", "orcid": "0000-0002-0077-4597", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ca22115b7c9444ab2056126a1c9d36d.json"}}, {"family": "Helgad\u00f3ttir", "given": "Hafd\u00eds T", "initials": "HT", "orcid": "0000-0003-4352-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce4dc1001c944a9d9dfe4c092cfda497.json"}}, {"family": "Bardin", "given": "Matthieu", "initials": "M", "orcid": "0000-0001-9755-8841", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4070871377c4fbcabf6e9a299d01277.json"}}, {"family": "Stefani", "given": "Fabiana", "initials": "F", "orcid": "0009-0008-8933-0773", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f3b815508714611a894e9853362b123.json"}}, {"family": "Wang", "given": "Depin", "initials": "D"}, {"family": "Chen", "given": "Ping", "initials": "P"}, {"family": "Franco", "given": "Irene", "initials": "I", "orcid": "0000-0002-4272-239X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eac8823b89543f09e9d2cb141bdb587.json"}}, {"family": "Rev\u00eachon", "given": "Gwladys", "initials": "G", "orcid": "0000-0002-4824-6793", "researcher": {"href": "https://publications.scilifelab.se/researcher/356dd0dbbdaa4d21957e516ce11bbd74.json"}}, {"family": "Eriksson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3233-2862", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca8641fd4d16471abf18990610fb89a1.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Nat Aging", "issn": "2662-8465", "volume": "5", "issue": "9", "pages": "1739-1749", "issn-l": null}, "abstract": "Aging is associated with a progressive decline in tissue function and regenerative capacity, partly due to genomic instability, one of the hallmarks of aging1,2. Genomic instability encompasses DNA damage and the accumulation of somatic mutations in post-zygotic cells, yet the specific impact of these mutations on age-related tissue dysfunction remains poorly understood. To address this, we developed a mouse model in which genomic instability was induced specifically in muscle progenitor cells3 through targeted deletion of the Msh2 (ref. 4) and Blm5 genes. This allowed us to assess how elevated DNA damage and somatic mutations, from single-nucleotide variants (SNVs) to structural variants, affect muscle regeneration following injury. These mice exhibited impaired muscle regeneration, characterized by smaller muscle fibers, reduced muscle mass gain and decreased grip strength. Importantly, similar muscle deficits were observed in a second mouse model where somatic mutations were elevated with less substantial DNA damage. These findings provide evidence that the accumulation of somatic mutations can potentially compromise the function of somatic cells, contributing to the aging phenotype in skeletal muscle.", "doi": "10.1038/s43587-025-00941-y", "pmid": "40836125", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12443595"}, {"db": "pii", "key": "10.1038/s43587-025-00941-y"}], "notes": [], "created": "2025-09-08T07:07:06.110Z", "modified": "2025-11-19T08:29:17.738Z"}, {"entity": "publication", "iuid": "d393109fcd1c4ba9be1fc99ed851ad05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d393109fcd1c4ba9be1fc99ed851ad05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d393109fcd1c4ba9be1fc99ed851ad05"}}, "title": "In-depth patient-specific analysis of tumor heterogeneity in melanoma brain metastasis: Insights from spatial transcriptomics and multi-region bulk sequencing.", "authors": [{"family": "Sharma", "given": "Nidhi", "initials": "N", "orcid": "0000-0002-2475-9340", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadc0f3bfb5443e8a14af7d785085324.json"}}, {"family": "R\u00e1jov\u00e1", "given": "Jana", "initials": "J"}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1bd1b94e1694de9a5c27fd8f331dc86.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Vikstr\u00f6m", "given": "Sofi", "initials": "S"}, {"family": "Baba\u010di\u0107", "given": "Haris", "initials": "H", "orcid": "0000-0003-0813-0005", "researcher": {"href": "https://publications.scilifelab.se/researcher/45a1c5d3d2d34a9e96d112877632784c.json"}}, {"family": "Jensdottir", "given": "Margret", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}, {"family": "Eriksson", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Transl Oncol", "issn": "1936-5233", "volume": "59", "pages": "102468", "issn-l": null}, "abstract": "Melanoma brain metastases (MBM) exhibit extensive intertumor and intratumor heterogeneity (ITH), driven by a complex tumor microenvironment. The aim of this study was to perform a detailed analysis of individual MBM patient tumors using a multiomics approach, integrating spatial transcriptomics with multi-region bulk exome, proteome, and transcriptome profiling for a small group of four patient samples. We identified significant patient-specific variations in immune cell infiltration, particularly in B/plasma cells, myeloid cells, and cancer-associated fibroblasts (CAFs). Notably, immunotherapy-treated patients showed enriched pathways related to epithelial-mesenchymal transition (EMT), interferon-gamma (IFN-\u03b3) signaling, oxidative phosphorylation, T-cell signaling, inflammation and DNA damage, which aligned with distinct cellular compositions observed in the spatial analysis. We also uncovered considerable ITH, especially at the protein level, revealing differential expression patterns of key tumor and immune-related markers. The correlation between mRNA and protein data highlighted consistent enrichment of critical pathways across multiomics layers. These findings highlight the molecular and cellular landscape of individual patient MBM, underscoring the importance of addressing tumor heterogeneity in the development of effective therapeutic strategies.", "doi": "10.1016/j.tranon.2025.102468", "pmid": "40669378", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12284558"}, {"db": "pii", "key": "S1936-5233(25)00199-8"}], "notes": [], "created": "2025-07-18T10:25:23.220Z", "modified": "2025-11-28T10:44:36.443Z"}, {"entity": "publication", "iuid": "68a7b049174f41e0a725288c665eede5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68a7b049174f41e0a725288c665eede5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68a7b049174f41e0a725288c665eede5"}}, "title": "Hot ductility behavior of new Ni-based superalloy G27: Influence of solution annealing on the liquation cracking susceptibility", "authors": [{"family": "Ariaseta", "given": "Achmad", "initials": "A", "orcid": "0000-0002-9520-0456", "researcher": {"href": "https://publications.scilifelab.se/researcher/c51dbaf873644924be646d70c5d2f45f.json"}}, {"family": "Hanning", "given": "Fabian", "initials": "F", "orcid": "0000-0002-1607-9177", "researcher": {"href": "https://publications.scilifelab.se/researcher/6737b910038f4c838703141e08aafd3a.json"}}, {"family": "Andersson", "given": "Joel", "initials": "J", "orcid": "0000-0001-9065-0741", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb14103bdd9b4df994ba97e3d17fb1c3.json"}}, {"family": "Ojo", "given": "Olanrewaju", "initials": "O"}], "type": "journal-article", "published": "2025-09-00", "journal": {"title": "Journal of Materials Research and Technology", "issn": "2238-7854", "volume": "38", "pages": "4133-4149", "issn-l": null}, "abstract": null, "doi": "10.1016/j.jmrt.2025.08.241", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "NanoSIMS": "Service"}, "xrefs": [], "notes": [], "created": "2026-03-10T07:24:20.430Z", "modified": "2026-03-10T14:20:41.619Z"}, {"entity": "publication", "iuid": "f77da0ef90c647a0af9d18b2b04042f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f77da0ef90c647a0af9d18b2b04042f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f77da0ef90c647a0af9d18b2b04042f0"}}, "title": "Gone With the Wind: Exploring a Vanished Rock Dove, Columba livia, Hybrid Zone in the Sahara Desert.", "authors": [{"family": "Hern\u00e1ndez-Alonso", "given": "Germ\u00e1n", "initials": "G", "orcid": "0000-0001-6065-1428", "researcher": {"href": "https://publications.scilifelab.se/researcher/408d39dcc0c24431816561f71350cb0f.json"}}, {"family": "van Grouw", "given": "Hein", "initials": "H"}, {"family": "Farahani", "given": "Motahare F", "initials": "MF"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "15", "issue": "9", "pages": "e72061"}, "abstract": "Rock doves (Columba livia) are the wild ancestor of domestic and feral pigeons and had a wide distribution across Eurasia and the northern part of Africa. West African rock doves have been identified as genetically distinct from all other populations, possibly representing a distinct species. This divergence is hypothesized to have arisen through cycles of allopatry during the dry and wet Sahara periods. Based on the Refugia Theory and observed admixture patterns, it was proposed that a hybrid zone existed in the Sahara during its last green period, playing a critical role in the speciation of West African rock doves. This project aims to test the existence and location of this vanished hybrid zone by analyzing whole-genome sequences from six historical rock doves from previously unsampled populations in the Central Sahara and West Africa, along with published genomic data. By exploring population structure, genetic diversity, and admixture patterns, our results confirm the existence of the hybrid zone, likely located around the mountainous regions of northwest Africa. To explain the observed genetic differentiation of West African rock doves, we propose a four-step scenario involving speciation by reinforcement. Finally, we support a species-level taxonomic arrangement to designate the West African rock dove as C. gymnocycla.", "doi": "10.1002/ece3.72061", "pmid": "40896089", "labels": {"Ancient DNA": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12391023"}, {"db": "pii", "key": "ECE372061"}, {"db": "figshare", "key": "10.6084/m9.figshare.29267132"}], "notes": [], "created": "2025-11-05T07:40:54.780Z", "modified": "2025-11-19T07:57:17.516Z"}, {"entity": "publication", "iuid": "99d94470f07541c2b23fad1eefd0f74b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b"}}, "title": "Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution.", "authors": [{"family": "Zervakis", "given": "Panagiotis-Ioannis", "initials": "PI", "orcid": "0000-0002-5197-3502", "researcher": {"href": "https://publications.scilifelab.se/researcher/295e9debf36c4641aa6c346e915b64ef.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Losvik", "given": "Aleksandra", "initials": "A", "orcid": "0000-0001-7669-9266", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85c35a0abd54a7087c94942290179be.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "Sol\u00e9r", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Churcher", "given": "Allison", "initials": "A", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "247", "issue": "6", "pages": "2964-2981"}, "abstract": "Distyly, an example of convergent evolution, is governed by a supergene, the S-locus, in several species. Recent studies highlight similar genomic architectures of independently evolved S-loci, but its mode of origin and whether similar regulatory pathways underlie the convergent evolution of distyly remains unclear. We examined the evolution of supergenes and mechanisms underlying distyly in Linum species that diverged c. 33 million years ago (Ma). Using haplotype-resolved genomes and population genomics, we identified and characterized the S-loci of Linum perenne (distylous) and Linum grandiflorum (style length dimorphic), and compared them to that of Linum tenue (distylous). We then tested for a conserved hormonal mechanism regulating style length polymorphism in Linum. The S-locus supergene was consistently hemizygous in short-styled individuals across all three species, although it showed variation in size, gene content, repeat elements and extent of recombination suppression. Two S-linked candidate genes, TSS1 (style length) and WDR-44 (anther height/pollen self-incompatibility), were conserved. Consistent with a brassinosteroid-dependent role of TSS1, epibrassinolide treatment revealed a conserved, morph-specific effect on style length. S-locus structural polymorphism, candidate distyly genes and mechanisms regulating style length remain conserved > 30 Ma in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism.", "doi": "10.1111/nph.70392", "pmid": "40682296", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371154"}], "notes": [], "created": "2025-08-19T13:25:54.698Z", "modified": "2025-11-19T10:24:41.159Z"}, {"entity": "publication", "iuid": "2cac753de106445cbf229064ef982197", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cac753de106445cbf229064ef982197.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cac753de106445cbf229064ef982197"}}, "title": "Genomic determinants of therapy response in ETV6::RUNX1 leukemia.", "authors": [{"family": "Oksa", "given": "Laura", "initials": "L", "orcid": "0000-0003-4468-9877", "researcher": {"href": "https://publications.scilifelab.se/researcher/5526f0f44427441bb2a49f27f00b5683.json"}}, {"family": "Moisio", "given": "Sanni", "initials": "S", "orcid": "0009-0009-4446-015X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de1112350e9042bfa9a8707d2c255bf5.json"}}, {"family": "Maqbool", "given": "Khurram", "initials": "K", "orcid": "0000-0003-2981-2582", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ea06b85057744018f754c373fef3ca5.json"}}, {"family": "Kramer", "given": "Roger", "initials": "R"}, {"family": "Nikkil\u00e4", "given": "Atte", "initials": "A"}, {"family": "Jayasingha", "given": "Buddika", "initials": "B"}, {"family": "M\u00e4kinen", "given": "Artturi", "initials": "A", "orcid": "0000-0002-5521-9216", "researcher": {"href": "https://publications.scilifelab.se/researcher/74542e2da6d542d8a40b93b692c7b760.json"}}, {"family": "Foroughi-Asl", "given": "Hassan", "initials": "H"}, {"family": "Rounioja", "given": "Samuli", "initials": "S"}, {"family": "Suhonen", "given": "Janne", "initials": "J"}, {"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Voutilainen", "given": "Miikka", "initials": "M", "orcid": "0000-0001-9367-3471", "researcher": {"href": "https://publications.scilifelab.se/researcher/390e63751ebb46e3873d801ce0c620d1.json"}}, {"family": "Lahnalampi", "given": "Mari", "initials": "M", "orcid": "0000-0003-4050-4935", "researcher": {"href": "https://publications.scilifelab.se/researcher/31d154912d9f4b9ca680f9d019035d46.json"}}, {"family": "Veps\u00e4l\u00e4inen", "given": "Kaisa", "initials": "K"}, {"family": "Huang", "given": "Sui", "initials": "S"}, {"family": "Duque-Afonso", "given": "Jesus", "initials": "J", "orcid": "0000-0002-8287-5673", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc78f208850b4a999859f110a3850bfa.json"}}, {"family": "Hauer", "given": "Julia", "initials": "J", "orcid": "0000-0002-4058-3058", "researcher": {"href": "https://publications.scilifelab.se/researcher/9387a9c586f74172a9d251fff4d71637.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Lohi", "given": "Olli", "initials": "O", "orcid": "0000-0001-9195-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11a59310dfc40e6a111367914fdba9e.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "issn-l": "0887-6924", "volume": "39", "issue": "9", "pages": "2125-2139"}, "abstract": "ETV6::RUNX1 leukemia is the second most common subtype of childhood B cell acute lymphoblastic leukemia (B-ALL). Although it generally has a low relapse risk, a significant proportion of B-ALL relapses occur within this subtype due to its relatively high incidence. Measurable residual disease at the end of induction therapy is a well-established biomarker predicting treatment outcomes, while no genomic biomarkers are routinely applied in clinics. In this study, we used multiomic data from ETV6::RUNX1 leukemias to identify genomic features predictive of therapy response at disease presentation. In the deeply characterized sub-cohort we discovered that fast-responding cases frequently exhibited the APOBEC mutational signature and the gene expression signature of high cell cycle activity. In contrast, rearrangements of IGK genes were more frequent in slow responders. Additionally, response-related mutations were identified in transcriptional regulators and tumor suppressor genes (INTS1, NF1, TP53). Copy number analysis revealed that fast responders harbored more frequent deletions of chr12 p-arm, leading to transcriptomic changes affecting genes associated with induction therapy response (KRAS, FKBP4), while a shorter gain in chr12 was more common in slow responders. The identified genetic and transcriptomic markers of treatment sensitivity pave the way for improved disease classification at presentation, potentially improving clinical outcomes.", "doi": "10.1038/s41375-025-02683-7", "pmid": "40634509", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12380598"}, {"db": "pii", "key": "10.1038/s41375-025-02683-7"}], "notes": [], "created": "2025-09-08T11:39:55.025Z", "modified": "2025-11-18T20:46:15.313Z"}, {"entity": "publication", "iuid": "7799feb1743049b29d4ce4b791a4dd02", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7799feb1743049b29d4ce4b791a4dd02.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7799feb1743049b29d4ce4b791a4dd02"}}, "title": "Genomic and morphological analysis reveals long-term mammoth hybridization in British Columbia, Canada.", "authors": [{"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Termes", "given": "Laura", "initials": "L"}, {"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "Moots", "given": "Hannah M", "initials": "HM"}, {"family": "Tubbesing", "given": "Florentine", "initials": "F"}, {"family": "Larsdotter", "given": "Juliana", "initials": "J"}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G"}, {"family": "Moreland", "given": "Kelsey", "initials": "K"}, {"family": "van Essen", "given": "Hans", "initials": "H"}, {"family": "Arbour", "given": "Victoria", "initials": "V"}, {"family": "Keddie", "given": "Grant", "initials": "G"}, {"family": "Richards", "given": "Michael P", "initials": "MP"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Lister", "given": "Adrian", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "21", "issue": "9", "pages": "20250305", "issn-l": "1744-9561"}, "abstract": "Climate changes profoundly impact species distributions and can drastically alter dynamics between formerly isolated taxa. The evolution of mammoths within North America was characterized by repeated cycles of dispersal and putative gene flow between woolly and Columbian mammoths. However, as genome-wide studies on mammoths have predominantly focused on Siberia, the consequences of these North American range shifts remain unclear. Here, we generated genome-wide and morphological data for two Late Pleistocene mammoth molars from British Columbia, Canada (BC), and jointly analysed these with previously published data. Our genome-wide analysis (n = 16) revealed gene flow between woolly and Columbian mammoths that would have gone undiscovered based on morphological (n = 48) and mitochondrial analysis (n = 124) alone. Consistent with their hybrid nature, our analyses suggest that these two BC mammoths had elevated genomic diversity. Our results highlight the importance of combining data types to reconstruct past evolutionary events. These findings demonstrate how the geographical range expansion of woolly mammoths resulted in long-term hybridization with local Columbian mammoths and enhance our understanding of the genomic and morphological consequences of climate-mediated dispersal.", "doi": "10.1098/rsbl.2025.0305", "pmid": "40994021", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12461089"}], "notes": [], "created": "2025-11-19T08:22:48.349Z", "modified": "2025-11-19T08:22:48.432Z"}, {"entity": "publication", "iuid": "f03b39792af64005a894aed97760ae28", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f03b39792af64005a894aed97760ae28.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f03b39792af64005a894aed97760ae28"}}, "title": "Fungal guild interactions slow decomposition of boreal forest pine litter and humus.", "authors": [{"family": "Mielke", "given": "Louis A", "initials": "LA", "orcid": "0000-0001-6948-3141", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f0d43b208d42798d423786eb4eb4cc.json"}}, {"family": "Klein", "given": "Julian", "initials": "J", "orcid": "0000-0002-4269-4974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdf08ca4a4cb44fbaa41db3c8549010f.json"}}, {"family": "Ekblad", "given": "Alf", "initials": "A", "orcid": "0000-0003-4384-5014", "researcher": {"href": "https://publications.scilifelab.se/researcher/55b407368cf342698c0b681ef8cf2ba9.json"}}, {"family": "Finlay", "given": "Roger D", "initials": "RD", "orcid": "0000-0002-3652-2930", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cf62270530f402faa530c435cb6829c.json"}}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD", "orcid": "0000-0002-3384-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a40688d33545a19c3c666940bda255.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "247", "issue": "5", "pages": "2367-2380", "issn-l": "0028-646X"}, "abstract": "Ericaceous understory shrubs and ericoid mycorrhizal fungal communities are ubiquitous in boreal forests, and their interactions with ectomycorrhizal and saprotrophic fungi may determine organic matter dynamics in forest soils. We followed decomposition of pine needle litter and mor-layer humus over 3 yr in a factorial shrub removal- and pine root exclusion experiment in an old-growth Scots pine (Pinus sylvestris) forest, to evaluate effects of fungal guilds on mass loss. Litter mass loss was 23% greater when ectomycorrhizal fungi were excluded suggesting increased saprotrophic activity, independently of ericoid shrub presence. However, this 'Gadgil effect' was only found after 17 months following a summer drought. By contrast, humus mass loss was overall stimulated by ectomycorrhizal fungi, while ericoid mycorrhizal shrubs appeared to counteract this effect, potentially caused by simultaneous addition of recalcitrant organic matter and inhibition of ectomycorrhizal decomposers. We conclude that competitive saprotrophic-ectomycorrhizal fungal interactions may slow early-stage litter decomposition, but this effect was small and inconsistent. Furthermore, interactions between ecto- and ericoid mycorrhizal guild members appear to determine the late-stage organic matter balance of boreal forest humus.", "doi": "10.1111/nph.70316", "pmid": "40552521", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12329171"}], "notes": [], "created": "2025-08-19T13:22:00.173Z", "modified": "2025-08-19T13:22:00.288Z"}, {"entity": "publication", "iuid": "f0dd1009dbcd4748808f41464cc0e1fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0dd1009dbcd4748808f41464cc0e1fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0dd1009dbcd4748808f41464cc0e1fc"}}, "title": "Fungal and arbuscular mycorrhizal communities unique to old grasslands in a Swedish agricultural landscape", "authors": [{"family": "Casta\u00f1o", "given": "Carles", "initials": "C"}, {"family": "Glimsk\u00e4r", "given": "Anders", "initials": "A"}, {"family": "Hallin", "given": "Sara", "initials": "S"}, {"family": "Maaroufi", "given": "Nadia I", "initials": "NI"}, {"family": "Sk\u00e5nes", "given": "Helle", "initials": "H"}, {"family": "Taylor", "given": "Astrid", "initials": "A"}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE"}], "type": "journal-article", "published": "2025-09-00", "journal": {"title": "Applied Soil Ecology", "issn": "0929-1393", "volume": "213", "pages": "106233", "issn-l": null}, "abstract": null, "doi": "10.1016/j.apsoil.2025.106233", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:42:00.613Z", "modified": "2025-11-28T10:42:00.617Z"}, {"entity": "publication", "iuid": "7168698f97694d46ba7aae5af6601e25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7168698f97694d46ba7aae5af6601e25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7168698f97694d46ba7aae5af6601e25"}}, "title": "Evaluation of TRPA1 as a Therapeutic Target in MYCN-Amplified Neuroblastoma.", "authors": [{"family": "Seger", "given": "Alexandra", "initials": "A", "orcid": "0000-0003-3191-5302", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfcd0a0a226c417eac8e0a48eedd4e7c.json"}}, {"family": "Adami\u010d", "given": "Dora", "initials": "D"}, {"family": "Olmos", "given": "Erick Muci\u00f1o", "initials": "EM"}, {"family": "Nilsson", "given": "Johannes", "initials": "J", "orcid": "0009-0004-3976-526X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1c6ff03f6da452e9bb867a959d84ab8.json"}}, {"family": "Granados-Aparici", "given": "Sofia", "initials": "S"}, {"family": "Vieco-Marti", "given": "Isaac", "initials": "I"}, {"family": "Esfandyari", "given": "Javanshir", "initials": "J"}, {"family": "Engstr\u00f6m", "given": "Matilda", "initials": "M"}, {"family": "Martinez", "given": "Julia", "initials": "J", "orcid": "0009-0004-4050-8439", "researcher": {"href": "https://publications.scilifelab.se/researcher/702e1de02611472097fd90ea328a0630.json"}}, {"family": "Ma\u00f1as", "given": "Adriana", "initials": "A", "orcid": "0000-0002-6955-1754", "researcher": {"href": "https://publications.scilifelab.se/researcher/7220571c605044f980abf2933374aa1a.json"}}, {"family": "Navarro", "given": "Samuel", "initials": "S"}, {"family": "Noguera", "given": "Rosa", "initials": "R"}, {"family": "Aaltonen", "given": "Kristina", "initials": "K", "orcid": "0000-0001-5104-735X", "researcher": {"href": "https://publications.scilifelab.se/researcher/68a63e2719d246a99fc51e8e3ed05cee.json"}}, {"family": "Bexell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9426-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda650768a264d93a80f40da6cb8d7e1.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Pediatr Blood Cancer", "issn": "1545-5017", "volume": "72", "issue": "9", "pages": "e31875", "issn-l": "1545-5009"}, "abstract": "Neuroblastoma (NB) is a childhood cancer with a high relapse rate despite intensive treatment. TRPA1 is a pain-sensing ion channel with downstream impacts on proliferative and pro-apoptotic pathways. Here, we evaluated TRPA1 expression in NB and performed pharmacological inhibition in preclinical models to assess its potential as a therapeutic target in NB.\n\nTRPA1 protein levels were assessed in NB patient tumors on tissue microarrays. Bulk and single-cell gene expression data were retrieved from publicly available databases. The effects of three TRPA1 inhibitors (AP-18, A967079, and Bay 390) on NB cell viability and cell death were evaluated using NB patient-derived xenograft (PDX)-derived organoids. In vivo testing was performed in a MYCN-amplified NB PDX model. Drug combination testing was performed using combination or sequential treatments and evaluated using drug synergy scores.\n\nTRPA1 is widely expressed in NB patient tumors and preclinical patient-derived NB models. Pharmacological TRPA1 inhibition decreased NB cell viability and increased cell death. In vivo TRPA1 inhibition alone did not significantly affect NB tumor growth. Pretreatment with TRPA1 inhibition prior to chemotherapy resulted in synergistic effects in vitro.\n\nTRPA1 is expressed in NB tumors, and pharmacological TRPA1 inhibition can be effective in vitro and synergistic when used as pretreatment to chemotherapy. However, the tested inhibitors did not show in vivo efficacy, at least as monotherapy.", "doi": "10.1002/pbc.31875", "pmid": "40556352", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:40:42.039Z", "modified": "2025-11-28T10:40:42.266Z"}, {"entity": "publication", "iuid": "b0aa84ad1a984c4d8b3eb1996eddfbe1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0aa84ad1a984c4d8b3eb1996eddfbe1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0aa84ad1a984c4d8b3eb1996eddfbe1"}}, "title": "Disease-specific U1 spliceosomal RNA mutations in mature B-cell neoplasms.", "authors": [{"family": "Nadeu", "given": "Ferran", "initials": "F", "orcid": "0000-0003-2910-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4654f6b3cd74ddfb4d859edff5fbc95.json"}}, {"family": "Shuai", "given": "Shimin", "initials": "S", "orcid": "0000-0002-9527-8018", "researcher": {"href": "https://publications.scilifelab.se/researcher/31c2a26041304b0390208fac7884e36c.json"}}, {"family": "Clot", "given": "Guillem", "initials": "G", "orcid": "0000-0003-2588-7413", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6a4380b01f4aa9a2fab0f19a0d34d9.json"}}, {"family": "Hilton", "given": "Laura K", "initials": "LK", "orcid": "0000-0002-6413-6586", "researcher": {"href": "https://publications.scilifelab.se/researcher/cebd0963fd1b4f7a836b380f3cb8a22d.json"}}, {"family": "Diaz-Navarro", "given": "Ander", "initials": "A"}, {"family": "Mart\u00edn", "given": "Silvia", "initials": "S"}, {"family": "Royo", "given": "Romina", "initials": "R"}, {"family": "Baumann", "given": "Tycho", "initials": "T"}, {"family": "Kulis", "given": "Marta", "initials": "M"}, {"family": "L\u00f3pez-Oreja", "given": "Irene", "initials": "I"}, {"family": "Cossio", "given": "Manuel", "initials": "M"}, {"family": "Lu", "given": "Junyan", "initials": "J", "orcid": "0000-0002-9211-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/08813991edd84a809d5a3e0e0bfaaa2e.json"}}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Young", "given": "Emma", "initials": "E"}, {"family": "Plevova", "given": "Karla", "initials": "K", "orcid": "0000-0002-6148-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a6c579cb91f4096a7f8a9143262ce9b.json"}}, {"family": "Knisbacher", "given": "Binyamin A", "initials": "BA"}, {"family": "Lin", "given": "Ziao", "initials": "Z"}, {"family": "Hahn", "given": "Cynthia K", "initials": "CK"}, {"family": "Bousquets", "given": "Pablo", "initials": "P", "orcid": "0000-0002-2969-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e3865ff15a94e8abfc95c039825adac.json"}}, {"family": "Alcoceba", "given": "Miguel", "initials": "M", "orcid": "0000-0002-3819-4846", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb06b84631cf4a259476737674499d1c.json"}}, {"family": "Gonz\u00e1lez", "given": "Marcos", "initials": "M"}, {"family": "Colado", "given": "Enrique", "initials": "E", "orcid": "0000-0001-8675-8207", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9a05ff8f434fbe81d1227335f431ae.json"}}, {"family": "Payer", "given": "\u00c1ngel R", "initials": "\u00c1R"}, {"family": "Aymerich", "given": "Marta", "initials": "M"}, {"family": "Terol", "given": "Mar\u00eda J", "initials": "MJ"}, {"family": "Rivas-Delgado", "given": "Alfredo", "initials": "A"}, {"family": "Enjuanes", "given": "Anna", "initials": "A"}, {"family": "Ruiz-Gasp\u00e0", "given": "S\u00edlvia", "initials": "S"}, {"family": "Chatzikonstantinou", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4105-1253", "researcher": {"href": "https://publications.scilifelab.se/researcher/428007841de74249a101c9cc5182cd5e.json"}}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a683cea1874ac290d91c325a648be8.json"}}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Stranska", "given": "Kamila", "initials": "K", "orcid": "0000-0001-7678-1163", "researcher": {"href": "https://publications.scilifelab.se/researcher/130a65c3d64a4c57bbd619d7dc033b45.json"}}, {"family": "Doubek", "given": "Michael", "initials": "M", "orcid": "0000-0002-1269-6282", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b574229235d455890fd703d2c722a17.json"}}, {"family": "van Gastel-Mol", "given": "Ellen J", "initials": "EJ"}, {"family": "Davis", "given": "Zadie", "initials": "Z"}, {"family": "Walewska", "given": "Renata", "initials": "R"}, {"family": "Scarf\u00f2", "given": "Lydia", "initials": "L", "orcid": "0000-0002-0844-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/47c4c336efb24d86b41c872d03836c78.json"}}, {"family": "Trentin", "given": "Livio", "initials": "L", "orcid": "0000-0003-1222-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/005d6d4e9e294ab7a1d7448c9aae45da.json"}}, {"family": "Visentin", "given": "Andrea", "initials": "A", "orcid": "0000-0003-0271-7200", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f11f2e170b04d83a4d0f0ee3fbffdec.json"}}, {"family": "Parikh", "given": "Sameer A", "initials": "SA", "orcid": "0000-0002-3221-7314", "researcher": {"href": "https://publications.scilifelab.se/researcher/88e9511c65bb4c069a0fbeb9d1f46872.json"}}, {"family": "Rabe", "given": "Kari G", "initials": "KG", "orcid": "0000-0002-7313-1875", "researcher": {"href": "https://publications.scilifelab.se/researcher/107eb83790e54331b7069c5eda2e2303.json"}}, {"family": "Moia", "given": "Riccardo", "initials": "R", "orcid": "0000-0001-7393-1138", "researcher": {"href": "https://publications.scilifelab.se/researcher/68e9d84703624f578568c1a2775f3442.json"}}, {"family": "Armand", "given": "Marine", "initials": "M", "orcid": "0000-0001-8906-3128", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d2e8c325db8415cb723a9718d49ae78.json"}}, {"family": "Rossi", "given": "Davide", "initials": "D"}, {"family": "Davi", "given": "Frederic", "initials": "F"}, {"family": "Gaidano", "given": "Gianluca", "initials": "G", "orcid": "0000-0002-4681-0151", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9af4cedf69e47a5a4ecf0da0ed88c8e.json"}}, {"family": "Kay", "given": "Neil E", "initials": "NE", "orcid": "0000-0002-5951-5055", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef074d0fdb0b4070b5216be063317bf8.json"}}, {"family": "Shanafelt", "given": "Tait D", "initials": "TD"}, {"family": "Ghia", "given": "Paolo", "initials": "P", "orcid": "0000-0003-3750-7342", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f24783739d44c7b73a1be28c344a35.json"}}, {"family": "Oscier", "given": "David", "initials": "D"}, {"family": "Langerak", "given": "Anton W", "initials": "AW", "orcid": "0000-0002-2078-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/769a5b06013b43d6af8d3e13804cd50c.json"}}, {"family": "Be\u00e0", "given": "S\u00edlvia", "initials": "S", "orcid": "0000-0001-7192-2385", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c087ad28194469892e86a69bdd4bab.json"}}, {"family": "L\u00f3pez-Guillermo", "given": "Armando", "initials": "A"}, {"family": "Neuberg", "given": "Donna", "initials": "D", "orcid": "0000-0003-2566-3145", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2f9cbb622f040bebdfcb68657035be1.json"}}, {"family": "Wu", "given": "Catherine J", "initials": "CJ", "orcid": "0000-0002-3348-5054", "researcher": {"href": "https://publications.scilifelab.se/researcher/049091c641354ab2855757db72404195.json"}}, {"family": "Getz", "given": "Gad", "initials": "G", "orcid": "0000-0002-0936-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/974b292190aa40c4a3b0c1d7ab735376.json"}}, {"family": "Pospisilova", "given": "Sarka", "initials": "S", "orcid": "0000-0001-7136-2680", "researcher": {"href": "https://publications.scilifelab.se/researcher/241cf7f1344c4016b40dfcf439c0b43d.json"}}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K", "orcid": "0000-0001-8529-640X", "researcher": {"href": "https://publications.scilifelab.se/researcher/772756566c154559b2c70c8f0f44d1ad.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}, {"family": "Huber", "given": "Wolfgang", "initials": "W"}, {"family": "Zenz", "given": "Thorsten", "initials": "T", "orcid": "0000-0001-7890-9845", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f6b107b1ec94de7bbc260f92f2dcc9f.json"}}, {"family": "Colomer", "given": "Dolors", "initials": "D", "orcid": "0000-0001-7486-8484", "researcher": {"href": "https://publications.scilifelab.se/researcher/0747c24c7c744799b7f0e73147dbbd05.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 I", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/06ccbd6b7051490fb2764ce9da7a418e.json"}}, {"family": "Delgado", "given": "Julio", "initials": "J", "orcid": "0000-0002-5157-4376", "researcher": {"href": "https://publications.scilifelab.se/researcher/def9787862d247299e08c4cdbfb6a993.json"}}, {"family": "Morin", "given": "Ryan D", "initials": "RD", "orcid": "0000-0003-2932-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1d13b9d68534df3a8a271742b55b240.json"}}, {"family": "Stein", "given": "Lincoln D", "initials": "LD"}, {"family": "Puente", "given": "Xose S", "initials": "XS", "orcid": "0000-0001-9525-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c757bd329184ea2a2aa9183802fefb1.json"}}, {"family": "Campo", "given": "El\u00edas", "initials": "E", "orcid": "0000-0001-9850-9793", "researcher": {"href": "https://publications.scilifelab.se/researcher/5642afaa4ed648dfabe66194e42bc01b.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "volume": "39", "issue": "9", "pages": "2076-2086", "issn-l": "0887-6924"}, "abstract": "Recurrent mutations in the third base of U1 spliceosomal RNA responsible for marked splicing and expression abnormalities have been described in chronic lymphocytic leukemia (CLL) and some solid tumors. However, the clinical significance of these mutations in large and independent CLL cohorts as well as their presence in other B-cell neoplasms is unknown. Here we characterized U1 mutations in 1670 CLL and 363 mature B-cell lymphomas. We confirmed that the g.3A>C U1 mutation is found in 3.5% of CLL, which conferred rapid disease progression independently of the main biological and clinical prognostic markers of the disease. Additionally, a recurrent g.9C>T mutation was found in 1.5% of CLL causing downstream splicing alterations and associated with adverse prognosis. We also identified a g.4C>T mutation in 10% of diffuse large B-cell lymphomas of the germinal center subtype and a g.7A>G mutation in 30% of EBV-negative Burkitt lymphomas, both of which altered the splicing pattern of multiple genes. This study reveals novel, recurrent, and tumor-specific U1 mutations in mature B-cell neoplasms with biological and prognostic implications, thus establishing U1 as a novel pan-B-cell malignancy driver gene.", "doi": "10.1038/s41375-025-02667-7", "pmid": "40588565", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12380619"}, {"db": "pii", "key": "10.1038/s41375-025-02667-7"}], "notes": [], "created": "2025-09-08T07:17:22.103Z", "modified": "2025-09-08T07:17:23.018Z"}, {"entity": "publication", "iuid": "886e256ac93c46fa8cb72b48aafa37a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/886e256ac93c46fa8cb72b48aafa37a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/886e256ac93c46fa8cb72b48aafa37a9"}}, "title": "Different plasma biomarker patterns associated with coronary atherosclerosis in low- versus high-risk individuals - an observational cross-sectional study.", "authors": [{"family": "Cederstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Lundman", "given": "Pia", "initials": "P"}, {"family": "Alfredsson", "given": "Joakim", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S"}, {"family": "Tornvall", "given": "Per", "initials": "P"}, {"family": "Jernberg", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Atherosclerosis", "issn": "1879-1484", "volume": "408", "pages": "120457", "issn-l": "0021-9150"}, "abstract": "Targeted omics techniques can be used to identify systemic blood biomarkers associated with coronary artery disease (CAD) and cardiovascular disease (CVD) events. Our aim was to study associations between plasma protein, metabolite biomarkers and subclinical CAD in a low and a high CVD risk population.\n\nThe Swedish CArdioPulmonary bioImage Study (SCAPIS) was used for inclusion of a study group without a history of atherosclerotic CVD stratified by cardiovascular risk; one low-risk group with a Systematic COronary Risk Evaluation 2 (SCORE2) of less than 5 % and one high-risk group with a SCORE2 above 7.5 %. In a cross-sectional study design, random forest and ordinal logistic regression models were used to analyse the relative importance of 409 proteins and metabolites for associations with the degree of coronary computed tomography angiography-detected subclinical coronary atherosclerosis, measured as coronary artery calcium score (CACS) and number of segments with coronary atherosclerosis (SIS) in the two groups.\n\nIn the low-risk group (n = 2063), branched-chain amino acids were associated with both CACS and SIS, while increased high-density lipoprotein (HDL) metabolites, with the exception of phospholipids, were associated with a lower CACS and SIS. In the high-risk group (n = 576), proteins involved in inflammatory processes showed negative associations with coronary atherosclerosis, while HDL metabolites did not show any protective effect. Renin and MMP12 were associated with subclinical CAD in both groups.\n\nDifferent plasma biomarker patterns associated with subclinical CAD (CACS and SIS) were identified in individuals with a low and a high CVD risk, which could be used to better understand protective and risk factors for CAD in primary prevention.", "doi": "10.1016/j.atherosclerosis.2025.120457", "pmid": "40729956", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9150(25)01355-3"}], "notes": [], "created": "2025-11-25T19:21:52.893Z", "modified": "2025-11-25T19:21:52.910Z"}, {"entity": "publication", "iuid": "907f0329d23245f887f3affd6c3c15d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/907f0329d23245f887f3affd6c3c15d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/907f0329d23245f887f3affd6c3c15d1"}}, "title": "Differences in inflammation biomarkers between patients with paroxysmal and persistent atrial fibrillation in the femoral vein and coronary sinus blood samples; a cohort study.", "authors": [{"family": "Valera Soria", "given": "Carlos", "initials": "C", "orcid": "0009-0000-9016-2924", "researcher": {"href": "https://publications.scilifelab.se/researcher/70fa02bee8884ce7b11face980c70edb.json"}}, {"family": "Carlh\u00e4ll", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0003-2198-9690", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9181ecd6ffc49f796475dd261b7c8af.json"}}, {"family": "Karlsson", "given": "Lars O", "initials": "LO", "orcid": "0000-0003-4852-3065", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bc038ac8bd45228000b22416019613.json"}}, {"family": "Lindb\u00e4ck", "given": "Johan", "initials": "J", "orcid": "0000-0002-6473-8798", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cea1044231d40b5a3bf186485d97cd4.json"}}, {"family": "Hijazi", "given": "Ziad", "initials": "Z", "orcid": "0000-0002-7420-743X", "researcher": {"href": "https://publications.scilifelab.se/researcher/03d1c858fbab4b7d9c9574adf5ad51af.json"}}, {"family": "Charitakis", "given": "Emmanouil", "initials": "E", "orcid": "0000-0002-2514-5324", "researcher": {"href": "https://publications.scilifelab.se/researcher/f74e5bef9c884d7781d01a6ff6acfd61.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Eur Heart J Open", "issn": "2752-4191", "volume": "5", "issue": "5", "pages": "oeaf089", "issn-l": null}, "abstract": "The association between inflammation and atrial fibrillation (AF) is evident, but assessing the specific inflammatory pathways involved in the pathogenesis remains complex. This study aimed to identify inflammatory biomarkers associated with paroxysmal (PAF) and persistent (PeAF) AF by evaluating blood samples from the intra- and extracardiac space.\n\nThis is an observational, cross-sectional, single-centre study. A total of 92 inflammatory biomarkers were analyzed from blood samples taken from the coronary sinus (CS) and the femoral vein (FV) in 88 patients with AF who had been referred for catheter ablation at the Link\u00f6ping University Hospital, Sweden. The concentrations of the biomarkers were compared between PAF and PeAF patients in the CS and FV. Significant differences in concentration were found in 36 of 92 biomarkers. Among these, 12 proteins stand out for exhibiting a higher concentration in PeAF patients: Interleukin 6 (IL-6), CUB domain-containing protein 1 (CDCP1), Interleukin 18 receptor 1 (IL-18R1) and cystatin D (CST5) in the FV, \u03b2 nerve growth factor (\u03b2-NGF) and tissue growth factor \u03b1 (TGF-\u03b1) at the CS level, as well as interleukin 18 (IL-18), chemokine ligand 3 (CCL-3) and tumour necrosis factor superfamily 14 (TNFSF-14) in both FV and CS. Moreover, chemokine ligand 25 (CCL-25), chemokine ligand 28 (CCL-28), and artemin (ARTN) were found at a higher concentration in the CS in the overall population.\n\nThis study supports the involvement of TNFSF-14, IL-6, and IL-18 in the pathogenesis and maintenance of PeAF. Furthermore, it identifies \u03b2-NGF and TGF-\u03b1 as potential participants in the pathogenesis and/or maintenance of PeAF locally in the atria. Novel inflammatory biomarkers, mainly chemokines, are also identified as possibly involved in the pathophysiology of AF.", "doi": "10.1093/ehjopen/oeaf089", "pmid": "40980715", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12448471"}, {"db": "pii", "key": "oeaf089"}], "notes": [], "created": "2025-11-25T19:21:54.951Z", "modified": "2025-11-25T19:21:55.162Z"}, {"entity": "publication", "iuid": "9d21fed99d724073b273c4111d795658", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d21fed99d724073b273c4111d795658.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d21fed99d724073b273c4111d795658"}}, "title": "Data-Driven Cluster Analysis of Cerebrospinal Fluid Proteome and Associations with Clinical Phenotypes in Systemic Lupus Erythematosus.", "authors": [{"family": "Grenmyr", "given": "Elsa", "initials": "E", "orcid": "0009-0001-2638-401X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a444ccb93e41482b89fc5701e9d1f112.json"}}, {"family": "Zervides", "given": "Kristoffer", "initials": "K", "orcid": "0000-0003-4311-1635", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d3d97e5524f4b96b9c1eec6a3046ad4.json"}}, {"family": "Najibi", "given": "Seyed Morteza", "initials": "SM", "orcid": "0000-0001-6756-508X", "researcher": {"href": "https://publications.scilifelab.se/researcher/57edb80d12c241ac81cee27e914bcc31.json"}}, {"family": "Gullstrand", "given": "Birgitta", "initials": "B", "orcid": "0000-0002-9172-990X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53a3099cf6d14f9e8a9cec8e6f305761.json"}}, {"family": "Welinder", "given": "Charlotte", "initials": "C", "orcid": "0000-0001-9626-0576", "researcher": {"href": "https://publications.scilifelab.se/researcher/924dc427398e4ba7b31eb5b4b47a89ca.json"}}, {"family": "Nystedt", "given": "Jessika", "initials": "J", "orcid": "0000-0002-7193-1828", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ca2947d930a471eb7fa23c622b7a5bb.json"}}, {"family": "Nilsson", "given": "Petra C", "initials": "PC"}, {"family": "Sundgren", "given": "Pia C", "initials": "PC", "orcid": "0000-0001-9237-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7c755205abb4ecfabb3d5f021b7a1f6.json"}}, {"family": "Kahn", "given": "Robin", "initials": "R", "orcid": "0000-0002-3167-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f81ea4fa0314830a81ceec70ec188da.json"}}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A", "orcid": "0000-0002-4418-5786", "researcher": {"href": "https://publications.scilifelab.se/researcher/894f8618182f401dafa8071e75ca57fa.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "ACR Open Rheumatol", "issn": "2578-5745", "volume": "7", "issue": "9", "pages": "e70089", "issn-l": null}, "abstract": "To explore the cerebrospinal fluid (CSF) proteome in systemic lupus erythematosus (SLE) and the associations between the CSF proteomic patterns and clinical manifestations.\n\nCSF samples from 29 female outpatients with SLE were analyzed with label-free liquid chromatography tandem mass spectrometry. Inclusion and CSF collection were conducted irrespective of clinical manifestations and disease duration. Proteomic data were used for sample clustering and analyzed for clinical variance. Proteins were clustered using Weighted Gene Co-expression Correlation Network Analysis. Modules were biologically characterized and analyzed for correlation to the clinical dataset.\n\nThree patient clusters were identified. Cluster 1 was characterized by the highest frequency of nephritis, depression, and cognitive dysfunction. Cluster 2 showed the highest frequency of alopecia and Sjogren disease antigen A-antibodies (anti-SSA) and a low frequency of cognitive impairment. Cluster 3 had a higher frequency of autonomic neuropathy and headache. Six protein modules were identified (module 1 [M1]-M6). Modules were characterized by nervous tissue proteins (M1), central nervous system (CNS) lipoproteins (M2), macrophage proteins (M3), plasma proteins (M4), Ig (M5), and intracellular metabolic proteins (M6). M1 and M2 proteins were most abundant in cluster 1 and correlated with nephritis, depression, and cognitive impairment. Increased abundance of M4 and M5 proteins were most distinct in cluster 2 and inversely correlated to cognitive impairment and brain atrophy.\n\nPatients clustered by their CSF proteomic pattern had different disease phenotypes. Nephritis and neuronal damage defined the group with higher levels of neuronal proteins in CSF, which may suggest shared pathogenetic pathways in SLE affecting the kidney and CNS.", "doi": "10.1002/acr2.70089", "pmid": "40874685", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12392285"}], "notes": [], "created": "2025-11-28T10:11:22.816Z", "modified": "2025-11-28T10:11:23.769Z"}, {"entity": "publication", "iuid": "52108fee7c594a488a7c040cda512718", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52108fee7c594a488a7c040cda512718.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52108fee7c594a488a7c040cda512718"}}, "title": "Combinations of BMI and metabolic syndrome and the risk of myocardial infarction, stroke, and heart failure.", "authors": [{"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Elmst\u00e5hl", "given": "S\u00f6lve", "initials": "S"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Titova", "given": "Olga E", "initials": "OE"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Nutr Metab Cardiovasc Dis", "issn": "1590-3729", "volume": "35", "issue": "9", "pages": "104102", "issn-l": null}, "abstract": "The relationship between uncommon phenotypes, such as metabolically healthy obesity and normal weight with metabolic syndrome (MetS), and cardiovascular disease (CVD) risk, remains unclear. We investigated how different combinations of body mass index (BMI) and MetS are associated with overall and specific CVDs and how the number of MetS components influences CVD risk in individuals with obesity.\n\nWe performed separate analyses and a meta-analysis of 36,233 individuals from four Swedish cohorts to assess the risk of incident CVDs across BMI/MetS combinations (normal-weight, overweight or obese/MetS yes or no). Participants were followed for CVDs and death through linkage to the Swedish National Registers. Compared to normal weight without MetS, overweight and obesity without MetS had most pronounced association with the risk of heart failure [multivariable hazard ratios, HR (95 % CI) = 1.37 (1.16-1.63) and 1.85 (1.37-2.48), respectively, p < 0.001]. In obese individuals, the risk of incident CVD (composite endpoint) increased with an increasing number of MetS components, but this relationship was not statistically significant in obese participants without additional MetS components, likely due to the small at-risk group. Normal-weight individuals with MetS had an increased risk of myocardial infarction [HR (95 % CI) 2.0 (1.51-2.64)], p < 0.001, and stroke [HR (95 % CI) 1.63 (1.17-2.28), p = 0.004].\n\nOverweight and obesity without MetS showed a greater impact on the risk of heart failure, whereas normal-weight individuals with MetS had a higher risk of myocardial infarction and stroke. In obese individuals, CVD risk increased as the number of MetS components increased.", "doi": "10.1016/j.numecd.2025.104102", "pmid": "40414765", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0939-4753(25)00256-X"}], "notes": [], "created": "2025-11-28T10:44:15.205Z", "modified": "2025-11-28T10:44:15.221Z"}, {"entity": "publication", "iuid": "663259e242554c7aa13f3a0303e14035", "links": {"self": {"href": "https://publications.scilifelab.se/publication/663259e242554c7aa13f3a0303e14035.json"}, "display": {"href": "https://publications.scilifelab.se/publication/663259e242554c7aa13f3a0303e14035"}}, "title": "Classification of Paediatric Celiac Disease Using RNA Sequencing and Real-Time PCR of Duodenal Biomarkers.", "authors": [{"family": "Bragde", "given": "Hanna Gustafsson", "initials": "HG", "orcid": "0000-0001-9104-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/7192535c27614e7a81122bef9fee9d42.json"}}, {"family": "Almer", "given": "Sven", "initials": "S", "orcid": "0000-0001-9334-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/b22467cf9a68465a93a27b11ace20713.json"}}, {"family": "S\u00f6derman", "given": "Jan", "initials": "J", "orcid": "0000-0001-7505-7210", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e27f9f58384d158dc7bb019e4a97db.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "J. Cell. Mol. Med.", "issn": "1582-4934", "volume": "29", "issue": "18", "pages": "e70854", "issn-l": "1582-1838"}, "abstract": "Celiac disease (CD) diagnosis in children with sub-threshold tissue transglutaminase autoantibody (anti-TG2) levels requires a small intestinal biopsy. Through RNA sequencing and real-time PCR of small intestinal biopsies, gene expression in such children was compared with the expression in children with active CD and anti-TG2 levels above the threshold, and with non-CD children. The study also included CD children with a non-diagnostic first biopsy to explore early gene expression changes in CD. The aim of the study was to explore gene expression in relation to anti-TG2 levels, investigate gene expression in Potential CD, and provide a gene expression profile to aid in CD diagnostics. The results showed that in active CD, expression changes involved genes associated with e.g., immune response, transport, angiogenesis, and epithelial barrier function, with even more pronounced changes of genes associated with cell cycle progression, absorption, lipid and lipoprotein processes, and retinoid metabolism in the active CD group with higher anti-TG2 levels. Gene expression changes in CD children with a non-diagnostic first biopsy showed large inter-individual variations, but in general, gene expressions were associated with many of the same biological contexts as in active CD, including epithelial barrier function. Overall, the results show that gene expression profiling has great potential as a complement to the histopathologic assessment in CD diagnostics, even early in the disease course, but probably cannot be used for prognostic purposes.", "doi": "10.1111/jcmm.70854", "pmid": "40977520", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12451401"}], "notes": [], "created": "2025-09-30T13:39:32.092Z", "modified": "2025-11-28T10:51:11.561Z"}, {"entity": "publication", "iuid": "1c2cfd0400784a32946fd5a6765d6bc5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c2cfd0400784a32946fd5a6765d6bc5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c2cfd0400784a32946fd5a6765d6bc5"}}, "title": "Circulating protein biomarkers and their association with vulnerable plaque characteristics - a PROSPECT II substudy.", "authors": [{"family": "Sharma", "given": "Tania", "initials": "T"}, {"family": "Maehara", "given": "Akiko", "initials": "A"}, {"family": "Maeng", "given": "Michael", "initials": "M"}, {"family": "Kj\u00f8ller-Hansen", "given": "Lars", "initials": "L"}, {"family": "Engstr\u00f8m", "given": "Thomas", "initials": "T"}, {"family": "Ben-Yehuda", "given": "Ori", "initials": "O"}, {"family": "Matsumura", "given": "Mitsuaki", "initials": "M"}, {"family": "Fr\u00f6bert", "given": "Ole", "initials": "O"}, {"family": "Persson", "given": "Jonas", "initials": "J"}, {"family": "Wiseth", "given": "Rune", "initials": "R"}, {"family": "Larsen", "given": "Alf Inge", "initials": "AI"}, {"family": "Koul", "given": "Sasha", "initials": "S"}, {"family": "Rylance", "given": "Rebecca", "initials": "R"}, {"family": "Mintz", "given": "Gary S", "initials": "GS"}, {"family": "Ali", "given": "Ziad A", "initials": "ZA"}, {"family": "James", "given": "Stefan K", "initials": "SK"}, {"family": "Stone", "given": "Gregg W", "initials": "GW"}, {"family": "Erlinge", "given": "David", "initials": "D"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Int J Cardiol Cardiovasc Risk Prev", "issn": "2772-4875", "volume": "26", "pages": "200440", "issn-l": null}, "abstract": "In the PROSPECT-II study, near infrared spectroscopy (NIRS) and intravascular ultrasound (IVUS) was used to characterize atherosclerotic plaques in the coronary arteries. NIRS-derived lipid core burden index (LCBI) and IVUS-derived plaque burden (PB) were able to identify plaques strongly associated with adverse cardiovascular events.\n\nOur aim was to identify biomarkers associated with LCBI or PB in the coronary arteries.\n\n898 patients with recent myocardial infarction underwent percutaneous coronary intervention. Blood samples to analyze plasma levels of 179 proteins associated with cardiovascular disease were procured and a combined NIRS-IVUS catheter was used to analyze the coronary arteries. Adjusted linear regression models were calculated between the biomarkers and the outcomes of interest, adjusted for multiplicity testing. Kaplan-Meier survival curves of biomarkers divided by median were assessed with the log-rank test. Adjusted Cox proportional models were calculated for major adverse cardiovascular events.\n\nA total of 24 proteins were associated with PB and 28 proteins with LCBI. Eight of these biomarkers were associated with both increased pan-coronary LCBI and PB; IL-18R1, CSF-1, VEGFA, EN-RAGE, cathepsin D, PCSK9, transferrin receptor protein 1 and OPN. After adjusting for multiplicity, angiopoietin like 3 (ANGPTL3) retained its association with LCBI, and IL-18R1 and CSF-1 retained their association with PB.\n\nWe were able to identify distinct biomarker patterns associated with PB and LCBI. IL-18R1 and CSF-1 had a strong relationship with PB. ANGPTL3 was associated with lipid rich plaques but not with PB, supporting its role in lipid accumulation and development of vulnerable plaques.", "doi": "10.1016/j.ijcrp.2025.200440", "pmid": "40503438", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12155917"}, {"db": "pii", "key": "S2772-4875(25)00078-9"}], "notes": [], "created": "2025-11-25T19:22:34.304Z", "modified": "2025-11-25T19:22:34.344Z"}, {"entity": "publication", "iuid": "c245dc8469a84cbdb2c65f2c31e9c295", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c245dc8469a84cbdb2c65f2c31e9c295.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c245dc8469a84cbdb2c65f2c31e9c295"}}, "title": "Applying Deep Learning to Quantify Drivers of Long-Term Ecological Change in a Swedish Marine Protected Area.", "authors": [{"family": "Nilsson", "given": "Christian L", "initials": "CL", "orcid": "0009-0005-6356-2152", "researcher": {"href": "https://publications.scilifelab.se/researcher/692506bc15454c6c99126379028d6d6b.json"}}, {"family": "Faurby", "given": "S\u00f8ren", "initials": "S"}, {"family": "Burman", "given": "Emil", "initials": "E"}, {"family": "Germishuys", "given": "Jurie", "initials": "J"}, {"family": "Obst", "given": "Matthias", "initials": "M", "orcid": "0000-0003-0264-9631", "researcher": {"href": "https://publications.scilifelab.se/researcher/03489369c77b4208b48f006a0db3bb84.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "15", "issue": "9", "pages": "e72091", "issn-l": "2045-7758"}, "abstract": "In this study, we trained an object-detection model to classify 17 benthic invertebrate taxa in archived footage of a study site on the northern west coast of Sweden (a wall section of the Koster Fjord) within the Swedish marine protected area Kosterhavet National Park. The model displayed a mean average precision score of 0.738 and was applied to footage from 1997 to 2023, generating a dataset of 72,369 occurrence records. The dataset was used to quantify depth distributions and abundance trends of both individual taxa and functional groups over time. Depth distributions for 15 of 17 taxa occurred at depths \u2265 45 m. Distributions of 11 taxa aligned with empirical observations, and for the remaining six taxa, we propose expanded depth distributions in the area. Abundances over time significantly increased for eight taxa and decreased for five taxa, while the overall community structure throughout the study period shifted toward smaller, more heat-tolerant suspension feeders. We found that temperature preference and size were significant drivers of the observed abundance trends in individual taxa. Community structure was altered by the loss of large, heat-sensitive taxa to greater depths due to increased temperatures. We also observed a strong trend of increasing abundances in the remaining community, including six trawling-sensitive taxa, highlighting the effectiveness of the park's protective measures. To protect key cold-water species, we suggest that current fishery regulations of the national park should be expanded to deeper (colder) waters and that new marine protected areas should also be established in deep waters. Our study demonstrates the application potential of video surveillance combined with deep-learning technology, and we recommend the implementation of standardized video monitoring in marine ecosystem management.", "doi": "10.1002/ece3.72091", "pmid": "40904377", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12404701"}, {"db": "pii", "key": "ECE372091"}], "notes": [], "created": "2025-11-28T10:39:55.103Z", "modified": "2025-11-28T10:39:55.173Z"}, {"entity": "publication", "iuid": "0677b45be8814334a65d2195c9099d8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0677b45be8814334a65d2195c9099d8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0677b45be8814334a65d2195c9099d8c"}}, "title": "Among-individual asynchrony but not genetic diversity is associated with temporal stability of tree growth in natural Quercus robur oak stands.", "authors": [{"family": "Hall", "given": "Marcus", "initials": "M", "orcid": "0000-0002-9556-1235", "researcher": {"href": "https://publications.scilifelab.se/researcher/18148df55a9145a993d4cb287a529519.json"}}, {"family": "Sunde", "given": "Johanna", "initials": "J", "orcid": "0000-0002-3145-1475", "researcher": {"href": "https://publications.scilifelab.se/researcher/972ff747b7044a6096583673286e9443.json"}}, {"family": "Franz\u00e9n", "given": "Markus", "initials": "M"}, {"family": "Forsman", "given": "Anders", "initials": "A", "orcid": "0000-0001-9598-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a605b671cd3414d9c75c2408b74d3de.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "21", "issue": "9", "pages": "20250180", "issn-l": "1744-9561"}, "abstract": "Theory, manipulation experiments and observational studies on biodiversity and ecosystem functioning largely concur that higher intraspecific diversity may increase the overall productivity of populations, buffer against environmental change and stabilize long-term productivity. However, evidence comes primarily from small and short-lived organisms. We tested for effects of genetic diversity on variation in forest growth by combining long-term data on annual individual growth rate (basal area increment (BAI)) with estimates of intrapopulation genetic variation (based on RAD-seq SNPs) for 18 natural Quercus robur pedunculate oak populations. Higher total or adaptive genetic variability of populations was neither associated with faster average growth nor with increased temporal or spatial stability of growth nor with among-individual asynchrony in growth. However, as expected, we found that greater asynchrony of growth responses within the populations increased their temporal stability. Together, these findings point towards a negligible role of genetic variation in structuring growth patterns in natural populations of tree species. Identifying which environmental factors and phenotypic traits (and its genetic basis) contribute to asynchronous growth responses is an important next step towards a better mechanistic understanding of the causes of temporal stability in tree growth and forest productivity.", "doi": "10.1098/rsbl.2025.0180", "pmid": "40925550", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12419903"}], "notes": [], "created": "2025-11-26T08:53:50.190Z", "modified": "2025-11-28T10:50:14.392Z"}, {"entity": "publication", "iuid": "b894c8f51e7b40e7b9e2c3472acdd17e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b894c8f51e7b40e7b9e2c3472acdd17e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b894c8f51e7b40e7b9e2c3472acdd17e"}}, "title": "A novel PML germline variant as a candidate predisposing genetic aberration in familial acute myeloid leukaemia.", "authors": [{"family": "Soussi", "given": "Thierry", "initials": "T", "orcid": "0000-0001-8184-3293", "researcher": {"href": "https://publications.scilifelab.se/researcher/fce7c1391f634a9684352a3c49401939.json"}}, {"family": "Kundu", "given": "Snehangshu", "initials": "S", "orcid": "0000-0003-3541-5583", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fa7619cacd842b6a6151964710315d2.json"}}, {"family": "Gerbaud", "given": "Pauline", "initials": "P"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Baskin", "given": "Berivan", "initials": "B"}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Delhommeau", "given": "Fran\u00e7ois", "initials": "F", "orcid": "0000-0002-4915-0734", "researcher": {"href": "https://publications.scilifelab.se/researcher/c51994ab468649ffb31f061f2a6f8023.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Br. J. Haematol.", "issn": "1365-2141", "volume": "207", "issue": "3", "pages": "1118-1121", "issn-l": "0007-1048"}, "abstract": null, "doi": "10.1111/bjh.20255", "pmid": "40954117", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12436221"}], "notes": [], "created": "2025-11-26T14:14:25.189Z", "modified": "2025-11-26T14:14:25.660Z"}, {"entity": "publication", "iuid": "2023de0c77cb44e4a8e75d4ca4ffc159", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2023de0c77cb44e4a8e75d4ca4ffc159.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2023de0c77cb44e4a8e75d4ca4ffc159"}}, "title": "A Unique Plasma Protein Signature Characterizes Squamous Cell Carcinoma of the Oral Tongue in Young Adults.", "authors": [{"family": "Gu", "given": "Xiaolian", "initials": "X", "orcid": "0000-0002-6574-3628", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b502390466749d18b3985c1930da1e0.json"}}, {"family": "Coates", "given": "Philip J", "initials": "PJ", "orcid": "0000-0003-1518-6306", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f0dd083f0964e72aac9864302cddbc4.json"}}, {"family": "Wang", "given": "Lixiao", "initials": "L"}, {"family": "Gnanasundram", "given": "Sivakumar Vadivel", "initials": "SV"}, {"family": "Sgaramella", "given": "Nicola", "initials": "N"}, {"family": "Attaran", "given": "Nima", "initials": "N"}, {"family": "Erdogan", "given": "Baris", "initials": "B"}, {"family": "Magan", "given": "Mustafa", "initials": "M"}, {"family": "Nylander", "given": "Karin", "initials": "K", "orcid": "0000-0002-4831-4100", "researcher": {"href": "https://publications.scilifelab.se/researcher/62805049d0b040aa8d9559d8bf448302.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "J. Oral Pathol. Med.", "issn": "1600-0714", "volume": "54", "issue": "8", "pages": "706-714", "issn-l": "0904-2512"}, "abstract": "The incidence of squamous cell carcinoma of the oral tongue (SCCOT) among young adults is increasing in several regions of the world. Age-dependent differences in the biology of SCCOT have been suspected.\n\nWe used the Olink Explore 3072 high-throughput platform to comprehensively quantify plasma proteins in 24 young (\u2264 40 years of age) and 50 old (> 50 years of age) individuals. Eight young and 20 old individuals were diagnosed with SCCOT, four young and nine old individuals with SCC at other oral subsites (SCCOO), and the remaining 12 young and 21 old individuals were healthy controls. Dimension reduction analysis, differential expression analysis, and functional enrichment analysis were performed to characterize young patient-specific biological signatures.\n\nPlasma levels of 2923 proteins were obtained. Principal component analysis indicated age-related expression patterns. Comparing young patients to young controls/old patients/old controls, differential abundance analysis showed that increases in protein levels of Peroxiredoxin 2 (PRDX2) and C-C motif chemokine ligand 26 (CCL26) and a decrease in Kallikrein related peptidase 4 (KLK4) were young patient-specific. Reactome pathway enrichment analysis identified \"Cellular response to chemical stress,\" \"Detoxification of reactive oxygen species\" and \"Cellular responses to stimuli\" as the top altered pathways in young patients with SCCOT.\n\nAbnormal cellular stress and aberrant immune regulation could thus be linked to cancer development in young patients. The unique plasma proteomic signature observed in young patients with SCCOT suggests that they constitute a specific group with distinct underlying pathophysiological processes.", "doi": "10.1111/jop.70020", "pmid": "40765509", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12419980"}], "notes": [], "created": "2025-11-25T19:19:06.154Z", "modified": "2025-11-25T19:21:48.766Z"}, {"entity": "publication", "iuid": "71f90935b7b14cb7a1cf3d07923b9c26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71f90935b7b14cb7a1cf3d07923b9c26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71f90935b7b14cb7a1cf3d07923b9c26"}}, "title": "Plasma proteomics in septic shock and alcohol-related pancreatitis: a hyaluronan-centered approach.", "authors": [{"family": "van der Heijden", "given": "Jaap", "initials": "J"}, {"family": "Mazubane", "given": "Asanda", "initials": "A"}, {"family": "Sallisalmi", "given": "Marko", "initials": "M"}, {"family": "Vorontsov", "given": "Egor", "initials": "E"}, {"family": "Tenhunen", "given": "Jyrki", "initials": "J"}, {"family": "Barrueta Tenhunen", "given": "Annelie", "initials": "A"}], "type": "journal article", "published": "2025-08-30", "journal": {"title": "Clin Proteomics", "issn": "1542-6416", "volume": "22", "issue": "1", "pages": "31", "issn-l": null}, "abstract": "Sepsis is a critical condition characterized by a dysregulated immune response to infection. As sepsis develops to septic shock, its most severe form, morbidity and mortality increases. Hyaluronan is a key component of the extracellular matrix and the endothelial glycocalyx. In sepsis, plasma hyaluronan concentrations are increased and correlate with disease severity. In this study we aimed to explore and compare the proteomic profiles of hyaluronan-associated proteins in patients with the dysregulated immune response of septic shock and the sterile inflammation of acute alcohol-related pancreatitis.\n\nThe present study involved proteomic analysis of patients with septic shock (n = 13), pancreatitis (n = 8), and healthy controls (n = 8). LC-MS/MS was conducted for peptide analysis. Hyaluronan-associated proteins were identified using the UniProt REST API, followed by functional and pathway enrichment analyses with GOATOOLS and GSEApy. Statistical analyses, including ANOVA and post hoc tests, were performed using Python and SPSS, with significance set at p < 0.05.\n\nFrom a total sum of 663 detected unique plasma proteins, 15 were identified as hyaluronan-related proteins. Plasma levels of 11/15 proteins separated septic shock from pancreatitis in a statistically significant manner. Between the groups differences were apparent on day 1 (8 proteins in septic shock versus 3 in pancreatitis) and day 4 (6 proteins in septic shock versus 3 in pancreatitis) relative to controls. Functional enrichment analysis revealed associations with extracellular matrix organization, proteolytic enzyme regulation, and hyaluronan metabolism. Notably, members of the inter-alpha-inhibitor family demonstrated distinct patterns, with ITIH3 levels increasing and ITIH1, ITIH2, and ITIH4 levels decreasing in septic shock compared to controls. Additionally, plasma hyaluronidase inhibition correlated positively with ITIH3 levels.\n\nThe present study explored the role of hyaluronan-related proteins in septic shock pathophysiology, revealing potential dysregulation associated with sepsis severity. The decrease in ITIH1, ITIH2 and ITIH4, as compared to the increase in ITIH3, suggest a complex alteration in the protein balance of the I\u03b1I-family in sepsis. Overall, the altered proteomic profile of hyaluronan-related proteins as reflected by the GO terms indicates a complex dysregulation not only in hyaluronan metabolism and extracellular matrix, but also in the regulation of several proteolytic enzymes. Future studies on this area are warranted.", "doi": "10.1186/s12014-025-09556-2", "pmid": "40885913", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12398169"}, {"db": "pii", "key": "10.1186/s12014-025-09556-2"}], "notes": [], "created": "2025-10-23T13:23:19.990Z", "modified": "2025-10-23T13:23:20.025Z"}, {"entity": "publication", "iuid": "97dcd02768fa4b35be175ba383846812", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97dcd02768fa4b35be175ba383846812.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97dcd02768fa4b35be175ba383846812"}}, "title": "Comparative Study of the Mitochondrial Proteome From Mesophyll, Vascular, and Guard Cells in Response to Carbon Starvation.", "authors": [{"family": "Boussardon", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0001-8313-3535", "researcher": {"href": "https://publications.scilifelab.se/researcher/63dace73d3684bf3b48c13b58c5f777f.json"}}, {"family": "Hussain", "given": "Shah", "initials": "S", "orcid": "0000-0003-4977-1167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f9c2bc4a6094b52b13737f26051bbd3.json"}}, {"family": "Keech", "given": "Olivier", "initials": "O", "orcid": "0000-0002-0546-7721", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbfa829eb0b74b67aed7865dda0e15d3.json"}}], "type": "journal article", "published": "2025-08-30", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "5", "pages": "e70465", "issn-l": "0031-9317"}, "abstract": "A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.", "doi": "10.1111/ppl.70465", "pmid": "40873255", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12391860"}], "notes": [], "created": "2025-11-27T13:03:24.119Z", "modified": "2025-11-27T13:03:24.590Z"}, {"entity": "publication", "iuid": "b77d222973e74c0a98eab34c342800bd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b77d222973e74c0a98eab34c342800bd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b77d222973e74c0a98eab34c342800bd"}}, "title": "A plasma protein profile of antidepressant response to omega-3 fatty acids.", "authors": [{"family": "Lindahl", "given": "Jesper", "initials": "J"}, {"family": "Stiernborg", "given": "Miranda", "initials": "M"}, {"family": "Ventorp", "given": "Filip", "initials": "F"}, {"family": "Suneson", "given": "Klara", "initials": "K"}, {"family": "S\u00f6derberg Veib\u00e4ck", "given": "Gustav", "initials": "G"}, {"family": "Tjernberg", "given": "Johanna", "initials": "J"}, {"family": "St\u00e5hl", "given": "Darya", "initials": "D"}, {"family": "Hj\u00e4rn", "given": "Marie", "initials": "M"}, {"family": "Lavebratt", "given": "Catharina", "initials": "C"}, {"family": "Lindqvist", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-08-30", "journal": {"title": "Prog. Neuropsychopharmacol. Biol. Psychiatry", "issn": "1878-4216", "volume": "141", "pages": "111481", "issn-l": "0278-5846"}, "abstract": "Previous studies suggest an antidepressant effect of omega-3 fatty acids (n-3 PUFAs). This effect may be larger in patients with low-grade inflammation, defined as mild elevations of high sensitivity C-reactive protein or other commonly used inflammatory markers. The antidepressant mechanisms of n-3 PUFAs are not fully understood but may involve modulation of immunometabolic processes and neurotrophic effects. Here we investigated inflammatory and cardiometabolic biomarkers in patients with major depressive disorder (MDD) and controls, how these biomarkers change with n-3 PUFA treatment, and their association with antidepressant response.\n\nNinety-four MDD patients were treated with 2.2 g eicosapentaenoic acid, 400 mg docosahexaenoic acid, and 800 mg other omega-3 fatty acids per day, added to stable antidepressant treatment for 8 weeks. Inflammatory and cardiometabolic plasma markers were assayed in MDD patients, before and after n-3 PUFA treatment, and in healthy controls (n = 76) using proximity extension assay technology. Treatment response was defined as \u226550 % reduction on the 17-item Hamilton Depression Rating Scale. Partial least squares discriminant analysis identified plasma proteins with differential levels between patients, controls, responders, and non-responders.\n\nAfter adjusting for relevant covariates and multiple comparisons, baseline levels of several biomarkers associated with immunometabolic functions and neurotrophic processes differed significantly between MDD patients and controls and between n-3 PUFA responders and non-responders. Some of these biomarkers, related to cell-cell communication and neurotrophy, increased significantly with treatment.\n\nThese findings provide new insights into the antidepressant mechanisms of n-3 PUFAs. Consistent with previous reports, we found evidence of pre-treatment immune activation in responders compared to non-responders, which could be used to personalize antidepressant n-3 PUFA treatment.", "doi": "10.1016/j.pnpbp.2025.111481", "pmid": "40882806", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "S0278-5846(25)00235-0"}], "notes": [], "created": "2025-11-25T19:21:44.532Z", "modified": "2025-11-25T19:21:44.554Z"}, {"entity": "publication", "iuid": "6091da69a89748ddb71ea83d5824cd31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6091da69a89748ddb71ea83d5824cd31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6091da69a89748ddb71ea83d5824cd31"}}, "title": "Whole genome transcriptional analysis of intestinal biopsies and blood cells indicate genes involved in antioxidant defense systems, amino acid metabolism and antigen presentation in the pathogenesis of celiac disease.", "authors": [{"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-0504-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcf3474dc7054c598cbe3a195deb8a1b.json"}}, {"family": "Sabbag", "given": "Shafir", "initials": "S"}, {"family": "Abrahamsson", "given": "Sanna", "initials": "S"}, {"family": "Gudj\u00f3nsd\u00f3ttir", "given": "Audur H", "initials": "AH"}, {"family": "Arnell", "given": "Henrik", "initials": "H"}, {"family": "Agardh", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-08-29", "journal": {"title": "BMC Med", "issn": "1741-7015", "volume": "23", "issue": "1", "pages": "507", "issn-l": "1741-7015"}, "abstract": "Celiac disease is associated with HLA-risk haplotypes, but non-HLA genes and environmental factors are also linked to disease susceptibility. In this study, we explore the molecular pathways involved in celiac disease by analyzing the differential expression of genes in both the gut and peripheral blood across various celiac disease phenotypes.\n\nWhole genome RNA sequencing was performed on 283 samples from intestinal mucosa and peripheral blood from 72 cases with either active, potential, or treated celiac disease and 73 disease controls. Enrichr pathway analysis of top differentially expressed genes was performed.\n\nOverall, 7565 genes in intestinal biopsies and 542 genes in blood samples were differentially expressed between cases and controls. Compared with controls, immunoglobulin heavy variable 5-51 (IGHV5-51) (p = 1.05 \u00d7 10-14) and tissue transglutaminase (TGM2) (p = 5.29 \u00d7 10-10), encoding for TG2, the main autoantigen in celiac disease, were two of the top up-regulated genes in intestinal biopsies from celiac cases. TGM2 was also slightly upregulated in blood cells from cases with active disease compared with controls (p = 0.05). The topmost differentially expressed genes in peripheral blood were HLA-DQB1, HLA-DQB2, and GSTM1. Among pathways identified containing transcriptionally differentiated genes were antioxidant defense systems (e.g., nuclear factor (erythroid-derived 2)-like 2 (Nrf2), glutathione, ergothioneine, and peroxisome metabolism), as well as MHC class 1 antigen presentation, amino acid transport, mTORC1, bilirubin and lipid metabolism, liver homeostasis, the complement system, and interferon signaling.\n\nDifferentially expressed genes in cases and controls indicate crosstalk between molecular pathways involved in antioxidant defense, immune regulation, and nutrient signaling in the pathogenesis of celiac disease.", "doi": "10.1186/s12916-025-04261-1", "pmid": "40883722", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12398127"}, {"db": "pii", "key": "10.1186/s12916-025-04261-1"}], "notes": [], "created": "2025-09-08T07:11:35.688Z", "modified": "2025-09-18T07:36:17.364Z"}, {"entity": "publication", "iuid": "588352e9404f4729b0d75cdc614fd16e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/588352e9404f4729b0d75cdc614fd16e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/588352e9404f4729b0d75cdc614fd16e"}}, "title": "Structure of the complete 14-subunit botulinum neurotoxin B complex reveals a unique anchoring through the narrow central pore of HA70.", "authors": [{"family": "Kr\u010d", "given": "Ajda", "initials": "A", "orcid": "0009-0007-5842-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/cda5c360c20149279692c5d69df7a694.json"}}, {"family": "Ko\u0161enina", "given": "Sara Persson", "initials": "SP", "orcid": "0000-0001-7893-0249", "researcher": {"href": "https://publications.scilifelab.se/researcher/9370d4ecf19c438bb205c43c23f94f26.json"}}, {"family": "Nowakowska", "given": "Maria B", "initials": "MB", "orcid": "0000-0003-2592-2442", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d7fb5e257e941fd8738d9ff147d6b61.json"}}, {"family": "Masuyer", "given": "Geoffrey", "initials": "G", "orcid": "0000-0002-9527-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/41dcc0806dba4a56bb04725812f3a000.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}], "type": "journal article", "published": "2025-08-29", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "35", "pages": "eadx5058", "issn-l": "2375-2548"}, "abstract": "Botulinum neurotoxin serotype B1 (BoNT/B) is a highly potent neurotoxin and therapeutic agent. Here, we present the structure of the complete 14-subunit (780 kDa) progenitor toxin complex (L-PTC) and of five subcomplexes. The structures show how the toxin interacts with its associated components in their role to protect and deliver BoNT/B across epithelial barriers. Each subcomplex, including the M-PTC, M-PTC-HA70, NTNH-HA70, and HA70 trimer, provides detailed understanding of the assembly mechanism, in which the NTNH-nLoop adopts a unique fold that locks the M-PTC into a central pore formed by HA70. The HA subcomplex presents a tripod architecture with flexible legs that may adapt to the rugged cell surface. Mass photometry reveals the pH dependence of BoNT/B release from the complex which is unexpectedly influenced by the presence of HA70. This study provides the complete L-PTC structure, offering insights into its assemblage and supporting the development of countermeasures and therapeutic applications.", "doi": "10.1126/sciadv.adx5058", "pmid": "40864696", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12383256"}], "notes": [], "created": "2025-09-03T12:07:51.156Z", "modified": "2025-11-24T10:54:02.699Z"}, {"entity": "publication", "iuid": "a572b67791f3483dbb7abb241e1938d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a572b67791f3483dbb7abb241e1938d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a572b67791f3483dbb7abb241e1938d3"}}, "title": "An Anti\u2010Myd88 Peptide Synergistically Enhances the Anti\u2010Inflammatory Effects of Extracellular Vesicles from Na\u00efve Umbilical Cord MSC or HEK293F CD24 Overexpressing Cells", "authors": [{"family": "Abas", "given": "Bur\u00e7in \u0130rem", "initials": "B\u0130", "orcid": "0000-0002-1018-5577", "researcher": {"href": "https://publications.scilifelab.se/researcher/941e021f937f43edab7eaed4003cbf7e.json"}}, {"family": "Bergqvist", "given": "Markus", "initials": "M", "orcid": "0009-0003-5716-3716", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d33e374d0642479a80683a989f095a.json"}}, {"family": "Yu", "given": "Lijuan", "initials": "L", "orcid": "0000-0003-3558-3800", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b0b4ca8553144b19c236bc09c1c9b81.json"}}, {"family": "Wang", "given": "Yi", "initials": "Y", "orcid": "0000-0002-4954-6317", "researcher": {"href": "https://publications.scilifelab.se/researcher/272a124e437a4787a233f9010f1b097f.json"}}, {"family": "Gimona", "given": "Mario", "initials": "M", "orcid": "0000-0002-2242-2015", "researcher": {"href": "https://publications.scilifelab.se/researcher/b34548020ae94f38872dc7c79cd44b76.json"}}, {"family": "Park", "given": "Kyong\u2010su", "initials": "K", "orcid": "0000-0003-0902-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e308b29fe144b49f4db27f4b819c18.json"}}, {"family": "L\u00f6tvall", "given": "Jan", "initials": "J", "orcid": "0000-0001-9195-9249", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cbcaf6b5698411c92e0de9e8fcf390f.json"}}], "type": "journal-article", "published": "2025-08-29", "journal": {"title": "Adv Materials Inter", "issn": "2196-7350", "issn-l": null}, "abstract": null, "doi": "10.1002/admi.202500252", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-05T13:25:34.023Z", "modified": "2025-11-05T13:25:34.577Z"}, {"entity": "publication", "iuid": "e3c4916f5c6c4103a058b9d484952882", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3c4916f5c6c4103a058b9d484952882.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3c4916f5c6c4103a058b9d484952882"}}, "title": "Structural and biochemical basis for activity of Aspergillus nidulans \u03b1-1,3-glucanases from glycoside hydrolase family 71", "authors": [{"family": "Mazurkewich", "given": "Scott", "initials": "S", "orcid": "0000-0002-9238-0615", "researcher": {"href": "https://publications.scilifelab.se/researcher/39a1e4f9d3a74121937087f8875a975a.json"}}, {"family": "Wid\u00e9n", "given": "Tove", "initials": "T", "orcid": "0009-0001-6830-9608", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cc9e7875b5a43f7b41f9b95a65d9634.json"}}, {"family": "Karlsson", "given": "Hampus", "initials": "H"}, {"family": "Even\u00e4s", "given": "Lars", "initials": "L", "orcid": "0000-0002-6580-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d5546ed87b0480aae72d8574db96911.json"}}, {"family": "Ramamohan", "given": "Poornima", "initials": "P"}, {"family": "Wohlert", "given": "Jakob", "initials": "J"}, {"family": "Br\u00e4nd\u00e9n", "given": "Gisela", "initials": "G", "orcid": "0000-0001-5615-7187", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0bd1188c26448398026757fef34469f.json"}}, {"family": "Larsbrink", "given": "Johan", "initials": "J", "orcid": "0000-0001-8386-2914", "researcher": {"href": "https://publications.scilifelab.se/researcher/99badc395dbc46d1a43ae5c3d39fd8aa.json"}}], "type": "journal-article", "published": "2025-08-28", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "issn-l": "2399-3642"}, "abstract": null, "doi": "10.1038/s42003-025-08696-3", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:05:25.939Z", "modified": "2025-11-27T08:05:26.165Z"}, {"entity": "publication", "iuid": "8e45f7b6f0c546ee93553d78ecbf4c23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e45f7b6f0c546ee93553d78ecbf4c23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e45f7b6f0c546ee93553d78ecbf4c23"}}, "title": "Morphological cell profiling for drug repurposing against SARS-CoV-2 infection", "authors": [{"family": "Asp", "given": "Elin", "initials": "E", "orcid": "0009-0006-6794-0779", "researcher": {"href": "https://publications.scilifelab.se/researcher/38e711145de94b0ba2e0a1891747a134.json"}}, {"family": "Rietdijk", "given": "Jonne", "initials": "J"}, {"family": "Tampere", "given": "Marianna", "initials": "M", "orcid": "0000-0001-5744-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c6c86cb20394d17abebb40db23407c8.json"}}, {"family": "Axelsson", "given": "Hanna", "initials": "H", "orcid": "0000-0003-2365-1749", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b88c4d11c443f39121c6d93fcff1f0.json"}}, {"family": "Njenda", "given": "Duncan", "initials": "D", "orcid": "0000-0001-8276-9726", "researcher": {"href": "https://publications.scilifelab.se/researcher/c14c27f4d60549da9949c97ed66a15b5.json"}}, {"family": "Potdar", "given": "Swapnil", "initials": "S", "orcid": "0000-0002-2778-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/f298f1f4f73048ab9266e9f5a0ab83da.json"}}, {"family": "Kalman", "given": "Adelinn", "initials": "A"}, {"family": "Georgieva", "given": "Polina", "initials": "P", "orcid": "0000-0001-8326-4738", "researcher": {"href": "https://publications.scilifelab.se/researcher/394f19ff3cff4b1c94d0a9a92e976b73.json"}}, {"family": "Lapins", "given": "Maris", "initials": "M"}, {"family": "Ballante", "given": "Flavio", "initials": "F", "orcid": "0000-0002-4831-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/20429d2a46f4479a9c262875794a3a9d.json"}}, {"family": "Soler", "given": "Alicia", "initials": "A"}, {"family": "de Kort", "given": "Martin", "initials": "M", "orcid": "0000-0002-7264-5436", "researcher": {"href": "https://publications.scilifelab.se/researcher/016a2e73e1254b84aeb5898e8a026f1b.json"}}, {"family": "Aittokallio", "given": "Tero", "initials": "T", "orcid": "0000-0002-0886-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/47e0db692d16440ea6779948c188713a.json"}}, {"family": "Zaliani", "given": "Andrea", "initials": "A"}, {"family": "Kuzikov", "given": "Maria", "initials": "M"}, {"family": "Gribbon", "given": "Philip", "initials": "P"}, {"family": "Lo", "given": "Donald", "initials": "D"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications.scilifelab.se/researcher/28ad5f6a1a064e52aca72780adc4bb96.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4645bc97a8024c548111802101b83571.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0001-5501-466X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0461a910ec4b4faa8668bb4044e76f61.json"}}], "type": "posted-content", "published": "2025-08-28", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.08.28.672794", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T11:34:50.011Z", "modified": "2025-12-18T19:09:56.756Z"}, {"entity": "publication", "iuid": "4a8447758bec4df191ec729e256f9f34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a8447758bec4df191ec729e256f9f34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a8447758bec4df191ec729e256f9f34"}}, "title": "De novo transcriptome assembly and annotation of the common freshwater amphipod (Gammarus pulex) a valuable resource for ecotoxicogenomics.", "authors": [{"family": "Escobar-Sierra", "given": "Camilo", "initials": "C", "orcid": "0000-0001-9105-4378", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed2b3eb0232f48d0ad3c685d72abd35a.json"}}, {"family": "Hassan", "given": "Sameer", "initials": "S"}, {"family": "Weichert", "given": "Fabian G", "initials": "FG"}, {"family": "Aronsson", "given": "Henrik", "initials": "H"}, {"family": "Lampert", "given": "Kathrin P", "initials": "KP"}, {"family": "Hollert", "given": "Henner", "initials": "H"}, {"family": "Backhaus", "given": "Thomas", "initials": "T"}, {"family": "Inostroza", "given": "Pedro A", "initials": "PA", "orcid": "0000-0001-7399-8308", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cea8a42ffc2454d86f5f829b5dd7eff.json"}}], "type": "dataset", "published": "2025-08-28", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "1502", "issn-l": "2052-4463"}, "abstract": "This study presents de novo transcriptome assemblies for Gammarus pulex, a freshwater amphipod widely used in ecotoxicology due to its ecological importance and sensitivity to pollution. Specimens were collected from 13 river sites in Germany and Sweden, encompassing a gradient of micropollutant exposure. Using high-throughput RNA sequencing, we generated transcriptomes for German, Swedish, and combined populations. The assemblies yielded up to 170,000 transcripts with strong metrics, including N50 values over 1,500 base pairs and completeness scores approaching 89%. Functional annotation revealed over 123,000 unique protein hits, nearly 99,000 BLASTx matches, and approximately 30,000 annotated KEGG pathways. We also identified thousands of conserved domains, signal peptides, and transmembrane proteins. These comprehensive resources provide valuable molecular insight into the stress responses of Gammarus pulex and will facilitate the development of gene-based biomarkers for freshwater monitoring. By improving the molecular toolkit for this key sentinel species, our study supports broader applications of ecotoxicogenomics in environmental assessment and conservation.", "doi": "10.1038/s41597-025-05872-2", "pmid": "40877247", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12394684"}, {"db": "pii", "key": "10.1038/s41597-025-05872-2"}], "notes": [], "created": "2025-11-28T10:46:48.868Z", "modified": "2025-11-28T10:46:48.977Z"}, {"entity": "publication", "iuid": "b287cd082dda431aa1c239aa37ea3454", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b287cd082dda431aa1c239aa37ea3454.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b287cd082dda431aa1c239aa37ea3454"}}, "title": "Spatial TCR clonality and clonal expansion in the in situ microenvironment of non-small cell lung cancer.", "authors": [{"family": "Yu", "given": "Hui", "initials": "H", "orcid": "0009-0000-0563-3243", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd698620e64b64949a408b5c2c6a22.json"}}, {"family": "Magoulopoulou", "given": "Anastasia", "initials": "A"}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM"}, {"family": "Chatzinikolaou", "given": "Maria Paraskevi", "initials": "MP"}, {"family": "Horie", "given": "Masafumi", "initials": "M"}, {"family": "Lindberg", "given": "Amanda", "initials": "A"}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A"}, {"family": "Backman", "given": "Max", "initials": "M"}, {"family": "Metousis", "given": "Andreas", "initials": "A"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Marincevic", "given": "Millaray", "initials": "M"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Mattsson", "given": "Johanna Sofia Margareta", "initials": "JSM"}, {"family": "K\u00e4rre", "given": "Klas", "initials": "K"}, {"family": "Leandersson", "given": "Karin", "initials": "K"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Strell", "given": "Carina", "initials": "C"}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "J Immunother Cancer", "issn": "2051-1426", "volume": "13", "issue": "8", "issn-l": null}, "abstract": "T-cell activation and clonal expansion are essential to effective immunotherapy responses in non-small cell lung cancer (NSCLC). The distribution of T-cell clones may offer insights into immunogenic mechanisms and imply potential prognostic and predictive information.\n\nWe analyzed \u03b1/\u03b2 T-cell receptor (TCR) clonality using RNA-sequencing of bulk frozen tumor tissue from 182 patients with NSCLC. The data was integrated with molecular and clinical characteristics, extensive in situ imaging, and spatial sequencing of the tumor immune microenvironment. TCR clonality was also determined in an independent cohort of nine patients with immune checkpoint-treated NSCLC.\n\nTCR clonality (Gini index) patterns ranged from high T-cell clone diversity with high evenness (low Gini index) to clonal dominance with low evenness (high Gini index). Generally, TCR clonality in cancer was lower than in matched normal lung parenchyma distant from the tumor (p=0.021). The TCR clonality distribution between adenocarcinoma and squamous cell carcinoma was similar; however, smokers showed a higher Gini index. While in the operated patient with NSCLC cohort, TCR clonality was not prognostic, in an immune checkpoint inhibitor-treated cohort, high TCR clonality was associated with better therapy response (p=0.016) and prolonged survival (p=0.003, median survival 13.8 vs 2.9 months). On the genomic level, a higher Gini index correlated strongly with a lower frequency of epidermal growth factor receptor (EGFR) and adenomatous polypsis coli (APC) gene mutations, but a higher frequency of P53 mutations, and a higher tumor mutation burden. In-depth characterization of the tumor tissue revealed that high TCR clonality was associated with an activated, inflamed tumor phenotype (PRF1, GZMA, GZMB, INFG) with exhaustion signatures (LAG3, TIGIT, IDO1, PD-1, PD-L1). Correspondingly, PD-1+, CD3+, CD8A+, CD163+, and CD138+immune cells infiltrated cancer tissue with high TCR clonality. In situ sequencing recovered single dominant T-cell clones within the patient tumor tissue, which were predominantly of the CD8 subtype and localized closer to tumor cells.\n\nOur robust analysis pipeline characterized diverse TCR repertoires linked to distinct genotypes and immunologic tumor phenotypes. The spatial clustering of expanded T-cell clones and their association with immunological activation underscores a functional, clinically relevant immune response, particularly in patients with NSCLC treated with checkpoint inhibitors.", "doi": "10.1136/jitc-2025-012089", "pmid": "40866291", "labels": {"In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12434955"}, {"db": "pii", "key": "jitc-2025-012089"}], "notes": [], "created": "2025-11-28T06:52:14.774Z", "modified": "2025-11-28T06:52:14.874Z"}, {"entity": "publication", "iuid": "9d97c09fe92948a999a721fbc9eca073", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d97c09fe92948a999a721fbc9eca073.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d97c09fe92948a999a721fbc9eca073"}}, "title": "SMAD3 and p300 complex scaffolding by long non-coding RNA LIMD1-AS1 promotes TGF-\u03b2-induced breast cancer cell plasticity.", "authors": [{"family": "Fan", "given": "Chuannan", "initials": "C", "orcid": "0000-0001-8754-4913", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a665d568ce94fcbaaee270c6c7701a5.json"}}, {"family": "Cats", "given": "Davy", "initials": "D", "orcid": "0000-0001-9684-220X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23de688650944eca98ed9f9c1e8f19bb.json"}}, {"family": "Selle", "given": "Miriam", "initials": "M"}, {"family": "Khorosjutina", "given": "Olga", "initials": "O"}, {"family": "Dhanjal", "given": "Soniya", "initials": "S"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B"}, {"family": "Mei", "given": "Hailiang", "initials": "H", "orcid": "0000-0003-1781-5508", "researcher": {"href": "https://publications.scilifelab.se/researcher/7899dde247724b2aacd8ccb6e27fbd49.json"}}, {"family": "Ten Dijke", "given": "Peter", "initials": "P", "orcid": "0000-0002-7234-342X", "researcher": {"href": "https://publications.scilifelab.se/researcher/299812073080446a91fc6228efbdc1c5.json"}}, {"family": "Wang", "given": "Qian", "initials": "Q"}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "53", "issue": "16", "pages": null}, "abstract": "Transforming growth factor (TGF)-\u03b2 signaling enhances cancer cell plasticity by inducing epithelial-to-mesenchymal transition (EMT). Here, we identified a TGF-\u03b2-induced long non-coding RNA, LIMD1 Antisense RNA 1 (LIMD1-AS1) that strengthens the SMAD-mediated transcriptional response to TGF-\u03b2. LIMD1-AS1 expression is upregulated in breast cancer tissues compared to normal breast tissues, and high LIMD1-AS1 expression is associated with poor prognosis in breast cancer patients. Depletion of LIMD1-AS1 hinders TGF-\u03b2-induced EMT, migration, and extravasation of breast cancer cells. Mechanistically, LIMD1-AS1 promotes the interaction between SMAD3 and its transcriptional coactivator p300, thereby enhancing SMAD3 transcriptional activity and TGF-\u03b2/SMAD signaling. We demonstrated that LIMD1-AS1 binds to the MAD homology 2 (MH2) domain of SMAD3 and the interferon-binding domain (IBiD) of p300. Displacing LIMD1-AS1 from p300 by its competitor interferon regulatory factor 3 (IRF3) suppressed the effects of LIMD1-AS1 on potentiating TGF-\u03b2/SMAD signaling. Furthermore, blockage of p300 acetyltransferase activity with a pharmacological inhibitor A-485 reduced the ability of LIMD1-AS1 to enhance SMAD3 transcriptional activity, TGF-\u03b2-induced EMT, and migration. This study identifies LIMD1-AS1 as a novel stimulator of TGF-\u03b2 signaling by establishing a positive feedback loop and highlights its potential as a therapeutic target for breast cancer.", "doi": "10.1093/nar/gkaf841", "pmid": "40889156", "labels": {"CRISPR Functional Genomics": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12400928"}, {"db": "pii", "key": "8245226"}], "notes": [], "created": "2025-09-05T13:25:16.080Z", "modified": "2026-03-18T09:37:05.489Z"}, {"entity": "publication", "iuid": "a054c0f7162b4df2b065275b4b1037bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a054c0f7162b4df2b065275b4b1037bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a054c0f7162b4df2b065275b4b1037bb"}}, "title": "Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome.", "authors": [{"family": "Zgadzay", "given": "Yury", "initials": "Y"}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Wanes", "given": "George", "initials": "G"}, {"family": "P\u00e1nek", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Chauhan", "given": "Prashant", "initials": "P", "orcid": "0000-0002-5160-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2ca3733447d4e38ae5cce50d1b4d165.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Z\u00edkov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Whitford", "given": "Paul C", "initials": "PC"}, {"family": "Gahura", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "Structure", "issn": "1878-4186", "issn-l": "0969-2126", "volume": null, "issue": null, "pages": null}, "abstract": "The biogenesis of the mitoribosomal small subunit involves a dynamic network of assembly factors. Conserved methyltransferases Mettl15 and Mettl17 act on the solvent-exposed surface of rRNA. Binding of Mettl17 is associated with the early assembly stage, whereas Mettl15 is involved in the late stage. Here, we integrate structural data from Trypanosoma brucei with mammalian homologs and molecular dynamics simulations. We reveal how the interplay of Mettl15 and Mettl17 in intermediate steps links the distinct stages of small subunit assembly. The analysis suggests a model wherein Mettl17 acts as a platform for Mettl15 recruitment. Subsequent release of Mettl17 allows a conformational change of Mettl15 for substrate recognition. Upon methylation, Mettl15 adopts a loosely bound state which leads to its replacement by initiation factors, concluding the assembly. Together, our results indicate that assembly factors Mettl15 and Mettl17 cooperate to regulate the biogenesis process.", "doi": "10.1016/j.str.2025.08.002", "pmid": "40882632", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0969-2126(25)00306-5"}], "notes": [], "created": "2025-09-08T06:24:34.626Z", "modified": "2025-11-21T11:42:45.696Z"}, {"entity": "publication", "iuid": "a820631626024f32811c8031777bf540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540"}}, "title": "Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation.", "authors": [{"family": "Atienza P\u00e1rraga", "given": "Alba", "initials": "A"}, {"family": "Nylund", "given": "Patrick", "initials": "P", "orcid": "0000-0002-1274-4010", "researcher": {"href": "https://publications.scilifelab.se/researcher/683976ea3c094b198998dabb0d433f4b.json"}}, {"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}}, {"family": "Garrido-Zabala", "given": "Berta", "initials": "B"}, {"family": "Tziola", "given": "Stefania Iliana", "initials": "SI"}, {"family": "Vasquez", "given": "Louella", "initials": "L", "orcid": "0000-0002-5758-6036", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479eadb09d44ece8523730e1e0fd0b1.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69051a0275c442c8c0d5621b4000929.json"}}, {"family": "Raykova", "given": "Doroteya", "initials": "D", "orcid": "0000-0001-6452-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a81c40491e349178167f148f2351875.json"}}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Ma", "given": "Anqi", "initials": "A", "orcid": "0000-0002-9293-4753", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c70ee5b7bd4136a74d7605ec7b1614.json"}}, {"family": "Jin", "given": "Jian", "initials": "J", "orcid": "0000-0002-3774-1609", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed488bfe2c024a6b874b3b964ce80b97.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 Ignacio", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/06ccbd6b7051490fb2764ce9da7a418e.json"}}, {"family": "\u00d6berg", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3609-1197", "researcher": {"href": "https://publications.scilifelab.se/researcher/c68243c8cc754cdb8b380db120f3b771.json"}}, {"family": "De Bruyne", "given": "Elke", "initials": "E", "orcid": "0000-0003-4012-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2715df4e920432c9723d8fdf4ff897b.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d1190dfa864e4089c58c864857b114.json"}}, {"family": "Jernberg Wiklund", "given": "Helena", "initials": "H"}, {"family": "Kalushkova", "given": "Antonia", "initials": "A", "orcid": "0000-0003-4535-506X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df89c7522b7b4af3b3cef8555380fe8c.json"}}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "31568"}, "abstract": "Comprehensive epigenomic studies in multiple myeloma (MM) that unravel the connections between major epigenetic regulators, their intertwined collaboration and the potential of combinatorial targeting remain limited. Utilizing ChIP-seq, ATAC-seq, RNA-seq, and DNA methylation (DNAme) data, we generated whole-genome chromatin annotations from normal plasma cells and MM patients, revealing epigenomic re-configuration affecting downstream genes involved in tumour growth and survival. Primary MM samples showed global DNA hypomethylation but site-specific hypermethylation was observed at transcription start sites, promoters, and enhancers. Moreover, increased deposition of H3K27me3 was observed in clinically relevant functional chromatin clusters. Combined EZH2 and DNMTs inhibition resulted in extensive epigenomic alterations activating apoptosis and cell cycle genes, leading to increased G2/M arrest and apoptosis in MM cell lines. Our findings provide novel insights into the role of epigenetic gene silencing in MM tumorigenesis and the interplay between the Polycomb repressive complex 2 and DNAme.\r\n\r\nThe online version contains supplementary material available at 10.1038/s41598-025-17093-z.", "doi": "10.1038/s41598-025-17093-z", "pmid": "40866476", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12391466"}, {"db": "pii", "key": "10.1038/s41598-025-17093-z"}], "notes": [], "created": "2025-09-08T07:11:30.283Z", "modified": "2025-10-06T12:40:33.288Z"}, {"entity": "publication", "iuid": "33a2971ff9da4d5cb94e7f2e92cc0592", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33a2971ff9da4d5cb94e7f2e92cc0592.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33a2971ff9da4d5cb94e7f2e92cc0592"}}, "title": "Chromogranin A and catestatin regulate pancreatic islet homeostasis, endocrine function, and neurotransmitter signaling.", "authors": [{"family": "Muntjewerff", "given": "Elke M", "initials": "EM", "orcid": "0000-0002-2281-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c231c8e176a4fdcbc1d531f15b62316.json"}}, {"family": "Epremidze", "given": "Dali", "initials": "D"}, {"family": "Nezhyva", "given": "Mariya", "initials": "M"}, {"family": "Kal", "given": "Satadeepa", "initials": "S"}, {"family": "Rohm", "given": "Theresa V", "initials": "TV"}, {"family": "Tang", "given": "Kechun", "initials": "K"}, {"family": "Singh", "given": "Kailash", "initials": "K"}, {"family": "Espes", "given": "Daniel", "initials": "D"}, {"family": "Jati", "given": "Suborno", "initials": "S"}, {"family": "Bootsma", "given": "Marleen", "initials": "M"}, {"family": "Mannaa", "given": "Atef Mahmoud", "initials": "AM"}, {"family": "Ikebuchi", "given": "Hiromi", "initials": "H"}, {"family": "Nilsson", "given": "Anna M", "initials": "AM"}, {"family": "Rajasekaran", "given": "Mahadevan", "initials": "M"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "Jansson", "given": "Erik T", "initials": "ET", "orcid": "0000-0002-0675-3412", "researcher": {"href": "https://publications.scilifelab.se/researcher/b896baf96b99439b941fcb6b5c53802e.json"}}, {"family": "Mahata", "given": "Sushil K", "initials": "SK", "orcid": "0000-0002-8300-9873", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fd4a0aa72a84aa49f0b2d2cb4455cfe.json"}}, {"family": "Christoffersson", "given": "Gustaf", "initials": "G", "orcid": "0000-0002-9640-9702", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4092dad56b342bca7a5ce9d8ed56dc2.json"}}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Chromogranin A (CgA), a neuroendocrine pro-hormone, undergoes proteolytic cleavage to yield bioactive peptides, notably catestatin (CST) and pancreastatin (PST), which exert opposing effects on metabolic and inflammatory processes. Using CgA and CST knockout (KO) mice, this study investigated their roles in pancreatic endocrine function, morphology, neurotransmitter dynamics, and systemic glucose homeostasis. CST deficiency induced insulin resistance, altered islet architecture, and heightened catecholamine levels, whereas CgA-KO mice lacking both CST and PST exhibited improved insulin sensitivity due to absence of PST. CST suppressed gluconeogenesis and enhanced glucagon regulation, while PST promoted insulin resistance and glucose production. Spatial mass spectrometry revealed altered neurotransmitter and polyamine profiles in pancreatic islets, implicating disrupted nerve-immune-islet interactions. CST's modulation of catecholaminergic and inflammatory pathways positions it as a key regulator in the neuro-immune-endocrine axis. These findings highlight the therapeutic potential of targeting CgA-derived peptides, especially CST, for managing diabetes and metabolic-inflammatory diseases through precise peptide-based interventions.", "doi": "10.1101/2024.11.29.626063", "pmid": "40909574", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12407687"}, {"db": "pii", "key": "2024.11.29.626063"}], "notes": [], "created": "2025-11-21T09:46:19.859Z", "modified": "2025-11-21T09:46:20.148Z"}, {"entity": "publication", "iuid": "de5a12f60a4f4c3187b8e9c6307307e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de5a12f60a4f4c3187b8e9c6307307e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de5a12f60a4f4c3187b8e9c6307307e2"}}, "title": "Short and long-term effects on the thyroid proteome after 131I exposure.", "authors": [{"family": "Bj\u00f6rk", "given": "Klara Insulander", "initials": "KI", "orcid": "0000-0002-8092-0389", "researcher": {"href": "https://publications.scilifelab.se/researcher/867f975e286142a2b97663e099d168fc.json"}}, {"family": "Langen", "given": "Britta", "initials": "B"}, {"family": "Schroff", "given": "Anja", "initials": "A"}, {"family": "Shubbar", "given": "Emman", "initials": "E"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Spetz", "given": "Johan", "initials": "J"}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E", "orcid": "0000-0002-7558-4368", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec65c90d3c3b45e6b51e5609b21398e4.json"}}], "type": "journal article", "published": "2025-08-26", "journal": {"title": "Radiat Prot Dosimetry", "issn": "1742-3406", "volume": "201", "issue": "13-14", "pages": "919-933", "issn-l": null}, "abstract": "131I is recognised, both for its significance in nuclear medicine, and for its association with a rise in paediatric but not adult thyroid cancer cases following the Chornobyl accident. However, the detailed radiobiological mechanisms underlying 131I effects on the thyroid remain unknown to date. In the present study, 1 kBq or 100 kBq 131I was administered to mice that were euthanised after 48 h, 3 weeks or 6 months. Thyroid glands were surgically removed, and proteins were extracted and analysed by tandem mass spectrometry. On a group-level, the results showed few alterations in protein abundance, mainly linked to RNA metabolism and DNA damage response. However, individual analysis of protein abundance changes in each animal showed distinct findings suggesting inhibited proliferation in a few individuals across various exposure levels and time points. Future studies should involve larger animal groups to better assess the frequency and variability of proteomic radiation responses.", "doi": "10.1093/rpd/ncaf073", "pmid": "40875266", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12392893"}, {"db": "pii", "key": "8242651"}], "notes": [], "created": "2025-11-20T18:09:02.602Z", "modified": "2025-11-20T18:09:02.814Z"}, {"entity": "publication", "iuid": "2339d2c2c2bf4b31a3d99eb35eeb5f9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2339d2c2c2bf4b31a3d99eb35eeb5f9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2339d2c2c2bf4b31a3d99eb35eeb5f9d"}}, "title": "Early proteomic response in thyroid gland after 131I administration in female Balb/c mice.", "authors": [{"family": "Rudqvist", "given": "Nils", "initials": "N"}, {"family": "Spetz", "given": "Johan", "initials": "J"}, {"family": "Sch\u00fcler", "given": "Emil", "initials": "E"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "Langen", "given": "Britta", "initials": "B"}, {"family": "Wallem", "given": "Carina Sihlbom", "initials": "CS"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E", "orcid": "0000-0002-7558-4368", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec65c90d3c3b45e6b51e5609b21398e4.json"}}], "type": "journal article", "published": "2025-08-26", "journal": {"title": "Radiat Prot Dosimetry", "issn": "1742-3406", "volume": "201", "issue": "13-14", "pages": "887-898", "issn-l": null}, "abstract": "131I (iodide) accumulates in the thyroid and may affect thyroid tissue. Mechanisms behind such effects are not known. The aim was to investigate early changes in protein expression in thyroid and plasma from mice injected with 131I as iodide. Female Balb/c nude mice were i.v. injected with 0 or 490 kBq 131I and killed after 24 h. Thyroid and blood samples were collected from each animal. Protein levels were determined by mass spectrometry. Data are available via ProteomeXchange with identifier PXD062861. Altogether, 17 and 20 proteins showed statistically significant altered levels in thyroid gland and plasma, respectively, after 131I exposure. Most of these proteins had decreased and increased levels in thyroid and plasma, respectively. Few of them were previously proposed radiation responsive proteins. Functional annotation suggests impact on haematopoiesis, reduced oxygen levels, and hypothyroidism. The role of CHIA and PGAM2 in radiation-induced response should be further examined, together with identification and validation of biomarkers of 131I exposure.", "doi": "10.1093/rpd/ncaf057", "pmid": "40875264", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12392886"}, {"db": "pii", "key": "8242649"}], "notes": [], "created": "2025-10-23T09:43:48.982Z", "modified": "2025-10-23T11:16:25.310Z"}, {"entity": "publication", "iuid": "73f861c471b841a1a1c4d70d50d7cc4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73f861c471b841a1a1c4d70d50d7cc4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73f861c471b841a1a1c4d70d50d7cc4c"}}, "title": "Decoupling processability of callose enriched aspen wood: the study of extractability of lignin and carbohydrates during autohydrolysis and kraft pulping", "authors": [{"family": "Kozlowski", "given": "Aleksandra Maria", "initials": "AM", "orcid": "0000-0002-3053-9854", "researcher": {"href": "https://publications.scilifelab.se/researcher/2617d05858a44b4f808fd59cd1d5c520.json"}}, {"family": "Bourdon", "given": "Matthieu", "initials": "M"}, {"family": "Helariutta", "given": "Yrj\u00f6", "initials": "Y"}, {"family": "Hasani", "given": "Merima", "initials": "M"}], "type": "journal-article", "published": "2025-08-26", "journal": {"issn": "0018-3830", "volume": "79", "issue": "8", "pages": "359-371", "issn-l": null}, "abstract": null, "doi": "10.1515/hf-2025-0004", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:06:16.825Z", "modified": "2025-11-27T08:06:16.882Z"}, {"entity": "publication", "iuid": "3bf8b914fe60405985064cab63ee13ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bf8b914fe60405985064cab63ee13ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bf8b914fe60405985064cab63ee13ff"}}, "title": "Biomarkers in the Newborn with Fetal Growth Retardation and Early Impairment of Heart Function.", "authors": [{"family": "\u00c4nghagen", "given": "Olov", "initials": "O"}, {"family": "Engvall", "given": "Jan", "initials": "J"}, {"family": "Gottvall", "given": "Tomas", "initials": "T"}, {"family": "Nelson Follin", "given": "Nina", "initials": "N"}, {"family": "Nylander", "given": "Eva", "initials": "E"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Rudholm Feldreich", "given": "Tobias", "initials": "T"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Bang", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2025-08-26", "journal": {"title": "Horm Res Paediatr", "issn": "1663-2826", "pages": "1-12", "issn-l": null}, "abstract": "Children born with lower birth weight face an increased risk of developing cardiovascular disease later in life. We hypothesize that cardiovascular protein biomarkers in cord blood, associated with birth weight SDS and systolic cardiac function, may reveal mechanisms behind early programming of cardiovascular function.\n\nWe investigated the association between birth weight SDS and plasma levels of 184 circulating proteins determined by Proximity Extension Assay (PEA) in cord blood from 48 children. The birth weight-associated proteins were correlated with left ventricular longitudinal strain (LVLS) determined by echocardiography at birth and 3 months of age.\n\nWe identified seven cardiovascular protein biomarkers associated with birth weight SDS: stem cell factor, leptin, elafin, insulin-like growth factor-binding protein-1, follastatin, paraoxonase, and epithelial cell adhesion molecule (Ep-CAM). Among these, Ep-CAM significantly correlated with LVLS at 3 months of age.\n\nPEA successfully identified both established and novel proteins associated with fetal growth and birth size, including one novel protein related to LVLS. This indicates that our approach is promising for uncovering biological pathways that may be involved in direct programming of cardiovascular function in children and affect the risk of cardiovascular disease in adulthood.", "doi": "10.1159/000548159", "pmid": "40875700", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12503826"}, {"db": "pii", "key": "000548159"}], "notes": [], "created": "2025-11-17T08:55:32.741Z", "modified": "2025-11-25T22:17:50.024Z"}, {"entity": "publication", "iuid": "fef01ac4b12d45f39b57e367d7f051d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fef01ac4b12d45f39b57e367d7f051d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fef01ac4b12d45f39b57e367d7f051d5"}}, "title": "Chemical mechanism of allosteric and asymmetric dark reversion in a bacterial phytochrome uncovered by cryo-EM.", "authors": [{"family": "Bodizs", "given": "Szabolcs A", "initials": "SA", "orcid": "0000-0002-3303-5897", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9848a63af6e4d019bbce45745b2bd8c.json"}}, {"family": "Fischer", "given": "Anna Lena M", "initials": "ALM", "orcid": "0009-0009-3310-5021", "researcher": {"href": "https://publications.scilifelab.se/researcher/979212c2ef024d249845258e2b322f0e.json"}}, {"family": "Cervenak", "given": "Miklos", "initials": "M", "orcid": "0009-0007-3048-5386", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b46abbe59c943c280314d23d1d7b982.json"}}, {"family": "Prodhan", "given": "Sayan", "initials": "S"}, {"family": "Maj", "given": "Michal", "initials": "M", "orcid": "0000-0003-1567-9514", "researcher": {"href": "https://publications.scilifelab.se/researcher/1be0f07d0c5f40adac62cf38f2244e79.json"}}, {"family": "Westenhoff", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-6961-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1519bb234b43c6a13833b04e6720b8.json"}}], "type": "posted-content", "published": "2025-08-24", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.08.21.671592", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-17T10:05:10.042Z", "modified": "2025-12-18T19:10:16.935Z"}, {"entity": "publication", "iuid": "8ed2bc92c9ef4a80aab66db3bcbdb8b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ed2bc92c9ef4a80aab66db3bcbdb8b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ed2bc92c9ef4a80aab66db3bcbdb8b1"}}, "title": "Wood-specific modification of glucuronoxylan can enhance growth in Populus.", "authors": [{"family": "Urbancsok", "given": "J\u00e1nos", "initials": "J", "orcid": "0000-0003-3237-6806", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6f0e25417543f49060959d3af92967.json"}}, {"family": "Donev", "given": "Evgeniy N", "initials": "EN", "orcid": "0000-0002-7279-0481", "researcher": {"href": "https://publications.scilifelab.se/researcher/26467c84e2664b4980a4ed04335860ad.json"}}, {"family": "Derba-Maceluch", "given": "Marta", "initials": "M", "orcid": "0000-0002-8034-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5be452cef9048e19a08fa8043b74329.json"}}, {"family": "Sivan", "given": "Pramod", "initials": "P", "orcid": "0000-0001-5297-2221", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bed5958298d4ca08df06860c94a3878.json"}}, {"family": "Barbut", "given": "F\u00e9lix R", "initials": "FR", "orcid": "0000-0001-5395-6776", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df5c17bbf0440fd8be22761c2df9a6f.json"}}, {"family": "Mitra", "given": "Madhusree", "initials": "M", "orcid": "0000-0002-8653-8770", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1827f45c7f4853888f15d857b7e414.json"}}, {"family": "Yassin", "given": "Zakiya", "initials": "Z", "orcid": "0000-0001-6878-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cd7ddc17274c0c9eabb07ae4e6c8e0.json"}}, {"family": "Cermanov\u00e1", "given": "Kate\u0159ina", "initials": "K"}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Karady", "given": "Michal", "initials": "M", "orcid": "0000-0002-5603-706X", "researcher": {"href": "https://publications.scilifelab.se/researcher/114911ccd31849e1a7584b5a52e9eb14.json"}}, {"family": "Scheepers", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-5630-1377", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a566216ee146d1bba50d7f8779a6f8.json"}}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2025-08-23", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "issn-l": "0022-0957"}, "abstract": "Xylem cells are surrounded by primary and secondary cell walls. Formation of primary walls is regulated by the cell wall integrity surveillance system, but it is unclear if the deposition of secondary walls is similarly regulated. To study this question, we introduced to aspen three different enzymes cleaving cell wall-localized xylan and we suppressed xylan synthase components either ubiquitously or specifically during secondary wall formation using Populus trichocarpa GT43B promoter. When xylan was ubiquitously altered, 95% of lines showed reduced growth, whereas when it was altered during secondary wall deposition, 30% of lines grew better with the rest having no growth impairment, suggesting opposite effects of primary and secondary wall disturbances. To detect mechanism of growth stimulation by disturbed deposition of secondary wall, we analyzed changes in wood quality traits, chemistry, transcriptomics, metabolomics and hormonomics in transgenic lines. We found increased tension wood production, reduced S- and H-lignin, and changes in several metabolites in common in these lines. Remorin REM1.3 and NRL2 (NPH3 family) transcripts increased and changes in jasmonates, ABA and SA occurred in secondary wall-forming xylem suggesting their involvement in secondary wall integrity surveyance and signaling. The data indicate that a unique program mediates responses to secondary wall impairment that induces growth.", "doi": "10.1093/jxb/eraf364", "pmid": "40847653", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "8240116"}], "notes": [], "created": "2025-11-18T12:16:27.291Z", "modified": "2025-11-18T12:16:27.407Z"}, {"entity": "publication", "iuid": "4ed7da9adac244919a18efaef8b67a03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ed7da9adac244919a18efaef8b67a03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ed7da9adac244919a18efaef8b67a03"}}, "title": "MALNC: a new mutant NPM1/IDH2R140 and PML-RARA-associated lncRNA with impact on AML cell proliferation, maturation and drug response.", "authors": [{"family": "Cozzi", "given": "Elisabetta", "initials": "E", "orcid": "0009-0003-5311-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6657fdce5a4c8e99ad05f000ef8de3.json"}}, {"family": "Neddermeyer", "given": "Anne", "initials": "A"}, {"family": "Zhong", "given": "Xiangfu", "initials": "X", "orcid": "0000-0002-1872-1186", "researcher": {"href": "https://publications.scilifelab.se/researcher/b625a888935a42a89d7df3522e249413.json"}}, {"family": "Gamboa-Cede\u00f1o", "given": "Angelica Mar\u00eda", "initials": "AM"}, {"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications.scilifelab.se/researcher/0921ab7566514fb0a3cd0daf2baabe6e.json"}}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "My", "initials": "M", "orcid": "0000-0002-2325-6012", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cc743cdb2604ffdbc78303d70985c48.json"}}, {"family": "Struyf", "given": "Nona", "initials": "N"}, {"family": "Karlsson", "given": "Kasper", "initials": "K"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "M\u00e5nsson", "given": "Alma", "initials": "A", "orcid": "0009-0006-1982-7712", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ccda3e6f49f43f5bcf5576d7acc16e5.json"}}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Nilsson", "given": "Christer", "initials": "C", "orcid": "0000-0003-0695-0050", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f78180b33fa48cd86474d5c3cdaa852.json"}}, {"family": "Fiskesund", "given": "Roland", "initials": "R"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Bartek", "given": "Jiri", "initials": "J"}, {"family": "Kallioniemi", "given": "Olli-Pekka", "initials": "OP"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2025-08-23", "journal": {"title": "Cancer Gene Ther", "issn": "1476-5500", "issn-l": null}, "abstract": "As the non-coding genome remains poorly characterized in acute myeloid leukemia (AML), we aimed to identify and functionally characterize novel long non-coding RNAs (lncRNAs) relevant to AML biology and treatment. We first identified lncRNAs overexpressed in AML blasts and, among them, discovered a novel transcript, which we named myeloid and AML-associated intergenic long non-coding RNA (MALNC). MALNC is overexpressed in AML, particularly in cases with the PML-RARA fusion or IDH2R140/NPM1 co-mutations, and is associated with a distinct gene expression profile. Functional studies showed that MALNC knockout impairs AML cell proliferation and colony formation, enhances ATRA-induced differentiation, and sensitizes cells to arsenic trioxide. Transcriptomic analysis revealed that MALNC loss alters the expression of retinoic acid pathway genes, and chromatin binding studies showed that MALNC binds to genes related to the retinoic acid and Rho GTPase pathways. In conclusion, we have identified MALNC as a novel lncRNA that promotes leukemic cell proliferation, counteracts ATRA-induced differentiation, and modulates drug sensitivity in AML.", "doi": "10.1038/s41417-025-00954-0", "pmid": "40849353", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41417-025-00954-0"}], "notes": [], "created": "2025-09-08T07:03:20.085Z", "modified": "2025-11-14T11:06:29.062Z"}, {"entity": "publication", "iuid": "2c0506e9af41449186a19fdeda9397c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c0506e9af41449186a19fdeda9397c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c0506e9af41449186a19fdeda9397c7"}}, "title": "Brain-region-specific lipid dysregulation in L-DOPA-induced dyskinesia in a primate model of Parkinson's disease.", "authors": [{"family": "Kaya", "given": "Ibrahim", "initials": "I"}, {"family": "Vallianatou", "given": "Theodosia", "initials": "T"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Bj\u00e4rterot", "given": "Patrik", "initials": "P"}, {"family": "Shariatgorji", "given": "Reza", "initials": "R"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Bezard", "given": "Erwan", "initials": "E"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}], "type": "journal article", "published": "2025-08-23", "journal": {"title": "NPJ Parkinsons Dis", "issn": "2373-8057", "volume": "11", "issue": "1", "pages": "258", "issn-l": null}, "abstract": "L-DOPA-induced dyskinesia (LID) is a significant and treatment-limiting complication in Parkinson's disease (PD) therapy, yet its mechanisms remain poorly understood. We used high-resolution mass spectrometry imaging to map brain-region-specific alterations of glycerophospholipids and sphingolipids in a female macaque model of PD with and without LID following chronic L-DOPA treatment. LID was associated with depletion of antioxidant plasmalogen phosphatidylcholines in the globus pallidus interna, claustrum, and precentral gyrus-regions critical for motor function-and elevations of polyunsaturated fatty acid-containing glycerophospholipids, indicative of increased membrane fluidity. This lipid profile differed from similarly treated non-dyskinetic animals, suggesting lipid composition mediates differential susceptibility to LID. Lipid alterations correlated strongly with dyskinesia severity, dopamine, and L-DOPA concentrations, supporting a mechanistic link between lipid metabolism, neurotransmitter dysregulation, and LID. This comprehensive spatial lipidomic analysis identifies region-specific lipid dysregulation as a novel aspect of LID pathology, highlighting lipid pathways as potential therapeutic targets for mitigating dyskinesia.", "doi": "10.1038/s41531-025-01109-6", "pmid": "40849420", "labels": {"Spatial Mass Spectrometry": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12374971"}, {"db": "pii", "key": "10.1038/s41531-025-01109-6"}], "notes": [], "created": "2025-11-21T09:59:50.610Z", "modified": "2025-11-21T09:59:50.625Z"}, {"entity": "publication", "iuid": "6631693c2e9b45d592f5de7f7e539554", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6631693c2e9b45d592f5de7f7e539554.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6631693c2e9b45d592f5de7f7e539554"}}, "title": "Machine learning framework for investigating nano- and micro-scale particle diffusion in colonic mucus.", "authors": [{"family": "Tjakra", "given": "Marco", "initials": "M"}, {"family": "Lidayov\u00e1", "given": "Krist\u00edna", "initials": "K"}, {"family": "Avenel", "given": "Christophe", "initials": "C"}, {"family": "Bergstr\u00f6m", "given": "Christel A S", "initials": "CAS"}, {"family": "Hossain", "given": "Shakhawath", "initials": "S"}], "type": "journal article", "published": "2025-08-22", "journal": {"title": "J Nanobiotechnology", "issn": "1477-3155", "issn-l": null, "volume": "23", "issue": "1", "pages": "583"}, "abstract": "Biosimilar artificial mucus models that mimic native mucus facilitate efficient, lab-based drug diffusion studies, addressing the costly and challenging preclinical phase of drug development, especially for nano- and micro-scale particle-based colonic drug delivery. This study presents a machine-learning-driven framework that integrates microrheological features into diffusional fingerprinting to characterize nano- and micro-scale particle diffusion patterns in mucus and assess the effect of mucus microrheology on such movements. We investigated the diffusion of fluorescent-labeled polystyrene particles in native pig mucus and two artificial mucus models. Particles (100, 200, and 1000 nm in diameter) with carboxylate- or amine-modified surfaces were tracked during passive diffusion. From each particle trajectory, 20 features -including microrheology-based parameters- were extracted. Based on these features, seven supervised machine learning models were applied to classify or identify similarities among mucus hydrogels. Of these, gradient boosting achieved the highest accuracy. SHapley Additive exPlanations analysis identified creep compliance as the most influential feature in distinguishing the mucus models. In native mucus, smaller negatively charged nanoparticles exhibited the highest mobility, with fewer particles being in the immobile and subdiffusive states. Microrheology data further indicated that larger particles experienced greater restriction owing to the elastic properties of native mucus. In contrast, smaller particles interacted more with the viscous liquid phase. A comprehensive feature-wide analysis revealed that hydroxyethyl cellulose (HEC)-based artificial mucus more closely resembled native pig mucus than the polyacrylic acid-based model. In conclusion, the machine-learning-driven fingerprinting approach, incorporating microrheological features, successfully differentiated the microstructural characteristics and rheological properties of the three mucus models. It also supported the selection of HEC-based artificial mucus as a viable substitute for native colonic mucus.", "doi": "10.1186/s12951-025-03659-6", "pmid": "40847404", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12372352"}, {"db": "pii", "key": "10.1186/s12951-025-03659-6"}], "notes": [], "created": "2025-11-25T12:50:39.442Z", "modified": "2025-11-28T10:52:50.049Z"}, {"entity": "publication", "iuid": "a8fbcd4a221c4de2a1151348bd4c9304", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8fbcd4a221c4de2a1151348bd4c9304.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8fbcd4a221c4de2a1151348bd4c9304"}}, "title": "Diverse oncogenes use common mechanisms to drive growth of major forms of human cancer.", "authors": [{"family": "Kauko", "given": "Otto", "initials": "O", "orcid": "0000-0001-8948-9452", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5390cad42a0409f8b66f56ab23ca232.json"}}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Pihlajamaa", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0001-9725-6907", "researcher": {"href": "https://publications.scilifelab.se/researcher/1171591a6a724f50a631d34948c6f14a.json"}}, {"family": "H\u00e4kkinen", "given": "Antti", "initials": "A", "orcid": "0000-0002-8081-1588", "researcher": {"href": "https://publications.scilifelab.se/researcher/b00bca666f344d4980a97bbdba20361e.json"}}, {"family": "Queiroz", "given": "Rayner M L", "initials": "RML"}, {"family": "P\u00e4\u00e4kk\u00f6nen", "given": "Mirva", "initials": "M"}, {"family": "Ventel\u00e4", "given": "Sami", "initials": "S"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL", "orcid": "0000-0003-2363-4287", "researcher": {"href": "https://publications.scilifelab.se/researcher/916e190e150e465c9e6afc11911bae04.json"}}, {"family": "Murgia", "given": "Antonio", "initials": "A"}, {"family": "Sahu", "given": "Biswajyoti", "initials": "B", "orcid": "0000-0001-6576-5440", "researcher": {"href": "https://publications.scilifelab.se/researcher/283b12ad225d4fb2b4e38b7f10c026d4.json"}}, {"family": "Routila", "given": "Johannes", "initials": "J", "orcid": "0000-0001-5385-7065", "researcher": {"href": "https://publications.scilifelab.se/researcher/71ee18226e6e4a42ae83b7106ca8b343.json"}}, {"family": "Wei", "given": "Gong-Hong", "initials": "G"}, {"family": "Irjala", "given": "Heikki", "initials": "H", "orcid": "0000-0003-3054-4677", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf759b807e9640aab8fcadbad0c60662.json"}}, {"family": "Griffin", "given": "Julian L", "initials": "JL", "orcid": "0000-0003-1336-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/98e91146412f4bd2a0bed9331efee8d2.json"}}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS", "orcid": "0000-0003-0594-6543", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b4e7e18a88455199308070d6da7ea3.json"}}, {"family": "Kivioja", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7732-2177", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c318f57c5ce4f4bb747e19514caa907.json"}}, {"family": "Hautaniemi", "given": "Sampsa", "initials": "S", "orcid": "0000-0002-7749-2694", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29cabf8ec5e4f78b9d14984a60c3e84.json"}}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}], "type": "journal article", "published": "2025-08-22", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "11", "issue": "34", "pages": "eadt1798"}, "abstract": "Mutations in numerous genes contribute to human cancer, with different oncogenic lesions prevalent in different cancer types. However, the malignant phenotype is simple, characterized by unrestricted cell growth, invasion, and often metastasis. One possible hypothesis explaining this dichotomy is that cancer genes regulate common targets, which then function as master regulators of essential cancer phenotypes. To identify mechanisms that drive the most fundamental feature shared by all tumors-unrestricted cell proliferation-we used a multiomic approach, which identified translation and ribosome biogenesis as common targets of major oncogenic pathways across cancer types. Proteomic analysis of tumors and functional studies of cell cultures established nucleolar and coiled-body phosphoprotein 1 as a key node, whose convergent regulation, both transcriptionally and posttranslationally, is critical for tumor cell proliferation. Our results indicate that lineage-specific oncogenic pathways regulate the same set of targets for growth control, revealing key downstream nodes that could be targeted for therapy or chemoprevention.", "doi": "10.1126/sciadv.adt1798", "pmid": "40834066", "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC13155486"}], "notes": [], "created": "2025-11-25T16:41:01.046Z", "modified": "2026-05-25T19:26:02.282Z"}, {"entity": "publication", "iuid": "dd0afad963a94899b6d550a9f7f21965", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd0afad963a94899b6d550a9f7f21965.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd0afad963a94899b6d550a9f7f21965"}}, "title": "An encompassing Mendelian randomization study of the causes and consequences of major depressive disorder.", "authors": [{"family": "Pasman", "given": "Jo\u00eblle A", "initials": "JA", "orcid": "0000-0001-7558-0482", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bb78c586bfc443b92436572de80cb90.json"}}, {"family": "Bergstedt", "given": "Jacob", "initials": "J", "orcid": "0000-0002-9279-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e8ca729357b421588628aa2eb06c2f8.json"}}, {"family": "Harder", "given": "Arvid", "initials": "A"}, {"family": "Gong", "given": "Tong", "initials": "T"}, {"family": "Xiong", "given": "Ying", "initials": "Y", "orcid": "0000-0001-7644-014X", "researcher": {"href": "https://publications.scilifelab.se/researcher/72484ccb61b140ca946294b68042c330.json"}}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Fang", "given": "Fang", "initials": "F", "orcid": "0000-0002-3310-6456", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ab8a681a053477b81f093cbd6232947.json"}}, {"family": "Treur", "given": "Jorien L", "initials": "JL"}, {"family": "Choi", "given": "Karmel W", "initials": "KW", "orcid": "0000-0002-3914-2431", "researcher": {"href": "https://publications.scilifelab.se/researcher/999aa3a1fbe943458b8db7c41bcc4965.json"}}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Lu", "given": "Yi", "initials": "Y"}], "type": "journal article", "published": "2025-08-22", "journal": {"title": "Nat Ment Health", "issn": "2731-6076", "volume": "3", "issue": "9", "pages": "1002-1011", "issn-l": null}, "abstract": "Major depressive disorder (MDD) is a prevalent and debilitating disorder whose causes and consequences remain insufficiently understood. Genetic variants can be used to study causal relationships with other traits. Here we reviewed 201 MDD-associated traits and performed genetic correlation analyses for 115 traits, two-sample Mendelian randomization for 89 of them, and one-sample Mendelian randomization for an additional 43 outcomes, applying sensitivity tests and power analyses. We show that MDD liability increases risk for poorer circadian, cognitive, diet, medical disease, endocrine, functional, inflammatory, metabolic, mortality, physical activity, reproduction, risk behavior, social, socioeconomic and suicide outcomes. Most associations were bidirectional, although with weaker evidence for diet, disease and endocrine traits causing MDD risk. These findings provide a systematic overview of traits putatively causally linked to MDD-confirming known links and identifying new ones-and underscore MDD as a cross-cutting risk factor across medical, functional and psychosocial domains.", "doi": "10.1038/s44220-025-00471-x", "pmid": "40932904", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12417207"}, {"db": "pii", "key": "471"}], "notes": [], "created": "2025-11-28T10:48:08.055Z", "modified": "2025-11-28T10:48:08.228Z"}, {"entity": "publication", "iuid": "3edf2b6f02ab49bf87dfe223379d93cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3edf2b6f02ab49bf87dfe223379d93cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3edf2b6f02ab49bf87dfe223379d93cd"}}, "title": "Environmental and Inflammatory Factors Drive Perinuclear-Antineutrophil Cytoplasmic Antibodies (pANCA) in Ulcerative Colitis: A European Twin Study.", "authors": [{"family": "Bergemalm", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1906-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50a7ccd948a492f900b8d44d5fc7f3b.json"}}, {"family": "Amcoff", "given": "Karin", "initials": "K"}, {"family": "Pierik", "given": "Marie J", "initials": "MJ"}, {"family": "Colombel", "given": "Jean-Frederic", "initials": "JF"}, {"family": "Vermeire", "given": "Severine", "initials": "S", "orcid": "0000-0001-9942-3019", "researcher": {"href": "https://publications.scilifelab.se/researcher/132301a81e47490aa57a40a699b4bd10.json"}}, {"family": "Bodin", "given": "Lennart", "initials": "L"}, {"family": "Carlson", "given": "Marie", "initials": "M"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2025-08-21", "journal": {"title": "United European Gastroenterol J", "issn": "2050-6414", "issn-l": null}, "abstract": "Perinuclear-antineutrophil cytoplasmic antibodies (pANCA) have been identified in familial ulcerative colitis (UC), but the mechanism underlying their expression remains elusive. We assessed the role of genetic predisposition, environmental factors and systemic subclinical inflammation in the development of pANCA in a twin cohort with UC.\n\nA total of 48 twin pairs (Leuven, Belgium n = 4, Maastricht, The Netherlands n = 6 and \u00d6rebro, Sweden n = 38) with UC were included. Among these, 18 were monozygotic (3 concordant and 15 discordant for UC) and 30 were dizygotic (1 concordant and 29 discordant for UC). P-ANCA was detected through standardised ELISA, an indirect immunofluorescence assay and DNase treatment. In addition to high sensitivity C-reactive protein (hs-CRP), 92 inflammatory protein markers were measured in serum by proximity extension assay.\n\nPerinuclear-ANCA was present in 15/52 (29%) of UC twins vs. 4/44 (9%) healthy twin siblings (p = 0.02). No agreement in the presence of pANCA or their levels was observed between twin siblings in monozygotic pairs discordant for UC [intraclass correlation coefficient (ICC) = 0.09] or dizygotic pairs (ICC = -0.20). Female sex was associated with an increased likelihood of pANCA (odds ratio, OR 5.25; 95% confidence interval, CI 1.36-20.30) and higher ANCA levels (ratio of geometric means 1.86; 95% CI 1.18-2.93). Active smoking was associated with lower concentrations of ANCA (ratio of geometric means 0.31; 95% CI 0.14-0.68) and potentially reduced the likelihood of pANCA (OR 0.20; 95% CI 0.03-1.34) in twins with UC but not in their healthy siblings. In healthy twin siblings, significant correlations between ANCA levels and hs-CRP, CDCP1, IL17 A, CXCL9 and IL5 (correlation coefficients 0.36-0.41, p-values < 0.05) were observed.\n\nFemale sex and tobacco smoking outweighed genetics regarding the generation and levels of pANCA and ANCA antibodies. The correlations between ANCA levels and inflammatory markers in healthy twin siblings suggest that pANCA may result from subclinical inflammation.", "doi": "10.1002/ueg2.70101", "pmid": "40839417", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-25T19:20:59.702Z", "modified": "2025-11-25T19:20:59.748Z"}, {"entity": "publication", "iuid": "6631db4df635414dbbbe505ccbd190ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6631db4df635414dbbbe505ccbd190ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6631db4df635414dbbbe505ccbd190ce"}}, "title": "Discovery of tumour indicating morphological changes in benign prostate biopsies through AI.", "authors": [{"family": "Chelebian", "given": "Eduard", "initials": "E"}, {"family": "Avenel", "given": "Christophe", "initials": "C"}, {"family": "J\u00e4remo", "given": "Helena", "initials": "H"}, {"family": "Andersson", "given": "Pernilla", "initials": "P"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C"}], "type": "journal article", "published": "2025-08-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "30770", "issn-l": "2045-2322"}, "abstract": "Diagnostic needle biopsies that miss clinically significant prostate cancer (PCa) often sample benign tissue near hidden cancers. Such benign samples might still display subtle morphological signs of cancer elsewhere in the prostate. This study examined if artificial intelligence (AI) could detect these morphological clues in benign biopsies from men with elevated prostate-specific antigen (PSA) levels to predict subsequent diagnosis of clinically significant PCa within 30 months. We analysed biopsies from 232 men initially diagnosed as benign, matched for age, diagnosis year, and PSA levels-half were later diagnosed with PCa, while the rest remained cancer-free for at least eight years. The AI model accurately predicted future PCa diagnosis from initial benign biopsies (AUC = 0.82), highlighting patterns such as changes in stromal collagen and altered glandular epithelial cells. This demonstrates that AI analysis of routine haematoxylin-eosin biopsy sections can detect subtle signs indicating clinically significant PCa before it becomes histologically apparent. Such morphological patterns shed light on the broader tissue alterations induced by prostate cancer, even in benign tissue, potentially enhancing early detection and clinical decision-making.", "doi": "10.1038/s41598-025-15105-6", "pmid": "40841408", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12370971"}, {"db": "pii", "key": "10.1038/s41598-025-15105-6"}], "notes": [], "created": "2025-11-25T12:52:52.168Z", "modified": "2025-11-25T12:52:52.171Z"}, {"entity": "publication", "iuid": "9b5649744c38405dbf38188c2431d979", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b5649744c38405dbf38188c2431d979.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b5649744c38405dbf38188c2431d979"}}, "title": "Smart Microscopy: Current Implementations and a Roadmap for Interoperability", "authors": [{"family": "Hinderling", "given": "Lucien", "initials": "L", "orcid": "0000-0002-3956-9363", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c639b9c76754da490fb7685c24cf81a.json"}}, {"family": "Heil", "given": "Hannah S", "initials": "HS", "orcid": "0000-0003-4279-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/6847d2e9b3134366a621dcd3b1bb9a3d.json"}}, {"family": "Rates", "given": "Alfredo", "initials": "A", "orcid": "0000-0001-6154-873X", "researcher": {"href": "https://publications.scilifelab.se/researcher/004ea795284a4ecda44c2c261722e633.json"}}, {"family": "Seidel", "given": "Philipp", "initials": "P", "orcid": "0000-0003-0097-9768", "researcher": {"href": "https://publications.scilifelab.se/researcher/007be887d4c040baa22b205a7d0ba0be.json"}}, {"family": "Gunkel", "given": "Manuel", "initials": "M", "orcid": "0000-0002-5363-8943", "researcher": {"href": "https://publications.scilifelab.se/researcher/7164065b12744c27a54ed195bbc68a10.json"}}, {"family": "Diederich", "given": "Benedict", "initials": "B", "orcid": "0000-0003-0453-6286", "researcher": {"href": "https://publications.scilifelab.se/researcher/895a73b7251849c8a249b01999a37bf8.json"}}, {"family": "Guilbert", "given": "Thomas", "initials": "T", "orcid": "0000-0001-5069-0730", "researcher": {"href": "https://publications.scilifelab.se/researcher/97a3a1881bc94f4596233a238e09802a.json"}}, {"family": "Torro", "given": "R\u00e9my", "initials": "R", "orcid": "0000-0002-4903-8304", "researcher": {"href": "https://publications.scilifelab.se/researcher/4381c9d35c5a4cb599808d36cb4ee491.json"}}, {"family": "Bouchareb", "given": "Otmane", "initials": "O"}, {"family": "Demeautis", "given": "Claire", "initials": "C", "orcid": "0009-0004-7834-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6befc2ff6f403a983658dd3db99432.json"}}, {"family": "Martin", "given": "C\u00e9lia", "initials": "C"}, {"family": "Brooks", "given": "Scott", "initials": "S", "orcid": "0009-0002-4748-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f747e713465409596e2031272fb84af.json"}}, {"family": "Sisamakis", "given": "Evangelos", "initials": "E"}, {"family": "Grandgirard", "given": "Erwan", "initials": "E", "orcid": "0000-0002-5263-2144", "researcher": {"href": "https://publications.scilifelab.se/researcher/955165560ba34b4dbb883a70f34a16d5.json"}}, {"family": "Mutterer", "given": "Jerome", "initials": "J", "orcid": "0000-0002-0722-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/55316e9f0e4b42e9b5c4d8bac14dd682.json"}}, {"family": "Oatman", "given": "Harrison", "initials": "H", "orcid": "0000-0002-2699-6374", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6818c59f877414b949e276d5cce74c5.json"}}, {"family": "Toettcher", "given": "Jared", "initials": "J", "orcid": "0000-0002-1546-4030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5464a4c3a5f4b76a94999c2164af0d0.json"}}, {"family": "Rogov", "given": "Andrii", "initials": "A"}, {"family": "Antonovaite", "given": "Nelda", "initials": "N", "orcid": "0000-0001-9080-0324", "researcher": {"href": "https://publications.scilifelab.se/researcher/30bcb20ca0364be598b3371e5ef62534.json"}}, {"family": "Johansson", "given": "Karl", "initials": "K", "orcid": "0000-0002-4140-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffe93a2e29f54a448becf3d7f82af27d.json"}}, {"family": "Ahnlinde", "given": "Johannes K", "initials": "JK", "orcid": "0000-0002-8136-8928", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d5a19c2b844431bb8539e85491256f1.json"}}, {"family": "Andr\u00e9", "given": "Oscar", "initials": "O", "orcid": "0000-0003-1732-9454", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb45098164e438f8db95715e2d46a1e.json"}}, {"family": "Nordenfelt", "given": "Philip", "initials": "P", "orcid": "0000-0002-9481-9951", "researcher": {"href": "https://publications.scilifelab.se/researcher/7aa3418ab23a4ec48c037d6d6ddea5b5.json"}}, {"family": "Nordenfelt", "given": "Pontus", "initials": "P", "orcid": "0000-0002-9481-9951", "researcher": {"href": "https://publications.scilifelab.se/researcher/7aa3418ab23a4ec48c037d6d6ddea5b5.json"}}, {"family": "Pfander", "given": "Claudia", "initials": "C", "orcid": "0000-0002-9574-9553", "researcher": {"href": "https://publications.scilifelab.se/researcher/46902321e1c041b992dd455ca966260a.json"}}, {"family": "Reymann", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Lambert", "given": "Talley", "initials": "T", "orcid": "0000-0002-2409-0181", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a3cf6c909954f19960ed2bb3de0b19a.json"}}, {"family": "Cosenza", "given": "Marco R", "initials": "MR", "orcid": "0000-0003-1744-5973", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c2ecb6e752f490f880d193a4cb1f1ee.json"}}, {"family": "Korbel", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-2798-3794", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed72e69cece749b08191bb9367887af8.json"}}, {"family": "Pepperkok", "given": "Rainer", "initials": "R", "orcid": "0000-0002-9762-3583", "researcher": {"href": "https://publications.scilifelab.se/researcher/e93cb4819a6544d9b1350391f545fd0f.json"}}, {"family": "Kapitein", "given": "Lukas C", "initials": "LC", "orcid": "0000-0001-9418-6739", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d00025167d4ccc85878c8195a36f2e.json"}}, {"family": "Pertz", "given": "Olivier", "initials": "O", "orcid": "0000-0001-8579-4919", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ce679783be64951a3c507bf0200f538.json"}}, {"family": "Norlin", "given": "Nils", "initials": "N", "orcid": "0000-0003-1970-3198", "researcher": {"href": "https://publications.scilifelab.se/researcher/904d237ef4cb45fc9c3284095c227f6c.json"}}, {"family": "Halavatyi", "given": "Aliaksandr", "initials": "A", "orcid": "0000-0002-9002-457X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2a1680338840d5be54c92ff5efebd2.json"}}, {"family": "Camacho", "given": "Rafael", "initials": "R", "orcid": "0000-0003-2325-6407", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a7a8cfe28634821984b078ce3246343.json"}}], "type": "posted-content", "published": "2025-08-20", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.08.18.670881", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Technology development"}, "xrefs": [], "notes": [], "created": "2025-11-05T13:52:25.254Z", "modified": "2025-12-18T19:10:58.884Z"}, {"entity": "publication", "iuid": "f9fa93241c55420684d17c40a4900126", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9fa93241c55420684d17c40a4900126.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9fa93241c55420684d17c40a4900126"}}, "title": "Environmental DNA from peck marks shows potential for non\u2011invasive monitoring of woodpeckers.", "authors": [{"family": "Sharif", "given": "Muhammad Bilal", "initials": "MB", "orcid": "0000-0002-0581-0542", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7d50e00ad8a448abafe330b8f92bbfe.json"}}, {"family": "Ferry", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-6372-4298", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d8ad3e349a54ad48dcd2f76f53a107e.json"}}, {"family": "Fuchs", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Cronholm", "given": "Bodil", "initials": "B"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2025-08-20", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "8", "pages": "e0328831", "issn-l": "1932-6203"}, "abstract": "Monitoring species' occurrences is essential for understanding ecosystem dynamics, tracking biodiversity changes, and guiding conservation efforts. Traditional monitoring methods, such as visual surveys, are challenging, particularly for elusive and endangered species. This proof-of-concept study explores the potential of environmental DNA (eDNA) collected from peck marks as a non-invasive tool for detecting and identifying woodpecker species. We collected nine samples from fresh peck marks on birch and spruce trees in the forests of Swedish Lapland. In two samples, we successfully amplified an 81 base-pair fragment of the woodpecker mitochondrial 16S rRNA gene. Taxonomic assignment identified the Eurasian three-toed woodpecker (Picoides tridactylus), a species classified as \"Near Threatened\" in Sweden. We collected an additional 15 samples from 4-19 years old peck marks preserved inside the trunks of birch and pine trees in the same area. No woodpecker DNA was detected in these samples, likely due to DNA degradation. Our findings demonstrate the potential of using eDNA from peck marks as a non-invasive approach for monitoring elusive woodpecker species.", "doi": "10.1371/journal.pone.0328831", "pmid": "40833950", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12367160"}, {"db": "pii", "key": "PONE-D-25-05526"}], "notes": [], "created": "2025-12-05T13:13:48.040Z", "modified": "2025-12-05T13:13:48.321Z"}, {"entity": "publication", "iuid": "56648ea2596d4aa49555ce26d1055513", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56648ea2596d4aa49555ce26d1055513.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56648ea2596d4aa49555ce26d1055513"}}, "title": "Repeated polyploidization shapes divergence in floral morphology in Lithophragma bolanderi (Saxifragaceae).", "authors": [{"family": "Gross", "given": "Karin", "initials": "K", "orcid": "0000-0002-2363-452X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f4362c55ecf40ada48792ac03f1425a.json"}}, {"family": "Yazdi", "given": "Homa Papoli", "initials": "HP", "orcid": "0000-0001-8667-6279", "researcher": {"href": "https://publications.scilifelab.se/researcher/608729115444421b8c6db7eb852a059a.json"}}, {"family": "Schlager", "given": "Elisabeth", "initials": "E"}, {"family": "Lilley", "given": "Jodie", "initials": "J"}, {"family": "Romero-Bravo", "given": "Andr\u00e9s", "initials": "A"}, {"family": "Runemark", "given": "Anna", "initials": "A", "orcid": "0000-0002-8976-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/e914e2d1ccbd4d35ae574187762ae01f.json"}}, {"family": "Thompson", "given": "John N", "initials": "JN", "orcid": "0000-0001-5941-6498", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5702a533123466c8ae723cc5732e72f.json"}}, {"family": "Friberg", "given": "Magne", "initials": "M", "orcid": "0000-0003-4779-7881", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d19106d6be748d99ee049ea616fc9c2.json"}}], "type": "journal article", "published": "2025-08-19", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "33", "pages": "e2505119122", "issn-l": "0027-8424"}, "abstract": "Polyploidization is an important driver of evolution and diversification in flowering plants. Here, we assess how repeated polyploidization may have shaped diversification of floral morphology in Lithophragma bolanderi (Saxifragaceae). This species comprises multiple cytotypes and varies geographically in its interactions with specialized pollinating moths in the genus Greya (Prodoxidae). Past studies have shown that coevolution with these moths has favored particular suites of floral characters but does not fully explain local and regional floral diversification. We combined phenotypic and genomic data from more than 1,800 individuals from 40 L. bolanderi populations spread across its entire range. Flow-cytometric analyses revealed a geographic mosaic of populations comprising one to four of three dominant (diploid, tetraploid, hexaploid) and three rare (triploid, pentaploid, octoploid) cytotypes. Whole-genome resequencing of a subset of populations suggested that polyploids arose from multiple autopolyploidization events, rather than a single event and/or through hybridization, albeit with some signals consistent with low levels of introgression from the congener Lithophragma glabrum. Quantification of flower traits from plants grown in a common garden showed that cytotype explained more than 15% of the variation in floral morphology, with polyploids showing more variability than diploids. Experimental induction of neopolyploids directly induced phenotypic changes but also indicated that local selection may have favored subsequent convergence in floral morphology among cytotypes in natural populations. Collectively, this comprehensive and integrative approach provides insights into how variability generating processes, such as polyploidization integrates with selection from species interactions to shape local floral diversification.", "doi": "10.1073/pnas.2505119122", "pmid": "40802687", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12377753"}], "notes": [], "created": "2025-11-21T15:15:36.277Z", "modified": "2025-11-28T10:48:23.989Z"}, {"entity": "publication", "iuid": "347f024c53aa429a82d7673a17eca4dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/347f024c53aa429a82d7673a17eca4dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/347f024c53aa429a82d7673a17eca4dc"}}, "title": "Epigenetic biomarkers predict macrovascular events in individuals with type 2 diabetes.", "authors": [{"family": "Garc\u00eda-Calz\u00f3n", "given": "Sonia", "initials": "S"}, {"family": "Maguolo", "given": "Alice", "initials": "A"}, {"family": "Eichelmann", "given": "Fabian", "initials": "F"}, {"family": "Edsfeldt", "given": "Andreas", "initials": "A"}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Maziarz", "given": "Marlena", "initials": "M"}, {"family": "Lindstr\u00f6m", "given": "Axel", "initials": "A"}, {"family": "Sun", "given": "Jiangming", "initials": "J"}, {"family": "Briviba", "given": "Monta", "initials": "M"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}, {"family": "Klovins", "given": "Janis", "initials": "J"}, {"family": "Ahlqvist", "given": "Emma", "initials": "E"}, {"family": "Gon\u00e7alves", "given": "Isabel", "initials": "I"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2025-08-19", "journal": {"title": "Cell Reports Medicine", "issn": "2666-3791", "volume": "6", "issue": "8", "pages": "102290", "issn-l": "2666-3791"}, "abstract": "Prediction of incident macrovascular events (iMEs) in individuals with type 2 diabetes (T2D) remains suboptimal. We aim to discover blood-based epigenetic biomarkers predicting iMEs in 752 newly diagnosed individuals with T2D, among whom 102 developed iMEs during follow-up. 461 DNA methylation sites, e.g., near ARID3A, GATA5, HDAC4, IRS2, and TMEM51, associate with iMEs. Using cross-validation, a methylation risk score (MRS) containing 87 sites predicts iMEs with an area under the curve (AUC) of 0.81 and an AUC of 0.84 for the combination of MRS and clinical risk factors, better than SCORE2-Diabetes (Systematic Coronary Risk Evaluation 2-Diabetes), UKPDS (United Kingdom Prospective Diabetes Study), Framingham, and polygenic risk scores (AUCs = 0.54-0.62). This epigenetic biomarker has a negative predictive value of 95.9% and improves the classification of iMEs with continuous net reclassification improvement (NRI) showing 90.2% improvement versus clinical factors. Atherosclerotic versus non-atherosclerotic aortas show 78 differentially methylated sites. We validate 32 sites in EPIC-Potsdam and 43 in OPTIMED cohorts, including an MRS (AUC = 0.80). Together, blood-based epigenetic biomarkers predict iMEs better than clinical risk factors, supporting its future clinical use.", "doi": "10.1016/j.xcrm.2025.102290", "pmid": "40780200", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12432358"}, {"db": "pii", "key": "S2666-3791(25)00363-5"}], "notes": [], "created": "2025-10-30T13:33:55.135Z", "modified": "2025-10-30T13:33:55.146Z"}, {"entity": "publication", "iuid": "8a944c22f1ab482e8a31f8af3b240aa9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a944c22f1ab482e8a31f8af3b240aa9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a944c22f1ab482e8a31f8af3b240aa9"}}, "title": "An in vivo mimetic liver-lobule-chip (LLoC) for stem cell maturation, and zonation of hepatocyte-like cells on chip.", "authors": [{"family": "Dalsbecker", "given": "Philip", "initials": "P", "orcid": "0000-0002-9762-2935", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9f86bdd978e4ac399fa9da18dba97ae.json"}}, {"family": "Suominen", "given": "Siiri", "initials": "S"}, {"family": "Faridi", "given": "Muhammad Asim", "initials": "MA"}, {"family": "Mahdavi", "given": "Reza", "initials": "R"}, {"family": "Johansson", "given": "Julia", "initials": "J"}, {"family": "Blomqvist", "given": "Charlotte Hamngren", "initials": "CH"}, {"family": "Goks\u00f6r", "given": "Mattias", "initials": "M"}, {"family": "Aalto-Set\u00e4l\u00e4", "given": "Katriina", "initials": "K"}, {"family": "Viiri", "given": "Leena E", "initials": "LE"}, {"family": "Adiels", "given": "Caroline B", "initials": "CB", "orcid": "0000-0002-2403-2213", "researcher": {"href": "https://publications.scilifelab.se/researcher/029f8a8f2f704d358b8743d821c03bd7.json"}}], "type": "journal article", "published": "2025-08-19", "journal": {"title": "Lab Chip", "issn": "1473-0189", "volume": "25", "issue": "17", "pages": "4328-4344", "issn-l": null}, "abstract": "In vitro cell culture models play a crucial role in preclinical drug discovery. To achieve optimal culturing environments and establish physiologically relevant organ-specific conditions, it is imperative to replicate in vivo scenarios when working with primary or induced pluripotent cell types. However, current approaches to recreating in vivo conditions and generating relevant 3D cell cultures still fall short. In this study, we validate a liver-lobule-chip (LLoC) containing 21 artificial liver lobules, each representing the smallest functional unit of the human liver. The LLoC facilitates diffusion-based perfusion via sinusoid-mimetic structures, providing physiologically relevant shear stress exposure and radial nutrient concentration gradients within each lobule. We demonstrate the feasibility of long term cultures (up to 14 days) of viable and functional HepG2 cells in a 3D discoid tissue structure, serving as initial proof of concept. Thereafter, we successfully differentiate sensitive, human induced pluripotent stem cell (iPSC)-derived cells into hepatocyte-like cells over a period of 20 days on-chip, exhibiting advancements in maturity compared to traditional 2D cultures. Further, hepatocyte-like cells cultured in the LLoC exhibit zonated protein expression profiles, indicating the presence of metabolic gradients characteristic of liver lobules. Our results highlight the suitability of the LLoC for long-term discoid tissue cultures, specifically for iPSCs, and their differentiation in a perfused environment. We envision the LLoC as a starting point for more advanced in vitro models, allowing for the combination of multiple liver cell types to create a comprehensive liver model for disease-onchip studies. Ultimately, when combined with stem cell technology, the LLoC offers a promising and robust on-chip liver model that serves as a viable alternative to primary hepatocyte cultures-ideally suited for preclinical drug screening and personalized medicine applications.", "doi": "10.1039/d4lc00509k", "pmid": "40485317", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-05T13:48:17.697Z", "modified": "2025-11-05T13:48:17.823Z"}, {"entity": "publication", "iuid": "5736722e01b74b29baf8fe43d4ce6819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819"}}, "title": "RNA-seq analysis identifies key genes enhancing hoof strength to withstand barefoot racing in Standardbred trotters.", "authors": [{"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Alameddine", "given": "Asmaa", "initials": "A"}, {"family": "Sp\u00f6rndly-Nees", "given": "Ellinor", "initials": "E"}, {"family": "Montigny", "given": "Mathilde", "initials": "M"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R", "orcid": "0000-0002-3610-4341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae740ff060a5499fa477891138e95117.json"}}, {"family": "Jansson", "given": "Anna", "initials": "A"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}], "type": "journal article", "published": "2025-08-18", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "751", "issn-l": "1471-2164"}, "abstract": "Racing without protective shoes is common in the Swedish harness racing industry, as it can enhance horses' performance on the track. Trainers typically decide whether a horse will race barefoot based on practical experience rather than objective measures. However, this practice can sometimes lead to excessive hoof wear, posing potential welfare concerns for racing horses. Gene expression differences may help reveal the underlying genetic mechanisms associated with different phenotypic traits. To explore an objective measure for assessing which horses are best suited for barefoot racing, we conducted a polyA-selected RNA-seq experiment on tissue from the growth zone at the coronary band of the hoof. This experiment compared tissues from Standardbred trotters capable of repeatedly racing barefoot without injury (n = 11) to those that could not (n = 7). By combining stringent phenotyping with racing records and trainer interviews, we aimed to elucidate the biological factors related to hoof strength in barefoot racing, focusing on differential abundant genes.\n\nThe RNA-seq analysis identified five significantly downregulated genes in horses capable of competing barefoot across consecutive races. These genes are associated with various biological processes relevant for hoof strength: ACCS, IRX2 and TRAPPAC6A contribute to enhancing the structural integrity of the hoof; MT2A regulates its metal homeostasis and SLC35F3 likely influences local vasoconstriction in the hoof. These gene findings suggest a coordinated genetic basis for structural reinforcement and physiological support of the hoof, which may be critical for sustaining performance under barefoot conditions.\n\nOur findings suggest that the ability of Standardbred trotters to race barefoot in consecutive events is reflected in distinct gene expression patterns, underscoring a genetic basis for hoof strength. This supports further genome-wide scans aimed at identifying genetic markers for hoof durability in these horses. The focused design of our study- comparing horses that could consistently race barefoot with those that could not- enabled us to isolate a select group of genes involved in diverse aspects of hoof biology essential for quality and resilience of horse hooves. This insight could ultimately be applied to augment both the performance and wellbeing of equine athletes across disciplines.", "doi": "10.1186/s12864-025-11814-4", "pmid": "40826322", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12363045"}, {"db": "pii", "key": "10.1186/s12864-025-11814-4"}], "notes": [], "created": "2025-09-08T07:04:42.067Z", "modified": "2025-09-09T13:14:43.091Z"}, {"entity": "publication", "iuid": "ce4033f0d9fc495bb5eaed500136d045", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce4033f0d9fc495bb5eaed500136d045.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce4033f0d9fc495bb5eaed500136d045"}}, "title": "Glucuronoyl Esterase Expressed in Aspen Xylem Affects \u03b3-Ester Linkages Between Lignin and Glucuronoxylan Reducing Recalcitrance and Accelerating Growth.", "authors": [{"family": "Derba-Maceluch", "given": "Marta", "initials": "M", "orcid": "0000-0002-8034-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5be452cef9048e19a08fa8043b74329.json"}}, {"family": "Garc\u00eda Roma\u00f1ach", "given": "Laura", "initials": "L", "orcid": "0000-0003-1188-5193", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0a86fa91e6745e0ac048cf33e1ecda5.json"}}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M", "orcid": "0000-0002-0903-6662", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db0f81a369741b0847c6f79746d82aa.json"}}, {"family": "Mitra", "given": "Madhusree", "initials": "M", "orcid": "0000-0002-8653-8770", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1827f45c7f4853888f15d857b7e414.json"}}, {"family": "Donev", "given": "Evgeniy N", "initials": "EN", "orcid": "0000-0002-7279-0481", "researcher": {"href": "https://publications.scilifelab.se/researcher/26467c84e2664b4980a4ed04335860ad.json"}}, {"family": "Urbancsok", "given": "J\u00e1nos", "initials": "J", "orcid": "0000-0003-3237-6806", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6f0e25417543f49060959d3af92967.json"}}, {"family": "Yassin", "given": "Zakiya", "initials": "Z", "orcid": "0000-0001-6878-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cd7ddc17274c0c9eabb07ae4e6c8e0.json"}}, {"family": "Gandla", "given": "Madhavi L", "initials": "ML", "orcid": "0000-0003-2798-6298", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1e32323239243999cbb5f1dcc06279a.json"}}, {"family": "Sivan", "given": "Pramod", "initials": "P", "orcid": "0000-0001-5297-2221", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bed5958298d4ca08df06860c94a3878.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Scheepers", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-5630-1377", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a566216ee146d1bba50d7f8779a6f8.json"}}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ", "orcid": "0000-0003-3866-0111", "researcher": {"href": "https://publications.scilifelab.se/researcher/1769e674df8649ce82a0d058f0a309dc.json"}}, {"family": "Vilaplana", "given": "Francisco", "initials": "F", "orcid": "0000-0003-3572-7798", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ee4f3eaece8487fb5cb34ce6cfbbcbf.json"}}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2025-08-17", "journal": {"title": "Plant Biotechnol. J.", "issn": "1467-7652", "issn-l": "1467-7644"}, "abstract": "Wood is the most abundant renewable natural resource composed of different polysaccharides and lignin, but its utilisation is hampered by intermolecular linkages between these components forming lignin-carbohydrate complexes (LCCs) causing recalcitrance. The links between glucuronoxylan and the \u03b3-C of lignin (\u03b3-ester linkages) are thought to contribute to one-third of LCCs, but direct evidence for their natural occurrence and their role in recalcitrance has been scarce so far. To address these issues, Phanerochaete carnosa glucuronoyl esterase (PcGCE), hydrolysing \u03b3-ester linkages, was expressed in cell walls of developing wood in hybrid aspen (Populus tremula L. \u00d7 tremuloides Michx.). The enzyme reduced HSQC 2D NMR signals corresponding to the \u03b3-esters and xylan in dioxane-extracted LCCs without altering glucuronoxylan content or structure. This increased acid solubility of lignin and lignin content. Reduced wood recalcitrance was shown by increased sugar yields and glucose production rates (by approx. 20%) in saccharification without pretreatment and increased xylan extractability by subcritical water (by approx. 70%). Moreover, trees expressing PcGCE exhibited greater primary and secondary growth. Transcriptomics and metabolomics analyses in developing wood suggested that growth could have been induced by a higher transcription of SMR2 and RPOTmp, which was likely triggered by the secondary cell wall integrity signalling. The results provide evidence for the natural existence of LCC \u03b3-esters and their significant contribution to lignocellulose recalcitrance. Furthermore, they show that reducing \u03b3-ester linkages could increase plant productivity.", "doi": "10.1111/pbi.70301", "pmid": "40819283", "labels": {"Swedish NMR Centre": "Collaborative", "Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-10T14:26:46.012Z", "modified": "2025-11-18T12:07:29.246Z"}, {"entity": "publication", "iuid": "b523e0bb42a74513b082b7459e71438f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b523e0bb42a74513b082b7459e71438f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b523e0bb42a74513b082b7459e71438f"}}, "title": "Image based subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing.", "authors": [{"family": "Tampere", "given": "Marianna", "initials": "M"}, {"family": "H Le", "given": "Trang", "initials": "T"}, {"family": "Asp", "given": "Elin", "initials": "E"}, {"family": "Kalman", "given": "Adelinn", "initials": "A"}, {"family": "Kaimal", "given": "Jayasankar Mohanakrishnan", "initials": "JM"}, {"family": "Njenda", "given": "Duncan", "initials": "D", "orcid": "0000-0001-8276-9726", "researcher": {"href": "https://publications.scilifelab.se/researcher/c14c27f4d60549da9949c97ed66a15b5.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e276634741d45249c7cec0b46a7d9f4.json"}}, {"family": "Axelsson", "given": "Hanna", "initials": "H", "orcid": "0000-0003-2365-1749", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b88c4d11c443f39121c6d93fcff1f0.json"}}, {"family": "Marabita", "given": "Francesco", "initials": "F", "orcid": "0000-0001-6180-0106", "researcher": {"href": "https://publications.scilifelab.se/researcher/05a6497e6561419f86f3227618e536fa.json"}}, {"family": "Moussaud-Lamodi\u00e8re", "given": "Elisabeth", "initials": "E", "orcid": "0000-0002-2359-6519", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a0f932253042239c1d38ea00ca0018.json"}}, {"family": "Sepulveda", "given": "Carolina Oses", "initials": "CO", "orcid": "0000-0001-8194-1168", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9dd54ba67d4f10a5ba6d0b4ede67bc.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4645bc97a8024c548111802101b83571.json"}}, {"family": "Vernersson", "given": "Caroline", "initials": "C"}, {"family": "Mirazimi", "given": "Ali", "initials": "A"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0001-5501-466X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0461a910ec4b4faa8668bb4044e76f61.json"}}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}], "type": "journal article", "published": "2025-08-16", "journal": {"title": "Biomed Pharmacother", "issn": "1950-6007", "volume": "191", "pages": "118447", "issn-l": null}, "abstract": "The COVID-19 pandemic has resulted in millions of deaths and affected socioeconomic structure worldwide and the search for new antivirals and treatments are still ongoing. In the search for new drug targets and to increase our understanding of the disease, we applied large-scale immunofluorescence profiling to explore host cell response to SARS-CoV-2 infection. Among the 602 host proteins studied in this host response profiling, changes in abundance and subcellular localization were observed for 97 proteins, with 45 proteins showing increased abundance and 10 reduced abundance. 20 proteins displayed changed localization upon infection and an additional 22 proteins displayed altered abundance and localization, together contributing to diverse reshuffling of the host cell protein landscape during infection. We then selected existing and approved small-molecule drugs (n = 123) against our identified host response proteins and identified one compound - elesclomol, that significantly reduced antiviral activity. Our study introduces a novel, targeted and systematic approach based on host protein profiling, to identify new targets for drug repurposing. The dataset of > 100,000 immunofluorescence images from this study are published as a resource available for further studies. AUTHOR SUMMARY: In this study we have evaluated a new approach for identifying drugs that could be used as antiviral drugs, in this case demonstrated for SARS CoV-2. By mining the literature for reported interactions between SARS CoV-2 viral components and host cell proteins, we identified a few hundred host proteins suggested to interact with the virus upon infection. To explore these viral-host interaction proteins further, we developed an image based assay using immunofluorescence and confocal microscopy to visualize the host proteins within infected and non infected cells. This was possible due to the proteome wide collection of antibodies generated within the Human Protein Atlas project, with the aim to systematically map the human proteome in cells and across tissues. The host proteins that altered their location or abundance level upon infection were regarded as putative targets for drug repurposing and we subsequently tested 123 drugs that were targeting a subset of these host proteins. Applying these drugs on two different cell types infected with SARS-CoV-2, revealed a non toxic antiviral effect for one compound that can be explored further as a treatment regimen for SARS-CoV-2 infection. The approach is novel since it combines a targeted approach for drug repurposing screening, giving insight into mechanism of action from start. As such it has the potential to accelerate drug repurposing or identification of targets for new drugs.", "doi": "10.1016/j.biopha.2025.118447", "pmid": "40819539", "labels": {"Spatial Proteomics": "Collaborative", "Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0753-3322(25)00641-9"}], "notes": [], "created": "2025-08-19T14:16:21.879Z", "modified": "2025-10-17T13:04:26.503Z"}, {"entity": "publication", "iuid": "f317e27f226041d0a08da9a63eb7e924", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f317e27f226041d0a08da9a63eb7e924.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f317e27f226041d0a08da9a63eb7e924"}}, "title": "Body weight reduction by increased weight loading in mice is associated with sensory signaling in the dorsal horn of the lumbar spinal cord.", "authors": [{"family": "Anesten", "given": "Fredrik", "initials": "F"}, {"family": "Zlatkovic", "given": "Jovana", "initials": "J"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "L\u00f6ken", "given": "Line", "initials": "L"}, {"family": "H\u00e4gg", "given": "Daniel", "initials": "D"}, {"family": "Jansson", "given": "John-Olov", "initials": "JO"}], "type": "journal article", "published": "2025-08-16", "journal": {"title": "Neuroscience", "issn": "1873-7544", "volume": "581", "pages": "157-163", "issn-l": null}, "abstract": "Previously, we demonstrated that increased weight loading suppresses body weight and food intake in rodents. Our earlier studies suggested that the hind limbs sense this increased load and transmit signals to the Nucleus of the Solitary Tract (NTS) in the brainstem. However, the pathway of this signal transmission was unclear. To investigate if sensory neurons contribute to this signaling, mice were implanted subcutaneously with two capsules weighing \u223c15 % (Load) or \u223c2.5 % (Control) of their body weight in total. Five days post-implantation, neuronal activation was measured by FosB immunoreactivity. An increase of FosB expression was found in Load mice compared to Control specifically at the lumbar L3-L5 segments in the superficial laminae (I-III) of the dorsal horn (DH). These segments receive input via sensory nerves from deeper parts of the hind limbs. Intrathecal injection of the drug capsaicin, blocking sensory nerve signaling, at L3-L5 attenuated Load-induced FosB expression at the lumbar L3-L5 segments and body weight reduction. In summary, increased weight loading increases FosB expression at segments L3-L5 of the DH and reduces body weight via sensory nerves. We propose that increased weight loading enhances compression of weight-bearing bones in the hind limbs, resulting in sensory nerve transmission to cell bodies in L3-L5, which in turn reduces food intake and body weight.", "doi": "10.1016/j.neuroscience.2025.07.009", "pmid": "40645323", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S0306-4522(25)00771-7"}], "notes": [], "created": "2025-11-05T13:27:12.078Z", "modified": "2025-11-05T13:27:12.191Z"}, {"entity": "publication", "iuid": "4c1a02cb06334542b3c2ae4a126bf000", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c1a02cb06334542b3c2ae4a126bf000.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c1a02cb06334542b3c2ae4a126bf000"}}, "title": "Setting up mother-infant pair lactation studies with biobanking for research according to regulatory requirements.", "authors": [{"family": "Hansson", "given": "Mats", "initials": "M", "orcid": "0000-0002-4053-8468", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6d5921e61b44f85ba27bbb3f00029c4.json"}}, {"family": "Bj\u00f6rkgren", "given": "Ida", "initials": "I", "orcid": "0000-0001-6678-2672", "researcher": {"href": "https://publications.scilifelab.se/researcher/005fcf59837243adb45d09cf066fe6dd.json"}}, {"family": "Svedenkrans", "given": "Jenny", "initials": "J", "orcid": "0000-0002-6194-5118", "researcher": {"href": "https://publications.scilifelab.se/researcher/5659e409f229463a85dfd25655907503.json"}}, {"family": "Backman", "given": "Helena", "initials": "H", "orcid": "0000-0002-2691-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/018d1cdcba874cd7a0a587d3f99a0e22.json"}}, {"family": "Hellman", "given": "Jarl", "initials": "J", "orcid": "0000-0001-6187-5511", "researcher": {"href": "https://publications.scilifelab.se/researcher/66f3b000e6ac4a928cdabf4e91d53a5f.json"}}, {"family": "Englund-\u00d6gge", "given": "Linda", "initials": "L", "orcid": "0000-0001-8334-2070", "researcher": {"href": "https://publications.scilifelab.se/researcher/eedec4bed3034b2d9885f41a4a0df99f.json"}}, {"family": "Magnusson", "given": "Mikaela", "initials": "M"}, {"family": "Lindstr\u00f6m", "given": "Inger", "initials": "I"}, {"family": "Wutte", "given": "Andrea", "initials": "A"}, {"family": "Sundell", "given": "Erica", "initials": "E"}, {"family": "Baranczewski", "given": "Pawel", "initials": "P", "orcid": "0000-0001-5772-6791", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f7af2466c14275a42aad4a431b2dcb.json"}}, {"family": "Shaughnessy", "given": "Laura", "initials": "L"}], "type": "case reports", "published": "2025-08-15", "journal": {"title": "Br J Clin Pharmacol", "issn": "1365-2125", "issn-l": null}, "abstract": "Within the ConcePTION project we set out to design two mother-infant pair studies collecting breast milk and plasma from the mother and plasma from the infant (for metformin and prednisolone) in order to demonstrate the premises and conditions for investigating potential drug transfer in association with breastfeeding. It is essential that the information from lactation studies is trustworthy and fulfils regulatory standards and requirements for the results to be fit for label. In this paper we describe the premises and conditions for mother-infant pair studies and biobanking for research of collected samples as laid down in regulatory requirements. The studies on metformin are still ongoing. At the time of the study (June 2025), 18 participants had been included in the metformin study and 20 in the prednisolone study. Evidence for the use of medicines in association with breastfeeding is urgently needed, both for already approved and used drugs, and for the development of new drugs. Based on our experiences within the IMI-ConcePTION project, we have described the premises for mother-infant pair studies to be adhered to.", "doi": "10.1002/bcp.70201", "pmid": "40817578", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-08-25T10:22:04.716Z", "modified": "2025-10-17T13:05:07.223Z"}, {"entity": "publication", "iuid": "4cb1f3bbbd73476d85743dd1a3b24932", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932"}}, "title": "Early germline sequestration in a basidiomycete fungus.", "authors": [{"family": "Thor\u00e9n", "given": "Markus Hiltunen", "initials": "MH", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Olsson", "given": "Boel", "initials": "B", "orcid": "0009-0006-4157-2664", "researcher": {"href": "https://publications.scilifelab.se/researcher/219a75999b65464ca3d405ac20898743.json"}}, {"family": "Vonk", "given": "Peter Jan", "initials": "PJ", "orcid": "0000-0001-5325-7430", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5684212a1f5478cab0943d5064e74a7.json"}}, {"family": "Siljestam", "given": "Mattias", "initials": "M", "orcid": "0000-0002-3720-4926", "researcher": {"href": "https://publications.scilifelab.se/researcher/653d5e0ec2bc4925a19db2697ad61a2d.json"}}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-1518-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/db7ebacfd8764a988ee41f2e5ab23e50.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2025-08-14", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "389", "issue": "6761", "pages": "720-723"}, "abstract": "In sexual organisms, inheritance of new mutations is highly dependent on the timing of germline definition. Here, we used the fairy ring-forming fungus Marasmius oreades to challenge the general assumption of a late germline separation in the Fungi. We collected mushrooms from different parts of rings over a 7-year period and identified new mutations in different tissues by whole-genome sequencing. We found evidence that fertile and sterile tissues had accumulated different mutations, suggesting that the germ line, destined for spore production, is already defined in the mycelium in this species. Moreover, the germ line carried fewer mutations than sterile tissues, indicating a lower mutation rate. Our findings suggest that early germline sequestration is more widespread than previously considered across multicellular life.", "doi": "10.1126/science.adu8580", "pmid": "40811541", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-08-29T12:41:10.841Z", "modified": "2025-11-21T13:14:48.967Z"}, {"entity": "publication", "iuid": "f6b93bc63d7447ab8768a84e8c6aa42a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6b93bc63d7447ab8768a84e8c6aa42a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6b93bc63d7447ab8768a84e8c6aa42a"}}, "title": "Systems analysis of clinical malaria reveals proteomic perturbation and innate-adaptive crosstalk linked to disease severity.", "authors": [{"family": "Lautenbach", "given": "Maximilian Julius", "initials": "MJ"}, {"family": "Wyss", "given": "Katja", "initials": "K"}, {"family": "Yman", "given": "Victor", "initials": "V"}, {"family": "Foroogh", "given": "Fariba", "initials": "F"}, {"family": "Satarvandi", "given": "Donya", "initials": "D"}, {"family": "Mousavian", "given": "Zaynab", "initials": "Z"}, {"family": "Sond\u00e9n", "given": "Klara", "initials": "K"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Sundling", "given": "Christopher", "initials": "C"}, {"family": "F\u00e4rnert", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-08-12", "journal": {"title": "Immunity", "issn": "1097-4180", "issn-l": "1074-7613", "volume": "58", "issue": "8", "pages": "2120-2136.e5"}, "abstract": "Malaria presents with varying degrees of severity. To improve clinical management and prevention, it is crucial to understand the pathogenesis and host response. We analyzed 1,463 plasma proteins during and after acute Plasmodium falciparum malaria in adult travelers and linked responses to peripheral immune cells by integrating with single-cell RNA sequencing (RNA-seq) data from a subset of donors. We identified extensive perturbations in over 250 proteins with diverse origins, including many not previously analyzed in malaria patients, such as hormones, circulating receptors, and intracellular or membrane-bound proteins from affected tissues. The protein profiles clustered participants according to disease severity, enabling the identification of a compressed 11-protein signature enriched in severe malaria. Conceptually, this study advances our understanding of malaria by linking systemic proteomic changes to immune cell communication and organ-specific responses. This resource, which includes an interactive platform to explore data, opens new avenues for hypothesis generation, biomarker discovery, and therapeutic target identification.", "doi": "10.1016/j.immuni.2025.06.014", "pmid": "40664217", "labels": {"Affinity Proteomics Stockholm": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Affinity Proteomics Uppsala": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(25)00283-3"}], "notes": [], "created": "2025-11-17T08:54:30.240Z", "modified": "2025-11-26T11:07:57.819Z"}, {"entity": "publication", "iuid": "2919c9b7380148cc900abda76763fd0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2919c9b7380148cc900abda76763fd0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2919c9b7380148cc900abda76763fd0a"}}, "title": "Epigenetic control of topoisomerase 1 activity presents a cancer vulnerability.", "authors": [{"family": "Lee", "given": "Tae-Hee", "initials": "TH", "orcid": "0000-0002-6263-6499", "researcher": {"href": "https://publications.scilifelab.se/researcher/b33aadc34b0e4884923829c5b183bc68.json"}}, {"family": "Qiao", "given": "Colina X", "initials": "CX"}, {"family": "Kuzin", "given": "Vladislav", "initials": "V"}, {"family": "Shi", "given": "Yuepeng", "initials": "Y"}, {"family": "Farkas", "given": "Marina", "initials": "M"}, {"family": "Zhao", "given": "Zhiyan", "initials": "Z"}, {"family": "Ramanarayanan", "given": "Vijayalalitha", "initials": "V"}, {"family": "Wu", "given": "Tongyu", "initials": "T"}, {"family": "Guan", "given": "Tianyi", "initials": "T"}, {"family": "Zhou", "given": "Xianzhen", "initials": "X", "orcid": "0009-0005-9862-6347", "researcher": {"href": "https://publications.scilifelab.se/researcher/10a47cfaa39147f98dfba981bb218c47.json"}}, {"family": "Corujo", "given": "David", "initials": "D", "orcid": "0000-0001-7930-0935", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f4d5e98aee5476d8f155afb367bb5cb.json"}}, {"family": "Buschbeck", "given": "Marcus", "initials": "M", "orcid": "0000-0002-3218-4567", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab121e4ccfe74986af0ed6dffaf4daf2.json"}}, {"family": "Baranello", "given": "Laura", "initials": "L", "orcid": "0000-0001-6039-1849", "researcher": {"href": "https://publications.scilifelab.se/researcher/a33e20ca8e284b5db1cca13e5e6d7940.json"}}, {"family": "Oberdoerffer", "given": "Philipp", "initials": "P", "orcid": "0000-0002-2484-1440", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fe8cc357c67450e885f33db1f83fdbc.json"}}], "type": "journal article", "published": "2025-08-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "7458", "issn-l": "2041-1723"}, "abstract": "DNA transactions introduce torsional constraints that pose an inherent risk to genome integrity. While topoisomerase 1 (TOP1) activity is essential for DNA supercoil removal, the aberrant stabilization of TOP1:DNA cleavage complexes (TOP1ccs) can result in cytotoxic DNA lesions. What protects genomic hot spots of topological stress from excessive TOP1cc accumulation remains unknown. Here, we identify chromatin context as an essential means to coordinate TOP1cc resolution. Through its ability to bind poly(ADP-ribose) (PAR), the histone variant macroH2A1.1 facilitates TOP1cc repair factor recruitment and lesion turnover, thereby preventing DNA damage in response to transcription-associated topological stress. The alternatively spliced macroH2A1.2 isoform is unable to bind PAR or protect from TOP1ccs. Impaired macroH2A1.1 splicing, a frequent cancer feature, was predictive of increased sensitivity to TOP1 poisons in a pharmaco-genomic screen in breast cancer cells, and macroH2A1.1 inactivation mirrored this effect. We propose macroH2A1 alternative splicing as an epigenetic modulator of TOP1-associated genome maintenance and a potential cancer vulnerability.", "doi": "10.1038/s41467-025-62598-w", "pmid": "40796804", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12343833"}, {"db": "pii", "key": "10.1038/s41467-025-62598-w"}], "notes": [], "created": "2025-11-28T10:45:50.886Z", "modified": "2025-11-28T10:45:51.087Z"}, {"entity": "publication", "iuid": "a58a549ff82149ffa87c6ec256ec94ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a58a549ff82149ffa87c6ec256ec94ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a58a549ff82149ffa87c6ec256ec94ef"}}, "title": "Unraveling Nitrogen Uptake and Metabolism: Gene Families, Expression Dynamics, and Functional Insights in Aspen (Populus tremula).", "authors": [{"family": "Zhang", "given": "Yupeng", "initials": "Y", "orcid": "0000-0001-9461-8554", "researcher": {"href": "https://publications.scilifelab.se/researcher/307e4bb258054d37bda861e64d5f893f.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S"}, {"family": "Renstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Luomaranta", "given": "Mikko", "initials": "M"}, {"family": "Chantreau", "given": "Maxime", "initials": "M"}, {"family": "Fleig", "given": "Verena", "initials": "V"}, {"family": "Gaboreanu", "given": "Ioana", "initials": "I"}, {"family": "Grones", "given": "Carolin", "initials": "C"}, {"family": "Nilsson", "given": "Ove", "initials": "O", "orcid": "0000-0002-1033-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/729146afe5e24eb0a6f107db10e95e01.json"}}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "Tuominen", "given": "Hannele", "initials": "H", "orcid": "0000-0002-4949-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d.json"}}], "type": "journal article", "published": "2025-08-11", "journal": {"title": "Tree Physiol", "issn": "1758-4469", "issn-l": "0829-318X"}, "abstract": "The influence of nitrogen on wood formation is well established. To gain insight into the underlying molecular mechanism, we first identified genes in fourteen gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. This study provides insight into the genetic basis of nitrogen uptake and assimilation and its connection to wood formation, providing interesting targets for improving nitrogen use efficiency and growth of aspen trees.", "doi": "10.1093/treephys/tpaf099", "pmid": "40795931", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "8230290"}], "notes": [], "created": "2025-08-29T10:02:04.420Z", "modified": "2025-11-14T11:08:03.834Z"}, {"entity": "publication", "iuid": "c1a6072bf7ac4b2ab7b22b6938ed192f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1a6072bf7ac4b2ab7b22b6938ed192f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1a6072bf7ac4b2ab7b22b6938ed192f"}}, "title": "Significant Interplay Between Lipids, Cytokines, Chemokines, Growth Factors, and Blood Cells in an Outpatient Cohort.", "authors": [{"family": "Eriksson", "given": "Mats B", "initials": "MB", "orcid": "0000-0002-3178-4210", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfcf6caaeeea422997c259d802e7e6f8.json"}}, {"family": "Eriksson", "given": "Lars B", "initials": "LB", "orcid": "0009-0002-1818-7347", "researcher": {"href": "https://publications.scilifelab.se/researcher/44d17c21be93409fb4d5bc5de121b497.json"}}, {"family": "Larsson", "given": "Anders O", "initials": "AO", "orcid": "0000-0003-3161-0402", "researcher": {"href": "https://publications.scilifelab.se/researcher/2276de26382b402aa384ac231f30f156.json"}}], "type": "journal article", "published": "2025-08-11", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "16", "issn-l": null}, "abstract": "Cardiovascular disease (CVD) remains the leading global cause of morbidity and mortality, largely driven by atherosclerosis, a chronic inflammatory process involving lipids and immune cells. Although traditional lipid biomarkers such as low-density lipoprotein (LDL) and high-density lipoprotein (HDL) are well-established in CVD risk stratification, the interplay between cytokines, chemokines, growth factors (CCGFs), lipid metabolism, and hematological parameters in non-cardiac populations remains underexplored. We investigated associations between plasma cytokines and lipid-related biomarkers and their relationships with circulating blood cell counts in a cohort of 164 essentially healthy adults aged 18-44 years. CCGF profiling was performed using a proximity extension assay (PEA), and statistical correlations were adjusted for multiple testing using false discovery rate (FDR) correction. The CCGFs that were associated with HDL and apolipoprotein A1 all displayed negative associations. Several pro-inflammatory cytokines, including CCL3, IL-6, and TNFSF10, showed strong positive associations with triglycerides, remnants, non-HDL, and body mass index (BMI). Furthermore, triglycerides and remnants were consistently correlated with elevated leukocyte, neutrophil, and platelet counts. HGF and FGF-21, mainly considered as anti-inflammatory, were positively associated with BMI and negatively associated with HDL, which is compliant with a multitude of actions, depending on the local milieu and the cellular interplay. Our results support the existence of a complex immunometabolic network involving lipids, CCGFs, and blood cells, even in non-diseased individuals. The observed patterns underscore the importance of understanding the intricate cytokine-lipid-cell interactions that may occur in early pathophysiological processes and highlight their potential utility in refining cardiovascular risk assessment beyond traditional lipid metrics.", "doi": "10.3390/ijms26167746", "pmid": "40869066", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12387115"}, {"db": "pii", "key": "ijms26167746"}], "notes": [], "created": "2025-11-25T19:21:46.609Z", "modified": "2025-11-25T19:21:46.738Z"}, {"entity": "publication", "iuid": "741f4c91234245268da4ddfa1e0b9efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/741f4c91234245268da4ddfa1e0b9efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/741f4c91234245268da4ddfa1e0b9efa"}}, "title": "Lrig3-deficient mice exhibit strain-specific alterations in liver fat accumulation, intestinal morphology, and middle ear inflammation.", "authors": [{"family": "Herdenberg", "given": "Carl", "initials": "C"}, {"family": "Henriksson", "given": "Roger", "initials": "R"}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0001-6891-6996", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b1b2d57a55e415aa17acbd0318a019e.json"}}, {"family": "Rondahl", "given": "Veronica", "initials": "V"}], "type": "journal article", "published": "2025-08-10", "journal": {"title": "Gene", "issn": "1879-0038", "issn-l": "0378-1119", "volume": "960", "issue": null, "pages": "149539"}, "abstract": "The transmembrane protein leucine-rich repeats and immunoglobulin-like domains 3 (LRIG3) regulates fat metabolism and bone morphogenetic protein (BMP) signaling. Lrig3-deficient mice exhibit impaired development of the snout and the inner ear lateral canal, neural defects, and cardiac hypertrophy in adulthood. However, no thorough and unbiased analysis of the physiological functions of Lrig3 has previously been performed. To address this knowledge gap, we performed histopathological examination of 42 tissues and organs from 1-year-old female C57BL/6JBomTac and 129S1-U mice with different Lrig3 genotypes. Among the scored pathologies, three were significantly associated with Lrig3 genotype: spontaneous macrovesicular hepatocellular degeneration (hepatocellular steatosis) was less prevalent in Lrig3-deficient C57BL/6JBomTac mice, whereas dilated or flaccid ileum and otitis media were more common in Lrig3-deficient 129S1-U mice. To further investigate hepatic steatosis phenotypes, 8-week-old C57BL/6JBomTac mice of both sexes and different Lrig3 genotypes were subjected to consuming a high-fat diet (HFD) for 8 weeks. The HFD regimen led to relatively few cases of hepatocellular steatosis, with no significant differences among the genotypes; however, female Lrig3-deficient mice presented reduced microvesicular hepatocellular degeneration compared with their wild-type littermates. This study revealed that Lrig3 regulates liver fat accumulation, intestinal morphology, and middle ear inflammation in a mouse strain-dependent manner.", "doi": "10.1016/j.gene.2025.149539", "pmid": "40320098", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S0378-1119(25)00327-0"}], "notes": [], "created": "2025-09-08T07:06:55.862Z", "modified": "2025-11-19T13:14:56.377Z"}, {"entity": "publication", "iuid": "60643192a0e04fbe8262b3c6e3cfce9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60643192a0e04fbe8262b3c6e3cfce9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60643192a0e04fbe8262b3c6e3cfce9e"}}, "title": "Ribosome biogenesis in plants requires the nuclear envelope and mitochondria localized OPENER complex.", "authors": [{"family": "Wang", "given": "Wei", "initials": "W", "orcid": "0000-0003-3400-4889", "researcher": {"href": "https://publications.scilifelab.se/researcher/df33096e9d6345469215380ba9b8ff55.json"}}, {"family": "Mahboubi", "given": "Amir", "initials": "A", "orcid": "0000-0002-0660-0555", "researcher": {"href": "https://publications.scilifelab.se/researcher/75a9b8d8749843c2b908b8712e39096e.json"}}, {"family": "Zhu", "given": "Shaochun", "initials": "S", "orcid": "0000-0001-9945-6718", "researcher": {"href": "https://publications.scilifelab.se/researcher/50c472868ea0437bb9a5a1b0a574bc39.json"}}, {"family": "Hanson", "given": "Johannes", "initials": "J", "orcid": "0000-0002-5605-7984", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d9c9973ca994461ad9f5c27b4341ddb.json"}}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-6870-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/d79942eca68f4b2d8c2e72cf258f1213.json"}}, {"family": "Niittyl\u00e4", "given": "Totte", "initials": "T", "orcid": "0000-0001-8029-1503", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2b8823dc6cf44eaa309fcf157b1f28a.json"}}], "type": "journal article", "published": "2025-08-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "7301", "issn-l": "2041-1723"}, "abstract": "Eukaryotic ribosome biogenesis proceeds from nucleolus to cytosol assisted by various assembly factors. The process is evolutionarily conserved across eukaryotes but differences between the kingdoms are emerging. Here, we describe how the OPENER (OPNR) protein complex is required for 60S ribosome assembly in the model plant Arabidopsis thaliana. The complex is observed on both nuclear envelope and mitochondria, and contains OPNR, OPENER ASSOCIATED PROTEIN 1 (OAP1), OAP2, Cell Division Cycle 48 D (CDC48D) and Calmodulin-interacting protein 111 (CIP111). Depletion of the OPNR complex components results in reproductive lethality and cytoplasmic retention of assembly factors on 60S ribosomes. Subsequent biochemical analyses and structural modelling suggest that OPNR, OAP1 and OAP2 form a claw-like trimer which grabs the ribosome assembly factor RIBOSOMAL PROTEIN L24C (RPL24C) on the pre-60S ribosome. Our results reveal previously unrecognised subcellular complexity of ribosome biogenesis in plants, and point to mitochondria association as a feature to ensure sufficient translational capacity.", "doi": "10.1038/s41467-025-62652-7", "pmid": "40775240", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12332008"}, {"db": "pii", "key": "10.1038/s41467-025-62652-7"}], "notes": [], "created": "2025-08-12T07:59:40.338Z", "modified": "2025-08-12T07:59:41.047Z"}, {"entity": "publication", "iuid": "d55fcfdd3aa04ce7988e0a08c686feee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d55fcfdd3aa04ce7988e0a08c686feee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d55fcfdd3aa04ce7988e0a08c686feee"}}, "title": "Inflammation-profiling reveals activated pathways and biomarkers with predictive potential in oligoarticular juvenile idiopathic arthritis.", "authors": [{"family": "Wen", "given": "Xingzhao", "initials": "X"}, {"family": "Aulin", "given": "Cecilia", "initials": "C"}, {"family": "Sundberg", "given": "Erik", "initials": "E"}, {"family": "Qu", "given": "Heshuang", "initials": "H"}, {"family": "Struglics", "given": "Andr\u00e9", "initials": "A"}, {"family": "Merritt", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Altman", "given": "Maria", "initials": "M"}, {"family": "Harris", "given": "Helena Erlandsson", "initials": "HE"}], "type": "journal article", "published": "2025-08-07", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1599747", "issn-l": "1664-3224"}, "abstract": "We set out to profile the immune mechanisms active in treatment-na\u00efve oligoarticular JIA (oJIA) to improve the knowledge of its immunopathogenesis, to identify potential biomarkers that can aid diagnosis, predictions and that correlate with clinical disease parameters.\n\nUsing Olink proteomics (inflammation panel measuring 92 markers), we defined and compared the inflammation profiles of 38 plasma and 62 synovial fluid (SF) oJIA samples, 38 plasma samples from healthy age- and sex-matched controls (HC), 12 SF samples from non-arthritic controls and 26 SF samples from knee injury patients. Clinical data for the oJIA cohort were retrieved from the Swedish pediatric rheumatology quality register and medical charts.\n\nPlasma inflammation profiles of oJIA and HC were largely overlapping, with IL6 and MMP-1 significantly upregulated in oJIA. In SF, 48 differentially expressed proteins (DEPs) were identified in oJIA, highlighting immune pathways like leukocyte migration, cell chemotaxis and adaptive immunity. Comparative analysis revealed 13 proteins specific to oJIA. Correlations were found between DEPs in oJIA SF and clinical parameters (cJADAS-71, pain, health impact score). In plasma, IL6 and MMP-1 showed strong correlation with disease activity and pain, respectively. CXCL9, CXCL10 and CXCL11 were identified as potential predictive biomarkers for disease progression.\n\nThe overlap in plasma inflammation profiles of oJIA and HCs suggests local rather than systemic inflammation in oJIA and underlines the need to study oJIA immunopathogenesis using SF samples. The oJIA SF inflammation profiles indicative of adaptive immune reactions separated oJIA from knee-injury patients and can be exploited for diagnostic purposes. Increased SF levels of CXCL9, CXCL10 and CXCL11 were associated with chronic disease progression and could serve as prognostic biomarkers and early treatment targets.", "doi": "10.3389/fimmu.2025.1599747", "pmid": "40852723", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12367756"}], "notes": [], "created": "2025-11-25T21:26:18.099Z", "modified": "2025-11-25T21:26:18.110Z"}, {"entity": "publication", "iuid": "3a76478c25bc4050bf24534f1284a51e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a76478c25bc4050bf24534f1284a51e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a76478c25bc4050bf24534f1284a51e"}}, "title": "Implementing a Nordic-Baltic Federated Health Data Network: A Case Report.", "authors": [{"family": "Chomutare", "given": "Taridzo", "initials": "T"}, {"family": "Barbic", "given": "Aleksandar", "initials": "A"}, {"family": "Peltonen", "given": "Laura-Maria", "initials": "LM"}, {"family": "Elunurm", "given": "Silja", "initials": "S"}, {"family": "Lundberg", "given": "Peter", "initials": "P"}, {"family": "J\u00f6nsson", "given": "Arne", "initials": "A"}, {"family": "Eneling", "given": "Emma", "initials": "E"}, {"family": "Gerstenberger", "given": "Ciprian-Virgil", "initials": "CV"}, {"family": "Siggaard", "given": "Troels", "initials": "T"}, {"family": "Kolde", "given": "Raivo", "initials": "R"}, {"family": "Jerdhaf", "given": "Oskar", "initials": "O"}, {"family": "Hansson", "given": "Martin", "initials": "M"}, {"family": "Makhlysheva", "given": "Alexandra", "initials": "A"}, {"family": "Muzny", "given": "Miroslav", "initials": "M"}, {"family": "Ylip\u00e4\u00e4", "given": "Erik", "initials": "E"}, {"family": "Brunak", "given": "S\u00f8ren", "initials": "S"}, {"family": "Dalianis", "given": "Hercules", "initials": "H"}], "type": "journal article", "published": "2025-08-07", "journal": {"title": "Stud Health Technol Inform", "issn": "1879-8365", "volume": "329", "pages": "1241-1245", "issn-l": null}, "abstract": "Centralized collection and processing of healthcare data across national borders pose significant challenges, including privacy concerns, data heterogeneity, and legal barriers. To study some of these challenges, we formed an interdisciplinary consortium to develop a federated health data network, comprised of six institutions across five countries, to facilitate Nordic-Baltic cooperation on secondary use of health data. The objective of this report is to offer early insights into our experiences developing this network. We employed a mixed-methods approach, combining both experimental design and implementation science to assess the factors influencing the implementation of our network. Technically, our experiments indicate that the network functions without significant performance degradation compared to centralized simulation. While use of interdisciplinary approaches holds a potential to solve challenges associated with establishing such collaborative networks, our findings turn the spotlight on the uncertain regulatory landscape playing catch up and the significant operational costs.", "doi": "10.3233/SHTI251037", "pmid": "40776055", "labels": {"AIDA Data Hub": "Service"}, "xrefs": [{"db": "pii", "key": "SHTI251037"}], "notes": [], "created": "2025-11-25T13:14:10.464Z", "modified": "2025-11-25T13:14:10.488Z"}, {"entity": "publication", "iuid": "9acee79fe2d04a89b9bbe5324622bbbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9acee79fe2d04a89b9bbe5324622bbbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9acee79fe2d04a89b9bbe5324622bbbe"}}, "title": "Insulin resistance as a potential driving force of parental obesity-induced adverse metabolic programming mechanisms in children with obesity.", "authors": [{"family": "Jurado-Sumariva", "given": "Luc\u00eda", "initials": "L"}, {"family": "Gonz\u00e1lez-Dom\u00ednguez", "given": "\u00c1lvaro", "initials": "\u00c1"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Dom\u00ednguez-Riscart", "given": "Jes\u00fas", "initials": "J"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Gonz\u00e1lez-Dom\u00ednguez", "given": "Ra\u00fal", "initials": "R"}], "type": "journal article", "published": "2025-08-05", "journal": {"title": "BMC Med", "issn": "1741-7015", "volume": "23", "issue": "1", "pages": "458", "issn-l": "1741-7015"}, "abstract": "Parental obesity has been identified as one of the most important early risk factors for childhood obesity, but molecular mechanisms driving this greater predisposition remain to be elucidated.\n\nIn this study, we recruited a cohort comprising children with obesity (body mass index over two z-scores above the age/sex-adjusted mean of the Spanish reference population, age range: 6-12 years), born to parents with obesity (N = 18) or without obesity (N = 41), as well as matched healthy controls (N = 26). Plasma and erythrocyte samples were collected for comprehensive biochemical and metabolomics analyses, this latter by applying high-throughput liquid chromatography-mass spectrometry. Then, a combination of multivariate and univariate statistical tools was applied to unravel the molecular pathogenic impairments that parental obesity may imprint in the offspring.\n\nInterestingly, we found parental obesity to be associated with exacerbated unhealthy metabolic outcomes in the offspring with obesity, as mirrored in higher fasting insulin levels (p = 2.8 \u00d7 10-8) and HOMA-IR scores (p = 1.3 \u00d7 10-8). This was in turn accompanied by altered concentrations in 87 plasma and 51 erythroid metabolites (p < 0.05) involved in a variety of obesity-related pathways that are known to be tightly regulated by insulin action, namely energy-related metabolism, branched-chain amino acids, nitrogen homeostasis, redox systems, and steroid synthesis (i.e., steroid hormones, bile acids). Additional analyses demonstrated that most metabolomics associations were largely attenuated after adjusting for the HOMA-IR scores.\n\nTherefore, we hypothesize that insulin resistance could be a major driving force in mediating deleterious programming mechanisms induced by parental obesity in the offspring.", "doi": "10.1186/s12916-025-04282-w", "pmid": "40764579", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12326771"}, {"db": "pii", "key": "10.1186/s12916-025-04282-w"}], "notes": [], "created": "2025-11-27T11:24:05.491Z", "modified": "2025-11-27T11:24:05.508Z"}, {"entity": "publication", "iuid": "ab9b4fd3312a411fa7600da6cc9fc651", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651"}}, "title": "Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling.", "authors": [{"family": "Wenson", "given": "Leonie", "initials": "L", "orcid": "0000-0002-1864-1258", "researcher": {"href": "https://publications.scilifelab.se/researcher/989e0534adbd426386cec5526c5e9668.json"}}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Erbilgin", "given": "Y\u00fccel", "initials": "Y"}, {"family": "Salman", "given": "Bar\u0131\u015f", "initials": "B", "orcid": "0000-0002-7657-8576", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb919f7fcc794c8898fe800056d42f38.json"}}, {"family": "Sundqvist", "given": "Anders", "initials": "A"}, {"family": "Schaal", "given": "Wesley", "initials": "W", "orcid": "0000-0001-6770-0878", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab184845a24f4effb22ec2b338ab8960.json"}}, {"family": "Sandbaumh\u00fcter", "given": "Friederike A", "initials": "FA"}, {"family": "Jansson", "given": "Erik T", "initials": "ET"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Davidsson", "given": "Anton", "initials": "A"}, {"family": "Stenerl\u00f6w", "given": "Bo", "initials": "B", "orcid": "0000-0001-8878-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/22437ff9315d43089232926973feb0d2.json"}}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael", "initials": "M", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}], "type": "journal article", "published": "2025-08-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "7130"}, "abstract": "The ability to analyze whether DNA contains lesions is essential in identifying mutagenic substances. Currently, the detection of single-stranded DNA breaks (SSBs) lacks precision. To address this limitation, we develop a method for sequence-templated erroneous end-labelling sequencing (STEEL-seq), which enables the mapping of SSBs. The method requires a highly error-prone DNA polymerase, so we engineer a chimeric DNA polymerase, Sloppymerase, capable of replicating DNA in the absence of one nucleotide. Following the omission of a specific nucleotide (e.g., dATP) from the reaction mixture, Sloppymerase introduces mismatches directly downstream of SSBs at positions where deoxyadenosine should occur. This mismatch pattern, coupled with the retention of sequence information flanking these sites, ensures that the identified hits are bona fide SSBs. STEEL-seq is compatible with a variety of sequencing technologies, as demonstrated using Sanger, Illumina, PacBio, and Nanopore systems. Using STEEL-seq, we determine the SSB/base pair frequency in the human genome to range between 0.7 and 3.8 \u00d7 10-6 with an enrichment in active promoter regions.", "doi": "10.1038/s41467-025-62512-4", "pmid": "40759655", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12322144"}, {"db": "pii", "key": "10.1038/s41467-025-62512-4"}], "notes": [], "created": "2025-08-19T13:16:23.958Z", "modified": "2025-11-28T10:45:45.544Z"}, {"entity": "publication", "iuid": "5ba497c8921c4350b7bfaa2f24b254e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ba497c8921c4350b7bfaa2f24b254e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ba497c8921c4350b7bfaa2f24b254e0"}}, "title": "Inflammatory imbalance and activation deficits in T cells of myasthenia gravis patients revealed by proteomic profiling.", "authors": [{"family": "Bhandage", "given": "Amol K", "initials": "AK"}, {"family": "Punga", "given": "Anna Rostedt", "initials": "AR"}], "type": "journal article", "published": "2025-08-04", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1648020", "issn-l": "1664-3224"}, "abstract": "Myasthenia gravis (MG) is a heterogeneous autoimmune disorder characterized by neuromuscular transmission failure and skeletal muscle fatigability, with a pathophysiology involving both cellular and humoral immune components. Despite growing interest in the immunological etiology of MG, few functional studies have addressed the role of T cells, and most existing work has focused on quantifying immune cell subsets using flow cytometry. In this study, a comparative in vitro analysis of resting and activated CD4+ and CD8+ T cells from MG patients and healthy controls (HC) was performed using the multiplex Proximity Extension Assay (PEA) proteomics to assess the secretion of inflammatory proteins, including cytokines and chemokines, and to define the inflammatory status of T cells in MG. Data analysis was performed using the Boruta algorithm to detect both linear and non-linear patterns, followed by multiple testing corrections, and correlation analyses. The results revealed distinct alterations in the secretion profiles of several inflammatory proteins in MG compared to HC across both T cell subsets, regardless of activation state. Notably, resting CD4+ T cells from MG patients secreted higher levels of VEGFA, TNFRSF9, TWEAK, CCL20, HGF, CCL19, TRAIL, IL18, and TNF-\u03b2 whereas resting CD8+ T cells secreted higher levels of IL-12B, TRAIL, CCL23, CD244, CXCL11, CCL20, VEGFA, PD-L1, and OSM relative to HC. In contrast, activated CD4+ and CD8+ cells from MG patients exhibited a blunted secretion profile compared to HC, suggesting functional exhaustion. Furthermore, MG-ADL scores correlated with the secretion levels of 14 proteins from resting CD4+ cells, including seven cytokines, five chemokines, and two matrix metalloproteins. Some of the CD4+ T cell secreted proteins also correlated with their corresponding serum or plasma levels in vivo. Overall, these findings indicate that T cells in MG exhibit a skewed inflammatory profile characterized by heightened basal activation and impaired inducibility, suggestive of an exhausted phenotype. The interplay between these altered T cell functions and aberrant B cell responses in MG warrants further investigation and may provide novel insights into disease immunopathophysiology as well as opportunities for targeted immunomodulatory therapies.", "doi": "10.3389/fimmu.2025.1648020", "pmid": "40831557", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12358477"}], "notes": [], "created": "2025-11-25T19:21:50.755Z", "modified": "2025-11-25T19:21:50.759Z"}, {"entity": "publication", "iuid": "d92378d3b8974814af478f714c0337fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d92378d3b8974814af478f714c0337fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d92378d3b8974814af478f714c0337fb"}}, "title": "Temporal genomic change in the Scandinavian Arctic fox (Vulpes lagopus)", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "Hasselgren", "given": "Malin", "initials": "M"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Farelo", "given": "Liliana", "initials": "L"}, {"family": "Wall\u00e9n", "given": "Johan", "initials": "J"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Eide", "given": "Nina E", "initials": "NE"}, {"family": "Landa", "given": "Arild", "initials": "A"}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Melo-Ferreira", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0003-4473-1908", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2343a14dc6f4ca4910c45d551a6908b.json"}}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal-article", "published": "2025-08-01", "journal": {"issn": "0024-4082", "volume": "204", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.1093/zoolinnean/zlaf078", "pmid": null, "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-10-30T13:23:09.560Z", "modified": "2025-11-14T11:08:09.295Z"}, {"entity": "publication", "iuid": "bf8f3c333e934ca6989a77551e9e1a73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf8f3c333e934ca6989a77551e9e1a73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf8f3c333e934ca6989a77551e9e1a73"}}, "title": "Genomic and secretomic analyses of Blastobotrys yeasts reveal key xylanases for biomass decomposition.", "authors": [{"family": "Ravn", "given": "Jonas", "initials": "J", "orcid": "0000-0003-4328-2530", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e5ad3ac36c49678bf382fb87b43e42.json"}}, {"family": "Ristinmaa", "given": "Amanda S", "initials": "AS", "orcid": "0000-0003-0120-0330", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e92b57ec1b14304be945f243b66717a.json"}}, {"family": "Mazurkewich", "given": "Scott", "initials": "S", "orcid": "0000-0002-9238-0615", "researcher": {"href": "https://publications.scilifelab.se/researcher/39a1e4f9d3a74121937087f8875a975a.json"}}, {"family": "Dias", "given": "Guilherme B", "initials": "GB", "orcid": "0000-0002-1459-3148", "researcher": {"href": "https://publications.scilifelab.se/researcher/73778a1096e04b5d94f8d5c6f3584d99.json"}}, {"family": "Larsbrink", "given": "Johan", "initials": "J", "orcid": "0000-0001-8386-2914", "researcher": {"href": "https://publications.scilifelab.se/researcher/99badc395dbc46d1a43ae5c3d39fd8aa.json"}}, {"family": "Geijer", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-4158-2938", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad8eab8b087d47c4bce77ee2661628fb.json"}}], "type": "journal article", "published": "2025-08-01", "journal": {"title": "Appl. Microbiol. Biotechnol.", "issn": "1432-0614", "issn-l": "0175-7598", "volume": "109", "issue": "1", "pages": "175"}, "abstract": "Xylanolytic enzyme systems in ascomycetous yeasts remain underexplored, despite the presence of yeasts in various xylan-rich ecological niches. In this study, we investigated the secreted xylanolytic machineries of three Blastobotrys species-B. mokoenaii, B. illinoisensis, and B. malaysiensis-by integrating genome annotation, bioinformatics, and secretome analyses of cultures grown on beechwood glucuronoxylan. Our findings demonstrate that these yeasts effectively hydrolyze xylan through the secretion of xylanases from the glycoside hydrolase (GH) family 11, which play a central role in cleaving the xylan backbone. Additionally, the yeasts produce a diverse array of other CAZymes, including members of GH families 3, 5, and 67, with putative roles in xylan degradation. We also report on the heterologous expression and functional characterization of the GH30_7 xylanase BmXyn30A from B. mokoenaii, which exhibits both glucuronoxylanase and xylobiohydrolase activities. We demonstrate additive effects between GH family 30 BmXyn30A and GH family 11 BmXyn11A during the hydrolysis of beechwood glucuronoxylan, where the enzymes exhibit complementary roles that enhance the deconstruction of this complex hemicellulose substrate. These findings broaden our understanding of the xylanolytic systems in yeasts and underscore the potential of Blastobotrys species as cell factories and natural xylanase producers. The enzymes they produce hold promise for biorefining applications, enabling efficient utilization of renewable xylan-rich plant biomass resources. KEY POINTS: \u2022 Extracellular GH11 xylanases dominate glucuronoxylan degradation in Blastobotrys yeasts. \u2022 Yeast GH30_7 enzyme shows multifaceted activity, supporting complex xylan breakdown. \u2022 Blastobotrys yeasts show promise as cell factories for industrial biotechnology applications.", "doi": "10.1007/s00253-025-13556-5", "pmid": "40748385", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12316802"}, {"db": "pii", "key": "10.1007/s00253-025-13556-5"}], "notes": [], "created": "2025-08-19T13:52:12.110Z", "modified": "2025-11-17T16:43:09.377Z"}, {"entity": "publication", "iuid": "822a69d3b0ec4aa3a59daedca9d107c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/822a69d3b0ec4aa3a59daedca9d107c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/822a69d3b0ec4aa3a59daedca9d107c8"}}, "title": "The role of metabolism in shaping enzyme structures over 400 million years.", "authors": [{"family": "Lemke", "given": "Oliver", "initials": "O", "orcid": "0000-0002-5104-1836", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ea9f0d77148491fa18aaa7330268348.json"}}, {"family": "Heineike", "given": "Benjamin Murray", "initials": "BM"}, {"family": "Viknander", "given": "Sandra", "initials": "S"}, {"family": "Cohen", "given": "Nir", "initials": "N", "orcid": "0000-0002-5634-1643", "researcher": {"href": "https://publications.scilifelab.se/researcher/897f1026754d4934956ca3024635d936.json"}}, {"family": "Li", "given": "Feiran", "initials": "F", "orcid": "0000-0001-9155-5260", "researcher": {"href": "https://publications.scilifelab.se/researcher/249bec020dae419caad38538e87331f2.json"}}, {"family": "Steenwyk", "given": "Jacob Lucas", "initials": "JL", "orcid": "0000-0002-8436-595X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3c9d722f73b46f8a34cca4938cf2d5c.json"}}, {"family": "Spranger", "given": "Leonard", "initials": "L", "orcid": "0000-0002-4316-2961", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7e784debe4c419194c7e85cc05c4ddf.json"}}, {"family": "Agostini", "given": "Federica", "initials": "F", "orcid": "0000-0002-4255-4867", "researcher": {"href": "https://publications.scilifelab.se/researcher/311b5e1b9fbb423f94855e86642bd1e3.json"}}, {"family": "Lee", "given": "Cory Thomas", "initials": "CT"}, {"family": "Aulakh", "given": "Simran Kaur", "initials": "SK"}, {"family": "Berman", "given": "Judith", "initials": "J", "orcid": "0000-0002-8577-0084", "researcher": {"href": "https://publications.scilifelab.se/researcher/749d11eaff8d4a50affd2711bfe85700.json"}}, {"family": "Rokas", "given": "Antonis", "initials": "A", "orcid": "0000-0002-7248-6551", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31b5f559903407bb94fc180e9aaff61.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Gossmann", "given": "Toni Ingolf", "initials": "TI", "orcid": "0000-0001-6609-4116", "researcher": {"href": "https://publications.scilifelab.se/researcher/50c218f57a5b4dc9b33d846db03cef53.json"}}, {"family": "Zelezniak", "given": "Aleksej", "initials": "A", "orcid": "0000-0002-3098-9441", "researcher": {"href": "https://publications.scilifelab.se/researcher/4328a7ff130a44cc90e5282e4a18a2d7.json"}}, {"family": "Ralser", "given": "Markus", "initials": "M", "orcid": "0000-0001-9535-7413", "researcher": {"href": "https://publications.scilifelab.se/researcher/254766a4f72a4223a719f1341daed59f.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "644", "issue": "8075", "pages": "280-289", "issn-l": "0028-0836"}, "abstract": "Advances in deep learning and AlphaFold2 have enabled the large-scale prediction of protein structures across species, opening avenues for studying protein function and evolution1. Here we analyse 11,269 predicted and experimentally determined enzyme structures that catalyse 361 metabolic reactions across 225 pathways to investigate metabolic evolution over 400 million years in the Saccharomycotina subphylum2. By linking sequence divergence in structurally conserved regions to a variety of metabolic properties of the enzymes, we reveal that metabolism shapes structural evolution across multiple scales, from species-wide metabolic specialization to network organization and the molecular properties of the enzymes. Although positively selected residues are distributed across various structural elements, enzyme evolution is constrained by reaction mechanisms, interactions with metal ions and inhibitors, metabolic flux variability and biosynthetic cost. Our findings uncover hierarchical patterns of structural evolution, in which structural context dictates amino acid substitution rates, with surface residues evolving most rapidly and small-molecule-binding sites evolving under selective constraints without cost optimization. By integrating structural biology with evolutionary genomics, we establish a model in which enzyme evolution is intrinsically governed by catalytic function and shaped by metabolic niche, network architecture, cost and molecular interactions.", "doi": "10.1038/s41586-025-09205-6", "pmid": "40634610", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12328220"}, {"db": "pii", "key": "10.1038/s41586-025-09205-6"}], "notes": [], "created": "2025-11-28T10:46:32.237Z", "modified": "2025-11-28T10:46:32.679Z"}, {"entity": "publication", "iuid": "7382f4dc1f364e9198563a2b1fd3f450", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7382f4dc1f364e9198563a2b1fd3f450.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7382f4dc1f364e9198563a2b1fd3f450"}}, "title": "System-wide targeted analysis of oxylipins and lipoproteins in chronic peripheral neuropathic pain-an explorative study.", "authors": [{"family": "J\u00f6nsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-8668-4241", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dca09627dc64b06a807765008b3775c.json"}}, {"family": "B\u00e4ckryd", "given": "Emmanuel", "initials": "E"}, {"family": "Ljunggren", "given": "Stefan", "initials": "S"}, {"family": "Ottosson", "given": "Nina", "initials": "N"}, {"family": "Jauregi-Miguel", "given": "Amaia", "initials": "A"}, {"family": "Liin", "given": "Sara I", "initials": "SI"}, {"family": "Checa", "given": "Antonio", "initials": "A"}, {"family": "Wheelock", "given": "Craig E", "initials": "CE"}, {"family": "Ghafouri", "given": "Bijar", "initials": "B"}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Pain Rep", "issn": "2471-2531", "volume": "10", "issue": "4", "pages": "e1305", "issn-l": null}, "abstract": "Neuroinflammation and oxidative dysfunction, and their reciprocal interplay, are critically involved in the pathophysiology of chronic neuropathic pain (NeuP). Numerous studies have investigated the crosstalk between inflammatory biomolecules such as cytokines, chemokines, and neuronal cells. However, the impact of immunomodulatory lipoproteins and oxylipins in NeuP pathophysiology is far less explored.\n\nUsing a combination of techniques, we uncovered altered lipoprotein composition in high-density lipoproteins (HDLs) and low-density lipoproteins (LDLs) with complementary alterations in the plasma profile of oxylipins and cytokines among patients.\n\nLower level of apolipoproteins in patient HDL and 2 isoforms of acute phase serum amyloid A (SAA) with higher levels in patients was found. The constitutively expressed SAA4 was detected in 6 isoforms in patients, but only 2 isoforms were detected in healthy controls. In LDL, lysozyme C and 2 isoforms of SAA were exclusive to patients. Analysis of protein carbonylation showed oxidation of 6 proteins in HDL, of which 3 were unique to patients. No oxidized proteins were observed in LDL. Oxylipin analysis revealed 13 octadecanoids that were significantly downregulated in patients, of which 7 demonstrated significant activating effects on the Kv7.2/7.3 channel, which is anticipated to dampen neuronal signalling in sensory afferents. Among the significant octadecanoids, 9-HODE showed most prominent facilitating effects on Kv7.2/7.3 channel activation.\n\nThese results present a previously unexplored network of integrated alterations of lipoproteins, octadecanoids, and cytokines in patients suffering from NeuP, indicative of deviant immuno-protective functioning across several biological systems including lipid metabolic processes, inflammation, and Kv7.2/7.3 signalling.", "doi": "10.1097/PR9.0000000000001305", "pmid": "40612405", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12226002"}, {"db": "pii", "key": "PAINREPORTS-D-24-0282"}], "notes": [], "created": "2025-11-18T09:19:59.841Z", "modified": "2025-11-18T09:19:59.933Z"}, {"entity": "publication", "iuid": "794f95243a174ac1bfe74ed38354bcbc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/794f95243a174ac1bfe74ed38354bcbc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/794f95243a174ac1bfe74ed38354bcbc"}}, "title": "Sublytic Activity of a Pore-Forming Protein From Commensal Bacteria Causes Epigenetic Modulation of Tumour-Affiliated Protein Expression.", "authors": [{"family": "Toh", "given": "Eric", "initials": "E"}, {"family": "Baryalai", "given": "Palwasha", "initials": "P"}, {"family": "Nadeem", "given": "Aftab", "initials": "A"}, {"family": "Aung", "given": "Kyaw Min", "initials": "KM"}, {"family": "Myint", "given": "Si Lhyam", "initials": "SL"}, {"family": "Zlatkov", "given": "Nikola", "initials": "N"}, {"family": "Alidadi", "given": "Hadis", "initials": "H"}, {"family": "Zhu", "given": "Shaochun", "initials": "S"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Raina", "given": "Deepak Bushan", "initials": "DB"}, {"family": "Ramstedt", "given": "Madeleine", "initials": "M"}, {"family": "Uhlin", "given": "Bernt Eric", "initials": "BE"}, {"family": "Wai", "given": "Sun Nyunt", "initials": "SN", "orcid": "0000-0003-4793-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/261986c5cf8f48878b74c4f60cc7af69.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "J Extracell Vesicles", "issn": "2001-3078", "volume": "14", "issue": "8", "pages": "e70149", "issn-l": "2001-3078"}, "abstract": "Cytolysin A (ClyA) is a pore-forming protein from a strongly silenced gene in non-pathogenic Escherichia coli, including typical commensal isolates in the intestinal microbiome of healthy mammalian hosts. Upon overproduction, ClyA-expressing bacteria display a cytolytic phenotype. However, it remains unclear whether sublytic amounts of native ClyA play a role in commensal E. coli-host interactions in vivo. Here, we show that sublytic amounts of ClyA are released via outer membrane vesicles (OMVs) and affect host cells in a remarkable manner. OMVs isolated from ClyA+ E. coli were internalised into cultured colon cancer cells. The OMV-associated ClyA caused reduced levels of cancer-activating proteins such as H3K27me3, CXCR4, STAT3 and MDM2 via the EZH2/H3K27me3/microRNA 622/CXCR4 signalling axis. Our results demonstrate that sublytic amounts of ClyA in OMVs from non-pathogenic E. coli can influence the stability of the EZH2 protein, reducing its activity in epigenetic regulation, causing elevated level of the tumour suppressor protein p53.", "doi": "10.1002/jev2.70149", "pmid": "40825567", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12360854"}], "notes": [], "created": "2025-10-30T12:03:18.918Z", "modified": "2025-10-30T12:03:18.934Z"}, {"entity": "publication", "iuid": "98b0419415a549f5811c2936f54fd763", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98b0419415a549f5811c2936f54fd763.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98b0419415a549f5811c2936f54fd763"}}, "title": "Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex.", "authors": [{"family": "MacLean", "given": "Andrew E", "initials": "AE"}, {"family": "Shikha", "given": "Shikha", "initials": "S", "orcid": "0000-0002-7878-1463", "researcher": {"href": "https://publications.scilifelab.se/researcher/2de6231587194596b907dddf06be1b45.json"}}, {"family": "Ferreira Silva", "given": "Mariana", "initials": "M"}, {"family": "Gramelspacher", "given": "Max J", "initials": "MJ", "orcid": "0000-0003-3090-9314", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fb639abc4534915b60c4ac9de0e26ac.json"}}, {"family": "Nilsen", "given": "Aaron", "initials": "A"}, {"family": "Liebman", "given": "Katherine M", "initials": "KM"}, {"family": "Pou", "given": "Sovitj", "initials": "S"}, {"family": "Winter", "given": "Rolf W", "initials": "RW"}, {"family": "Meir", "given": "Amit", "initials": "A", "orcid": "0000-0001-9635-1021", "researcher": {"href": "https://publications.scilifelab.se/researcher/75240761defd4310a72f84c79a5114be.json"}}, {"family": "Riscoe", "given": "Michael K", "initials": "MK", "orcid": "0000-0002-1343-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d664bd5cf8d4e2db165759312e43e65.json"}}, {"family": "Doggett", "given": "J Stone", "initials": "JS", "orcid": "0000-0002-6098-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/08880b0318d44f23ac4264bf0d967ed5.json"}}, {"family": "Sheiner", "given": "Lilach", "initials": "L", "orcid": "0000-0001-5909-2307", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e426f417f194a75ae9fbc76ea24040e.json"}}, {"family": "M\u00fchleip", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1877-2282", "researcher": {"href": "https://publications.scilifelab.se/researcher/921b5acb5b7c402fa06c8c148cbd5340.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "32", "issue": "8", "pages": "1424-1433", "issn-l": "1545-9985"}, "abstract": "The apicomplexan mitochondrial electron transport chain is essential for parasite survival and displays a divergent subunit composition. Here we report cryo-electron microscopy structures of an apicomplexan III2-IV supercomplex and of the drug target complex III2. The supercomplex structure reveals how clade-specific subunits form an apicomplexan-conserved III2-IV interface with a unique, kinked architecture, suggesting that supercomplexes evolved independently in different eukaryotic lineages. A knockout resulting in supercomplex disassembly challenges the proposed role of III2-IV in electron transfer efficiency as suggested for mammals. Nevertheless, knockout analysis indicates that III2-IV is critical for parasite fitness. The complexes from the model parasite Toxoplasma gondii were inhibited with the antimalarial atovaquone, revealing interactions underpinning species specificity. They were also inhibited with endochin-like quinolone (ELQ)-300, an inhibitor in late-stage preclinical development. Notably, in the apicomplexan binding site, ELQ-300 is flipped compared with related compounds in the mammalian enzyme. On the basis of the binding modes and parasite-specific interactions discovered, we designed more potent ELQs with subnanomolar activity against T. gondii. Our findings reveal critical evolutionary differences in the role of supercomplexes in mitochondrial biology and provide insight into cytochrome b inhibition, informing future drug discovery.", "doi": "10.1038/s41594-025-01531-7", "pmid": "40389671", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12350165"}, {"db": "pii", "key": "10.1038/s41594-025-01531-7"}], "notes": [], "created": "2025-11-13T09:40:20.527Z", "modified": "2025-11-13T09:40:21.380Z"}, {"entity": "publication", "iuid": "06ca672ce48846a38877306910ec4cd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06ca672ce48846a38877306910ec4cd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06ca672ce48846a38877306910ec4cd1"}}, "title": "Small\u2010scale thermal habitat variability may not determine seagrass resilience to climate change", "authors": [{"family": "Hattich", "given": "Giannina S I", "initials": "GSI", "orcid": "0000-0003-4660-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/86fec49ce8324a27aa3da020810cd115.json"}}, {"family": "Jahnke", "given": "Marlene", "initials": "M", "orcid": "0000-0001-7262-315X", "researcher": {"href": "https://publications.scilifelab.se/researcher/88ddc399062a4cc792c36feb725f3ecd.json"}}, {"family": "Enge", "given": "Swantje", "initials": "S", "orcid": "0000-0003-4292-0051", "researcher": {"href": "https://publications.scilifelab.se/researcher/d92a4e95bf294c34855b27f30ba39dce.json"}}, {"family": "Niemi", "given": "Niklas", "initials": "N", "orcid": "0009-0008-8279-4049", "researcher": {"href": "https://publications.scilifelab.se/researcher/65c382595e5140b18c6ffa7b504f3434.json"}}, {"family": "Bernal\u2010G\u00f3mez", "given": "Maru", "initials": "M", "orcid": "0009-0006-0275-6620", "researcher": {"href": "https://publications.scilifelab.se/researcher/09f54c2d6291411c87843cf10056e32d.json"}}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Havenhand", "given": "Jonathan N", "initials": "JN", "orcid": "0000-0003-0253-3428", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d1c6ad9fb0a40418db6e99f127ea8ab.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Limnol Oceanogr", "issn": "0024-3590", "volume": "70", "issue": "8", "pages": "2039-2052", "issn-l": null}, "abstract": null, "doi": "10.1002/lno.70049", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:11:32.834Z", "modified": "2025-11-14T11:05:36.890Z"}, {"entity": "publication", "iuid": "8a1c0d0e49ab4ddaaca2551db8330fbc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a1c0d0e49ab4ddaaca2551db8330fbc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a1c0d0e49ab4ddaaca2551db8330fbc"}}, "title": "Optimization of the Isolation Method for Large\u2010Scale Production of Synthetic Bacterial Vesicles for Cancer Immunotherapy", "authors": [{"family": "Ordouzadeh", "given": "Negar", "initials": "N"}, {"family": "Crescitelli", "given": "Rossella", "initials": "R"}, {"family": "Zimmer", "given": "Agnes", "initials": "A"}, {"family": "Tj\u00e4rnlund", "given": "Petra", "initials": "P"}, {"family": "L\u00e4sser", "given": "Cecilia", "initials": "C"}, {"family": "L\u00f6tvall", "given": "Jan", "initials": "J"}, {"family": "Park", "given": "Kyong\u2010Su", "initials": "K", "orcid": "0000-0003-0902-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e308b29fe144b49f4db27f4b819c18.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Advanced Therapeutics", "issn": "2366-3987", "volume": "8", "issue": "8", "issn-l": null}, "abstract": null, "doi": "10.1002/adtp.202500084", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-05T13:58:52.094Z", "modified": "2025-11-05T13:58:52.148Z"}, {"entity": "publication", "iuid": "e081c532d4de40fea93e6cad64023850", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e081c532d4de40fea93e6cad64023850.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e081c532d4de40fea93e6cad64023850"}}, "title": "Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification.", "authors": [{"family": "Brunet", "given": "Sofia", "initials": "S"}, {"family": "Grankvist", "given": "Anna", "initials": "A"}, {"family": "Jaen-Luchoro", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5988-6227", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a821a703a144b5aa5a783e7f8043d86.json"}}, {"family": "Bergdahl", "given": "Maria", "initials": "M"}, {"family": "Tison", "given": "Jean-Luc", "initials": "JL"}, {"family": "Wester", "given": "Annica", "initials": "A"}, {"family": "Elfving", "given": "Karin", "initials": "K"}, {"family": "Brandenburg", "given": "Jule", "initials": "J"}, {"family": "Gullsby", "given": "Karolina", "initials": "K"}, {"family": "Lindsten", "given": "Christoffer", "initials": "C"}, {"family": "Arvidsson", "given": "Lars-Ola", "initials": "LO"}, {"family": "Larsson", "given": "Helena", "initials": "H", "orcid": "0000-0002-6851-3297", "researcher": {"href": "https://publications.scilifelab.se/researcher/21f2cca2f6b74c5393c0fc33bcf15ee6.json"}}, {"family": "Eilers", "given": "Hinnerk", "initials": "H"}, {"family": "Strand", "given": "Anna S\u00f6derlund", "initials": "AS"}, {"family": "Lannefors", "given": "Mimi", "initials": "M"}, {"family": "Keskitalo", "given": "Johanna", "initials": "J"}, {"family": "Rylander", "given": "Felicia", "initials": "F"}, {"family": "Welander", "given": "Jenny", "initials": "J"}, {"family": "Jungestrom", "given": "Malin Bergman", "initials": "MB"}, {"family": "Ge\u00f6rg", "given": "Miriam", "initials": "M"}, {"family": "Kaden", "given": "Rene", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications.scilifelab.se/researcher/018870b1d0034ee09552a3ae451d5504.json"}}, {"family": "Karlsson", "given": "Ida", "initials": "I"}, {"family": "Linde", "given": "Anna-Malin", "initials": "AM"}, {"family": "Mernelius", "given": "Sara", "initials": "S"}, {"family": "Berglind", "given": "Linda", "initials": "L"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Kerje", "given": "Susanne", "initials": "S", "orcid": "0000-0002-2944-9288", "researcher": {"href": "https://publications.scilifelab.se/researcher/078ca525f2cc4a68a430f2655e45efce.json"}}, {"family": "Karlsson", "given": "Linda", "initials": "L", "orcid": "0000-0003-2704-1788", "researcher": {"href": "https://publications.scilifelab.se/researcher/9942f9d57c094401a1bb9b965f300092.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Guerra-Blomqvist", "given": "Lina", "initials": "L"}, {"family": "Wallin", "given": "Frans", "initials": "F"}, {"family": "Fagerstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0002-6276-8811", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8dc177a668c4256be2893eb98abddd4.json"}}, {"family": "Vondracek", "given": "Martin", "initials": "M"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Hallb\u00e4ck", "given": "Erika T\u00e5ng", "initials": "ET"}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Eur. J. Clin. Microbiol. Infect. Dis.", "issn": "1435-4373", "volume": "44", "issue": "8", "pages": "1907-1916", "issn-l": "0934-9723"}, "abstract": "Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration coordinated by Genomic Medicine Sweden.\n\nThirteen mock samples comprised of various bacterial strains and an External Quality Assessment (EQA) panel from QCMD (Quality Control for Molecular Diagnostics) were analysed by 20 microbiological laboratories across Sweden, using the recent v14 chemistry. Most laboratories generated full-length 16S rRNA sequencing libraries using an optimized protocol for the 16S Barcoding Kit 24, while two laboratories employed in-house PCR coupled with the Ligation Sequencing Kit. The commercial 16S bioinformatic pipeline from 1928 Diagnostics (1928-16S) was evaluated and compared with the open-sourced gms_16S pipeline that is based on the EMU classification tool (GMS-16S).\n\nSeventeen out of 20 laboratories successfully sequenced and analysed the samples. Laboratories that used sodium acetate-containing elution buffers faced compatibility issues during library construction, resulting in reduced read count. High bacterial load samples were generally well-characterized, whereas hard-to-lyse bacteria such as Gram-positive strains were detected at lower abundance. The GMS-16S tool provided improved species-level identification compared to the 1928-16S pipeline, particularly for closely related taxa within the Streptococcus and Staphylococcus genera.\n\nNanopore sequencing demonstrated promising potential for bacterial identification in a clinical setting. The results prompt further optimization of the protocol to improve detection of a broader range of species. This multicentre study highlights the feasibility of implementing Nanopore sequencing into clinical microbiological laboratories, for improved national precision diagnostics.", "doi": "10.1007/s10096-025-05158-w", "pmid": "40348924", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12321653"}, {"db": "pii", "key": "10.1007/s10096-025-05158-w"}], "notes": [], "created": "2025-07-08T13:51:52.338Z", "modified": "2025-11-26T14:14:27.926Z"}, {"entity": "publication", "iuid": "b442a8117224474d8136e0a8102a8ab9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b442a8117224474d8136e0a8102a8ab9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b442a8117224474d8136e0a8102a8ab9"}}, "title": "Moving towards better risk assessment for invertebrate conservation", "authors": [{"family": "Goodsell", "given": "Robert M", "initials": "RM", "orcid": "0000-0002-3349-1876", "researcher": {"href": "https://publications.scilifelab.se/researcher/84f42755a394403b95486707bf4a83bd.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}, {"family": "Ronquist", "given": "Fredrik", "initials": "F"}, {"family": "van Dijk", "given": "Laura J A", "initials": "LJA"}, {"family": "Iwaszkiewicz\u2010Eggebrecht", "given": "Elzbieta", "initials": "E", "orcid": "0000-0003-1015-8496", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c9432c19234fd5bc5dfc0a037dae0f.json"}}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Vanhatalo", "given": "Jarno", "initials": "J", "orcid": "0000-0002-6831-0211", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c665f3fd6a94f099bf9171533623cc7.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Ecography", "issn": "0906-7590", "volume": "2025", "issue": "8", "issn-l": null}, "abstract": null, "doi": "10.1002/ecog.07819", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:40:05.316Z", "modified": "2025-11-28T10:40:05.539Z"}, {"entity": "publication", "iuid": "f94b305344964e2abd50b277f36990ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f94b305344964e2abd50b277f36990ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f94b305344964e2abd50b277f36990ad"}}, "title": "Mast Cell Phenotypic Heterogeneity Impacts the Interplay with Pathogenic Salmonella Typhimurium Bacteria.", "authors": [{"family": "von Beek", "given": "Christopher", "initials": "C", "orcid": "0000-0001-6310-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ea7730832f4f45ae6583076d90418a.json"}}, {"family": "Prensa", "given": "Grisna I", "initials": "GI", "orcid": "0009-0002-7101-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d030d78925948d993999b66e1959acc.json"}}, {"family": "Andersson", "given": "Julia H M", "initials": "JHM"}, {"family": "Pejler", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-6779-391X", "researcher": {"href": "https://publications.scilifelab.se/researcher/97b2d5f8dec04bc3b7631370d77a2236.json"}}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Eur. J. Immunol.", "issn": "1521-4141", "volume": "55", "issue": "8", "pages": "e70040", "issn-l": "0014-2980"}, "abstract": "Mast cells (MCs) lodge within barrier tissues and respond to infectious microbes. Recent work demonstrated that MCs differentiate their cytokine response to extracellular versus invasive Gram-negative enterobacteria by a two-step activation mechanism that integrates Toll-like-receptor (TLR) sensing with signals elicited by type-III-secretion-system (TTSS) effectors during bacterial invasion. However, multiple MC subtypes exist, and it remains unclear how their phenotypic heterogeneity impacts microbial interactions. We find that murine MCs maintained in IL-3, or differentiated toward a connective-tissue phenotype (CT-MCs), respond potently to the enteropathogen Salmonella enterica Typhimurium (S.Tm) through two-step activation, with the TLR component explained by functional TLR4 and TLR2. By contrast, murine mucosal mast cells (M-MCs) express insignificant levels of these TLRs, therefore being unresponsive to extracellular S.Tm, but still mounting a response to invasive bacteria. Following invasion, MC granule maintenance by serglycin restricts S.Tm vacuolar and cytosolic colonization. Notably, this has no impact on the cytokine release from infected MCs, thus uncoupling S.Tm\u00b4s intracellular life-cycle from the MC cytokine response. Finally, human LUVA MCs employ a variant of two-step activation where TLR2/6 signaling combines with the TTSS-elicited signals. Together, this study explains how MC subtypes can respond differently to S.Tm-infection depending on their TLR expression and granule features.", "doi": "10.1002/eji.70040", "pmid": "40838737", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12369454"}], "notes": [], "created": "2025-09-08T07:06:53.513Z", "modified": "2025-09-09T13:13:50.740Z"}, {"entity": "publication", "iuid": "919cf2bb62074bd48782a3c7c7263536", "links": {"self": {"href": "https://publications.scilifelab.se/publication/919cf2bb62074bd48782a3c7c7263536.json"}, "display": {"href": "https://publications.scilifelab.se/publication/919cf2bb62074bd48782a3c7c7263536"}}, "title": "Large-scale genome-wide analyses with proteomics integration reveal novel loci and biological insights into frailty.", "authors": [{"family": "Mak", "given": "Jonathan K L", "initials": "JKL", "orcid": "0000-0003-4454-8580", "researcher": {"href": "https://publications.scilifelab.se/researcher/4994e82ef4784f06aff8017a9cf9ad1c.json"}}, {"family": "Qin", "given": "Chenxi", "initials": "C"}, {"family": "Kr\u00fcger", "given": "Moritz", "initials": "M", "orcid": "0009-0005-7754-1950", "researcher": {"href": "https://publications.scilifelab.se/researcher/868a1b17a99c4fa1ac629e65f0dd636f.json"}}, {"family": "Kuukka", "given": "Anna", "initials": "A"}, {"family": "FinnGen", "given": "", "initials": ""}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d010dfe5d84a33b6a6c7ec815ca3dc.json"}}, {"family": "Lin", "given": "Jake", "initials": "J"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J", "orcid": "0000-0003-0250-4491", "researcher": {"href": "https://publications.scilifelab.se/researcher/5193964678264255adaaf5005ab59a87.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Nat Aging", "issn": "2662-8465", "volume": "5", "issue": "8", "pages": "1589-1600", "issn-l": null}, "abstract": "Frailty is a clinically relevant phenotype with notable gaps in our understanding of its etiology. Using the Hospital Frailty Risk Score (HFRS) to define frailty, we performed a genome-wide association study in FinnGen (N = 500,737), replicated the results in the UK Biobank (N = 407,463) and performed a meta-analysis. We prioritized genes through colocalization with expression, splicing and protein quantitative trait loci and proteomics integration. We identified 53 independent lead variants associated with frailty (P < 5 \u00d7 10-8), of which 45 were novel and not previously reported in the GWAS Catalog. Replication at the individual variant and polygenic risk score of the HFRS (P = 1.86 \u00d7 10-522) levels and meta-analysis largely confirmed the findings. Colocalization analysis supported a causal role for several genes, including CHST9, C6orf106 (ILRUN), KHK, MET, APOE, CGREF1 and PPP6C. Additionally, plasma levels of MET, CGREF1 and APOE were associated with HFRS. Our results reveal new genetic contributions to frailty and shed light on its biological basis.", "doi": "10.1038/s43587-025-00925-y", "pmid": "40764432", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12350161"}, {"db": "pii", "key": "10.1038/s43587-025-00925-y"}], "notes": [], "created": "2025-11-28T10:47:40.805Z", "modified": "2025-11-28T10:47:41.026Z"}, {"entity": "publication", "iuid": "3b9b5a866e2a4139b03c9bbe033fc083", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b9b5a866e2a4139b03c9bbe033fc083.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b9b5a866e2a4139b03c9bbe033fc083"}}, "title": "Landscape connectivity and genetic structure of animal populations in urban ponds", "authors": [{"family": "Yildirim", "given": "Yeserin", "initials": "Y"}, {"family": "Hyseni", "given": "Chaz", "initials": "C", "orcid": "0000-0003-2567-8013", "researcher": {"href": "https://publications.scilifelab.se/researcher/7327304d59cb41a7a97cdcba953f9cdc.json"}}, {"family": "Heino", "given": "Jani", "initials": "J"}, {"family": "Bini", "given": "Luis Mauricio", "initials": "LM", "orcid": "0000-0003-3398-9399", "researcher": {"href": "https://publications.scilifelab.se/researcher/490cfde8f1824571a07f21bf11ea61f0.json"}}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Johansson", "given": "Frank", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Conserv Genet", "issn": "1566-0621", "volume": "26", "issue": "4", "pages": "703-714", "issn-l": null}, "abstract": null, "doi": "10.1007/s10592-025-01697-z", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:17:17.339Z", "modified": "2025-09-09T13:13:41.822Z"}, {"entity": "publication", "iuid": "c878486c08b744719c249a5e651964c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c878486c08b744719c249a5e651964c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c878486c08b744719c249a5e651964c0"}}, "title": "Genotypic and Phenotypic Characterization of Seven Individuals With Predicted Bone Morphogenetic Protein 2 (BMP2) Haploinsufficiency.", "authors": [{"family": "Stavr\u00e9n-Eriksson", "given": "Elin", "initials": "E"}, {"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "Pigg", "given": "Maritta Hellstr\u00f6m", "initials": "MH"}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Clin. Genet.", "issn": "1399-0004", "volume": "108", "issue": "2", "pages": "199-205", "issn-l": "0009-9163"}, "abstract": "Bone morphogenetic protein 2 (BMP-2), encoded by the BMP2 gene located in chromosomal region 20p12, is a signalling protein involved in formation of bone and cartilage and other developmental processes such as cardiac and neural development. Haploinsufficiency of BMP2 has been associated with distinct facial features, short stature, skeletal malformations and cardiac abnormalities. The degree of developmental delay is still controversial. We summarise clinical and genetic findings from seven individuals with BMP2 haploinsufficiency. The study participants were identified by genetic testing and their phenotypic data was collected retrospectively from medical records. One individual had a novel frameshift variant in BMP2, and six individuals had 1.3-3.7 Mb microdeletions, including BMP2. In our cohort, delayed language development (4/5) and secretory otitis media (4/5) were common. Our results, together with previous studies, suggest that individuals with sequence variants or small microdeletions can have mild developmental delay or delay in one area (e.g., verbal development or gross motor development). We propose that global developmental delay is either a rare part or not part of the phenotype. Based on our observations, we propose that evaluation of language development and regular controls of the middle ear should be included in the surveillance of these individuals.", "doi": "10.1111/cge.14727", "pmid": "39970956", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12215207"}], "notes": [], "created": "2025-11-18T20:45:19.134Z", "modified": "2025-11-18T20:45:19.165Z"}, {"entity": "publication", "iuid": "a97b36bc55b94119b54060180a6e6305", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a97b36bc55b94119b54060180a6e6305.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a97b36bc55b94119b54060180a6e6305"}}, "title": "Genome-wide identification of modulators of Chlamydia trachomatis parasitophorous vacuole stability highlights an important role for sphingolipid supply.", "authors": [{"family": "Babu Sait", "given": "Mohammed Rizwan", "initials": "MR"}, {"family": "Jachmann", "given": "Lana H", "initials": "LH"}, {"family": "T\u00fcrk\u00f6z", "given": "G\u00f6zde", "initials": "G"}, {"family": "Milivojevic", "given": "Milica", "initials": "M"}, {"family": "Llorente-S\u00e1ez", "given": "Celia", "initials": "C"}, {"family": "Dhanjal", "given": "Soniya", "initials": "S"}, {"family": "Schumacher", "given": "Fabian", "initials": "F"}, {"family": "Henriksson", "given": "Sara", "initials": "S", "orcid": "0000-0003-1615-0583", "researcher": {"href": "https://publications.scilifelab.se/researcher/934e6f18e3c94684be715e7bdc28d9b7.json"}}, {"family": "Gayathri Vegesna", "given": "Naga Venkata", "initials": "NV"}, {"family": "Seddik", "given": "Noha", "initials": "N"}, {"family": "Chaban", "given": "Anastasiia", "initials": "A"}, {"family": "Mohanty", "given": "Partha", "initials": "P"}, {"family": "\u00d6lander", "given": "Magnus", "initials": "M"}, {"family": "Muraleedharan", "given": "Samada", "initials": "S"}, {"family": "Farmand Azadeh", "given": "Sepideh", "initials": "S"}, {"family": "Kleuser", "given": "Burkhard", "initials": "B"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Sixt", "given": "Barbara S", "initials": "BS", "orcid": "0000-0002-5607-8902", "researcher": {"href": "https://publications.scilifelab.se/researcher/998ac876b31f45c5b10d36f0d10c7390.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "issn-l": "1544-9173", "volume": "23", "issue": "8", "pages": "e3003297"}, "abstract": "A mechanistic understanding of how intracellular pathogens evade the intrinsic defenses of their host cells could open up intriguing therapeutic opportunities. Here, we applied a genome-wide genetic screening approach to investigate the nature of the defensive host cell death response suppressed by the membrane trafficking modulator CpoS, an effector protein secreted by the obligate intracellular bacterial pathogen Chlamydia trachomatis. Initially, this work revealed a CpoS-deficient mutant to exhibit a markedly increased dependence on host cellular synthesis of ceramides, the precursors of complex sphingolipids. Using novel microscopic reporters, we then established CpoS' role in defense evasion to occur by preserving the integrity of Chlamydia's parasitophorous vacuole (the inclusion) via ensuring an adequate sphingolipid supply. More specifically, we observed CpoS deficiency to destabilize inclusions, initially characterized by a release of individual bacteria into the host cell cytosol, then followed by inclusion rupture concomitant with host cell death. Exogenous addition of sphingosine stabilized CpoS-deficient inclusions, whereas disruption of host cellular ceramide synthesis destabilized wild-type inclusions. In combination, CpoS deficiency and impaired ceramide synthesis - presumably disrupting both Chlamydia's vesicular and non-vesicular sphingolipid supply routes - destabilized inclusions even earlier, resulting in infection clearance and host cell survival rather than host cell death. Overall, this study highlights how the vacuolar pathogen C. trachomatis maintains vacuole integrity by ensuring a steady sphingolipid supply, potentially offering inspiration and directions for future therapeutic strategies targeting parasitophorous vacuoles.", "doi": "10.1371/journal.pbio.3003297", "pmid": "40794560", "labels": {"CRISPR Functional Genomics": "Collaborative", "Integrated Microscopy Technologies Ume\u00e5": "Technology development", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Chemical Biology Consortium Sweden": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12342332"}, {"db": "pii", "key": "PBIOLOGY-D-24-02720"}], "notes": [], "created": "2025-09-04T09:04:13.790Z", "modified": "2026-03-18T09:37:39.227Z"}, {"entity": "publication", "iuid": "952ed8e7e59d4100b61d6cf634d568fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/952ed8e7e59d4100b61d6cf634d568fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/952ed8e7e59d4100b61d6cf634d568fd"}}, "title": "Genetics of monozygotic twins reveals the impact of environmental sensitivity on psychiatric and neurodevelopmental phenotypes.", "authors": [{"family": "Assary", "given": "Elham", "initials": "E", "orcid": "0000-0001-9788-0478", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4b6d4805e24466a860f5366c30d7ea8.json"}}, {"family": "Coleman", "given": "Jonathan R I", "initials": "JRI", "orcid": "0000-0002-6759-0944", "researcher": {"href": "https://publications.scilifelab.se/researcher/91f9f96c887447918926b36de9cfc820.json"}}, {"family": "Hemani", "given": "Gibran", "initials": "G", "orcid": "0000-0003-0920-1055", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd71462e306f446bae17d8991b97b24e.json"}}, {"family": "van de Weijer", "given": "Margot P", "initials": "MP", "orcid": "0000-0001-9720-9481", "researcher": {"href": "https://publications.scilifelab.se/researcher/92d34b4941224694adccc703a15696dc.json"}}, {"family": "Howe", "given": "Laurence J", "initials": "LJ"}, {"family": "Palviainen", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7847-8384", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcbc4c92052b4819b5d7d821c0c421b0.json"}}, {"family": "Grasby", "given": "Katrina L", "initials": "KL", "orcid": "0000-0001-8539-0228", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e9d35817bc460ea594b892e5d2030e.json"}}, {"family": "Ahlskog", "given": "Rafael", "initials": "R"}, {"family": "Nygaard", "given": "Marianne", "initials": "M", "orcid": "0000-0003-0703-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d68eda16735460d81993dc39006d5a5.json"}}, {"family": "Cheesman", "given": "Rosa", "initials": "R", "orcid": "0000-0002-6543-0402", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4c5f583a67b418cb5535f55e74a453e.json"}}, {"family": "Lim", "given": "Kai", "initials": "K"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Ordo\u00f1ana", "given": "Juan R", "initials": "JR", "orcid": "0000-0001-7779-6017", "researcher": {"href": "https://publications.scilifelab.se/researcher/68390af477eb46efadef77a93cc2d5c1.json"}}, {"family": "Colodro-Conde", "given": "Lucia", "initials": "L", "orcid": "0000-0002-9004-364X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3d04cc447a34470a5063ae581eb9030.json"}}, {"family": "Gordon", "given": "Scott", "initials": "S", "orcid": "0000-0001-7623-328X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8815739662214e75b60f71f0b1ca58a6.json"}}, {"family": "Madrid-Valero", "given": "Juan J", "initials": "JJ", "orcid": "0000-0002-3450-1159", "researcher": {"href": "https://publications.scilifelab.se/researcher/168d9ef0279a4cd792ffc3dafbc45293.json"}}, {"family": "Thalamuthu", "given": "Anbupalam", "initials": "A", "orcid": "0000-0002-7114-1260", "researcher": {"href": "https://publications.scilifelab.se/researcher/440c1694c55e4092a30a69dc495e47d9.json"}}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ", "orcid": "0000-0002-5668-2368", "researcher": {"href": "https://publications.scilifelab.se/researcher/75553b594b1f4255833de730f7f7d170.json"}}, {"family": "Mengel-From", "given": "Jonas", "initials": "J", "orcid": "0000-0003-1573-8908", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4dbeb78e51b441399c96921567e636f.json"}}, {"family": "Armstrong", "given": "Nicola J", "initials": "NJ", "orcid": "0000-0002-4477-293X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de6e46b360454a4f8185cfa7d4ac7134.json"}}, {"family": "Sachdev", "given": "Perminder S", "initials": "PS", "orcid": "0000-0002-9595-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec82937a4354f4c8247bcce974f4771.json"}}, {"family": "Lee", "given": "Teresa", "initials": "T"}, {"family": "Brodaty", "given": "Henry", "initials": "H", "orcid": "0000-0001-9487-6617", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa888d67cbac4c5db0782146e17e53e0.json"}}, {"family": "Trollor", "given": "Julian N", "initials": "JN", "orcid": "0000-0002-7685-2977", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b1bbca91f8345d8a1d36e1eacb18613.json"}}, {"family": "Wright", "given": "Margaret", "initials": "M", "orcid": "0000-0001-7133-4970", "researcher": {"href": "https://publications.scilifelab.se/researcher/da35d18966cb418ba5207c85b040ae98.json"}}, {"family": "Ames", "given": "David", "initials": "D"}, {"family": "Catts", "given": "Vibeke S", "initials": "VS", "orcid": "0000-0002-9892-0547", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abf66f90553491f82b01293572b5ec7.json"}}, {"family": "Latvala", "given": "Antti", "initials": "A"}, {"family": "Within Family Consortium", "given": "", "initials": ""}, {"family": "Vuoksimaa", "given": "Eero", "initials": "E"}, {"family": "Mallard", "given": "Travis", "initials": "T", "orcid": "0000-0002-3265-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/de1d5003d2c641129c1f6518787bf606.json"}}, {"family": "Paige Harden", "given": "K", "initials": "K", "orcid": "0000-0002-1557-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed28dc61f14a48828402ba8db84d7062.json"}}, {"family": "Tucker-Drob", "given": "Elliot M", "initials": "EM", "orcid": "0000-0001-5599-6237", "researcher": {"href": "https://publications.scilifelab.se/researcher/3057f100241341d5becce265f1b983f5.json"}}, {"family": "Oskarsson", "given": "Sven", "initials": "S", "orcid": "0000-0001-8698-2866", "researcher": {"href": "https://publications.scilifelab.se/researcher/892fdebfc99b44249b90fe801db41436.json"}}, {"family": "Hammond", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3227-2620", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17349aecfab4cb2b9b376b53c6e97aa.json"}}, {"family": "Christensen", "given": "Kaare", "initials": "K", "orcid": "0000-0002-5429-5292", "researcher": {"href": "https://publications.scilifelab.se/researcher/e79ea43d09544efc95351b52ac682910.json"}}, {"family": "Taylor", "given": "Mark", "initials": "M"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-7235-8499", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0e069eb1cd349c4b05c11eded6dca5e.json"}}, {"family": "Larsson", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6851-3297", "researcher": {"href": "https://publications.scilifelab.se/researcher/21f2cca2f6b74c5393c0fc33bcf15ee6.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Mather", "given": "Karen A", "initials": "KA", "orcid": "0000-0003-4143-8941", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec0c7f15235d4be4848b56025d5ff4f0.json"}}, {"family": "Medland", "given": "Sarah E", "initials": "SE", "orcid": "0000-0003-1382-380X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da1f0230a912425c9237830be85aa642.json"}}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "Martin", "given": "Nicholas G", "initials": "NG", "orcid": "0000-0003-4069-8020", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b445e5935f74fd6a71b2e92a9dac176.json"}}, {"family": "Plomin", "given": "Robert", "initials": "R", "orcid": "0000-0002-0756-3629", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e3ca0c39ff4a5087146d5125e0190f.json"}}, {"family": "Bartels", "given": "Meike", "initials": "M", "orcid": "0000-0002-9667-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a91c095e993411b99e81e21f40d8597.json"}}, {"family": "Lichtenstein", "given": "Paul", "initials": "P", "orcid": "0000-0003-3037-5287", "researcher": {"href": "https://publications.scilifelab.se/researcher/4db67c51837b4cdfa18cacbc3fca1173.json"}}, {"family": "Kaprio", "given": "Jaakko", "initials": "J", "orcid": "0000-0002-3716-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/814d362333844b72a70cba9ebcf61e6f.json"}}, {"family": "Eley", "given": "Thalia C", "initials": "TC", "orcid": "0000-0001-6458-0700", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5eb736ac79d451c82ed6c18414ccad4.json"}}, {"family": "Davies", "given": "Neil M", "initials": "NM", "orcid": "0000-0002-2460-0508", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ab6ffbb98594ea69b9fee350cc221e2.json"}}, {"family": "Munroe", "given": "Patricia B", "initials": "PB", "orcid": "0000-0002-4176-2947", "researcher": {"href": "https://publications.scilifelab.se/researcher/657544a7f921459f926aae5cd0e2065c.json"}}, {"family": "Keers", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Nat Hum Behav", "issn": "2397-3374", "volume": "9", "issue": "8", "pages": "1683-1696", "issn-l": null}, "abstract": "Individual sensitivity to environmental exposures may be genetically influenced. This genotype-by-environment interplay implies differences in phenotypic variance across genotypes, but these variants have proven challenging to detect. Genome-wide association studies of monozygotic twin differences are conducted through family-based variance analyses, which are more robust to the systemic biases that impact population-based methods. We combined data from 21,792 monozygotic twins (10,896 pairs) from 11 studies to conduct one of the largest genome-wide association study meta-analyses of monozygotic phenotypic differences, in children, adolescents and adults separately, for seven psychiatric and neurodevelopmental phenotypes: attention deficit hyperactivity disorder symptoms, autistic traits, anxiety and depression symptoms, psychotic-like experiences, neuroticism and wellbeing. The proportions of phenotypic variance explained by single-nucleotide polymorphisms in these phenotypes were estimated (h2 = 0-18%), but were imprecise. We identified 13 genome-wide significant associations (single-nucleotide polymorphisms, genes and gene sets), including genes related to stress reactivity for depression, growth factor-related genes for autistic traits and catecholamine uptake-related genes for psychotic-like experiences. This is the largest genetic study of monozygotic twins to date by an order of magnitude, evidencing an alternative method to study the genetic architecture of environmental sensitivity. The statistical power was limited for some analyses, calling for better-powered future studies.", "doi": "10.1038/s41562-025-02193-7", "pmid": "40494901", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12367547"}, {"db": "pii", "key": "10.1038/s41562-025-02193-7"}], "notes": [], "created": "2025-09-08T11:34:10.493Z", "modified": "2025-09-08T11:34:12.043Z"}, {"entity": "publication", "iuid": "1d0370becf604d269d8bc287ea19cd6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d0370becf604d269d8bc287ea19cd6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d0370becf604d269d8bc287ea19cd6b"}}, "title": "Genetic diversity and structure among Acropora austera populations in Mozambique suggest low resilience potential of one of the world\u2019s most charismatic coral reefs", "authors": [{"family": "Duvane", "given": "Jossias Alberto", "initials": "JA", "orcid": "0009-0008-6595-3415", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23044e5482b4936bb376823b8dee593.json"}}, {"family": "Dupont", "given": "Sam", "initials": "S"}, {"family": "Sola", "given": "Erwan", "initials": "E"}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O"}, {"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Coral Reefs", "issn": "0722-4028", "volume": "44", "issue": "4", "pages": "1185-1195", "issn-l": null}, "abstract": null, "doi": "10.1007/s00338-025-02679-w", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:17:08.995Z", "modified": "2025-09-08T07:17:09.074Z"}, {"entity": "publication", "iuid": "6848f75298734c12a8cad5501012e437", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6848f75298734c12a8cad5501012e437.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6848f75298734c12a8cad5501012e437"}}, "title": "Fatty acid biomarkers reveal landscape influences on linkages between aquatic and terrestrial food webs", "authors": [{"family": "Burdon", "given": "Francis J", "initials": "FJ", "orcid": "0000-0002-5398-4993", "researcher": {"href": "https://publications.scilifelab.se/researcher/853e9aa4ce714858a8ea19175bf20b35.json"}}, {"family": "Sargac", "given": "Jasmina", "initials": "J"}, {"family": "Ramberg", "given": "Ellinor", "initials": "E"}, {"family": "Popescu", "given": "Cristina", "initials": "C"}, {"family": "Darmina", "given": "Nita", "initials": "N"}, {"family": "Bradu", "given": "Corina", "initials": "C"}, {"family": "Forio", "given": "Marie A E", "initials": "MAE", "orcid": "0000-0001-6675-4751", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed5fdbe42d1b4054bcc3d674eba113e5.json"}}, {"family": "Witing", "given": "Felix", "initials": "F"}, {"family": "Kupilas", "given": "Benjamin", "initials": "B"}, {"family": "Lau", "given": "Danny C P", "initials": "DCP", "orcid": "0000-0002-3246-7508", "researcher": {"href": "https://publications.scilifelab.se/researcher/28aa8ed05fc64662b9a72cf4bde0e59b.json"}}, {"family": "Volk", "given": "Martin", "initials": "M"}, {"family": "R\u00ee\u015fnoveanu", "given": "Geta", "initials": "G"}, {"family": "Goethals", "given": "Peter", "initials": "P"}, {"family": "Friberg", "given": "Nikolai", "initials": "N"}, {"family": "Johnson", "given": "Richard K", "initials": "RK"}, {"family": "McKie", "given": "Brendan G", "initials": "BG"}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Ecological Monographs", "issn": "0012-9615", "volume": "95", "issue": "3", "issn-l": null}, "abstract": null, "doi": "10.1002/ecm.70025", "pmid": null, "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-19T10:50:13.565Z", "modified": "2025-11-19T10:50:13.738Z"}, {"entity": "publication", "iuid": "a1230f19911a42d48a23d2dc916d5bdc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1230f19911a42d48a23d2dc916d5bdc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1230f19911a42d48a23d2dc916d5bdc"}}, "title": "Exploring novel genomic biomarkers for response and survival after neoadjuvant chemotherapy and radical cystectomy of muscle-invasive bladder cancer.", "authors": [{"family": "Holmsten", "given": "K", "initials": "K"}, {"family": "De Laere", "given": "B", "initials": "B"}, {"family": "Sj\u00f6dahl", "given": "G", "initials": "G"}, {"family": "Lindberg", "given": "J", "initials": "J"}, {"family": "Costa Svedman", "given": "F", "initials": "F"}, {"family": "\u00d6stling", "given": "P", "initials": "P"}, {"family": "Eriksson", "given": "P", "initials": "P"}, {"family": "Liedberg", "given": "F", "initials": "F"}, {"family": "Ull\u00e9n", "given": "A", "initials": "A"}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "ESMO Open", "issn": "2059-7029", "volume": "10", "issue": "8", "pages": "105512", "issn-l": null}, "abstract": "Neoadjuvant cisplatin-based combination chemotherapy (NAC) is standard perioperative treatment of patients with muscle-invasive urothelial bladder cancer (MIBC); however, about half of the patients experience recurrence of the disease. Biomarkers for response and survival represent an unmet medical need. We used tumor specimens from transurethral resections of the bladder to explore genomic alterations and their association with response and survival in MIBC patients treated by NAC and radical cystectomy.\n\nA pan cancer panel with single-nucleotide polymorphism backbone-based sequencing approach with coverage of the most commonly perturbed cancer genes and low-pass whole genome sequencing was applied for genomic characterization of 110 clinical routine patients treated with NAC before radical cystectomy. Pathological response rates, recurrence-free and overall survival were assessed.\n\nAmplifications of genes on chromosome 6p22.3, particularly of the E2F3 and SOX4 gene loci, were associated with improved response and survival to NAC. Patients harboring these alterations had a high pathological treatment response rate and all remained recurrence-free during a median follow-up of 5 years. Conversely, patients with FGFR3 mutations demonstrated impaired response and survival, whereas CDKN1A mutations appeared not related to treatment response but may serve as a biomarker for poor prognosis.\n\nWe found the panel-based sequencing approach feasible for exploring genomic alterations associated with clinical benefits of NAC and radical cystectomy. Amplifications of genes on chromosome 6p22.3 and FGFR3 and CDKN1A mutations hold promise as biomarkers associated with response and survival to NAC.", "doi": "10.1016/j.esmoop.2025.105512", "pmid": "40664147", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12281969"}, {"db": "pii", "key": "S2059-7029(25)01381-X"}], "notes": [], "created": "2025-11-18T20:46:22.612Z", "modified": "2025-11-18T20:46:22.635Z"}, {"entity": "publication", "iuid": "a2eeb64d4b934f20a9bb9b1bb34dcd34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2eeb64d4b934f20a9bb9b1bb34dcd34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2eeb64d4b934f20a9bb9b1bb34dcd34"}}, "title": "Effects of boreal ground layer shrubs and bryophytes on the diversity, biomass and composition of lichen communities across contrasting ecosystems", "authors": [{"family": "Fanin", "given": "Nicolas", "initials": "N", "orcid": "0000-0003-4195-855X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7494a4ecb6c44cb9aa68b43cbe5dd7c9.json"}}, {"family": "Asplund", "given": "Johan", "initials": "J", "orcid": "0000-0001-5610-4480", "researcher": {"href": "https://publications.scilifelab.se/researcher/fba6230f8274434db7ec265290d84c3f.json"}}, {"family": "Gundale", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-2447-609X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69996ee5fff4524a3912055239f8b3d.json"}}, {"family": "Kardol", "given": "Paul", "initials": "P", "orcid": "0000-0001-7065-3435", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b89b05e397d47af942e0dbb8ca23676.json"}}, {"family": "Nilsson", "given": "Marie\u2010Charlotte", "initials": "M", "orcid": "0000-0002-9254-2223", "researcher": {"href": "https://publications.scilifelab.se/researcher/32f05190f0254333aab0ce402c19df9c.json"}}, {"family": "Wardle", "given": "David A", "initials": "DA", "orcid": "0000-0002-0476-7335", "researcher": {"href": "https://publications.scilifelab.se/researcher/570a8bd46088437cb7edc3e607f84e7b.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Oikos", "issn": "0030-1299", "volume": "2025", "issue": "8", "issn-l": null}, "abstract": null, "doi": "10.1002/oik.11099", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-08-19T13:53:03.296Z", "modified": "2025-08-19T13:53:03.410Z"}, {"entity": "publication", "iuid": "a4c2b66aa3bc44a9b753a11fb03b83a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4c2b66aa3bc44a9b753a11fb03b83a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4c2b66aa3bc44a9b753a11fb03b83a9"}}, "title": "Ectomycorrhizal decomposers and their niche(s) in boreal forests", "authors": [{"family": "Packard", "given": "Erica E", "initials": "EE", "orcid": "0000-0002-3175-090X", "researcher": {"href": "https://publications.scilifelab.se/researcher/086fa0579672428fa8845eacdf4da74f.json"}}, {"family": "P\u00e9rez\u2010Izquierdo", "given": "Leticia", "initials": "L", "orcid": "0000-0002-5200-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/25e9fb4343c24736b87268bb20d5aa28.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Dahlberg", "given": "Anders", "initials": "A", "orcid": "0000-0002-3669-6797", "researcher": {"href": "https://publications.scilifelab.se/researcher/a62efad22b414d618531b66ad404f689.json"}}, {"family": "Spohn", "given": "Marie", "initials": "M", "orcid": "0000-0002-1010-7317", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4f9aa10fc7e490a8b8ff24eba5bef44.json"}}, {"family": "Stendahl", "given": "Johan", "initials": "J", "orcid": "0000-0002-9944-0297", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85527eadcb54545844e20d97954fb11.json"}}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD", "orcid": "0000-0002-3384-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a40688d33545a19c3c666940bda255.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Functional Ecology", "issn": "0269-8463", "volume": "39", "issue": "8", "pages": "1998-2014", "issn-l": null}, "abstract": null, "doi": "10.1111/1365-2435.70085", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-08-19T13:28:05.546Z", "modified": "2025-11-28T10:50:35.099Z"}, {"entity": "publication", "iuid": "67fab09bb8ea4fdcad3e53e8d0da7021", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67fab09bb8ea4fdcad3e53e8d0da7021.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67fab09bb8ea4fdcad3e53e8d0da7021"}}, "title": "Diplodia tip blight (Diplodia sapinea) and site conditions shape Scots pine (Pinus sylvestris) endophytic mycobiome", "authors": [{"family": "Brodde", "given": "Laura", "initials": "L", "orcid": "0000-0003-3048-079X", "researcher": {"href": "https://publications.scilifelab.se/researcher/52ace940a7744b7aa2e70e1af653f1a8.json"}}, {"family": "Mi\u00f1ana-Posada", "given": "Silvia", "initials": "S", "orcid": "0009-0001-5316-6181", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f96c2b26e8847bb831fc9323c483f97.json"}}, {"family": "Tudoran", "given": "Amelia", "initials": "A", "orcid": "0000-0001-7307-3938", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f3f1524af4a4210b67e53be4811e064.json"}}, {"family": "Angel Redondo", "given": "Miguel", "initials": "M"}, {"family": "Elfstrand", "given": "Malin", "initials": "M", "orcid": "0000-0002-0214-5284", "researcher": {"href": "https://publications.scilifelab.se/researcher/2957dac173f4495a9245f0d8a9750606.json"}}, {"family": "Oliva", "given": "Jon\u00e1s", "initials": "J", "orcid": "0000-0003-2418-2542", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea605d40772449298a04cbf0b4b01de5.json"}}, {"family": "Stenlid", "given": "Jan", "initials": "J", "orcid": "0000-0002-5344-2094", "researcher": {"href": "https://publications.scilifelab.se/researcher/eac6fc31e38c4552a986310015fcb1b4.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Forest Ecology and Management", "issn": "0378-1127", "volume": "589", "pages": "122781", "issn-l": null}, "abstract": null, "doi": "10.1016/j.foreco.2025.122781", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-08-19T13:20:58.202Z", "modified": "2025-08-19T13:20:58.506Z"}, {"entity": "publication", "iuid": "db8859e1f60843cfb22193244670316d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db8859e1f60843cfb22193244670316d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db8859e1f60843cfb22193244670316d"}}, "title": "Deep sequencing combined with high-throughput screening enables efficient development of a pH-dependent high-affinity binding domain targeting HER3.", "authors": [{"family": "M\u00f6ller", "given": "Marit", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Malin", "initials": "M"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "L\u00f6fblom", "given": "John", "initials": "J"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "34", "issue": "8", "pages": "e70247", "issn-l": "0961-8368"}, "abstract": "In vitro methods for developing binding domains have been well-established for many years, owing to the cost-efficient synthesis of DNA and high-throughput selection and screening technologies. However, generating high-affinity binding domains often requires the development of focused maturation libraries for a second selection, which typically demands a detailed understanding of the binding surfaces from the initial selection, a process that can be time-consuming. In this study, we accelerated this process by using deep sequencing data from the first selection to guide the design of the maturation library. Additionally, we employed a high-throughput screening system using flow cytometry based on Escherichia coli display to identify conditional binding domains from the selection output. This approach enabled the development of a high-affinity binder targeting the cancer biomarker HER3, with a binding affinity of 3.3 nM at extracellular pH 7.4, 100 times higher than the first-generation binding domain. Notably, the binding domain features a pH-dependent release mechanism, enabling rapid release in slightly acidic environments (pH \u22486), which resemble endosomal conditions. When conjugated to the cytotoxin mertansine (DM1), the binding domain demonstrated specific cytotoxic activity against HER3-expressing cell lines, with an IC50 of 2-5 nM. The presented approach enables the efficient development of conditional binding domains which hold promise for therapeutic applications.", "doi": "10.1002/pro.70247", "pmid": "40716110", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-21T18:09:51.575Z", "modified": "2025-11-21T18:09:51.723Z"}, {"entity": "publication", "iuid": "1ea24dddd57b41208480279c592968f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ea24dddd57b41208480279c592968f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ea24dddd57b41208480279c592968f1"}}, "title": "Complex relationship between soil fungi and conservation value assessments in boreal forests.", "authors": [{"family": "Kyaschenko", "given": "Julia", "initials": "J", "orcid": "0000-0001-8831-8483", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f85920960014681b0a1b7199253ba3e.json"}}, {"family": "Mielke", "given": "Louis", "initials": "L", "orcid": "0000-0001-6948-3141", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f0d43b208d42798d423786eb4eb4cc.json"}}, {"family": "J\u00f6nsson", "given": "Mari", "initials": "M", "orcid": "0000-0002-5465-7820", "researcher": {"href": "https://publications.scilifelab.se/researcher/18583af858a540c19c5c143acd1c08ba.json"}}, {"family": "Hekkala", "given": "Anne-Maarit", "initials": "AM", "orcid": "0000-0002-8023-0425", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec3c2c2c458443218444e462efd0b756.json"}}, {"family": "K\u00e4rvemo", "given": "Simon", "initials": "S", "orcid": "0000-0003-0954-7312", "researcher": {"href": "https://publications.scilifelab.se/researcher/9816d3d619c845bbbf833bb6141506cc.json"}}, {"family": "Sj\u00f6gren", "given": "J\u00f6rgen", "initials": "J", "orcid": "0000-0002-0538-8265", "researcher": {"href": "https://publications.scilifelab.se/researcher/08946e047aeb45f5be5aa3797113346d.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Strengbom", "given": "Joachim", "initials": "J", "orcid": "0000-0002-1720-5016", "researcher": {"href": "https://publications.scilifelab.se/researcher/3311ed539845455b9bad3e84907133de.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Conservation Biology", "issn": "1523-1739", "volume": "39", "issue": "4", "pages": "e70012", "issn-l": "0888-8892"}, "abstract": "Large-scale industrial forestry is a threat to biodiversity and imposes long-lasting changes to many forested biomes. Preserving forests as reserves is an important component of the strategy for safeguarding forest biodiversity. Yet, the selection of forests of high biodiversity value is usually based on proxies (i.e., subsets of aboveground habitat characteristics) rather than on direct assessments of species occurrences. This approach is based on the assumption that the diversity and community composition of all organism groups are well represented by the assessed habitat characteristics. We investigated how conservation value, assessed according to common practices based on aboveground habitat heterogeneity, corresponded to the abundance, richness, and community composition of 12 taxonomic and ecological groups of soil fungi across northern and southern Swedish forests. Overall, the assessed conservation value reflected the abundance, diversity, and community composition of deadwood-associated saprotrophs well, likely because they depend directly on the availability of the structures that the assessment is based on. However, the conservation assessment value failed to capture the overall variability for most of the soil-dwelling fungal guilds. Although the assessed value was positively associated with the diversity of ectomycorrhizal fungi, root-associated Ascomycota, and saprotrophic Basidiomycota in the southern region, no such association was evident in the northern region. Soil fertility was the best predictor of the variation in community composition in all fungal guilds. The relative abundance and diversity of most saprotrophic guilds increased as soil fertility increased, whereas root-associated guilds decreased as soil fertility increased. Current methods for assessing conservation value captured only specific subsets of soil fungi, and the predictability of capturing fungal diversity varied depending on the region. To more comprehensively preserve soil fungi, assessment methods should incorporate additional environmental parameters, especially those linked to fungal community composition, such as soil fertility.", "doi": "10.1111/cobi.70012", "pmid": "40070243", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-08-19T13:58:34.455Z", "modified": "2025-08-19T13:58:34.710Z"}, {"entity": "publication", "iuid": "508dbf0c7a8540809bc38d4710d43948", "links": {"self": {"href": "https://publications.scilifelab.se/publication/508dbf0c7a8540809bc38d4710d43948.json"}, "display": {"href": "https://publications.scilifelab.se/publication/508dbf0c7a8540809bc38d4710d43948"}}, "title": "Clinical whole genome sequencing in pediatric epilepsy: Genetic and phenotypic spectrum of 733 individuals.", "authors": [{"family": "Henry", "given": "Olivia J", "initials": "OJ", "orcid": "0000-0002-4717-8346", "researcher": {"href": "https://publications.scilifelab.se/researcher/1226db94b02c4ceda75fd5903c4815a0.json"}}, {"family": "Ygberg", "given": "Sofia", "initials": "S"}, {"family": "Barbaro", "given": "Michela", "initials": "M"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Karlsson", "given": "Leif", "initials": "L", "orcid": "0000-0001-6274-9330", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a90f592b91c4f3b9568cb086f568a98.json"}}, {"family": "Pe\u00f1a-P\u00e9rez", "given": "Luc\u00eda", "initials": "L"}, {"family": "B\u00e5vner", "given": "Ann", "initials": "A"}, {"family": "T\u00f6h\u00f6nen", "given": "Virpi", "initials": "V"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "St\u00f6dberg", "given": "Tommy", "initials": "T"}, {"family": "Wedell", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Epilepsia", "issn": "1528-1167", "volume": "66", "issue": "8", "pages": "2966-2979", "issn-l": "0013-9580"}, "abstract": "A large proportion of pediatric epilepsies have an underlying genetic etiology. Limited studies have explored the efficacy of whole genome sequencing (WGS) in a clinical setting. Our academic-clinical center implemented clinical whole exome sequencing (WES) in 2014, then transitioned to WGS from 2015. We report the diagnostic yield, genetic and phenotypic findings, and prognostic factors following WGS/WES in pediatric epilepsy.\n\nThe cohort included 733 families with pediatric epilepsy who received clinical WGS/WES between 2014 and 2022. WGS/WES was performed at the Genomic Medicine Center Karolinska for Rare Diseases and analyzed at the Center for Inherited Metabolic Diseases at Karolinska University Hospital. Phenotypic information was extracted from referrals and medical records. Genetic and phenotypic data were analyzed using descriptive statistics, and univariable and multivariable analyses.\n\nThe median age at seizure onset was 9 months. Developmental delay and/or intellectual disability (DD/ID) was observed in 61.3% of the cohort; 38.1% of individuals received an International League Against Epilepsy epilepsy syndrome diagnosis. WGS/WES was performed in 640 (87.3%) and 143 (19.5%) families, respectively, totaling 2029 individuals. A molecular diagnosis was identified in 278 of 733 individuals (37.9%), including 51 of 211 individuals analyzed more than once (24.2% of reanalyzed cases). Independent predictors for receiving a genetic diagnosis included female sex (adjusted odds ratio [aOR] = 1.8, 95% confidence interval [CI] = 1.3-2.4, p < .001), neonatal seizure onset (aOR = 2.5, 95% CI = 1.6-4, p < .001), mortality (aOR = 2.2, 95% CI = 1.3-4.0, p = .0048), and an ID/DD/developmental and epileptic encephalopathy (DEE) diagnosis (aOR = 1.8, 95% CI = 1.2-2.5, p = .0019). The strongest independent predictor of ID/DD/DEE was microcephaly (aOR = 7.8, 95% CI = 2-53, p = .0099). In the solved cohort, gene group did not predict cognitive outcome.\n\nClinical WGS is an effective diagnostic tool in pediatric epilepsy. We identified female sex as a novel prognostic factor for receiving a genetic diagnosis and highlight the value of reanalyzing previously unsolved cases to improve diagnostic yield.", "doi": "10.1111/epi.18403", "pmid": "40183601", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371643"}], "notes": [], "created": "2025-11-18T20:45:27.809Z", "modified": "2025-11-18T20:45:27.863Z"}, {"entity": "publication", "iuid": "a4f9fbd843ba40c1819a1c0eca22b281", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4f9fbd843ba40c1819a1c0eca22b281.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4f9fbd843ba40c1819a1c0eca22b281"}}, "title": "Carbonation of quicklimes during cooling in moderate and high CO2 atmospheres", "authors": [{"family": "Ma", "given": "Charlie", "initials": "C", "orcid": "0000-0002-0555-5924", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfe1a7690d74481f8f301a43e338a923.json"}}, {"family": "Eriksson", "given": "Matias", "initials": "M"}, {"family": "Wilhelmsson", "given": "Bodil", "initials": "B"}, {"family": "Wendel", "given": "Mikael", "initials": "M"}, {"family": "Brostr\u00f6m", "given": "Markus", "initials": "M"}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Thermochimica Acta", "issn": "0040-6031", "volume": "750", "pages": "180022", "issn-l": null}, "abstract": null, "doi": "10.1016/j.tca.2025.180022", "pmid": null, "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-03T14:34:07.854Z", "modified": "2025-11-03T14:34:07.895Z"}, {"entity": "publication", "iuid": "7aa42d25cae04535af39ca526f08d568", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7aa42d25cae04535af39ca526f08d568.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7aa42d25cae04535af39ca526f08d568"}}, "title": "Cafestol and kahweol concentrations in workplace machine coffee compared with conventional brewing methods.", "authors": [{"family": "Orrje", "given": "Erik", "initials": "E"}, {"family": "Fristedt", "given": "Rikard", "initials": "R"}, {"family": "Rosqvist", "given": "Fredrik", "initials": "F"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Iggman", "given": "David", "initials": "D"}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Nutr Metab Cardiovasc Dis", "issn": "1590-3729", "volume": "35", "issue": "8", "pages": "103933", "issn-l": null}, "abstract": "Unfiltered coffee contains high concentrations of cholesterol-raising diterpenes. We aimed to measure the levels of diterpenes in machine coffee.\n\nCoffee samples were collected from Swedish workplaces and compared with home-made coffee brews. Concentrations of cafestol and kahweol were measured by liquid chromatography-mass spectrometry. The median (range) cafestol and kahweol concentrations were 176 (24-444) mg/L and 142 (18-434) mg/L for brewing machines (n = 11), 8 (2-343) mg/L and 7 (2-288) mg/L for liquid-model machines (n = 3), and 12 (4-24) mg/L and 8 (3-19) mg/l for home-brewed, paper-filtered coffees (n = 5). Boiled coffee had high concentrations of cafestol and kahweol, 939 mg/L and 678 mg/L, but having it poured through a fabric filter reduced the concentrations to 28 and 21 mg/L. Other coffee brews (percolator, French press) contained intermediate levels of cafestol (\u223c90 mg/L) and kahweol (\u223c70 mg/L), with the exception of some espresso samples with high levels (up to 2447 mg/L cafestol).\n\nMost coffees from workplace brewing machines contain higher diterpene concentrations than paper-filtered coffee, but lower than unfiltered coffee. Intake of insufficiently filtered coffee during working hours could be an overlooked factor for cardiovascular health due to its effect on plasma cholesterol concentrations.", "doi": "10.1016/j.numecd.2025.103933", "pmid": "40089392", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0939-4753(25)00087-0"}], "notes": [], "created": "2025-12-01T05:42:42.046Z", "modified": "2025-12-01T05:42:42.049Z"}, {"entity": "publication", "iuid": "c0b630a30a1a46ce900790a05a054996", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0b630a30a1a46ce900790a05a054996.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0b630a30a1a46ce900790a05a054996"}}, "title": "Assessing Sperm Quality Parameters in Mass\u2010Spawning Norwegian Arctic Charr", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K", "orcid": "0000-0002-9852-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba96d1e78654b6992ef1c25035e93da.json"}}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Thomason", "given": "Benjamin", "initials": "B"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Aquaculture Fish &amp; Fisheries", "issn": "2693-8847", "volume": "5", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.1002/aff2.70111", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:02:14.701Z", "modified": "2025-09-09T13:12:28.648Z"}, {"entity": "publication", "iuid": "56d7b9a10ca7456c955235973fcb394e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56d7b9a10ca7456c955235973fcb394e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56d7b9a10ca7456c955235973fcb394e"}}, "title": "An east\u2013west distribution of genetic diversity in Nordic populations of caraway (Carum carvi L.) and its consequences for conservation prioritisation", "authors": [{"family": "de Haro Reyes", "given": "Bernardo", "initials": "B", "orcid": "0000-0003-0871-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bebf9f96b8ae43d38df1dc8a4f3ac389.json"}}, {"family": "Palm\u00e9", "given": "Anna", "initials": "A", "orcid": "0000-0002-8012-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa8ff1168d27459e9b02b7c59afa94f0.json"}}, {"family": "Fitzgerald", "given": "Heli", "initials": "H", "orcid": "0000-0002-6754-6409", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bdf20a416b49509431dd29201d28f2.json"}}, {"family": "G\u00f6ransson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-0081-2207", "researcher": {"href": "https://publications.scilifelab.se/researcher/13cca49312994a8fa45dc1fb7db8a42f.json"}}, {"family": "Lyytik\u00e4inen", "given": "Virva", "initials": "V", "orcid": "0009-0006-0207-9789", "researcher": {"href": "https://publications.scilifelab.se/researcher/315e8b253f184ca081297937e28c5225.json"}}, {"family": "Madsen", "given": "Bjarke", "initials": "B", "orcid": "0000-0002-4490-8710", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8a2e6641fec437f8624b6125d907bdd.json"}}, {"family": "Normand", "given": "Signe", "initials": "S", "orcid": "0000-0002-8782-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/c676988310824f518a646427dfed6600.json"}}, {"family": "Thorbj\u00f6rnsson", "given": "Hj\u00f6rtur", "initials": "H", "orcid": "0000-0003-1768-3699", "researcher": {"href": "https://publications.scilifelab.se/researcher/98e074fa60a24b3aa9ffcb54c238db8f.json"}}, {"family": "Treier", "given": "Urs Albert", "initials": "UA", "orcid": "0000-0003-4027-739X", "researcher": {"href": "https://publications.scilifelab.se/researcher/985ba0c9228a43f1a1132383266b7579.json"}}, {"family": "Hagenblad", "given": "Jenny", "initials": "J", "orcid": "0000-0002-9850-5546", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d1a751682448a3b6485cb67c6474f0.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Conserv Genet", "issn": "1566-0621", "volume": "26", "issue": "4", "pages": "771-785", "issn-l": null}, "abstract": null, "doi": "10.1007/s10592-025-01702-5", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:30:05.435Z", "modified": "2025-11-14T11:05:47.156Z"}, {"entity": "publication", "iuid": "5efe2eece54f4706b0bc9858c4ca29a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5efe2eece54f4706b0bc9858c4ca29a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5efe2eece54f4706b0bc9858c4ca29a1"}}, "title": "Adaptations for stealth in the wing-like flippers of a large ichthyosaur.", "authors": [{"family": "Lindgren", "given": "Johan", "initials": "J", "orcid": "0000-0002-0116-976X", "researcher": {"href": "https://publications.scilifelab.se/researcher/912abaa9b903468c86436671fd917df5.json"}}, {"family": "Lomax", "given": "Dean R", "initials": "DR", "orcid": "0000-0001-6985-3966", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dffba987e264deea55a2cb0d1933906.json"}}, {"family": "Sz\u00e1sz", "given": "Robert-Zolt\u00e1n", "initials": "RZ", "orcid": "0000-0001-5736-3126", "researcher": {"href": "https://publications.scilifelab.se/researcher/88752fee7d1f434aa1ff1952ebeffd4a.json"}}, {"family": "Marx", "given": "Miguel", "initials": "M"}, {"family": "Revstedt", "given": "Johan", "initials": "J"}, {"family": "G\u00f6ltz", "given": "Georg", "initials": "G"}, {"family": "Sachs", "given": "Sven", "initials": "S"}, {"family": "De La Garza", "given": "Randolph G", "initials": "RG"}, {"family": "Heing\u00e5rd", "given": "Miriam", "initials": "M"}, {"family": "Jarenmark", "given": "Martin", "initials": "M", "orcid": "0000-0002-3939-433X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8c79a5f2e8a47c3858424aa095c5624.json"}}, {"family": "Ydstr\u00f6m", "given": "Kristina", "initials": "K"}, {"family": "Sj\u00f6vall", "given": "Peter", "initials": "P", "orcid": "0000-0002-2696-7215", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a75fdbda2cc4424a478fa116dca4936.json"}}, {"family": "Osb\u00e6ck", "given": "Frank", "initials": "F"}, {"family": "Hall", "given": "Stephen A", "initials": "SA"}, {"family": "Op de Beeck", "given": "Michiel", "initials": "M"}, {"family": "Eriksson", "given": "Mats E", "initials": "ME"}, {"family": "Alwmark", "given": "Carl", "initials": "C", "orcid": "0000-0003-3153-4649", "researcher": {"href": "https://publications.scilifelab.se/researcher/19a9ed41e6834ba0a36e2f53468d5015.json"}}, {"family": "Marone", "given": "Federica", "initials": "F", "orcid": "0000-0002-3467-8763", "researcher": {"href": "https://publications.scilifelab.se/researcher/3740c6fd4c2d40589dbabcdb69b3f2cd.json"}}, {"family": "Liptak", "given": "Alexander", "initials": "A", "orcid": "0000-0003-1597-4193", "researcher": {"href": "https://publications.scilifelab.se/researcher/b79939b85db247a9aabf21b220631b01.json"}}, {"family": "Atwood", "given": "Robert", "initials": "R", "orcid": "0000-0001-6708-1085", "researcher": {"href": "https://publications.scilifelab.se/researcher/90f42a7c5ae448e89c53623ce3719c2b.json"}}, {"family": "Burca", "given": "Genoveva", "initials": "G", "orcid": "0000-0001-6867-9628", "researcher": {"href": "https://publications.scilifelab.se/researcher/e42cb3a829a543069ec270d7a8d496bc.json"}}, {"family": "Uvdal", "given": "Per", "initials": "P", "orcid": "0000-0002-2121-3377", "researcher": {"href": "https://publications.scilifelab.se/researcher/64a0f345a3ba48c6b35c7c1eca5b9aa5.json"}}, {"family": "Persson", "given": "Per", "initials": "P"}, {"family": "Nilsson", "given": "Dan-Eric", "initials": "DE", "orcid": "0000-0003-1028-9314", "researcher": {"href": "https://publications.scilifelab.se/researcher/227a4b4ff7314ff39b771699caa43649.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "644", "issue": "8078", "pages": "976-983", "issn-l": "0028-0836"}, "abstract": "With their superficially shark-like appearance, the Mesozoic ichthyosaurs provide a classic illustration of major morphological adaptations in an ancestrally terrestrial tetrapod lineage following the invasion of marine habitats1-3. Much of what is known about ichthyosaur soft tissues derives from specimens with body outlines4-6. However, despite offering insights into aspects of biology that are otherwise difficult to envisage from skeletal evidence alone (such as the presence of a crescentic fluke), information on their soft parts has hitherto been limited to a taxonomically narrow sample of small- to dolphin-sized animals2,4-6. Here we report the discovery of a metre-long front flipper of the large-bodied Jurassic ichthyosaur Temnodontosaurus, including unique details of its soft-tissue anatomy. In addition to revealing a wing-like planform, the fossil preserves a serrated trailing edge that is reinforced by novel cartilaginous integumental elements, herein denominated chondroderms. We also document chordwise-parallel skin ornamentations and a protracted fleshy distal tip that presumably acted like a flexible winglet in life. By integrating morphological and numerical data, we show that the observed features probably provided hydroacoustic benefits, and conclude that the visually guided7,8 Temnodontosaurus relied on stealth while hunting in dim-lit pelagic environments. This unexpected combination of control surface modifications represents a previously unrecognized mode of concealment, and underscores the importance of soft-tissue fossils when inferring aspects of palaeoethology and predator-prey palaeoecology.", "doi": "10.1038/s41586-025-09271-w", "pmid": "40670791", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12390834"}, {"db": "pii", "key": "10.1038/s41586-025-09271-w"}], "notes": [], "created": "2025-11-14T11:06:54.899Z", "modified": "2025-11-14T11:06:56.322Z"}, {"entity": "publication", "iuid": "8731474c0874412e8ff9f33c698c18a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8731474c0874412e8ff9f33c698c18a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8731474c0874412e8ff9f33c698c18a1"}}, "title": "Profiling of the microRNA transcriptome in feline whole blood.", "authors": [{"family": "Ohlsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-1116-0141", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d12e64d2d740669ec499319b66c22e.json"}}, {"family": "Han\u00e5s", "given": "Sofia", "initials": "S"}, {"family": "Holst", "given": "Bodil S", "initials": "BS"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "H\u00f6glund", "given": "Katja", "initials": "K"}, {"family": "Tidholm", "given": "Anna", "initials": "A"}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6617-0454", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b19ecb541c4d13a685b574390e8104.json"}}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0000-0003-3402-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e1779188e20402294f12861a8232e71.json"}}], "type": "journal article", "published": "2025-07-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "27962", "issn-l": "2045-2322"}, "abstract": "Circulating microRNAs (miRNAs) are potential biomarkers for numerous diseases. Characterization of the whole blood (WB) miRNA-transcriptome (miRNome) in cats is lacking, which limits the potential use of miRNAs as biomarkers for diseases such as feline cardiovascular disease. The aims of the present study were to profile and evaluate circulating miRNAs in feline WB by high-throughput sequencing of the total miRNome in WB from twelve domestic mixed breed (DOM) and Norwegian Forest (NFO) cats stringently diagnosed with or without preclinical hypertrophic cardiomyopathy (HCM). A total of 459 mature miRNAs were identified in feline WB, of which 40 were potential novel feline miRNAs. A majority, 85.3%, of the miRNAs showed sequence similarity with human miRNAs. An effect of breed was found, with up to thirteen WB miRNAs being differentially abundant between breeds. The majority of the significant breed-specific miRNAs in feline WB could be associated with regulation of haematopoietic cells. One miRNA, miR-204-5p, was potentially associated with preclinical HCM in NFO cats, but the results need to be confirmed in a larger and sex-unbiased cohort. In conclusion, here we used miRNome-sequencing to identify hundreds of circulating miRNAs in feline WB. Breed should be considered when evaluating the miRNome in feline WB.", "doi": "10.1038/s41598-025-09478-x", "pmid": "40745193", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12313912"}, {"db": "pii", "key": "10.1038/s41598-025-09478-x"}], "notes": [], "created": "2025-09-05T08:24:52.249Z", "modified": "2025-09-09T13:12:41.462Z"}, {"entity": "publication", "iuid": "c2b76b1e291f42adaf0bfad3e62eae4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2b76b1e291f42adaf0bfad3e62eae4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2b76b1e291f42adaf0bfad3e62eae4b"}}, "title": "X-ray computed tomography-based qualitative analysis of internal resinwood in Scots pine", "authors": [{"family": "Joevenller", "given": "Sheng", "initials": "S", "orcid": "0000-0002-6428-0422", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5a4a0a5104c410b85a00c660a4a0c77.json"}}, {"family": "Huber", "given": "Johannes A J", "initials": "JAJ", "orcid": "0000-0001-9196-0370", "researcher": {"href": "https://publications.scilifelab.se/researcher/137eb440e33141938c047f1cde3924d7.json"}}, {"family": "Svennerstam", "given": "Henrik", "initials": "H", "orcid": "0000-0002-3096-5028", "researcher": {"href": "https://publications.scilifelab.se/researcher/328e8c7fd2634fe9ae0c0d45be7d8d6e.json"}}, {"family": "Nysj\u00f6", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-2734-8149", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6a7de84caa941d59d3ba2c9cb84d75f.json"}}, {"family": "Karlsson", "given": "Olov", "initials": "O", "orcid": "0000-0002-7711-9267", "researcher": {"href": "https://publications.scilifelab.se/researcher/daead600c96146709875d1822366da8b.json"}}], "type": "journal-article", "published": "2025-07-30", "journal": {"title": "Wood Material Science &amp; Engineering", "issn": "1748-0272", "pages": "1-12", "issn-l": null}, "abstract": null, "doi": "10.1080/17480272.2025.2536725", "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T12:59:24.048Z", "modified": "2025-11-25T12:59:24.581Z"}, {"entity": "publication", "iuid": "6bfd9db1c38b49c49158044c0155d00d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6bfd9db1c38b49c49158044c0155d00d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6bfd9db1c38b49c49158044c0155d00d"}}, "title": "Thioredoxin Reductase 1 inhibition triggers ferroptosis in KRAS-independent lung cancers.", "authors": [{"family": "Andreani", "given": "Cristina", "initials": "C", "orcid": "0000-0003-3245-670X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac8d24e06e2949b59784539dc93e9a1e.json"}}, {"family": "Bartolacci", "given": "Caterina", "initials": "C", "orcid": "0000-0003-2002-7721", "researcher": {"href": "https://publications.scilifelab.se/researcher/4876eab40d6f496da30ea338ede8e8e1.json"}}, {"family": "Melegari", "given": "Margherita", "initials": "M", "orcid": "0000-0003-3565-5560", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ad61d725ed8433c9e4469312bcce77f.json"}}, {"family": "Sargentoni", "given": "Nicola", "initials": "N", "orcid": "0009-0009-2735-3440", "researcher": {"href": "https://publications.scilifelab.se/researcher/e478ff01e2e24fe8bbbf3331b125d093.json"}}, {"family": "Luciani", "given": "Lorenzo", "initials": "L", "orcid": "0000-0002-9000-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/806ba2ac1b9f461eb25549b4b81fd1d9.json"}}, {"family": "Marucci", "given": "Agnese", "initials": "A"}, {"family": "Galeazzi", "given": "Roberta", "initials": "R", "orcid": "0000-0003-1792-654X", "researcher": {"href": "https://publications.scilifelab.se/researcher/891fb9c56107468a8cce385d8bb402b6.json"}}, {"family": "DeNicola", "given": "Gina M", "initials": "GM", "orcid": "0000-0001-6611-6696", "researcher": {"href": "https://publications.scilifelab.se/researcher/e19a7cc8adae4fd482db8d1e44adbf23.json"}}, {"family": "Kilgore", "given": "Jessica", "initials": "J", "orcid": "0000-0001-9138-2099", "researcher": {"href": "https://publications.scilifelab.se/researcher/340f210063894be2b5a7a3edc73a9f64.json"}}, {"family": "Williams", "given": "Noelle", "initials": "N", "orcid": "0000-0003-1894-5742", "researcher": {"href": "https://publications.scilifelab.se/researcher/69f9dcee6ec441abbf0bc8d19b1cdeb2.json"}}, {"family": "Berto", "given": "Stefano", "initials": "S", "orcid": "0000-0001-9028-9458", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e144d40db50454caf117f24e57a320a.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Pattabhi", "given": "Prasad", "initials": "P", "orcid": "0000-0002-8437-7838", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ff340a9b68a46f7b87225a63767f6b9.json"}}, {"family": "Osman", "given": "Sagid S", "initials": "SS"}, {"family": "Mansour", "given": "Ahmad T", "initials": "AT"}, {"family": "Pucciarelli", "given": "Stefania", "initials": "S", "orcid": "0000-0003-2137-5517", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ee3c9bf3ffc485a8686a08aef7e4ca8.json"}}, {"family": "Galassi", "given": "Rossana", "initials": "R", "orcid": "0000-0002-8025-9615", "researcher": {"href": "https://publications.scilifelab.se/researcher/97a7ad071ad4410dad92fe45c56e61e4.json"}}, {"family": "Scaglioni", "given": "Pier Paolo", "initials": "PP", "orcid": "0000-0002-6036-5138", "researcher": {"href": "https://publications.scilifelab.se/researcher/898e0ff87b6949129b39faae85c5346c.json"}}], "type": "journal article", "published": "2025-07-30", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Lung cancers that harbor wild type KRAS (KRAS-WT) represent a molecularly diverse subset of tumors that often lack targeted therapeutic options. Using synthesized gold(I)-based inhibitors, a multi-omics approach, and functional validation, we identified Thioredoxin reductase 1 (TXNRD1), encoding as a selective vulnerability in KRAS-WT and oncogenic KRAS mutant (KM)-independent lung cancer (LC). Mechanistically, TRXR1 blockade induces ferroptosis through glutathione depletion, lipid reactive oxygen species (ROS) accumulation, and HMOX1-dependent iron overload in KRAS-WT LC both in vitro and in vivo. Furthermore, while KM LC cells are intrinsically resistant to TRXR1 inhibition, KMLC cells that acquire resistance to KRAS inhibitors (KRASi) undergo a redox shift that renders them sensitive to TRXR1 inhibition, uncovering a potential novel therapeutic vulnerability in KRASi-refractory tumors. These findings establish TRXR1 as a targetable redox checkpoint in KRAS-WT and KRASi-resistant lung cancers and support further development of TRXR1 inhibitors.", "doi": "10.1101/2025.07.25.666783", "pmid": "40766571", "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12324224"}, {"db": "pii", "key": "2025.07.25.666783"}, {"db": "figshare", "key": "10.25452/figshare.plus.24667905.v2"}], "notes": [], "created": "2025-11-25T16:35:13.732Z", "modified": "2025-11-25T16:42:16.937Z"}, {"entity": "publication", "iuid": "6a3d8633c23e4f38b7f95ceb3f097594", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6a3d8633c23e4f38b7f95ceb3f097594.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6a3d8633c23e4f38b7f95ceb3f097594"}}, "title": "Single-Entity Resolution Single-Cell Nanosensor Reveals Reactive Oxygen Species at Stress Granules Are Formed by Interfacial Redox Chemistry.", "authors": [{"family": "Gu", "given": "Hui", "initials": "H"}, {"family": "Gu", "given": "Chaoyi", "initials": "C"}, {"family": "Du Toit", "given": "Andre", "initials": "A"}, {"family": "Yu", "given": "Wen", "initials": "W"}, {"family": "Chen", "given": "Michael W", "initials": "MW"}, {"family": "Struckman", "given": "Heather L", "initials": "HL"}, {"family": "Silva", "given": "Jonathan R", "initials": "JR"}, {"family": "Dai", "given": "Yifan", "initials": "Y", "orcid": "0000-0002-1009-5790", "researcher": {"href": "https://publications.scilifelab.se/researcher/278a241ff01846b7913d280926534457.json"}}, {"family": "Ewing", "given": "Andrew G", "initials": "AG", "orcid": "0000-0002-2084-0133", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6ecb82dc7a6423fa0876822f5568e1b.json"}}], "type": "journal article", "published": "2025-07-30", "journal": {"title": "J. Am. Chem. Soc.", "issn": "1520-5126", "volume": "147", "issue": "30", "pages": "27020-27029", "issn-l": "0002-7863"}, "abstract": "The electrochemical activities of biomolecular condensates represent a new fundamental functioning mechanism in biochemistry and cell biology. However, our understanding of the underlying molecular mechanism and the interfacial field-dependent chemical activities remains limited. This is due to the lack of technology to probe such activities in real time and at a single-condensate level. Stress granules (SGs) are membraneless organelles that form in the cytoplasm to adapt to cell stress, which are found to encapsulate reactive oxygen species (ROS) in our lab. Here, we design and implement a collision-based electrochemical nanosensor that enables probing of the redox activities of SGs at a single-condensate level in live cells. We show that ex-vivo separated SGs drive the redox reactions depending on their own interfacial potentials and the constituents of the solution system. Surprisingly, we found that water molecules, rather than solvated oxygen (the main source of ROS produced by a conventional enzyme reaction in cells), are the main chemical origin of the redox activity of SGs. Finally, we demonstrate the application of this electrochemical nanosensor in real-time probing of the generation of hydrogen peroxide from SGs in mammalian cells and show that the electrochemical environment of the cells can regulate the redox activity of SGs. This work uncovers the likely mechanisms encoding nonenzymatic redox activities of SGs and demonstrates a key fundamental technological capability that can be highly useful in exploring the intracellular electroactive pathways of macroscale assemblies.", "doi": "10.1021/jacs.5c09338", "pmid": "40692136", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12314916"}], "notes": [], "created": "2025-11-05T13:50:45.342Z", "modified": "2025-11-05T13:50:45.408Z"}, {"entity": "publication", "iuid": "94bc601b34d44e4c92d9c87e8a71600f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94bc601b34d44e4c92d9c87e8a71600f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94bc601b34d44e4c92d9c87e8a71600f"}}, "title": "Sex-Biased Gene Expression Under Sexually Antagonistic and Sex-Limited Selection.", "authors": [{"family": "Wiberg", "given": "R Axel W", "initials": "RAW", "orcid": "0000-0002-8074-8670", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e9fd2f8f36a4be4a40b87ce2b65133c.json"}}, {"family": "Zwoinska", "given": "Martyna K", "initials": "MK", "orcid": "0000-0003-3356-7284", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f8ceb1ef19c4089bf685928da01b9e8.json"}}, {"family": "Kaufmann", "given": "Philipp", "initials": "P", "orcid": "0000-0002-7164-6867", "researcher": {"href": "https://publications.scilifelab.se/researcher/4214ade17fff4c30a690c13c43623ee7.json"}}, {"family": "Howie", "given": "James M", "initials": "JM", "orcid": "0000-0001-7142-5100", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1e0979df2194651916b36b39b11064f.json"}}, {"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}], "type": "journal article", "published": "2025-07-30", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "42", "issue": "8", "issn-l": "0737-4038"}, "abstract": "Sex differences in gene expression are ubiquitous, evolve quickly, and are expected to underlie phenotypic sexual dimorphism (SD). Despite long-standing interest, the impact of sex-specific selection on the transcriptome remains poorly understood. Here, we test fundamental questions on the role of constraints on gene expression evolution arising from the mode of selection and genetic architecture. We also test the relationship between sex-biased expression and evolved SD. We assess these using body size selection lines in the seed beetle, Callosobruchus maculatus, that have evolved variation in SD in response to either sex-limited (SL) or sexually antagonistic (SA). We find that sex differences in the phenotypic responses and expression changes are generally well aligned. SL selection, despite a phenotypic response similar to SA selection in males, but not in females, resulted in a more extensive expression differentiation and increase of sex-biased expression than SA selection. These patterns show that SA selection imposes a transcriptomic constraint and is not required for sex-bias to evolve. Sex-biased transcripts show lower cross-sex correlations in expression changes than unbiased transcripts, suggesting greater sex differences in their underlying genetic architecture. Although male-biased transcripts are disproportionately affected when selection targeted males, we find no support for a transcriptome-wide association between sex-bias and SD. In the light of these unique experimental insights into how sex-specific selection on size changes adult transcription, our findings have important implications for inferring selection history and mode from patterns of sex-biased gene expression in natural populations.", "doi": "10.1093/molbev/msaf178", "pmid": "40729508", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371189"}, {"db": "pii", "key": "8217438"}], "notes": [], "created": "2025-11-07T07:27:03.269Z", "modified": "2025-11-28T10:50:04.075Z"}, {"entity": "publication", "iuid": "79cda722345d4dddadc80c3f12903789", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79cda722345d4dddadc80c3f12903789.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79cda722345d4dddadc80c3f12903789"}}, "title": "Cytokines, chemokines and antibodies against histone-3/4 citrullinated peptides in rheumatoid arthritis patients with pulmonary fibrosis.", "authors": [{"family": "Johansson", "given": "Linda", "initials": "L", "orcid": "0000-0001-7071-4699", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b9129e8ce7846e5b35b50f1ff4493e2.json"}}, {"family": "Pratesi", "given": "Federico", "initials": "F", "orcid": "0000-0002-7226-0907", "researcher": {"href": "https://publications.scilifelab.se/researcher/978ceb177a5545c89fe32f0689843120.json"}}, {"family": "Errante", "given": "Fosca", "initials": "F", "orcid": "0000-0001-7790-9886", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f4b94b4ee454c8fa990418b921272ab.json"}}, {"family": "Pacini", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-0737-2213", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8e5edfce6ae432cb0b3333cd9a8ebfd.json"}}, {"family": "Migliorini", "given": "Paola", "initials": "P", "orcid": "0000-0001-6433-4964", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de011ca211242b3bb0639adc36c47e3.json"}}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}], "type": "journal article", "published": "2025-07-30", "journal": {"title": "Arthritis Res. Ther.", "issn": "1478-6362", "volume": "27", "issue": "1", "pages": "160", "issn-l": "1478-6354"}, "abstract": "Rheumatoid arthritis (RA) associated interstitial lung disease (ILD) is the most common pulmonary manifestations of RA, with a progressive course and a poor survival. An early detection and better treatment is essential to improve outcome. We evaluated 16 analytes that could be relevant for the development of RA ILD.\n\nIn an inception cohort of 1118 early RA patients, pulmonary fibrosis (PF) were identified in 60 patients after a mean follow-up of 5.3 years using high resolution computer tomography (HRCT). As controls, 124 early RA patients without PF and 94 matched population controls without known rheumatic disease were studied. Analysis of antibodies against histones 3 and 4 derived citrullinated peptides (CitH3/H4), and cytokines/chemokines levels were performed in plasma samples collected at RA diagnosis using in-house ELISA and Luminex analysis.\n\nAnti-CitH3(114-135) antibodies were the only antibody with increased frequency and levels in patients with PF versus without PF. The highest OR for PF development were found when combining positivity for anti-CitH3(114-135) and -CitH4(31-50) antibodies, OR 2.26. Levels of IL1\u03b1, IL1\u00df, TNF\u03b1, VEGFA and MIP\u03b1 remained significantly elevated in patients with PF compared without PF, after adjustments and Bonferroni corrections. Several of the cytokines/chemokines correlated significantly with the histone antibodies in patients without PF. Partial least squares discriminant analysis including antibodies against citrullinated histon peptides and cytokines/chemokines identified significantly in PF in non-smokers.\n\nAntibodies against CitH3 peptides and several of the analysed cytokines/chemokines in samples collected at diagnosis were associated with subsequent delevopment of PF in patients with RA.", "doi": "10.1186/s13075-025-03603-x", "pmid": "40739515", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12308956"}, {"db": "pii", "key": "10.1186/s13075-025-03603-x"}], "notes": [], "created": "2025-11-21T11:45:04.126Z", "modified": "2025-11-21T11:45:04.707Z"}, {"entity": "publication", "iuid": "f3e20a54efbe442c83ae530df3eecba2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3e20a54efbe442c83ae530df3eecba2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3e20a54efbe442c83ae530df3eecba2"}}, "title": "Disease activity and treatment response in early rheumatoid arthritis: an exploratory metabolomic profiling in the NORD-STAR cohort.", "authors": [{"family": "Fatima", "given": "Tahzeeb", "initials": "T"}, {"family": "Zhang", "given": "Yuan", "initials": "Y"}, {"family": "Vasileiadis", "given": "Georgios K", "initials": "GK"}, {"family": "Rawshani", "given": "Araz", "initials": "A"}, {"family": "van Vollenhoven", "given": "Ronald", "initials": "R"}, {"family": "Lampa", "given": "Jon", "initials": "J"}, {"family": "Gudbjornsson", "given": "Bjorn", "initials": "B"}, {"family": "Haavardsholm", "given": "Espen A", "initials": "EA"}, {"family": "Nordstr\u00f6m", "given": "Dan", "initials": "D"}, {"family": "Gr\u00f6ndal", "given": "Gerdur", "initials": "G"}, {"family": "H\u00f8rslev-Petersen", "given": "Kim", "initials": "K"}, {"family": "Lend", "given": "Kristina", "initials": "K"}, {"family": "Heiberg", "given": "Marte S", "initials": "MS"}, {"family": "Hetland", "given": "Merete Lund", "initials": "ML"}, {"family": "Nurmohamed", "given": "Michael", "initials": "M"}, {"family": "\u00d8stergaard", "given": "Mikkel", "initials": "M"}, {"family": "Uhlig", "given": "Till", "initials": "T"}, {"family": "Sokka-Isler", "given": "Tuulikki", "initials": "T"}, {"family": "Rudin", "given": "Anna", "initials": "A"}, {"family": "Maglio", "given": "Cristina", "initials": "C"}], "type": "journal article", "published": "2025-07-26", "journal": {"title": "Arthritis Res. Ther.", "issn": "1478-6362", "volume": "27", "issue": "1", "pages": "156", "issn-l": "1478-6354"}, "abstract": "The variability in treatment response in people with rheumatoid arthritis (RA) warrants the prediction of patients at high risk of treatment failure. Identification of biomarkers linked to clinical remission in RA is currently a challenge. Metabolomics may help to identify such biomarkers as it allows for a comprehensive exploration of disease-related variations that extends beyond the genome and proteome. This hypothesis-free exploratory metabolomics study aimed to profile serum metabolic alterations in early RA to understand the metabolic changes associated with disease activity and therapeutic response.\n\nThe study included 220 early RA participants from the NORD-STAR study, randomized at baseline into four arms, ranging from conventional anti-rheumatic treatment to biological drugs: methotrexate combined with prednisolone (1), certolizumab (2), abatacept (3), or tocilizumab (4). Untargeted metabolomics was performed in serum samples at baseline and 24-week follow-up. Participants achieving clinical disease activity index remission at 24 weeks were defined as responders. Machine learning models for treatment response were constructed using random forest, logistic regression, support vector machine and extreme gradient boosting algorithms based on selected features.\n\nWe identified 278 metabolites, of which 39 were associated with baseline disease activity, including several acylcarnitines and amino acids. We also found 17 baseline metabolites associated with remission at 24 weeks in the overall cohort, including malic acid (\u03b2=-0.4), cytidine (\u03b2 = 0.4), arginine (\u03b2 = 0.3), and citrulline (\u03b2 = 0.2), as well as specific metabolites and metabolic pathways associated with remission in the four treatment arms. Fifteen features were identified using machine learning-based multivariable selection. The best predictive model using logistic regression achieved AUC of 0.75 in training and 0.73 in the test set.\n\nOur study has identified several baseline metabolites and metabolic pathways associated with disease activity and response to different treatments in early RA. By integrating metabolomics and clinical data, we developed predictive models for response to treatment in early RA, though their predictive performance remains limited.", "doi": "10.1186/s13075-025-03616-6", "pmid": "40713837", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12297794"}, {"db": "pii", "key": "10.1186/s13075-025-03616-6"}], "notes": [], "created": "2025-11-18T12:07:38.351Z", "modified": "2025-11-18T12:07:38.356Z"}, {"entity": "publication", "iuid": "90b8a5b9723c42228207d46e91919ff8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90b8a5b9723c42228207d46e91919ff8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90b8a5b9723c42228207d46e91919ff8"}}, "title": "Topical MTH1 Inhibition Suppresses SKP2-WNT5a-Driven Psoriatic Hyperproliferation", "authors": [{"family": "Bivik Eding", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-2769-0016", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe41fe488cc34311a78037b2c7cee09b.json"}}, {"family": "K\u00f6hler", "given": "Ines", "initials": "I", "orcid": "0000-0002-9260-8528", "researcher": {"href": "https://publications.scilifelab.se/researcher/38cf202fae2a4a9fb1a892023899a497.json"}}, {"family": "Moparthi", "given": "Lavanya", "initials": "L", "orcid": "0000-0002-6030-3084", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2207da5d7d34dd2a8def5239eaf351d.json"}}, {"family": "Sj\u00f6gren", "given": "Florence", "initials": "F"}, {"family": "Andersson", "given": "Blanka", "initials": "B", "orcid": "0000-0002-9562-0872", "researcher": {"href": "https://publications.scilifelab.se/researcher/df74d95228ec4e4583fd0a7f9dfd0317.json"}}, {"family": "Das", "given": "Debojyoti", "initials": "D", "orcid": "0000-0001-6811-3333", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c763bab024a492d8e534a1e541c21dc.json"}}, {"family": "Verma", "given": "Deepti", "initials": "D"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Warpman Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Enerb\u00e4ck", "given": "Charlotta", "initials": "C", "orcid": "0000-0003-1769-3790", "researcher": {"href": "https://publications.scilifelab.se/researcher/492c35e3b7b44e23933cb0f91c721af3.json"}}], "type": "journal-article", "published": "2025-07-25", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "15", "pages": "7174", "issn-l": null}, "abstract": null, "doi": "10.3390/ijms26157174", "pmid": null, "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-08-06T13:43:31.717Z", "modified": "2025-08-06T13:44:10.161Z"}, {"entity": "publication", "iuid": "0d182c82543e4dbaa9df359980262f0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d182c82543e4dbaa9df359980262f0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d182c82543e4dbaa9df359980262f0b"}}, "title": "The 3D genome of pediatric B-cell precursor acute lymphoblastic leukemia", "authors": [{"family": "Moura-Castro", "given": "Larissa H", "initials": "LH", "orcid": "0000-0001-9063-5592", "researcher": {"href": "https://publications.scilifelab.se/researcher/d326f608c7744622a92cc73768f23afb.json"}}, {"family": "Ayd\u0131n", "given": "Efe", "initials": "E"}, {"family": "Telliam Dushime", "given": "Gladys", "initials": "G"}, {"family": "Woodward", "given": "Eleanor L", "initials": "EL"}, {"family": "Castor", "given": "Anders", "initials": "A", "orcid": "0009-0007-4634-0704", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed2d2dab933049f5b69cdf0ff1e1d8a1.json"}}, {"family": "Gunnarsson", "given": "Rebeqa", "initials": "R", "orcid": "0000-0002-2283-786X", "researcher": {"href": "https://publications.scilifelab.se/researcher/12601745d2c74562bf83d22879f212eb.json"}}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H", "orcid": "0000-0001-8703-1173", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a75300e8c346858ce8dd8f64ecae85.json"}}, {"family": "Olsson-Arvidsson", "given": "Linda", "initials": "L"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Johansson", "given": "Bertil", "initials": "B", "orcid": "0000-0001-8829-4813", "researcher": {"href": "https://publications.scilifelab.se/researcher/fed657adae7f49f2b8d052cff36eac07.json"}}, {"family": "J\u00e4r\u00e5s", "given": "Marcus", "initials": "M", "orcid": "0000-0003-4080-7055", "researcher": {"href": "https://publications.scilifelab.se/researcher/65cacd8558004a8689985676a798ae90.json"}}, {"family": "Hagstr\u00f6m-Andersson", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-2904-1311", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc93a87c663d471ba64fc3be63212a89.json"}}, {"family": "Yang", "given": "Minjun", "initials": "M"}, {"family": "Paulsson", "given": "Kajsa", "initials": "K", "orcid": "0000-0001-7950-222X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2033b23811f1432c90ad860dd993e7a8.json"}}], "type": "posted-content", "published": "2025-07-25", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.07.22.666073", "pmid": null, "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-06T09:11:41.063Z", "modified": "2025-12-18T19:11:22.125Z"}, {"entity": "publication", "iuid": "65d5c997675d4e2f85e9fc2e08debdf6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65d5c997675d4e2f85e9fc2e08debdf6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65d5c997675d4e2f85e9fc2e08debdf6"}}, "title": "Incentivising cooperation by judging a group's performance by its weakest member in neuroevolution and reinforcement learning.", "authors": [{"family": "Schossau", "given": "Jory", "initials": "J"}, {"family": "Shirmohammadi", "given": "Bamshad", "initials": "B"}, {"family": "Hintze", "given": "Arend", "initials": "A"}], "type": "journal article", "published": "2025-07-25", "journal": {"title": "Front Robot AI", "issn": "2296-9144", "volume": "12", "pages": "1599676", "issn-l": null}, "abstract": "Autonomous agents increasingly interact within social domains such as customer service, transportation, and healthcare, often acting collectively on behalf of humans. In many of these scenarios, individually greedy strategies can diminish overall performance, exemplified by phenomena such as stop-and-go traffic congestion or network service disruptions due to competing interests. Thus, there is a growing need to develop decision-making strategies for autonomous agents that balance individual efficiency with group equitability.\n\nWe propose a straightforward approach for rewarding groups of autonomous agents within evolutionary and reinforcement learning frameworks based explicitly on the performance of the weakest member of the group. Rather than optimizing each agent's individual rewards independently, we align incentives by using a \"weakest-link\" metric, thereby encouraging collective strategies that support equitable outcomes.\n\nOur results demonstrate that this weakest-member reward system effectively promotes equitable behavior among autonomous agents. Agents evolve or learn to balance collective benefit with individual performance, resulting in fairer outcomes for the entire group. Notably, the introduced approach improves overall efficiency, as equitably-minded agents collectively achieve greater stability and higher individual outcomes than agents pursuing purely selfish strategies.\n\nThis methodology aligns closely with biological mechanisms observed in nature, specifically group-level selection and inclusive fitness theory. By tying the evolutionary and learning objectives to the group's weakest member, we mimic natural processes that favor cooperative and equitable behaviors. Our findings highlight the importance of incentive structures that consider the collective well-being to optimize both group fairness and individual agent success. Future research should explore how this reward framework generalizes across broader domains and more complex agent interactions.", "doi": "10.3389/frobt.2025.1599676", "pmid": "40786653", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12331510"}, {"db": "pii", "key": "1599676"}], "notes": [], "created": "2025-11-28T10:54:39.267Z", "modified": "2025-11-28T10:54:39.290Z"}, {"entity": "publication", "iuid": "19dc9b80218f459f85baeddd7d825f66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19dc9b80218f459f85baeddd7d825f66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19dc9b80218f459f85baeddd7d825f66"}}, "title": "cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads.", "authors": [{"family": "Petri", "given": "Alexander J", "initials": "AJ", "orcid": "0009-0005-9397-0341", "researcher": {"href": "https://publications.scilifelab.se/researcher/87c33c340c454e8c8cb82938ab4259c3.json"}}, {"family": "Thi-Huyen Nguyen", "given": "Mai", "initials": "M", "orcid": "0009-0002-7680-1464", "researcher": {"href": "https://publications.scilifelab.se/researcher/50e89828a6064cc6a99a8944ab6a6a6f.json"}}, {"family": "Rajwar", "given": "Anjali", "initials": "A"}, {"family": "Benson", "given": "Erik", "initials": "E"}, {"family": "Sahlin", "given": "Kristoffer", "initials": "K", "orcid": "0000-0001-7378-2320", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7fcc3f1dbb448659ee971c81fc45651.json"}}], "type": "journal article", "published": "2025-07-24", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "7", "pages": "e0321246", "issn-l": "1932-6203"}, "abstract": "Synthetic combinatorial DNA libraries are widely used to produce protein variants, optimize binders, and for high-throughput studies of protein-DNA interactions. The libraries can be made by researchers or vendors, and high-throughput sequencing is used for both quality control and to study the outcome of selection experiments. Oxford nanopore sequencing (ONT) is well suited to this as it allows for long read lengths and can be done rapidly with low-cost instrumentation. However, it suffers from a lower overall read accuracy and an uneven error profile. No current bioinformatics tools are well-suited to the challenge of deducing the composition and order of constituent members of combinatorial libraries from ONT reads. We introduce cONcat, an algorithm to identify the makeup of concatenated DNA fragments in a set of ONT sequencing reads from a pool of known fragments. cONcat uses an edit distance-based recursive covering algorithm for finding the best possible matchings between the fragments and the reads. In our experiments on simulated and experimental data, cONcat accurately detects the correct fragment coverings given the short fragment sizes (< 20 bp) and the sequencing errors present in ONT reads. However, we find that the high error rates in the start of ONT reads make it challenging to get confident coverage there, inferring a need for experimental strategies to avoid key sequence information in the start of reads.", "doi": "10.1371/journal.pone.0321246", "pmid": "40705736", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12289010"}, {"db": "pii", "key": "PONE-D-25-11429"}], "notes": [], "created": "2025-11-28T10:54:08.697Z", "modified": "2025-11-28T10:54:08.793Z"}, {"entity": "publication", "iuid": "b541a4128e1345e8bf9d8db8209ae7a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b541a4128e1345e8bf9d8db8209ae7a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b541a4128e1345e8bf9d8db8209ae7a3"}}, "title": "Transcription of GABAA receptor subunits in circulating monocytes and association to emotional brain function in premenstrual dysphoric disorder.", "authors": [{"family": "Stiernman", "given": "Louise", "initials": "L", "orcid": "0000-0002-9662-981X", "researcher": {"href": "https://publications.scilifelab.se/researcher/168bd84159814cd88be040d84a4c57a7.json"}}, {"family": "Comasco", "given": "Erika", "initials": "E"}, {"family": "Johansson", "given": "Maja", "initials": "M"}, {"family": "Bixo", "given": "Marie", "initials": "M", "orcid": "0000-0002-4988-1967", "researcher": {"href": "https://publications.scilifelab.se/researcher/defb095eecec4c33b25851f9553fc320.json"}}], "type": "journal article", "published": "2025-07-23", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "volume": "15", "issue": "1", "pages": "255", "issn-l": "2158-3188"}, "abstract": "Premenstrual dysphoric disorder (PMDD) has been hypothesized to be related to an altered sensitivity of the \u03b3-aminobutyric acid type A (GABAA) receptor to progesterone-derived neurosteroids. GABAA receptor sensitivity to neurosteroid-modulation is dependent on its subunit composition. In the present study, we used quantitative reverse transcription polymerase chain reactions (RT-qPCR) to compare messenger ribonucleic acid (mRNA) expression of GABAA receptor subunits in peripheral mononuclear cells (PBMCs) across the menstrual cycle in 29 women with PMDD and 27 controls. We related mRNA subunit expression to serum levels of neurosteroids and to functional activation of the amygdala, a key brain region involved in emotion generation, measured using functional magnetic resonance imaging (fMRI). Women with PMDD had lower mRNA expression of the delta GABAA receptor subunit during the symptomatic, luteal phase (compared to the asymptomatic, follicular phase) of the menstrual cycle. Lower delta mRNA expression was related to higher amygdala activation in PMDD women. GABAA receptors incorporating the delta subunit are especially sensitive to neurosteroid modulation. It is possible that the mood symptoms of PMDD are mediated by an inability to effectively adjust the expression of this receptor type in response to neurosteroid fluctuations, leading to dysregulation GABAergic tone and increased activity in emotion-generating brain circuits.", "doi": "10.1038/s41398-025-03465-6", "pmid": "40701967", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12287299"}, {"db": "pii", "key": "10.1038/s41398-025-03465-6"}], "notes": [], "created": "2025-11-26T09:17:53.937Z", "modified": "2025-11-26T09:17:54.289Z"}, {"entity": "publication", "iuid": "3f3eeca95ed34ac385bdad9bbf4f1a2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f3eeca95ed34ac385bdad9bbf4f1a2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f3eeca95ed34ac385bdad9bbf4f1a2f"}}, "title": "Predicting immune responsiveness in ER-positive breast cancer for personalized therapy: a population-based study.", "authors": [{"family": "Stenmark Tullberg", "given": "Axel", "initials": "A"}, {"family": "Woxlin", "given": "Sara", "initials": "S"}, {"family": "Sj\u00f6lin", "given": "Filippa", "initials": "F"}, {"family": "Ittner", "given": "Ella", "initials": "E"}, {"family": "Kov\u00e0cs", "given": "Anik\u00f2", "initials": "A"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Holmberg", "given": "Erik", "initials": "E"}, {"family": "Karlsson", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2025-07-23", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "250", "issn-l": null}, "abstract": "The immune system's role in estrogen receptor (ER)-positive breast cancer is poorly understood. A population-based cohort of 428 breast cancer patients with clinical and molecular data was analyzed to assess how immune biomarkers can inform treatment decisions. Tumor-intrinsic immune responsiveness and local immune infiltration were quantified, and epithelial cell states were derived using EcoTyper. The interaction between ProliferativeIndex and Immunescore predicted risk of local recurrence in ER-positive tumors (HR 0.56, 95% CI 0.36-0.88, p = 0.012). EcoTyper identified two epithelial cell states, S04 and S05, with distinct immunomodulatory properties. S04 tumors showed higher proliferation, enrichment for M1 macrophages, CD8 effector T-cells, and plasma cells, alongside hypomethylation of immune-related pathways and hypermethylation of the PI3K signaling pathway. In contrast, S05-enriched tumors were associated with fibroblast activation, immune exclusion, and enrichment for glycosylation-related pathways. These findings suggest that epithelial cell states shape immune responsiveness in ER-positive breast cancer and may inform biomarker-driven treatment strategies.", "doi": "10.1038/s41698-025-01035-z", "pmid": "40702082", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12287262"}, {"db": "pii", "key": "10.1038/s41698-025-01035-z"}], "notes": [], "created": "2025-09-08T07:07:03.551Z", "modified": "2025-09-08T07:07:03.584Z"}, {"entity": "publication", "iuid": "8e3c080a6b6f4c1494f64bbfe3ee1dc4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e3c080a6b6f4c1494f64bbfe3ee1dc4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e3c080a6b6f4c1494f64bbfe3ee1dc4"}}, "title": "Identification of a small molecule targeting EPLIN as a novel strategy for the treatment of pediatric neuroblastoma and medulloblastoma.", "authors": [{"family": "Lindell", "given": "Emma", "initials": "E", "orcid": "0009-0001-2785-946X", "researcher": {"href": "https://publications.scilifelab.se/researcher/667fca56e7c74aa7984daf5dac4bbc2e.json"}}, {"family": "Guo", "given": "Jing", "initials": "J", "orcid": "0000-0002-6399-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e778f67395b491daec1b80d805ab6bd.json"}}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N"}, {"family": "Lu", "given": "Xi", "initials": "X"}, {"family": "Wacker", "given": "Tabea", "initials": "T"}, {"family": "Zhong", "given": "Lei", "initials": "L"}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Svanberg", "given": "Sara", "initials": "S"}, {"family": "Chowdhury", "given": "Azazul I", "initials": "AI"}, {"family": "Bergsten", "given": "Peter", "initials": "P"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Bexell", "given": "Daniel", "initials": "D"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Zhang", "given": "Xiaonan", "initials": "X", "orcid": "0000-0003-4359-9079", "researcher": {"href": "https://publications.scilifelab.se/researcher/306b1ef8c6904d6b936e11442b4515f4.json"}}], "type": "journal article", "published": "2025-07-23", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "issn-l": "2041-4889", "volume": "16", "issue": "1", "pages": "554"}, "abstract": "Amplification of the MYCN proto-oncogene serves as a key marker of aggressive disease and poor treatment outcomes in certain pediatric tumors originating from the nervous system, including neuroblastoma and medulloblastoma. However, the complex nature of the challenging MYCN protein underscores the urgent need for additional targets and therapies to tackle neuroblastoma and medulloblastoma. In this study, with a primary focus on neuroblastoma and the aim of also benefiting children with medulloblastoma, we identified FLIX5, a small compound that exhibits broad cytotoxicity against both neuroblastoma and medulloblastoma cells, primarily by triggering apoptosis. Furthermore, FLIX5 enhances the cholesterol dependency of neuroblastoma cells under conditions where mitochondrial function is impaired. FLIX5 as well shows a synergistic effect when combined with vincristine, a conventional anticancer drug, against neuroblastoma cells and organoids. Through proteome integral solubility alteration, computational molecular docking predictions, and cellular thermal shift assays for target identification and validation, FLIX5 reveals EPLIN (Epithelial Protein Lost In Neoplasm) as a previously unexplored drug target. EPLIN is involved in several cellular processes, including cholesterol uptake and mitochondrial function. The discovery of FLIX5 targeting EPLIN presents new opportunities for treating malignant pediatric tumors, with the potential to target chemoresistant dormant cancer cells and broaden its therapeutic applications to other tumor types.", "doi": "10.1038/s41419-025-07876-7", "pmid": "40701975", "labels": {"NGI Single cell": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Chemical Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12287531"}, {"db": "pii", "key": "10.1038/s41419-025-07876-7"}], "notes": [], "created": "2025-09-30T09:25:55.225Z", "modified": "2025-11-25T17:06:41.935Z"}, {"entity": "publication", "iuid": "5c371c3254f24f45930def1fa3ba5c42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c371c3254f24f45930def1fa3ba5c42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c371c3254f24f45930def1fa3ba5c42"}}, "title": "Wide-scale geographical analysis of genetic ancestry in the South African Coloured population.", "authors": [{"family": "Lankheet", "given": "Imke", "initials": "I"}, {"family": "Hammar\u00e9n", "given": "Rickard", "initials": "R", "orcid": "0000-0001-9017-591X", "researcher": {"href": "https://publications.scilifelab.se/researcher/01a7b62a04c14b99bd73fb436006e4ff.json"}}, {"family": "Alva Caballero", "given": "Luc\u00eda Ximena", "initials": "LX"}, {"family": "Larena", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8799-7645", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d580f1f3e584c809f5f22d7355f154f.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Jolly", "given": "Cecile", "initials": "C"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "de Jongh", "given": "Michael", "initials": "M"}, {"family": "Schlebusch", "given": "Carina", "initials": "C", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2025-07-22", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "23", "issue": "1", "pages": "219", "issn-l": "1741-7007"}, "abstract": "The South African Coloured (SAC) population, a prominent admixed population in South Africa, reflects centuries of migration, admixture, and historical segregation. Descendants of local Khoe-San and Bantu-speaking populations, European settlers, and enslaved individuals from Africa and Asia, SAC individuals embody diverse ancestries. This study investigates the genetic makeup of SAC individuals, utilizing autosomal genotypes, mitochondrial DNA and Y-chromosome data. We analyse new genotype data for 125 SAC individuals from seven locations.\n\nOur analysis, based on a dataset comprising 356 SAC individuals from 22 geographic locations, revealed significant regional variations in ancestry. Khoe-San ancestry predominates in 14 locations, highlighting its lasting influence. Inland regions exhibit higher proportions of Khoe-San ancestry, eastern regions show more Bantu-speaker/West African ancestry, and western/coastal areas, particularly around Cape Town, display increased Asian ancestry. Additionally, sex-biased admixture ratios show male-biased admixture from East Africans and Europeans, and female-biased admixture from Khoe-San populations, which is supported by mitochondrial and Y-chromosome data.\n\nThe observed patterns of significant regional variation in ancestry reflect historical migrations and settlement patterns. This research underscores the importance of studying the SAC population to understand South Africa's historical migrations, providing insights into the complex genetic heritage of South Africans.", "doi": "10.1186/s12915-025-02317-5", "pmid": "40696318", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12281806"}, {"db": "pii", "key": "10.1186/s12915-025-02317-5"}], "notes": [], "created": "2025-08-19T13:34:50.043Z", "modified": "2025-11-14T11:08:46.149Z"}, {"entity": "publication", "iuid": "271af7d523044be1ba7f3093ac752ba5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/271af7d523044be1ba7f3093ac752ba5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/271af7d523044be1ba7f3093ac752ba5"}}, "title": "Cytoskeleton-associated protein 4 affects podocyte cytoskeleton dynamics in diabetic kidney disease.", "authors": [{"family": "Boi", "given": "Roberto", "initials": "R"}, {"family": "Lass\u00e9n", "given": "Emelie", "initials": "E"}, {"family": "Johansson", "given": "Alva", "initials": "A"}, {"family": "Liu", "given": "Peidi", "initials": "P"}, {"family": "Chaudhari", "given": "Aditi", "initials": "A"}, {"family": "Tati", "given": "Ramesh", "initials": "R"}, {"family": "M\u00fcller-Deile", "given": "Janina", "initials": "J"}, {"family": "Schiffer", "given": "Mario", "initials": "M"}, {"family": "Ebefors", "given": "Kerstin", "initials": "K"}, {"family": "Nystr\u00f6m", "given": "Jenny", "initials": "J"}], "type": "journal article", "published": "2025-07-22", "journal": {"title": "JCI Insight", "issn": "2379-3708", "volume": "10", "issue": "14", "issn-l": "2379-3708"}, "abstract": "Podocytes are kidney glomerular cells that depend on rigorously regulated cytoskeleton components and integrins to form and maintain the so-called foot processes, apparatuses that attach podocytes to the glomerular basement membrane and connect them to neighboring podocytes. In diabetic kidney disease (DKD) these foot processes are effaced as a result of cytoskeleton dysregulation, a phenomenon that gradually reduces glomerular filtration. Cytoskeleton-associated protein 4 (CKAP4) is a known linker between the endoplasmic reticulum, integrins, and microtubular cytoskeleton. Since CKAP4 gene expression is downregulated in glomeruli from patients with DKD but not in other chronic kidney diseases, we hypothesized a role for CKAP4 in the mechanisms leading to foot process effacement (FPE) in DKD. CKAP4 mRNA reduction in podocytes in DKD was demonstrated in human kidney biopsies. Knockdown of CKAP4 in vivo in zebrafish resulted in edema, proteinuria, and foot process effacement, all typical features of DKD. Knockdown of CKAP4 in vitro led to disruption of the actin cytoskeleton and of the microtubular orientation. Moreover, it caused a downregulation of several integrins. These findings indicate that CKAP4 is crucial for foot process dynamics of podocytes. Its reduction, unique to DKD, is mechanistically connected to the pathophysiological processes leading to podocyte FPE.", "doi": "10.1172/jci.insight.181298", "pmid": "40493405", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12288980"}, {"db": "pii", "key": "181298"}], "notes": [], "created": "2025-11-20T18:09:48.096Z", "modified": "2025-11-20T18:09:48.101Z"}, {"entity": "publication", "iuid": "9b2a4c60a4bc4b7ba65120b1198c46a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b2a4c60a4bc4b7ba65120b1198c46a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b2a4c60a4bc4b7ba65120b1198c46a0"}}, "title": "Sustainable production of exopolysaccharides from quinoa stalk hydrolysates using halotolerant Bacillus swezeyi: fermentation kinetics and product characterization", "authors": [{"family": "Miranda", "given": "Diego A", "initials": "DA"}, {"family": "Carrasco", "given": "Cristhian", "initials": "C"}, {"family": "Romero\u2010Soto", "given": "Luis", "initials": "L"}, {"family": "Lundqvist", "given": "Jenny", "initials": "J"}, {"family": "Sundman", "given": "Ola", "initials": "O"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Gorzs\u00e1s", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Brostr\u00f6m", "given": "Markus", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}, {"family": "Mart\u00edn", "given": "Carlos", "initials": "C", "orcid": "0000-0002-4258-0512", "researcher": {"href": "https://publications.scilifelab.se/researcher/7300805a6af44b9687438bb882be7e71.json"}}], "type": "journal-article", "published": "2025-07-21", "journal": {"title": "Biofuels Bioprod Bioref", "issn": "1932-104X", "issn-l": null}, "abstract": null, "doi": "10.1002/bbb.70021", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-09-10T14:26:43.175Z", "modified": "2025-10-17T13:03:52.260Z"}, {"entity": "publication", "iuid": "f0fcb0e459e6426fab71064e0db96eee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0fcb0e459e6426fab71064e0db96eee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0fcb0e459e6426fab71064e0db96eee"}}, "title": "Parathyroidectomy Restores Muscle Strength and Transcriptome in Individuals with Primary Hyperparathyroidism.", "authors": [{"family": "Bj\u00f6rnsdotter-\u00d6berg", "given": "Sofia", "initials": "S"}, {"family": "Koman", "given": "Anna", "initials": "A", "orcid": "0000-0003-3196-7057", "researcher": {"href": "https://publications.scilifelab.se/researcher/518d3806b27d4b19822b8572b90f36a5.json"}}, {"family": "Skorpil", "given": "Mikael", "initials": "M"}, {"family": "Ryd\u00e9n", "given": "Henric", "initials": "H"}, {"family": "Lanner", "given": "Johanna T", "initials": "JT"}, {"family": "Krook", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Inga-Lena", "initials": "IL"}, {"family": "Pillon", "given": "Nicolas J", "initials": "NJ"}, {"family": "Nyl\u00e9n", "given": "Carolina", "initials": "C", "orcid": "0000-0002-8445-7221", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb57024f0b2492988a3dbad9fafe198.json"}}], "type": "journal article", "published": "2025-07-21", "journal": {"title": "J. Clin. Endocrinol. Metab.", "issn": "1945-7197", "issn-l": "0021-972X"}, "abstract": "Primary hyperparathyroidism leads to hypercalcemia and muscle dysfunction. Muscle weakness is associated with increased morbidity and mortality but is overlooked in surgical treatment guidelines. While parathyroidectomy is the only curative treatment, its effects on skeletal muscle strength and molecular remodelling remain underexplored.\n\nDetermining functional and molecular changes in skeletal muscle before and after parathyroidectomy.\n\nA prospective observational study was conducted in the spring and fall of 2023.\n\nPatients underwent surgery at the Endocrine and Sarcoma section at the Karolinska University Hospital in Stockholm, Sweden.\n\n21 postmenopausal women with primary hyperparathyroidism planned for surgery were included, whereof 15 completed the study protocol. Participants had no disabling comorbidities.\n\nMuscle function tests, muscle biopsies, MRI, and biochemical panels were analyzed before and after parathyroidectomy.\n\nMuscle composition of m. vastus lateralis was tested with MRI and transcriptomic analysis of muscle biopsies. Leg strength was evaluated with timed stands test and peak torque tests. Activity level was estimated from questionnaires.\n\nParathyroidectomy normalized calcium levels (p<0.001) and improved muscle strength (p<0.005). Muscle volume increased (p=0.023) and fat fraction was reduced (p=0.013), without changes in physical activity levels. Transcriptomic analysis identified 981 differentially expressed genes post-surgery, enriched in pathways mirroring exercise-induced adaptations.\n\nThese findings highlight the impact of parathyroidectomy on skeletal muscle function and suggest that muscle assessments should be included in surgical referral criteria to address age-related muscle decline and improve long-term outcomes.", "doi": "10.1210/clinem/dgaf418", "pmid": "40690900", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "8210038"}], "notes": [], "created": "2025-11-28T14:57:00.299Z", "modified": "2025-11-28T14:57:00.643Z"}, {"entity": "publication", "iuid": "e4171e3c321d427eab5134bacfa87814", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4171e3c321d427eab5134bacfa87814.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4171e3c321d427eab5134bacfa87814"}}, "title": "Cross-generational genomic prediction of Norway spruce (Picea abies) wood properties: an evaluation using independent validation.", "authors": [{"family": "Hayatgheibi", "given": "Haleh", "initials": "H"}, {"family": "Hallingb\u00e4ck", "given": "Henrik R", "initials": "HR"}, {"family": "Gezan", "given": "Salvador A", "initials": "SA"}, {"family": "Lundqvist", "given": "Sven-Olof", "initials": "SO"}, {"family": "Grahn", "given": "Thomas", "initials": "T"}, {"family": "Scheepers", "given": "Gerhard", "initials": "G"}, {"family": "Ranade", "given": "Sonali Sachin", "initials": "SS"}, {"family": "K\u00e4rkk\u00e4inen", "given": "Katri", "initials": "K"}, {"family": "Garc\u00eda Gil", "given": "M Rosario", "initials": "MR"}], "type": "journal article", "published": "2025-07-21", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "680", "issn-l": "1471-2164"}, "abstract": "The evaluation of genomic selection (GS) efficiency in forestry has primarily relied on cross-validation schemes that split the same population within a single generation for both training and validation. While useful, this approach may not be reliable for multigenerational breeding. To our knowledge, this is the first study to assess genomic prediction in Norway spruce using a large dataset spanning two generations in two environments. We trained pedigree-based (ABLUP) and marker-based (GBLUP) prediction models under three approaches: forward prediction, backward prediction, and across-environment prediction. The models were evaluated for ring-width, solid-wood and tracheid characteristics, using ~ 6,000 phenotyped and ~ 2,500 genotyped individual. Predictive ability (PA) and prediction accuracy (ACC) were estimated using an independent validation method, ensuring no individuals were shared between training and validation datasets. To assess the trade-off between comprehensive radial history and practical direct methods, we compared GBLUP models trained with cumulative area-weighted density (AWE-GBLUP) and single annual-ring density (SAD-GBLUP) from mother plus-trees. These models were validated using early and mature-stage progeny density measurements across two trials.\n\nDespite the smaller number of individuals used in the GBLUP models, both PA and ACC were generally comparable to those of the ABLUP model, particularly for cross-environment predictions. Overall, forward and backward predictions were significantly higher for density-related and tracheid properties, suggesting that across-generation predictions are feasible for wood properties but may be challenging for growth and low-heritability traits. Notably, SAD-GBLUP provided comparable prediction accuracies to AWE-GBLUP, supporting the use of more practical and cost-effective phenotyping methods in operational breeding programs.\n\nOur findings highlight the need for context-specific models to improve the accuracy and reliability of genomic prediction in forest tree breeding. Future efforts might aim to expand training populations, incorporate non-additive genetic effects, and validate model performance across cambial ages while accounting for climatic variability during the corresponding growth years. Overall, this study offers a valuable foundation for implementing GS in Norway spruce breeding programs.", "doi": "10.1186/s12864-025-11861-x", "pmid": "40691535", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12278512"}, {"db": "pii", "key": "10.1186/s12864-025-11861-x"}], "notes": [], "created": "2025-11-17T16:50:45.625Z", "modified": "2025-11-17T16:50:45.629Z"}, {"entity": "publication", "iuid": "f5c04bc9cc13408387b5cb7cbcd3cbc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5c04bc9cc13408387b5cb7cbcd3cbc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5c04bc9cc13408387b5cb7cbcd3cbc6"}}, "title": "The invasion phenotypes of glioblastoma depend on plastic and reprogrammable cell states.", "authors": [{"family": "Doroszko", "given": "Milena", "initials": "M"}, {"family": "Stockgard", "given": "Rebecka", "initials": "R"}, {"family": "Uppman", "given": "Irem", "initials": "I", "orcid": "0000-0003-3602-5544", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29421803962496880443d5772f4c97a.json"}}, {"family": "Heinold", "given": "Josephine", "initials": "J"}, {"family": "Voukelatou", "given": "Faidra", "initials": "F", "orcid": "0009-0007-4281-3041", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b89b587bcc740e691e8d0253a03e161.json"}}, {"family": "Mangukiya", "given": "Hitesh Bhagavanbhai", "initials": "HB", "orcid": "0000-0002-8460-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/d32958c394c749d19d7444dac9fe6c3b.json"}}, {"family": "Millner", "given": "Thomas O", "initials": "TO"}, {"family": "Skepp\u00e5s", "given": "Madeleine", "initials": "M", "orcid": "0009-0003-3741-4143", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0b0193e1c804b738dc4b2d5d735d53e.json"}}, {"family": "Ballester Bravo", "given": "Mar", "initials": "M"}, {"family": "Elgendy", "given": "Ramy", "initials": "R", "orcid": "0000-0002-2592-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a5ce4db4317446bb1ef113f7c6e8eb5.json"}}, {"family": "Berglund", "given": "Maria", "initials": "M"}, {"family": "Elfineh", "given": "Ludmila", "initials": "L"}, {"family": "Krona", "given": "Cecilia", "initials": "C"}, {"family": "Kundu", "given": "Soumi", "initials": "S", "orcid": "0000-0002-0759-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/e48ddbc3493247e4930203374878f4b7.json"}}, {"family": "Koltowska", "given": "Katarzyna", "initials": "K", "orcid": "0000-0002-6841-8900", "researcher": {"href": "https://publications.scilifelab.se/researcher/06a8aeda504340c1af3ab893fd413a65.json"}}, {"family": "Marino", "given": "Silvia", "initials": "S", "orcid": "0000-0002-9612-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d040a587c9417b925d42b8e39a43e6.json"}}, {"family": "Larsson", "given": "Ida", "initials": "I", "orcid": "0000-0001-5422-4243", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ac604ca793048e9b6ddaa3459b4e97a.json"}}, {"family": "Nelander", "given": "Sven", "initials": "S", "orcid": "0000-0003-1758-1262", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d684fc3b26d4741b850790ba0571c96.json"}}], "type": "journal article", "published": "2025-07-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "6662", "issn-l": "2041-1723"}, "abstract": "Glioblastoma (GBM) is the most common primary brain cancer. It causes death mainly by local invasion via several routes, including infiltration of white matter tracts and penetration of perivascular spaces. However, the pathways that mediate these invasion routes are only partly known. Here, we conduct an integrative study to identify cell states and central drivers of route-specific invasion in GBM. Combining single-cell profiling and spatial protein detection in patient-derived xenograft models and clinical tumor samples, we demonstrate a close association between the differentiation state of GBM cells and their choice of invasion route. Computational modeling identifies ANXA1 as a driver of perivascular involvement in GBM cells with mesenchymal differentiation and the transcription factors RFX4 and HOPX as orchestrators of growth and differentiation in diffusely invading GBM cells. Ablation of these targets in tumor cells alters their invasion route, redistributes the cell states, and extends survival in xenografted mice. Our results define a close association between GBM cell differentiation states and invasion routes, identify functional biomarkers of route-specific invasion, and point toward targeted modulation of specific invasive cell states as a therapeutic strategy in GBM.", "doi": "10.1038/s41467-025-61999-1", "pmid": "40683881", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12276355"}, {"db": "pii", "key": "10.1038/s41467-025-61999-1"}], "notes": [], "created": "2025-09-30T08:40:58.966Z", "modified": "2025-11-21T11:52:14.274Z"}, {"entity": "publication", "iuid": "ec61d27d2c1246fd953c84e68a7f1129", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec61d27d2c1246fd953c84e68a7f1129.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec61d27d2c1246fd953c84e68a7f1129"}}, "title": "Interplay between antipredator behavior, parasitism, and gut microbiome in wild stickleback populations.", "authors": [{"family": "Varg", "given": "Javier Edo", "initials": "JE", "orcid": "0000-0002-7895-4563", "researcher": {"href": "https://publications.scilifelab.se/researcher/72cb1019516e49f7b8f39b18924babc2.json"}}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC", "orcid": "0000-0001-7068-2017", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeb2930d582f4483afc1f5bd52e37818.json"}}, {"family": "Benha\u00efm", "given": "David", "initials": "D"}, {"family": "Losada-Germain", "given": "Rafael", "initials": "R"}, {"family": "Boughman", "given": "Janette W", "initials": "JW"}], "type": "journal article", "published": "2025-07-19", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "11", "issue": "1", "pages": "138", "issn-l": "2055-5008"}, "abstract": "The impact of microbial composition on stress-related behavior in aquatic organisms is poorly understood. This study explored the link between antipredator behavior, parasitism, and the gut microbiome in wild stickleback from two lakes: clear, spring-fed Galtab\u00f3l and turbid, glacial-fed \u00deristikla. Behavioral analysis revealed differences between populations, with each exhibiting unique baseline behaviors. Microbiome analysis showed that a small proportion of its variation was explained by population, likely reflecting differences in lake environments. Only the marine genus Pseudoalteromonas abundance differed between populations. Our findings suggest that behavior and microbiome correlations may primarily reflect environmental adaptations and parasite status rather than direct gut-brain interactions. However, some tentative evidence suggests a potential innate connection between some antipredator behavior and microbiome composition. The study highlights the complexity of the gut-brain axis in wild populations and suggests future research directions, including experimental manipulations to uncover causal relationships between microbiome composition and behavior.", "doi": "10.1038/s41522-025-00758-y", "pmid": "40683872", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12276351"}, {"db": "pii", "key": "10.1038/s41522-025-00758-y"}], "notes": [], "created": "2025-09-08T11:37:13.990Z", "modified": "2025-09-09T13:13:05.326Z"}, {"entity": "publication", "iuid": "09be553050f342ae982025de836a0afd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09be553050f342ae982025de836a0afd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09be553050f342ae982025de836a0afd"}}, "title": "Tissue origin and virus specificity shape human CD8+ T cell cytotoxicity.", "authors": [{"family": "Niessl", "given": "Julia", "initials": "J", "orcid": "0000-0001-8852-1924", "researcher": {"href": "https://publications.scilifelab.se/researcher/710f1dd1e63e45d39a11d52eb21a5e88.json"}}, {"family": "M\u00fcller", "given": "Thomas R", "initials": "TR", "orcid": "0000-0001-5331-5522", "researcher": {"href": "https://publications.scilifelab.se/researcher/b411684ce1eb401fb8917def9c2a75a0.json"}}, {"family": "Constantz", "given": "Christian", "initials": "C"}, {"family": "Cai", "given": "Curtis", "initials": "C", "orcid": "0000-0002-3490-4361", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ea25e71e96246d89437270a12cc9e47.json"}}, {"family": "Nils\u00e9n", "given": "Vera", "initials": "V"}, {"family": "Rivera Ballesteros", "given": "Olga", "initials": "O", "orcid": "0000-0001-6949-4270", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b48f38b946d4fbc9d687da130f2e661.json"}}, {"family": "Adamo", "given": "Sarah", "initials": "S", "orcid": "0000-0002-6161-3156", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbdfb6f121014c29a448232b60f32585.json"}}, {"family": "Kammann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-8433-036X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ead9a21a35e34fd092774ae13a211255.json"}}, {"family": "Mouchtaridi", "given": "Elli", "initials": "E"}, {"family": "Gao", "given": "Yu", "initials": "Y"}, {"family": "Akhirunnesa", "given": "Mily", "initials": "M", "orcid": "0000-0003-3136-9284", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbce6754eaea4ebfa2437f9572f180ae.json"}}, {"family": "Raineri", "given": "Elisa J M", "initials": "EJM", "orcid": "0000-0002-5468-276X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fe9b94230d5498f8550c7ad897254e9.json"}}, {"family": "Weigel", "given": "Whitney", "initials": "W"}, {"family": "Kokkinou", "given": "Efthymia", "initials": "E"}, {"family": "Stamper", "given": "Christopher", "initials": "C", "orcid": "0000-0002-5568-8880", "researcher": {"href": "https://publications.scilifelab.se/researcher/19710b0b30ca436ca1d29bc89a376ddc.json"}}, {"family": "Marchalot", "given": "Anne", "initials": "A", "orcid": "0000-0002-3042-8206", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b674db5dc349eaa4438563f2256290.json"}}, {"family": "Bassett", "given": "John", "initials": "J", "orcid": "0009-0002-5785-5088", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cc9841bc436476492288239d3bb0fff.json"}}, {"family": "Ferreira", "given": "Sabrina", "initials": "S"}, {"family": "Rodahl", "given": "Inga", "initials": "I"}, {"family": "Wild", "given": "Nicole", "initials": "N", "orcid": "0000-0002-4009-473X", "researcher": {"href": "https://publications.scilifelab.se/researcher/17325f3df80248f7a1b4985094a86d7c.json"}}, {"family": "Stellaccio", "given": "Teresa", "initials": "T", "orcid": "0009-0002-5224-0893", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddfda0141dd948a6b1cd6289b2c5e7f2.json"}}, {"family": "Brownlie", "given": "Demi", "initials": "D", "orcid": "0000-0001-5932-6425", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e879a6ef8ff45bea049986707480e99.json"}}, {"family": "Ringqvist", "given": "Emma", "initials": "E", "orcid": "0000-0001-6303-6076", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfad17442063471cb570d5be1c4dbc48.json"}}, {"family": "Flodstr\u00f6m-Tullberg", "given": "Malin", "initials": "M", "orcid": "0000-0003-2685-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6d04afbe8141c2b9297854de64dab8.json"}}, {"family": "Llewellyn-Lacey", "given": "Sian", "initials": "S", "orcid": "0000-0002-4703-0413", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a952db761ab4e66b251f69c00d14990.json"}}, {"family": "Tibbitt", "given": "Chris", "initials": "C", "orcid": "0000-0002-7730-7700", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d8a6804b0be4aba9a9256dd2df71656.json"}}, {"family": "Hammer", "given": "Quirin", "initials": "Q", "orcid": "0000-0003-2968-6061", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b6b2e5256c8401f83c3f89b5c5bb92f.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Price", "given": "David A", "initials": "DA", "orcid": "0000-0001-9416-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dd5567af7984233b164e6906d4daaca.json"}}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J", "orcid": "0000-0002-1119-0976", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcca878a7f314944bf1a4290cfd5d71d.json"}}, {"family": "Marquardt", "given": "Nicole", "initials": "N", "orcid": "0000-0003-3186-4752", "researcher": {"href": "https://publications.scilifelab.se/researcher/b87ccad53d354bdd80af490dc8a0c019.json"}}, {"family": "Sandberg", "given": "Johan K", "initials": "JK", "orcid": "0000-0002-6275-0750", "researcher": {"href": "https://publications.scilifelab.se/researcher/7468c415a46645a3a4c3d28badcff954.json"}}, {"family": "Sekine", "given": "Takuya", "initials": "T", "orcid": "0000-0001-7649-0593", "researcher": {"href": "https://publications.scilifelab.se/researcher/42434c4f0f504dcd82e5830a727d5a04.json"}}, {"family": "Jorns", "given": "Carl", "initials": "C", "orcid": "0000-0001-7727-8113", "researcher": {"href": "https://publications.scilifelab.se/researcher/59d387bd893f45bdb3663a0ef3aae88a.json"}}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}], "type": "journal article", "published": "2025-07-18", "journal": {"title": "Sci Immunol", "issn": "2470-9468", "volume": "10", "issue": "109", "pages": "eadq4881", "issn-l": null}, "abstract": "CD8+ T cells are classically defined by cytotoxic activity, but it has remained unclear whether cytotoxic programs are compartmentalized across tissues and memory subsets. Here, we established a human organ donor cohort and found that expression of conventional cytotoxic molecules-granulysin, perforin, and granzyme B-was most prominent among circulating memory CD8+ T cells and decreased progressively with tissue residency, inversely mirroring the expression of CD69 and CD103. Other cytotoxic molecules, including granzymes A, H, K, and M, were variably expressed across tissues, and memory CD8+ T cells targeting persistent viruses expressed multiple granzymes coordinately. In an in vitro tonsil system, transforming growth factor-\u03b2 induced discordant regulation of cytotoxic molecules and CD103. Combined with interleukin-15, this circuitry modulated proliferation and the acquisition of redirected killing activity via perforin and granzyme B. Our findings suggest that human memory CD8+ T cell cytotoxicity is intricately regulated by environmental cues reflecting tissue location and antigen specificity.", "doi": "10.1126/sciimmunol.adq4881", "pmid": "40680144", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2025-10-13T13:28:04.756Z", "modified": "2025-11-25T21:31:43.911Z"}, {"entity": "publication", "iuid": "3a670a7d749a49c1bc72990a94337d2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a670a7d749a49c1bc72990a94337d2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a670a7d749a49c1bc72990a94337d2a"}}, "title": "Sequencing airborne DNA to monitor crop pathogens and pests.", "authors": [{"family": "Mikko", "given": "Amanda", "initials": "A"}, {"family": "Villegas", "given": "Jose Antonio", "initials": "JA"}, {"family": "Svensson", "given": "Daniel", "initials": "D"}, {"family": "Karlsson", "given": "Edvin", "initials": "E"}, {"family": "Esseen", "given": "Per-Anders", "initials": "PA"}, {"family": "Albrectsen", "given": "Benedicte Riber", "initials": "BR"}, {"family": "Lundin", "given": "Ola", "initials": "O"}, {"family": "Forsman", "given": "Mats", "initials": "M"}, {"family": "Berlin", "given": "Anna", "initials": "A"}, {"family": "Stenberg", "given": "Per", "initials": "P", "orcid": "0000-0003-4738-4788", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e9b9949cf994f6c93d60261eb530d1b.json"}}], "type": "journal article", "published": "2025-07-18", "journal": {"title": "iScience", "issn": "2589-0042", "pages": "112912", "volume": "28", "issue": "7", "issn-l": "2589-0042"}, "abstract": "Crop pests and diseases increasingly challenge the global food system. To prepare for and detect outbreaks, surveillance plays an important role. Traditional monitoring methods are often organism-specific, making large-scale monitoring of crop pathogens and pests impractical. We here investigate the potential for using shotgun sequencing of airborne eDNA for large-scale surveillance of crop pathogens and pests. We show that it is possible to detect DNA from all types of organisms in air, and that DNA can be classified down to species level. However, the accuracy of the identification is highly dependent on the quality of reference genomes of both the pathogens or pests, and their close relatives present in the region. Finally, we find that observed degree of crop damages correlate with amount of DNA from crop pathogens and pests in air, showing the promise of this approach for surveillance of all types of crop pathogens and pests.", "doi": "10.1016/j.isci.2025.112912", "pmid": "40678541", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12269458"}, {"db": "pii", "key": "S2589-0042(25)01173-3"}], "notes": [], "created": "2025-06-30T07:24:39.046Z", "modified": "2025-11-14T11:06:13.683Z"}, {"entity": "publication", "iuid": "74e45b5f352b43f9bdfd21344a50e8f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74e45b5f352b43f9bdfd21344a50e8f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74e45b5f352b43f9bdfd21344a50e8f9"}}, "title": "Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species.", "authors": [{"family": "Ruiz-Ruano", "given": "Francisco J", "initials": "FJ", "orcid": "0000-0002-5391-301X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37ccedb49884e27aeffed3b49085ddf.json"}}, {"family": "Schlebusch", "given": "Stephen A", "initials": "SA"}, {"family": "Vontzou", "given": "Niki", "initials": "N"}, {"family": "Moreno", "given": "Hugo", "initials": "H"}, {"family": "Biegler", "given": "Matthew T", "initials": "MT"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Borges", "given": "In\u00eas", "initials": "I"}, {"family": "Pei", "given": "Yifan", "initials": "Y"}, {"family": "Rossini", "given": "Roberto", "initials": "R"}, {"family": "Albrecht", "given": "Tomas", "initials": "T"}, {"family": "Boman", "given": "Jesper", "initials": "J"}, {"family": "Borodin", "given": "Pavel", "initials": "P"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Cain", "given": "Kristal E", "initials": "KE"}, {"family": "Forstmeier", "given": "Wolfgang", "initials": "W"}, {"family": "Frankl-Vilches", "given": "Carolina", "initials": "C"}, {"family": "Gahr", "given": "Manfred", "initials": "M"}, {"family": "Griffith", "given": "Simon C", "initials": "SC"}, {"family": "Hill", "given": "Amy M", "initials": "AM"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Joseph", "given": "Leo", "initials": "L"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Kempenaers", "given": "Bart", "initials": "B"}, {"family": "Malinovskaya", "given": "Lyubov", "initials": "L"}, {"family": "Mueller", "given": "Jakob C", "initials": "JC"}, {"family": "de Oliveira", "given": "Edivaldo H C", "initials": "EHC"}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM"}, {"family": "Palinauskas", "given": "Vaidas", "initials": "V"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Reifova", "given": "Radka", "initials": "R"}, {"family": "Ridl", "given": "Jakub", "initials": "J"}, {"family": "Segami", "given": "J Carolina", "initials": "JC"}, {"family": "Tan", "given": "David J X", "initials": "DJX", "orcid": "0000-0001-7019-7871", "researcher": {"href": "https://publications.scilifelab.se/researcher/106b75b566b74e1f84893895c9727f6c.json"}}, {"family": "Torgasheva", "given": "Anna", "initials": "A"}, {"family": "Whibley", "given": "Annabel", "initials": "A"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2025-07-18", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Bird genomes are among the most stable in terms of synteny and gene content across vertebrates. However, germline-restricted chromosomes (GRCs) represent a striking exception where programmed DNA elimination confines large-scale genomic changes to the germline. GRCs are known to occur in songbirds (oscines), but have been studied only in a few species of Passerides such as the zebra finch, the key model for passerine genomics. Their presence and evolutionary dynamics in most major passerine lineages remain largely unexplored, with suboscines entirely unexamined by cytogenetic or genomic methods. Here, we present the most comprehensive comparative analysis of GRCs to date, spanning 44 million years of passerine evolution. By generating the first germline reference genomes of an oscine and a suboscine, 22 novel germline draft genomes spanning nearly all major passerine lineages and a germline draft genome of a parrot outgroup, we show that the GRC is likely present in 6,700 passerine species. Our results reveal that the GRC evolves rapidly and distinctly from the standard A chromosomes (autosomes and sex chromosomes), yet retains functionally important, selectively maintained genes. We observed gene and repeat turnover occuring orders of magnitude faster than on the A chromosomes. Some GRC genes, such as cpeb1 and pim1, are widespread from an ancient duplication. In contrast, other GRC genes, like mfsd2b and bmp15, have been independently duplicated onto the GRC multiple times, suggesting adaptive constraints. The discovery of zglp1 on the zebra finch GRC, initially copied from chromosome 30 and subsequently lost from it, indicates functional replacement, where the GRC permits gene loss from the standard genome. As the GRC harbors the only zglp1 copy in most of the ~4000 Passerides species, GRC loss would compromise essential germline functions. Our findings establish the GRC as a genomic innovator driving rapid germline evolution. This fact highlights its evolutionary significance for passerine diversification and suggests that programmed DNA elimination may be an overlooked yet phylogenetically widespread mechanism in many understudied animal lineages.", "doi": "10.1101/2025.07.16.664580", "pmid": "40791346", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12338730"}, {"db": "pii", "key": "2025.07.16.664580"}], "notes": [], "created": "2025-11-17T17:04:19.699Z", "modified": "2025-11-17T17:04:20.016Z"}, {"entity": "publication", "iuid": "53d03e91562b4e76b2cd0ba65cd9a3b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53d03e91562b4e76b2cd0ba65cd9a3b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53d03e91562b4e76b2cd0ba65cd9a3b3"}}, "title": "A Cyanobacterial Screening Platform for Rubisco Mutant Variants.", "authors": [{"family": "Hoffmann", "given": "Ute A", "initials": "UA", "orcid": "0000-0002-9658-2695", "researcher": {"href": "https://publications.scilifelab.se/researcher/b02ccaa2cd6a4ee49c7fa8baea449f50.json"}}, {"family": "Schuppe", "given": "Anna Z", "initials": "AZ", "orcid": "0009-0005-8564-1636", "researcher": {"href": "https://publications.scilifelab.se/researcher/276f2f37c5354d4fbfce87f6f6a194cb.json"}}, {"family": "Knave", "given": "Axel", "initials": "A"}, {"family": "Sporre", "given": "Emil", "initials": "E"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H"}, {"family": "Englund", "given": "Elias", "initials": "E", "orcid": "0000-0002-0190-5659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9e2c1874da74d95af104be659521645.json"}}, {"family": "Syr\u00e9n", "given": "Per-Olof", "initials": "PO"}, {"family": "Hudson", "given": "Elton P", "initials": "EP", "orcid": "0000-0003-1899-7649", "researcher": {"href": "https://publications.scilifelab.se/researcher/6613e8d72ae74b609bb087698039defb.json"}}], "type": "journal article", "published": "2025-07-18", "journal": {"title": "ACS Synth Biol", "issn": "2161-5063", "volume": "14", "issue": "7", "pages": "2619-2633", "issn-l": null}, "abstract": "Rubisco is the main entry point of inorganic carbon into the biosphere and a central player in the global carbon system. The relatively low specific activity and tendency to accept O2 as a substrate have made Rubisco an attractive but challenging target for enzyme engineering. We have developed an enzyme engineering and screening platform for Rubisco using the model cyanobacterium Synechocystis sp. PCC 6803. Starting with the Form II Rubisco from Gallionella, we first show that the enzyme can replace the native Form I Rubisco in Synechocystis and that growth rates become sensitive to CO2 and O2 levels. We address the challenge of designing a zero-shot input library of the Gallionella Rubisco, without prior experimental knowledge, by coupling the phylogenetically guided model EV mutation with \"in silico evolution\". This multisite mutagenesis library of Synechocystis (n = 16) was subjected to competitive growth in different gas feeds coupled to deep sequencing, in order to compare Rubisco variants. We identified an amino acid exchange that increased the thermostability of Gallionella Rubisco and conveyed resilience to otherwise detrimental amino acid exchanges. The platform is a first step toward high-throughput screening of Rubisco variants in Synechocystis and creating optimized enzyme variants to accelerate the Calvin-Benson-Bassham cycle in cyanobacteria and possibly chloroplasts.", "doi": "10.1021/acssynbio.5c00065", "pmid": "40622942", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12313052"}], "notes": [], "created": "2025-11-12T11:37:01.850Z", "modified": "2025-11-12T11:37:02.522Z"}, {"entity": "publication", "iuid": "ea0141d3c2e3447facf702d344e4d0f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea0141d3c2e3447facf702d344e4d0f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea0141d3c2e3447facf702d344e4d0f3"}}, "title": "Small RNA in sperm-Paternal contributions to human embryo development.", "authors": [{"family": "Isacson", "given": "Signe", "initials": "S", "orcid": "0000-0002-7590-8326", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0cb5b0f3f694a10abf049f9e9c298e3.json"}}, {"family": "Karlsson", "given": "Kajsa", "initials": "K", "orcid": "0009-0002-7481-6291", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f9727c26319451fab05d0646447c9c3.json"}}, {"family": "Zalavary", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5209-6655", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccbf5fd93a3471d828865b7da39571e.json"}}, {"family": "Asratian", "given": "Anna", "initials": "A", "orcid": "0000-0001-7696-0508", "researcher": {"href": "https://publications.scilifelab.se/researcher/420e14758e1f45e9bf5f8a37f0115eae.json"}}, {"family": "Kugelberg", "given": "Unn", "initials": "U"}, {"family": "Liffner", "given": "Susanne", "initials": "S"}, {"family": "\u00d6st", "given": "Anita", "initials": "A", "orcid": "0000-0003-0547-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7a222183b264e4b828a38c322a4090f.json"}}], "type": "journal article", "published": "2025-07-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "6571", "issn-l": "2041-1723"}, "abstract": "Sperm not only delivers the paternal genome to the oocyte but also regulatory small RNA (sRNA). However, the role of sRNA in fertilisation and human embryo development remains poorly understood. Here, couples undergoing IVF are recruited, and sperm sRNA analysed to investigate their role in IVF treatment. Differential expression of mitochondrial sRNA and Y-RNA are observed in relation to sperm concentration. For fertilisation rate, sRNA from a single locus are significantly changed. Expression of microRNA (miRNA) and ribosomal sRNA correlates positively and negatively, respectively, to high-quality embryos. Notably, the top miRNA have an area under ROC of >0.8. Predicted targets of these miRNA are relevant for development, suggesting a role for sperm-borne miRNA in embryo development. In conclusion, sperm-borne sRNA are biomarkers for sperm concentration and embryo quality in IVF. These findings may contribute to clinical strategies improving embryo quality, lowering costs and reducing the need for additional treatment cycles.", "doi": "10.1038/s41467-025-62015-2", "pmid": "40670377", "labels": {"Clinical Genomics Link\u00f6ping": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12267487"}, {"db": "pii", "key": "10.1038/s41467-025-62015-2"}], "notes": [], "created": "2025-08-11T10:09:40.254Z", "modified": "2025-08-11T10:09:40.970Z"}, {"entity": "publication", "iuid": "1ae1fed54a1143f7913b764b6403bb5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ae1fed54a1143f7913b764b6403bb5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ae1fed54a1143f7913b764b6403bb5d"}}, "title": "Phenotypic Screening Identifies Flunarizine as an Inhibitor of Radiotherapy-Induced Astrocyte Reactivity with Therapeutic Potential in Glioblastoma", "authors": [{"family": "Jeannot", "given": "Pauline", "initials": "P"}, {"family": "Rosberg", "given": "Rebecca", "initials": "R"}, {"family": "Lindgren", "given": "David", "initials": "D"}, {"family": "Dawson", "given": "John C", "initials": "JC"}, {"family": "Pracucci", "given": "Enrico", "initials": "E"}, {"family": "B\u00f6rjesson-Freitag", "given": "Cornelia", "initials": "C"}, {"family": "Martinez", "given": "Julia", "initials": "J", "orcid": "0009-0004-4050-8439", "researcher": {"href": "https://publications.scilifelab.se/researcher/702e1de02611472097fd90ea328a0630.json"}}, {"family": "Pantazopoulou", "given": "Vasiliki", "initials": "V"}, {"family": "Malmberg", "given": "Maria", "initials": "M", "orcid": "0000-0002-4506-0408", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3d76ad702314dc5aa6dc3bf9a1918f8.json"}}, {"family": "Smolag", "given": "Karolina I", "initials": "KI"}, {"family": "Manou", "given": "Dimitra", "initials": "D"}, {"family": "Elliott", "given": "Richard J R", "initials": "RJR"}, {"family": "Ceberg", "given": "Crister", "initials": "C"}, {"family": "Berg", "given": "Tracy J", "initials": "TJ"}, {"family": "Ahlenius", "given": "Henrik", "initials": "H"}, {"family": "Carragher", "given": "Neil O", "initials": "NO"}, {"family": "Pietras", "given": "Alexander", "initials": "A", "orcid": "0000-0002-5783-9347", "researcher": {"href": "https://publications.scilifelab.se/researcher/83b683e1098c4fa1b3615cce74e75c6d.json"}}], "type": "posted-content", "published": "2025-07-17", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.07.12.664538", "pmid": null, "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-10T10:14:49.321Z", "modified": "2025-12-18T19:11:42.071Z"}, {"entity": "publication", "iuid": "c0b267b08217465e9c9d03a6ade73a43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0b267b08217465e9c9d03a6ade73a43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0b267b08217465e9c9d03a6ade73a43"}}, "title": "Dual targeting of G9a and DNMTs induces anti-tumour effects in multiple myeloma", "authors": [{"family": "Nylund", "given": "Patrick William", "initials": "PW", "orcid": "0000-0002-1274-4010", "researcher": {"href": "https://publications.scilifelab.se/researcher/683976ea3c094b198998dabb0d433f4b.json"}}, {"family": "Garrido-Zabala", "given": "Berta", "initials": "B"}, {"family": "Tziola", "given": "Stefania Iliana", "initials": "SI"}, {"family": "Mohajershojai", "given": "Tabassom", "initials": "T", "orcid": "0000-0002-7364-5470", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a193b44e7c4c85997ec74c0fee29ae.json"}}, {"family": "Berglund", "given": "Hanna", "initials": "H", "orcid": "0009-0007-1754-1822", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad08d24abc17454dafb1415b1400a038.json"}}, {"family": "Muylaert", "given": "Catharina", "initials": "C"}, {"family": "Van Hemelrijck", "given": "Lien Ann", "initials": "LA"}, {"family": "Atienza P\u00e1rraga", "given": "Alba", "initials": "A"}, {"family": "Vasquez", "given": "Louella", "initials": "L", "orcid": "0000-0002-5758-6036", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479eadb09d44ece8523730e1e0fd0b1.json"}}, {"family": "Jacob", "given": "Jim", "initials": "J"}, {"family": "Bergquist", "given": "Eric", "initials": "E"}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 Ignacio", "initials": "JI"}, {"family": "\u00d6berg", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3609-1197", "researcher": {"href": "https://publications.scilifelab.se/researcher/c68243c8cc754cdb8b380db120f3b771.json"}}, {"family": "Karlsson", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Nestor", "given": "Marika", "initials": "M", "orcid": "0000-0003-4662-3142", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e9ff7b0cad949c48c808a1dedec7fe4.json"}}, {"family": "De Bruyne", "given": "Elke", "initials": "E", "orcid": "0000-0003-4012-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2715df4e920432c9723d8fdf4ff897b.json"}}, {"family": "Kalushkova", "given": "Antonia", "initials": "A"}, {"family": "Jernberg-Wiklund", "given": "Helena", "initials": "H"}], "type": "journal-article", "published": "2025-07-17", "journal": {"issn": "2473-9529", "title": "Blood Adv", "issn-l": null}, "abstract": null, "doi": "10.1182/bloodadvances.2023010571", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-08-22T08:45:25.194Z", "modified": "2025-08-22T08:45:26.051Z"}, {"entity": "publication", "iuid": "f40ae5d37dba407f9888378328f7bbf1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f40ae5d37dba407f9888378328f7bbf1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f40ae5d37dba407f9888378328f7bbf1"}}, "title": "Biomarkers of progressive multiple sclerosis decrease following autologous hematopoietic stem cell transplantation.", "authors": [{"family": "Erngren", "given": "Ida", "initials": "I"}, {"family": "Lundblad", "given": "Katarina", "initials": "K"}, {"family": "Pavlovic", "given": "Ivan", "initials": "I"}, {"family": "Al-Grety", "given": "Asma", "initials": "A"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Burman", "given": "Joachim", "initials": "J"}], "type": "journal article", "published": "2025-07-17", "journal": {"title": "J Neuroinflammation", "issn": "1742-2094", "volume": "22", "issue": "1", "pages": "186", "issn-l": "1742-2094"}, "abstract": "Autologous hematopoietic stem cell transplantation (AHSCT) has been increasingly used for treatment of relapsing-remitting multiple sclerosis (RRMS). Existing data suggest that AHSCT might alter the natural course of multiple sclerosis (MS) and postpone or even prevent the occurrence of progressive MS. This study aimed to investigate whether three cerebrospinal fluid biomarkers of progressive MS: Galectin-9, GDF-15, and YKL-40, were affected by treatment intervention with AHSCT for RRMS.\n\nRRMS patients treated with AHSCT at Uppsala University Hospital between 2011 and 2018 were considered for participation and included if CSF samples from baseline and at least one follow-up were available. CSF from healthy volunteers was included as controls. Galectin-9 and GDF-15 concentrations were determined with ELISA, and YKL-40 with electrochemiluminescence.\n\nThe final cohort comprised 45 RRMS patients and 32 controls. At baseline, MS patients had markedly higher CSF concentrations of Galectin-9 and YKL-40 and slightly higher GDF-15 than controls. Following AHSCT, biomarker concentrations decreased from baseline to the 1-year follow-up, with a median (IQR) of 454 (357-553) vs. 408 (328-495) pg/mL (P = 0.0002) for Galectin-9; 49 (38-79) vs. 45 (35 to 75) pg/mL (P = 0.012) for GDF-15, and 100 (54-164) vs. 58 (43-92) ng/mL (P < 0.0001) for YKL-40. Galectin-9 and YKL-40 concentrations decreased further and were even lower at the 2-year follow-up; median (IQR) 408 (328-495) vs. 376 (289-478) pg/mL (P = 0.0009) for Galectin-9; and 62 (37-96) vs. 56 (30-83) ng/mL (P < 0.0001) for YKL-40. Thereafter, the levels of all biomarkers were stable throughout the follow-up.\n\nTreatment with AHSCT was associated with sustained reductions in biomarkers linked to progressive MS, indicating its potential not only to achieve lasting remission but also to delay or prevent transition to SPMS. However, additional studies are necessary to confirm these findings and elucidate their long-term clinical significance.", "doi": "10.1186/s12974-025-03511-6", "pmid": "40676588", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12273295"}, {"db": "pii", "key": "10.1186/s12974-025-03511-6"}], "notes": [], "created": "2025-11-25T19:23:15.634Z", "modified": "2025-11-25T19:23:15.649Z"}, {"entity": "publication", "iuid": "309e4cb30adc40c79c9ac77e220eece6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/309e4cb30adc40c79c9ac77e220eece6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/309e4cb30adc40c79c9ac77e220eece6"}}, "title": "Validation of Guidelines for Genetic Investigation of Myeloid Neoplasms with Germline Predisposition: Results from a Prospective Cohort Study.", "authors": [{"family": "Tesi", "given": "Bianca", "initials": "B", "orcid": "0000-0002-8253-2507", "researcher": {"href": "https://publications.scilifelab.se/researcher/96a994cd257c4833a4efe79e26b900ff.json"}}, {"family": "Robelius", "given": "Anna", "initials": "A", "orcid": "0000-0002-8853-1863", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cfc6bb334e455d9f64172ff43e3428.json"}}, {"family": "Baskin", "given": "Berivan", "initials": "B", "orcid": "0000-0001-5994-9868", "researcher": {"href": "https://publications.scilifelab.se/researcher/97aa30696594447c999c200bd11f996b.json"}}, {"family": "Lazarevic", "given": "Vladimir", "initials": "V", "orcid": "0000-0002-1782-4423", "researcher": {"href": "https://publications.scilifelab.se/researcher/7113f0d0569247d4ac94b73ddc6ca74e.json"}}, {"family": "Deneberg", "given": "Stefan", "initials": "S", "orcid": "0000-0003-1888-5567", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1eb998009ee4a468be8e7f8109ef088.json"}}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Fogelstrand", "given": "Linda", "initials": "L", "orcid": "0000-0003-3698-8519", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39ff709aa0646b8ad5e520780a0ad49.json"}}, {"family": "Ungerstedt", "given": "Johanna", "initials": "J", "orcid": "0000-0002-0202-7296", "researcher": {"href": "https://publications.scilifelab.se/researcher/04b6b5dd2f4845e38f4ad133608fe022.json"}}, {"family": "Pandzic", "given": "Tatjana", "initials": "T", "orcid": "0009-0006-9032-4616", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b7ad159e7524989a3eacd65b251ca9f.json"}}, {"family": "Tobiasson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3633-5852", "researcher": {"href": "https://publications.scilifelab.se/researcher/37b88e8e02af4145b95cc379c68ebee9.json"}}, {"family": "Garelius", "given": "Hege Gravdahl", "initials": "HG", "orcid": "0000-0003-2553-7659", "researcher": {"href": "https://publications.scilifelab.se/researcher/25307333f50942bbb7db3f84e094f7f3.json"}}, {"family": "Kuchinskaya", "given": "Ekaterina", "initials": "E", "orcid": "0009-0009-3347-6658", "researcher": {"href": "https://publications.scilifelab.se/researcher/d229b0af7f884fcb9d2a2832f59888ff.json"}}, {"family": "Persson", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-5374-4770", "researcher": {"href": "https://publications.scilifelab.se/researcher/33f1e0d34d5844e5b9d042b4d68df22c.json"}}, {"family": "\u00c5gerstam", "given": "Helena", "initials": "H", "orcid": "0009-0002-8216-3876", "researcher": {"href": "https://publications.scilifelab.se/researcher/55f2c7f5067949dbbce9a4bf505807b6.json"}}, {"family": "Hallb\u00f6\u00f6k", "given": "Helene", "initials": "H", "orcid": "0000-0002-5764-3213", "researcher": {"href": "https://publications.scilifelab.se/researcher/2478793f7c5945ba9f00cde3f39b62c4.json"}}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Norberg", "given": "Anna", "initials": "A", "orcid": "0000-0003-2947-8879", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e3c81cf4da410db2feaac562e88846.json"}}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC", "orcid": "0000-0002-4018-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/829bcbc2bb734d848f7b370546aca35c.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S", "orcid": "0000-0001-8374-8978", "researcher": {"href": "https://publications.scilifelab.se/researcher/4be462a447404937857936f77677da2f.json"}}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Vennstr\u00f6m", "given": "Lovisa", "initials": "L", "orcid": "0009-0002-7300-5438", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3b702bc59b147d3adb508358d4e1a18.json"}}, {"family": "Ejerblad", "given": "Elisabeth", "initials": "E", "orcid": "0009-0009-8190-1073", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a6b1722a4b34be5a9f3f0780dd34261.json"}}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Cammenga", "given": "J\u00f6rg", "initials": "J", "orcid": "0009-0001-0668-607X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6daacdf33e7443c94c98bec4dec5cf5.json"}}, {"family": "J\u00e4dersten", "given": "Martin", "initials": "M", "orcid": "0000-0001-5217-3235", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5b56c006df74965adab16c28afeb453.json"}}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-7839-3743", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf8d52e24234fa8b348ad08f58d1d48.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "journal article", "published": "2025-07-15", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "volume": "31", "issue": "14", "pages": "3062-3071", "issn-l": "1078-0432"}, "abstract": "In a multicenter prospective cohort study, we assessed the diagnostic yield of the Nordic guidelines for germline investigation in myeloid neoplasms and mapped the spectrum of inherited and somatic variants.\n\nEighty-five patients (acute myeloid leukemia, n = 38; myelodysplastic syndromes, n = 26; thrombocytopenia, n = 14; and other, n = 7) fulfilling the Nordic criteria for germline investigation, based on (i) medical history or family history suggestive of a germline condition and (ii) relevant findings from the somatic diagnostic work-up (CytoMol), were recruited. The genetic analysis included enhanced whole-exome sequencing (n = 69) or sequencing of specific variants of interest (n = 16).\n\nPathogenic or likely pathogenic (P/LP) germline variants were identified in 35% of patients (30/85). The diagnostic yield varied from 6% (1/16) in the family history group to 52% (17/33) in the CytoMol group. Germline DDX41 P/LP variants were the most frequent finding (13/30, 43% of all positive cases) almost exclusively found within the CytoMol group (12/13). Seven variants of unknown significance were also detected (TERT n = 2 and DDX41, RTEL1, ETV6, PARN, and SAMD9 n = 1). Five patients carried a P/LP variant in genes associated with another hereditary cancer syndrome (BRCA1 n = 3; PALB2 n = 1; and CHEK2; n = 1). Survival analysis showed a trend for longer survival among patients with acute myeloid leukemia and confirmed or suspected germline predisposition that underwent allogeneic stem cell transplantation.\n\nThe implementation of the Nordic guidelines in a prospective Swedish cohort results in a high overall diagnostic yield (35%), proving the feasibility and utility of these or similar guidelines in a clinical setting.", "doi": "10.1158/1078-0432.CCR-24-4251", "pmid": "40388595", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12260513"}, {"db": "pii", "key": "762516"}], "notes": [], "created": "2025-11-06T06:30:44.017Z", "modified": "2025-11-26T14:14:22.824Z"}, {"entity": "publication", "iuid": "d5108740da8e45ba8da2b5476a7d0993", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5108740da8e45ba8da2b5476a7d0993.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5108740da8e45ba8da2b5476a7d0993"}}, "title": "Poincare guided geometric UNet for left atrial epicardial adipose tissue segmentation in Dixon MRI images.", "authors": [{"family": "Firouznia", "given": "Marjan", "initials": "M"}, {"family": "Ylip\u00e4\u00e4", "given": "Erik", "initials": "E"}, {"family": "Henningsson", "given": "Markus", "initials": "M"}, {"family": "Carlh\u00e4ll", "given": "Carl-Johan", "initials": "CJ"}], "type": "journal article", "published": "2025-07-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "25549", "issn-l": "2045-2322"}, "abstract": "Epicardial Adipose Tissue (EAT) is a recognized risk factor for cardiovascular diseases and plays a pivotal role in the pathophysiology of Atrial Fibrillation (AF). Accurate automatic segmentation of the EAT around the Left Atrium (LA) from Magnetic Resonance Imaging (MRI) data remains challenging. While Convolutional Neural Networks excel at multi-scale feature extraction using stacked convolutions, they struggle to capture long-range self-similarity and hierarchical relationships, which are essential in medical image segmentation. In this study, we present and validate PoinUNet, a deep learning model that integrates a Poincar\u00e9 embedding layer into a 3D UNet to enhance LA wall and fat segmentation from Dixon MRI data. By using hyperbolic space learning, PoinUNet captures complex LA and EAT relationships and addresses class imbalance and fat geometry challenges using a new loss function. Sixty-six participants, including forty-eight AF patients, were scanned at 1.5T. The first network identified fat regions, while the second utilized Poincar\u00e9 embeddings and convolutional layers for precise segmentation, enhanced by fat fraction maps. PoinUNet achieved a Dice Similarity Coefficient of 0.87 and a Hausdorff distance of 9.42 on the test set. This performance surpasses state-of-the-art methods, providing accurate quantification of the LA wall and LA EAT.", "doi": "10.1038/s41598-025-10110-1", "pmid": "40664735", "labels": {"AIDA Data Hub": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12263985"}, {"db": "pii", "key": "10.1038/s41598-025-10110-1"}], "notes": [], "created": "2025-11-25T13:12:40.133Z", "modified": "2025-11-25T13:12:40.136Z"}, {"entity": "publication", "iuid": "05c4a2e86e3440cdabf68373cd453878", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05c4a2e86e3440cdabf68373cd453878.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05c4a2e86e3440cdabf68373cd453878"}}, "title": "Plasma carotenoids are inversely correlated with granulocyte counts and soluble inflammatory markers in a middle-aged population: a cross-sectional study with mediation analysis.", "authors": [{"family": "Neelissen", "given": "Jan", "initials": "J"}, {"family": "Leanderson", "given": "Per", "initials": "P"}, {"family": "Nystr\u00f6m", "given": "Fredrik H", "initials": "FH"}, {"family": "Jonasson", "given": "Lena", "initials": "L"}, {"family": "Chung", "given": "Rosanna W S", "initials": "RWS"}], "type": "journal article", "published": "2025-07-15", "journal": {"title": "BMC Med", "issn": "1741-7015", "volume": "23", "issue": "1", "pages": "427", "issn-l": "1741-7015"}, "abstract": "High intake of fruits and vegetables is generally associated with reduced levels of inflammation. In line with this, plasma levels of carotenoids have shown inverse associations with inflammatory markers, in particular C-reactive protein (CRP) and leukocyte counts. However, it remains unclear to what extent carotenoids are associated with specific leukocyte subsets or other inflammatory markers. This study systematically assessed the inter-relationships among total and individual carotenoids, circulating leukocyte subsets, and soluble inflammatory markers in a middle-aged population.\n\nA subcohort of 1078 subjects, aged 50-64, was recruited from the Swedish CArdioPulmonary bioImage Study (SCAPIS) cohort. Leukocyte subsets were determined by whole blood flow cytometry. Five major carotenoids, namely lutein, \u03b2-cryptoxanthin, lycopene, \u03b1-carotene and \u03b2-carotene, and inflammatory markers including CRP, interleukin (IL)-6 and interleukin-18, matrix metalloproteinase (MMP)-9, and myeloperoxidase (MPO), were measured in plasma. Nutrient intake was estimated by validated food frequency questionnaires.\n\nAmong leukocyte subsets, only granulocytes showed independent and inverse associations with all carotenoids after adjustment. CRP, IL-18, and MMP-9 exhibited similar inverse relationships with most carotenoids. Mediation analysis revealed that the associations of carotenoids with CRP and MMP-9 were mediated by granulocyte counts. Lutein and \u03b2-cryptoxanthin remained independently associated with MMP-9 after accounting for the mediation effects of granulocyte counts. No estimated nutrient intake showed comparable associations with leukocyte subsets or inflammatory markers.\n\nTo our knowledge, this is the largest population-based study investigating relationships between plasma carotenoids, leukocyte subsets, and soluble inflammatory markers. It provides evidence that low levels of carotenoids in plasma are linked to low-grade chronic inflammation and, furthermore, that this relationship is mediated by granulocyte numbers.", "doi": "10.1186/s12916-025-04266-w", "pmid": "40660217", "labels": {"Affinity Proteomics Stockholm": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12261581"}, {"db": "pii", "key": "10.1186/s12916-025-04266-w"}], "notes": [], "created": "2025-09-19T15:17:30.474Z", "modified": "2025-11-25T20:05:42.460Z"}, {"entity": "publication", "iuid": "3a5b4226b65d4c05a3c20c75d6d2d57f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a5b4226b65d4c05a3c20c75d6d2d57f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a5b4226b65d4c05a3c20c75d6d2d57f"}}, "title": "HigH-ratiO partiaL proteolysiS with carriER proteome (HOLSER) Enables Global Structure Profiling and Site-resolved Elucidation of Ligand-Protein Interactions", "authors": [{"family": "Zhang", "given": "Xuepei", "initials": "X"}, {"family": "Sokolova", "given": "Bohdana", "initials": "B"}, {"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b3f220ebf947779d4b2638d2ccef1c.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85179acfa7e4916ad40ae478d6dcc0a.json"}}, {"family": "Lyu", "given": "Hezheng", "initials": "H", "orcid": "0009-0008-7995-6473", "researcher": {"href": "https://publications.scilifelab.se/researcher/de932cbcb2c341f7a6544104026c7b1c.json"}}, {"family": "Ata Saei", "given": "Amir", "initials": "A"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "posted-content", "published": "2025-07-15", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.07.11.664381", "pmid": null, "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2025-11-25T16:22:59.508Z", "modified": "2025-12-18T19:12:11.165Z"}, {"entity": "publication", "iuid": "19a4115c6ad14acaaf738a62c51e4f69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19a4115c6ad14acaaf738a62c51e4f69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19a4115c6ad14acaaf738a62c51e4f69"}}, "title": "Genome analyses suggest recent speciation and postglacial isolation in the Norwegian lemming.", "authors": [{"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Feinauer", "given": "Isabelle S", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "N\u00e4svall", "given": "Karin", "initials": "K", "orcid": "0000-0002-2970-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/9173164aadbe47b0b4132d2c6e654cf3.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications.scilifelab.se/researcher/5419b796720a47c8aa7a26ca663a96bd.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Kuzmina", "given": "Elena A", "initials": "EA"}, {"family": "Smirnov", "given": "Nickolay G", "initials": "NG"}, {"family": "Stewart", "given": "John R", "initials": "JR", "orcid": "0000-0002-3506-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e8f2e54f1a4f1d96d8f4ae1de97a93.json"}}, {"family": "Knul", "given": "Monika V", "initials": "MV", "orcid": "0000-0002-0650-0992", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff550d1088bb4857a28277ae1db41452.json"}}, {"family": "Noiret", "given": "Pierre", "initials": "P"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Ehrich", "given": "Dorothee", "initials": "D"}, {"family": "Pokrovsky", "given": "Ivan", "initials": "I"}, {"family": "Fedorov", "given": "Vadim B", "initials": "VB", "orcid": "0000-0003-3938-4200", "researcher": {"href": "https://publications.scilifelab.se/researcher/017b3cc7d41e46feb13e4e919b0c2dd5.json"}}, {"family": "Goropashnaya", "given": "Anna V", "initials": "AV", "orcid": "0009-0005-4712-6297", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e89f839e5c24f0dbef8deadb3a17f8d.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}], "type": "journal article", "published": "2025-07-15", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "122", "issue": "28", "pages": "e2424333122"}, "abstract": "The Norwegian lemming (Lemmus lemmus) is a small rodent distributed across the Fennoscandian mountain tundra and the Kola Peninsula. The Norwegian lemming likely evolved during the Late Pleistocene and inhabited Fennoscandia shortly prior to the Last Glacial Maximum. However, the exact timing and origins of the species, and its phylogenetic position relative to the closely related Siberian lemming (Lemmus sibiricus) remain disputed. Moreover, the presence of ancient or contemporary gene flow between both species is largely untested. The Norwegian lemming displays characteristic phenotypic and behavioral adaptations (e.g., coat color, aggression) that are not present in other Lemmus species. We generated a de novo genome assembly for the Norwegian lemming and resequenced nine modern and two ancient Lemmus spp. genomes. We show that all Lemmus species form distinct monophyletic clades, with concordant topology between the mitochondrial and nuclear genome phylogenies. The Siberian lemming is divided into two distinct but paraphyletic clades, one in the east and one in the west, where the western clade represents a sister taxon to the Norwegian lemming. We estimate that the Norwegian and western Siberian lemming diverged shortly before the Last Glacial Maximum, making the Norwegian lemming one of the youngest known mammalian species. We did not find any indication of gene flow between L. lemmus and L. sibiricus, suggesting postglacial isolation of L. lemmus. Furthermore, we identify species-specific genomic differences in genes related to coat color and fat transport, which are likely associated with the distinctive coloration and overwintering behavior observed in the Norwegian lemming.", "doi": "10.1073/pnas.2424333122", "pmid": "40587810", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12280882"}], "notes": [], "created": "2025-07-01T06:45:31.166Z", "modified": "2025-11-14T11:07:37.863Z"}, {"entity": "publication", "iuid": "3d5e24e8dc3542eab9713c6df3a7e8e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d5e24e8dc3542eab9713c6df3a7e8e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d5e24e8dc3542eab9713c6df3a7e8e5"}}, "title": "Reverse microdialysis of sucrose stimulates soil fungal and bacterial growth at the microscale.", "authors": [{"family": "Schneider", "given": "Andreas N", "initials": "AN"}, {"family": "Buckley", "given": "Scott", "initials": "S"}, {"family": "Lorenzo", "given": "Zulema Carracedo", "initials": "ZC"}, {"family": "Gratz", "given": "Regina", "initials": "R"}, {"family": "Nilsson", "given": "Lina", "initials": "L"}, {"family": "Swaine", "given": "Mark", "initials": "M"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Taylor", "given": "Andy F S", "initials": "AFS"}, {"family": "J\u00e4mtg\u00e5rd", "given": "Sandra", "initials": "S"}], "type": "journal article", "published": "2025-07-14", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "25", "issue": "1", "pages": "436", "issn-l": "1471-2180"}, "abstract": "The rhizosphere is a critical microenvironment that plays key roles in plant nutrient availability, largely due to root interactions with rhizospheric microbes. However, we lack suitable methods that can elucidate mechanisms determining rhizospheric community structure and function within the context of a dynamic, undisturbed soil. Microdialysis has been used for low intrusive soil nutrient sampling at the scale of a fine root, with small probes that also enable release of defined compounds. We evaluated whether microdialysis could simulate exudation, by the release of sucrose, and stimulate changes in a soil microbial community, allowing us to determine the microbes that responded most to carbon release.\n\nMicrodialysis successfully stimulated growth on probe surfaces of fungi and bacteria, which were extracted and sequenced for identification. Microbial growth was also visualized with scanning electron microscopy. The majority of the species stimulated were classified as fast growing or opportunistic, e.g. yeasts, moulds, proteobacteria and actinobacteriota, which are known to respond quickly (within days) to the release of simple sugars as exudates in the rhizosphere.\n\nThe study demonstrates the potential of using microdialysis as a tool to investigate interactions between root exudation and soil microbial community composition, initially for individual compounds and in the future for more complex compositions.", "doi": "10.1186/s12866-025-04082-5", "pmid": "40660105", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12257659"}, {"db": "pii", "key": "10.1186/s12866-025-04082-5"}], "notes": [], "created": "2025-10-30T11:57:11.876Z", "modified": "2025-11-28T10:52:39.912Z"}, {"entity": "publication", "iuid": "7d1ba25b67c9423e84e530a52b63a532", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d1ba25b67c9423e84e530a52b63a532.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d1ba25b67c9423e84e530a52b63a532"}}, "title": "Cell atlas of the developing human meninges reveals a dura origin of meningioma.", "authors": [{"family": "Vinsland", "given": "Elin", "initials": "E", "orcid": "0000-0001-9695-9192", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c7bf61b0d3348d9b966a7a018c8859d.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM"}, {"family": "Kapustov\u00e1", "given": "Ivana", "initials": "I"}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Webb", "given": "Simone", "initials": "S"}, {"family": "Li", "given": "Xiaofei", "initials": "X"}, {"family": "He", "given": "Xiaoling", "initials": "X"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Haniffa", "given": "Muzlifah", "initials": "M"}, {"family": "Barker", "given": "Roger", "initials": "R"}, {"family": "Persson", "given": "Oscar", "initials": "O"}, {"family": "Raleigh", "given": "David R", "initials": "DR"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}], "type": "journal article", "published": "2025-07-13", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The vertebrate central nervous system is enveloped by the meninges, consisting of the pia, arachnoid, and dura layers. The arachnoid is hypothesised to give rise to the most common primary intracranial tumours, meningiomas. However, molecular evidence supporting this hypothesis is lacking. There are no effective medical therapies to treat meningiomas that are resistant to local interventions, encumbered by our limited understanding of their cellular origin. To address this limitation in our understanding of meningioma biology, we generated a comprehensive reference single cell and spatial transcriptomic atlas of human fetal meninges at post-conceptional weeks 5-13. We found that the meningeal layers develop concurrently, and identified an inner CDH1-positive dura cell layer expressing tight junction genes consistent with barrier function. We show that transcriptionally, meningioma cells resemble dura-lineage cells, and that common meningioma driver genes were expressed preferentially in the dura lineage. Our findings suggest that meningiomas originate from dura lineage cells.", "doi": "10.1101/2025.07.08.663122", "pmid": "40672210", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12265625"}, {"db": "pii", "key": "2025.07.08.663122"}], "notes": [], "created": "2025-11-24T09:18:03.258Z", "modified": "2025-11-28T06:53:07.022Z"}, {"entity": "publication", "iuid": "4bfa745c2a514b2c8a47ec6ffc073c31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4bfa745c2a514b2c8a47ec6ffc073c31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4bfa745c2a514b2c8a47ec6ffc073c31"}}, "title": "Novel insights on remnant stomach following Roux-en-Y gastric bypass surgery based on histological evaluation and quantitative proteomics analysis.", "authors": [{"family": "Larson", "given": "Carl I W", "initials": "CIW"}, {"family": "F\u00e4ndriks", "given": "Lars", "initials": "L"}, {"family": "Casselbrant", "given": "Anna", "initials": "A"}, {"family": "Wallenius", "given": "Ville", "initials": "V"}], "type": "journal article", "published": "2025-07-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "25243", "issn-l": "2045-2322"}, "abstract": "Patients undergoing weight-reducing Roux-en-Y gastric bypass (RYGB) have immediate positive effects on metabolic health, including type 2 diabetes (T2D). Refeeding via the secluded stomach, either by a gastrotube or after gastro-gastric fistulation result in T2D relapse and weight regain. The stomach therefore seems to play an active role in metabolism. To explore histological and protein expression changes in the gastric mucosa before compared to after RYGB. Perioperatively, biopsies were taken in a non-paired manner from the stomach (fundus, corpus, antrum) in patients undergoing Sleeve Gastrectomy (SG) and patients > 8 months postoperatively after RYGB by balloon-enteroscopy. The included SG and RYGB patients did not display any obvious mucosal or luminal pathology during surgery or the balloon-enteroscopies. The gastric biopsies both at perioperatively and postoperatively were prepared f\u00f6r histological evaluation and for quantitative (comparative) non-targeted proteomics. The results were compared by Volcano plots, Principal Component Analysis and STRING functional protein association networks. Histologically the gastric mucosa looked normal in biopsies from all the different parts of the postoperative bypassed stomach with no clear differences compared to the perioperative samples. The perioperative biopsies generally contained significantly higher amounts of proteins involved in fatty acid metabolism, oxidative phosphorylation and ATP metabolic processes, citric acid cycle and the respiratory chain. Postoperative biopsies instead showed overall increased quantities of proteins associated with ribosomes, RNA-metabolic processes, the mitotic cycle and pancreatic secretion. The results provide novel insights into the mucosal proteome-changes in the secluded stomach following RYGB.", "doi": "10.1038/s41598-025-10114-x", "pmid": "40652086", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12255712"}, {"db": "pii", "key": "10.1038/s41598-025-10114-x"}], "notes": [], "created": "2025-10-23T11:13:55.730Z", "modified": "2025-10-23T11:13:55.738Z"}, {"entity": "publication", "iuid": "a596dad743e74d2c803822ac42670a7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a596dad743e74d2c803822ac42670a7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a596dad743e74d2c803822ac42670a7d"}}, "title": "Spatial mapping of proteins and their activity states in cancer models by multiplex in situ PLA", "authors": [{"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Xu", "given": "Bo", "initials": "B", "orcid": "0000-0002-5341-1722", "researcher": {"href": "https://publications.scilifelab.se/researcher/d262ebec52004d1f8bc77d43cafe0cc7.json"}}, {"family": "Sinha", "given": "Tanay Kumar", "initials": "TK"}, {"family": "Dahlstr\u00f6m", "given": "Caroline", "initials": "C"}, {"family": "Vennberg", "given": "Jonas", "initials": "J", "orcid": "0000-0002-8153-9934", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce37c5833d9402282f308ca16cfe3bb.json"}}, {"family": "Larsson Forss\u00e9n", "given": "Tore", "initials": "T"}, {"family": "Klaesson", "given": "Axel", "initials": "A"}, {"family": "Clausson", "given": "Carl Magnus", "initials": "CM"}, {"family": "Wang", "given": "Xuan", "initials": "X", "orcid": "0000-0002-6672-017X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea013f2f56894e698a1bce01a49dcf7a.json"}}, {"family": "Str\u00f6mberg-Olsson", "given": "Ulla", "initials": "U"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Zieba-Wicher", "given": "Agata", "initials": "A"}, {"family": "Landegren", "given": "Ulf", "initials": "U", "orcid": "0000-0002-7820-1000", "researcher": {"href": "https://publications.scilifelab.se/researcher/87392e51288f4ef9a38fe3989d10d180.json"}}], "type": "posted-content", "published": "2025-07-11", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.07.11.662357", "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Spatial Proteomics": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-25T12:57:35.337Z", "modified": "2026-03-06T09:57:26.506Z"}, {"entity": "publication", "iuid": "26b2d2e481ee4340b58cb2399170e18c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26b2d2e481ee4340b58cb2399170e18c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26b2d2e481ee4340b58cb2399170e18c"}}, "title": "Cross-population GWAS and proteomics improve risk prediction and reveal mechanisms in atrial fibrillation.", "authors": [{"family": "Yuan", "given": "Shuai", "initials": "S", "orcid": "0000-0001-5055-5627", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a51e0853b654cdcb2d42ebc5d73b52a.json"}}, {"family": "Chen", "given": "Jie", "initials": "J", "orcid": "0000-0002-4029-4192", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dbfd7fc4a2d4fe38a244f78cf48dce2.json"}}, {"family": "Ruan", "given": "Xixin", "initials": "X", "orcid": "0000-0002-4937-9168", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d92ee22a384cb0bc5a7bcdccb83d0e.json"}}, {"family": "Li", "given": "Yuying", "initials": "Y", "orcid": "0000-0002-3231-7542", "researcher": {"href": "https://publications.scilifelab.se/researcher/019bd04ea79a42eda01be14c54af5090.json"}}, {"family": "Abramowitz", "given": "Sarah A", "initials": "SA"}, {"family": "Wang", "given": "Lijuan", "initials": "L", "orcid": "0000-0002-9797-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/97af8fc0299a4c25aa4f31841007a8f8.json"}}, {"family": "Jiang", "given": "Fangyuan", "initials": "F"}, {"family": "Xiong", "given": "Ying", "initials": "Y", "orcid": "0000-0001-7644-014X", "researcher": {"href": "https://publications.scilifelab.se/researcher/72484ccb61b140ca946294b68042c330.json"}}, {"family": "Levin", "given": "Michael G", "initials": "MG", "orcid": "0000-0002-9937-9932", "researcher": {"href": "https://publications.scilifelab.se/researcher/d165b2fd025f41fab9959e82610492a3.json"}}, {"family": "Voight", "given": "Benjamin F", "initials": "BF", "orcid": "0000-0002-6205-9994", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d9e9de96ee4983ba97efc14eb3d79b.json"}}, {"family": "Gill", "given": "Dipender", "initials": "D", "orcid": "0000-0001-7312-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca049660534b4f18ab8a16da46ffca52.json"}}, {"family": "Burgess", "given": "Stephen", "initials": "S", "orcid": "0000-0001-5365-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd2dcaf4dbb4e4c91c2af460b8fa98f.json"}}, {"family": "\u00c5kesson", "given": "Agneta", "initials": "A", "orcid": "0000-0001-9594-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/f699e3a40b424acd9461ca03f288d6bc.json"}}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0001-6880-2577", "researcher": {"href": "https://publications.scilifelab.se/researcher/360d5c60409d415f8c6957d9e3373cd0.json"}}, {"family": "Damrauer", "given": "Scott M", "initials": "SM", "orcid": "0000-0001-8009-1632", "researcher": {"href": "https://publications.scilifelab.se/researcher/b878210396ae46eba9f04f78be5ff564.json"}}, {"family": "Larsson", "given": "Susanna C", "initials": "SC", "orcid": "0000-0003-0118-0341", "researcher": {"href": "https://publications.scilifelab.se/researcher/afe4b220a6c547e6aac27a10c5024a23.json"}}], "type": "journal article", "published": "2025-07-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "6426", "issn-l": "2041-1723"}, "abstract": "Atrial fibrillation (AF) is a common cardiac arrhythmia with strong genetic components, yet its underlying molecular mechanisms and potential therapeutic targets remain incompletely understood. We conducted a cross-population genome-wide meta-analysis of 168,007 AF cases and identified 525 loci that met genome-wide significance. Two loci of PITX2 and ZFHX3 genes were identified as shared across populations of different ancestries. Comprehensive gene prioritization approaches reinforced the role of muscle development and heart contraction while also uncovering additional pathways, including cellular response to transforming growth factor-beta. Population-specific genetic correlations uncovered common and unique circulatory comorbidities between Europeans and Africans. Mendelian randomization identified modifiable risk factors and circulating proteins, informing disease prevention and drug development. Integrating genomic data from this cross-population genome-wide meta-analysis with proteomic profiling significantly enhanced AF risk prediction. This study advances our understanding of the genetic etiology of AF while also enhancing risk prediction, prevention strategies, and therapeutic development.", "doi": "10.1038/s41467-025-61720-2", "pmid": "40645996", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12254421"}, {"db": "pii", "key": "10.1038/s41467-025-61720-2"}], "notes": [], "created": "2025-11-28T10:45:39.870Z", "modified": "2025-11-28T10:45:40.305Z"}, {"entity": "publication", "iuid": "3f94f51a9c5f47249cc487ebd66bad09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f94f51a9c5f47249cc487ebd66bad09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f94f51a9c5f47249cc487ebd66bad09"}}, "title": "Silk-Ovarioids: establishment and characterization of a human ovarian primary cell 3D-model system.", "authors": [{"family": "Di Nisio", "given": "Valentina", "initials": "V", "orcid": "0000-0002-8435-7925", "researcher": {"href": "https://publications.scilifelab.se/researcher/bee1509ba58840f597b7fccc778a0a20.json"}}, {"family": "Li", "given": "Tianyi", "initials": "T", "orcid": "0000-0003-2246-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9d609023a624d80ac76d112661918f8.json"}}, {"family": "Xiao", "given": "Zhijie", "initials": "Z"}, {"family": "Papaikonomou", "given": "Kiriaki", "initials": "K"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1"}, {"family": "Lebre", "given": "Filipa", "initials": "F"}, {"family": "Alfaro-Moreno", "given": "Ernesto", "initials": "E"}, {"family": "Pedersen", "given": "Mikael", "initials": "M", "orcid": "0000-0001-6540-4805", "researcher": {"href": "https://publications.scilifelab.se/researcher/99fbf942a9324124813072f70ef9e1ee.json"}}, {"family": "Svingen", "given": "Terje", "initials": "T", "orcid": "0000-0003-4650-7651", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1900781448d4715a287420203765a44.json"}}, {"family": "Zubarev", "given": "Roman", "initials": "R"}, {"family": "Acharya", "given": "Ganesh", "initials": "G"}, {"family": "Damdimopoulou", "given": "Pauliina", "initials": "P", "orcid": "0000-0001-8458-0855", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d258c0f0d9b417ea4608769fc3ebaaf.json"}}, {"family": "Salumets", "given": "Andres", "initials": "A", "orcid": "0000-0002-1251-8160", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dcf4bacf5c4792bbfd111495d43595.json"}}], "type": "journal article", "published": "2025-07-10", "journal": {"title": "Hum Reprod Open", "issn": "2399-3529", "volume": "2025", "issue": "3", "pages": "hoaf042", "issn-l": null}, "abstract": "What is the best protocol to establish a long-term stable three-dimensional (3D) model for human primary ovarian cells?\n\nWe developed and characterized long-term cultured 3D models of primary ovarian somatic cells isolated from adult tissues, using Biosilk as a scaffold.\n\nIn vitro models that mimic ovaries are crucial for elucidating the biological mechanisms underlying follicle activation and growth, hormonal activity, ovarian angiogenesis, damage in response to toxic exposures, and other biological mechanisms that enable the functionality of this complex organ. Three-dimensional systems are particularly relevant because they replicate heterogeneity and cell-cell communication among different ovarian cell types. However, complex models using human ovarian primary cells are yet to be developed.\n\nOvarian tissue samples were collected from five patients (age 26 \u00b1 5 years) who underwent gender-affirming surgery. The cortex and medulla were separated and dissociated into single-cell suspensions using mechanical and enzymatic methods. Three approaches were tested to establish a 3D model culture system: matrix-free ovarian spheroids (MFOS), a Matrigel-based three-layer gradient system (3LGS), and Biosilk scaffolds (Silk-Ovarioid). In parallel, paired controls from each patient and ovarian area were cultured in a standard 2D system for the same duration.\n\nThe 3D culture systems were monitored every second day to detect signs of aggregation and growth. Freshly fixed tissue, as well as 2D- and 3D-cultured samples were further processed for transcriptomic profiling after 42 days of culture using RNA sequencing. The culture of the 3D system was further characterized, regarding its protein profile and steroid and cytokine production, through proteomics and liquid chromatography-tandem mass spectrometry and the Luminex platform, respectively. The key findings from the high-throughput assays were finally validated through RNA fluorescent in situ hybridization (RNA-FISH) and immunofluorescence staining.\n\nThe 3D model systems MFOS (n = 120) and 3LGS (n = 18) failed to form aggregates capable of long-term maintenance in culture (MFOS: maximum of 15 days for both cortex and medulla; 3LGS: maximum of 11 days for medulla only). In contrast, we successfully established ovarian cortex- and medulla-derived 3D systems using Biosilk, termed Silk-Ovarioids (n = 120). Silk-Ovarioids were maintained for up to 42 days as free-floating culture without any signs of cell death, as confirmed by the absence of TUNEL, \u03b3-H2A.X, and cleaved caspase 3 fluorescent signals. The presence of key ovarian somatic cell types, including granulosa, stromal, endothelial, and perivascular cells, was confirmed by transcriptomics and proteomics in the majority of Silk-Ovarioids. Validation through RNA-FISH and immunostaining was performed using the following markers: AMHR2 for granulosa cells, PDGFR\u03b1 for stromal cells, CLDN5 and GPIHBP1 for endothelial cells, GJA4/Cx37 and MCAM for perivascular cells. Notably, Silk-Ovarioids exhibited the formation of a pro-angiogenic hypoxic core, as evidenced by the transcriptomic and proteomic data and visualized by the expression of hypoxia markers MMP2 and PDGFR\u03b2. This hypoxic environment led to development of vessel-like structures after 4-6 weeks of culture, which were positive for the angiogenic markers TGFBR2, BMP2, and PDGF\u03b1. The functionality of Silk-Ovarioids was further confirmed by the identification of de novo extracellular matrix secretion (Col1\u03b11 and Lam\u03b11), and by the detection of pro-angiogenic cytokines (e.g. IL-6, IL-8, and GM-CSF) and steroids (e.g. pregnenolone and epitestosterone) in the culture media.\n\nThe RNA-sequencing count matrix is deposited in Gene Expression Omnibus with accession number GSE253571. Raw data are deposited in Swedish National Data Service with the DOI https://doi.org/10.48723/h8cm-bs19. Single-cell RNA-seq data have been downloaded from the ArrayExpress database at EMBL-EBI with the accession codes 'E-MTAb - 8381'. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD048710. The code used for the analysis can be found in https://github.com/tialiv/Silk-Ovarioid_project.\n\nThe ovarian samples were collected from patients undergoing androgen treatment, raising the concern that androgen exposure may alter the behavior of cells in Silk-Ovarioids compared to those derived from androgen-unstimulated patients. Furthermore, the cell culture media used in this study were supplemented with fetal bovine serum and did not contain any supplements or growth factors that could be essential for the resemblance of Silk-Ovarioids to the tissue of origin.\n\nThe Silk-Ovarioids exhibited low intra-batch variability and long-term culture stability, underscoring their potential as a robust step toward developing a bioengineered, patient-specific artificial ovary. In addition, Silk-Ovarioids could be utilized as the first ovarian angiogenesis in vitro model, function as biological scaffold for in vitro folliculogenesis, and be used for toxicological and pharmacological studies targeting the ovaries.\n\nThis study was funded by: a research grant from the Center for Innovative Medicine (CIMED) at Karolinska Insitutet; European Union's Horizon 2020 Research and Innovation Programme (project ERIN no. 952516); a Horizon Europe grant (NESTOR, grant no. 101120075) of the European Commission; the Swedish Research Council for Sustainable Development FORMAS (2018-02280, 2020-01621); StratRegen Funding from Karolinska Institute, Swedish Research Council VR (grant no. 2020-02132); Swedish Childhood Cancer Fund (Reference PR2017-0044, PR2020-0096); Estonian Research Council (grant no. PRG1076); Swedish Research Council (grant no. 2024-02530); Novo Nordisk Foundation (grant no. NNF24OC0092384); European Union's H2020 project Sinfonia (no. 857253) (INL research); and SbDToolBox, with reference NORTE-01-0145-FEDER-000047, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (INL research). The authors have no conflicts of interest to declare.", "doi": "10.1093/hropen/hoaf042", "pmid": "40799620", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12343022"}, {"db": "pii", "key": "hoaf042"}], "notes": [], "created": "2025-11-28T14:58:05.868Z", "modified": "2025-11-28T14:58:06.995Z"}, {"entity": "publication", "iuid": "e59a3f9900274a389b62b4915dc79be9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e59a3f9900274a389b62b4915dc79be9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e59a3f9900274a389b62b4915dc79be9"}}, "title": "Intestinal estrogen receptor beta modulates the murine colon tumor immune microenvironment.", "authors": [{"family": "Birgersson", "given": "Madeleine", "initials": "M"}, {"family": "Holm", "given": "Matilda", "initials": "M"}, {"family": "Gallardo-Dodd", "given": "Carlos J", "initials": "CJ"}, {"family": "Chen", "given": "Baizhen", "initials": "B"}, {"family": "Stepanauskait\u0117", "given": "Lina", "initials": "L"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Kutter", "given": "Claudia", "initials": "C"}, {"family": "Archer", "given": "Amena", "initials": "A"}, {"family": "Williams", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2025-07-10", "journal": {"title": "Cancer Lett.", "issn": "1872-7980", "pages": "217661", "volume": "622", "issn-l": "0304-3835"}, "abstract": "Chronic inflammation contributes to the development of colorectal cancer, partly through its regulation of the microenvironment and antitumor immunity. Interestingly, women have a lower incidence of colorectal cancer, and estrogen treatment has been shown to reduce the occurrence of colorectal tumors. While intestinal estrogen receptor beta (ER\u03b2, Esr2) can protect against colitis and colitis-induced cancer in mice, its role in shaping the tumor microenvironment remains unknown. In this study, we performed RNA sequencing to analyze the transcriptome of colonic epithelia and tumors from azoxymethane/dextran sulfate sodium-treated wild-type and intestinal ER\u03b2 knockout (ER\u03b2KOVil) mice and vehicle-treated controls. This revealed significant differences in gene expression and enriched biological processes influenced by sex and genotype, with immune-related responses being overrepresented. Deconvolution supported differential immune cell abundance and immunostaining showed that tumors from ER\u03b2KOVil mice displayed significantly increased macrophage infiltration, decreased T cell infiltration, and impaired natural killer cell infiltration. Further, ER\u03b2 mRNA levels in clinical colorectal tumors correlated with immune signaling profiles and better survival. Our findings indicate that intestinal ER\u03b2 promotes an antitumor microenvironment and could potentially affect the effectiveness of immunotherapy. These insights highlight the importance of ER\u03b2 in modulating antitumor immunity and underscore its therapeutic potential in colorectal cancer.", "doi": "10.1016/j.canlet.2025.217661", "pmid": "40120798", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0304-3835(25)00227-7"}], "notes": [], "created": "2025-04-07T09:56:23.805Z", "modified": "2025-11-14T11:05:53.324Z"}, {"entity": "publication", "iuid": "d936680b828c47f8a2753c7de07ce0de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d936680b828c47f8a2753c7de07ce0de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d936680b828c47f8a2753c7de07ce0de"}}, "title": "DNA Methylation Reflects Cis-Genetic Differentiation Across the European Crow Hybrid Zone.", "authors": [{"family": "Merondun", "given": "Justin", "initials": "J", "orcid": "0000-0001-5077-4096", "researcher": {"href": "https://publications.scilifelab.se/researcher/38e6336366e1418685f36244f39ecde6.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}], "type": "journal article", "published": "2025-07-10", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e70026"}, "abstract": "Chromatin modifications provide a substrate for epigenetic variation with evolutionary potential. To quantify the contribution of this layer of variation during speciation in crows, we leveraged genome and methylome sequencing data from an incipient avian species: all-black carrion crows, grey-coated hooded crows, and their hybrids. Combining controlled experimentation under common garden conditions and sampling of natural genetic variation across the hybrid zone, we show that 5mC methylation variation was largely explained by genome properties and the ontogenetic programme of the organism. Taxonomically related methylation divergence clustered in intergenic space, with the only genomic region of strongly elevated genetic differentiation encoding the diagnostic colour contrast between taxa. We conclude that methylation variation with relevance to speciation largely follows cis-genetic polymorphism in this system and does not constitute an autonomous axis of evolution.", "doi": "10.1111/mec.70026", "pmid": "40637207", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T06:59:29.504Z", "modified": "2025-11-03T08:42:37.319Z"}, {"entity": "publication", "iuid": "be2bf86eb5d64f5d95d391903ab5b1cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be2bf86eb5d64f5d95d391903ab5b1cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be2bf86eb5d64f5d95d391903ab5b1cf"}}, "title": "Development of Anti-Inflammatory Extracellular Vesicles by Surface Expression of Syndecan-4", "authors": [{"family": "Yu", "given": "Lijuan", "initials": "L", "orcid": "0000-0003-3558-3800", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b0b4ca8553144b19c236bc09c1c9b81.json"}}, {"family": "Bergqvist", "given": "Markus", "initials": "M", "orcid": "0009-0003-5716-3716", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d33e374d0642479a80683a989f095a.json"}}, {"family": "Park", "given": "Kyong Su", "initials": "KS", "orcid": "0000-0003-0902-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e308b29fe144b49f4db27f4b819c18.json"}}, {"family": "L\u00e4sser", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-1279-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/e14e17d2cdb24a9f93991d83811c78b9.json"}}, {"family": "L\u00f6tvall", "given": "Jan", "initials": "J", "orcid": "0000-0001-9195-9249", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cbcaf6b5698411c92e0de9e8fcf390f.json"}}], "type": "posted-content", "published": "2025-07-09", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.07.05.663259", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-05T14:10:03.333Z", "modified": "2025-12-18T19:13:20.153Z"}, {"entity": "publication", "iuid": "c86bd10726ee4bf092f5650e7a9e86a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c86bd10726ee4bf092f5650e7a9e86a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c86bd10726ee4bf092f5650e7a9e86a7"}}, "title": "The association between the gut microbiome and 24-h blood pressure measurements in the SCAPIS study.", "authors": [{"family": "Lin", "given": "Yi-Ting", "initials": "YT", "orcid": "0000-0002-5833-0040", "researcher": {"href": "https://publications.scilifelab.se/researcher/899debb5e314439c8f35f255445b3674.json"}}, {"family": "Sayols-Baixeras", "given": "Sergi", "initials": "S", "orcid": "0000-0002-1181-6262", "researcher": {"href": "https://publications.scilifelab.se/researcher/cde59259b02342deb13d78874ce93124.json"}}, {"family": "Baldanzi", "given": "Gabriel", "initials": "G", "orcid": "0000-0003-3962-3953", "researcher": {"href": "https://publications.scilifelab.se/researcher/577652ffb15442e1a47a9aaffc3b52e7.json"}}, {"family": "Dekkers", "given": "Koen F", "initials": "KF", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Nguyen", "given": "Diem", "initials": "D", "orcid": "0000-0002-9680-5772", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78958133e474831ac76dacc36f68cbb.json"}}, {"family": "Nielsen", "given": "Nynne", "initials": "N", "orcid": "0009-0003-5603-3514", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae270d751a64bef8e6ecf9b3a9b423b.json"}}, {"family": "Eklund", "given": "Aron C", "initials": "AC", "orcid": "0000-0003-0861-1001", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1b0f6b48de45f7916e14d6a4defb09.json"}}, {"family": "Varotsis", "given": "Georgios", "initials": "G", "orcid": "0000-0002-3320-2448", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3db146258e467ab67f8848a048baa3.json"}}, {"family": "Holm", "given": "Jacob B", "initials": "JB", "orcid": "0000-0003-1756-0875", "researcher": {"href": "https://publications.scilifelab.se/researcher/359fa6a18dc549a8852dd3990ccde1f1.json"}}, {"family": "Nielsen", "given": "H Bj\u00f8rn", "initials": "HB", "orcid": "0000-0003-2281-5713", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1d5f2e0565a46bcbccfc973eec9e838.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}], "type": "journal article", "published": "2025-07-07", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "276", "issn-l": null}, "abstract": "There is mounting evidence supporting the role of the microbiota in hypertension from experimental studies and population-based studies. We aimed to investigate the relationship between specific characteristics of the gut microbiome and 24-h ambulatory blood pressure measurements.\n\nThe association of gut microbial species and microbial functions, determined by shotgun metagenomic sequencing of fecal samples, with 24-h ambulatory blood pressure measurements in 3695 participants and office blood pressure was assessed in multivariable-adjusted models in 2770 participants without antihypertensive medication from the Swedish CArdioPulmonary bioImage Study.\n\nGut microbiome alpha diversity was negatively associated with diastolic blood pressure variability. Additionally, four microbial species were associated with at least one of the 24-h blood pressure traits. Streptococcus sp001556435 was associated with higher systolic blood pressure, Intestinimonas massiliensis and Dysosmobacter sp001916835 with lower systolic blood pressure, Dysosmobacter sp001916835 with lower diastolic blood pressure, and ER4 sp900317525 with lower systolic blood pressure variability. Moreover, office blood pressure data from a subsample without ambulatory blood pressure measurements replicated the association of Intestinimonas massiliensis with systolic blood pressure and Dysosmobacter sp001916835 with diastolic blood pressure. Species associated with 24-h blood pressure were linked to a similar pattern of metabolites.\n\nIn this large cross-sectional analysis, gut microbiome alpha diversity negatively associates with diastolic blood pressure variability, and four gut microbial species associate with 24-h blood pressure traits.", "doi": "10.1038/s43856-025-00980-x", "pmid": "40624247", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12234806"}, {"db": "pii", "key": "10.1038/s43856-025-00980-x"}], "notes": [], "created": "2025-11-28T10:47:57.315Z", "modified": "2025-11-28T10:47:57.726Z"}, {"entity": "publication", "iuid": "f724e07d9a3f4f3089e31b1bd1bfe6e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f724e07d9a3f4f3089e31b1bd1bfe6e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f724e07d9a3f4f3089e31b1bd1bfe6e6"}}, "title": "Optimized Artificial Colonic Mucus Enabling Physiologically Relevant Diffusion Studies of Drugs, Particles, and Delivery Systems.", "authors": [{"family": "Tjakra", "given": "Marco", "initials": "M", "orcid": "0000-0003-2266-4011", "researcher": {"href": "https://publications.scilifelab.se/researcher/64d56ecd178f433bac46a0d277e619eb.json"}}, {"family": "Chakrapeesirisuk", "given": "Nopdanai", "initials": "N"}, {"family": "Jacobson", "given": "Magdalena", "initials": "M"}, {"family": "Sellin", "given": "Mikael E", "initials": "ME"}, {"family": "Eriksson", "given": "Jens", "initials": "J"}, {"family": "Teleki", "given": "Alexandra", "initials": "A", "orcid": "0000-0001-6514-8960", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f66123962cb40dab667805e777b9cf3.json"}}, {"family": "Bergstr\u00f6m", "given": "Christel A S", "initials": "CAS", "orcid": "0000-0002-8917-2612", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bb49fc33a4e4b73a4f5b723dcbcd752.json"}}], "type": "journal article", "published": "2025-07-07", "journal": {"title": "Mol. Pharm.", "issn": "1543-8392", "volume": "22", "issue": "7", "pages": "4032-4045", "issn-l": "1543-8384"}, "abstract": "Development of oral drug delivery systems that penetrate the colonic mucus remains challenging. Artificial models of porcine colonic mucus have been developed that mimic the rheology and viscosity of the native mucus and its contents of mucins, protein, and lipids. However, they are less representative with regard to the zeta potential, a factor of importance for charged molecules and particles. This study therefore aimed to improve the existing porcine artificial colonic mucus model by exchanging the polymer backbone (used for viscosity) to more closely mimic the charge of porcine native colonic mucus. Polymers studied were poly(acrylic acid), hydroxyethylcellulose, sodium hyaluronate, sodium alginate, and pectin. The resulting porcine artificial colonic mucus was assayed for apparent viscosity, storage modulus, pH, water content, zeta potential, and pore size. The two best-performing polymers (poly(acrylic acid) and hydroxyethylcellulose) were then assayed with diffusion of FITC-dextran, particle tracking of nanoparticles, and binding of FITC-dextran and contrasted to data generated in porcine native colonic mucus (PNCM). Of the two polymers, PACM based on HEC generated zeta potential and binding kinetics similar to those of PNCM. We conclude that the choice of polymer in PACMs is critical for improving their use in drug development. The extensive characterization of the PACMs further points toward the importance of complementary techniques to determine rheological characteristics, mesh, and pore size.", "doi": "10.1021/acs.molpharmaceut.5c00298", "pmid": "40492464", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12239078"}], "notes": [], "created": "2025-11-18T22:14:57.467Z", "modified": "2025-11-18T22:14:57.918Z"}, {"entity": "publication", "iuid": "018d4ddadbbb4063809bc76956670eab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/018d4ddadbbb4063809bc76956670eab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/018d4ddadbbb4063809bc76956670eab"}}, "title": "Fungal diversity in wood of living trees is higher in oak than in beech, maple or linden, and is affected by tree size and climate", "authors": [{"family": "Nord\u00e9n", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-2739-9774", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbc527defcc24463b13c9d7e50750ec1.json"}}, {"family": "Andreasen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-2390-8412", "researcher": {"href": "https://publications.scilifelab.se/researcher/f317685500284ff7a9bf51706c732511.json"}}, {"family": "Gran", "given": "Oskar", "initials": "O", "orcid": "0000-0002-7999-0478", "researcher": {"href": "https://publications.scilifelab.se/researcher/c10af52f4d2e436c92c304de277f7c9c.json"}}, {"family": "Menkis", "given": "Audrius", "initials": "A", "orcid": "0000-0002-6545-8907", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d4d16d281344b9f9cf2c3c27fb40f06.json"}}], "type": "journal-article", "published": "2025-07-05", "journal": {"title": "Biodivers Conserv", "issn": "0960-3115", "issn-l": null}, "abstract": null, "doi": "10.1007/s10531-025-03119-5", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-08-19T13:24:14.874Z", "modified": "2025-08-19T13:24:15.099Z"}, {"entity": "publication", "iuid": "d455b3d68f6e42e89fb9f9af444a61b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d455b3d68f6e42e89fb9f9af444a61b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d455b3d68f6e42e89fb9f9af444a61b2"}}, "title": "Discovery and characterization of novel pyridone and furan substituted ligands of choline acetyltransferase.", "authors": [{"family": "Baidya", "given": "Anurag Tk", "initials": "AT"}, {"family": "Dante", "given": "Davide", "initials": "D"}, {"family": "Das", "given": "Bhanuranjan", "initials": "B"}, {"family": "Wang", "given": "Lisha", "initials": "L"}, {"family": "Darreh-Shori", "given": "Taher", "initials": "T"}, {"family": "Kumar", "given": "Rajnish", "initials": "R"}], "type": "journal article", "published": "2025-07-05", "journal": {"title": "Eur J Pharmacol", "issn": "1879-0712", "volume": "998", "pages": "177638", "issn-l": null}, "abstract": "The key to the management of two devastating diseases, namely Alzheimer's Disease (AD) and Amyotrophic Lateral Sclerosis (ALS) lies in an early diagnosis, which is difficult due to its multifactorial nature. However, a common hallmark of AD and ALS is degeneration of cholinergic system. Choline acetyltransferase (ChAT) has been proposed as a potential target for development of cholinergic-specific biomarker. However, lack of selective, potent, brain permeable molecular probes of ChAT hinder development of ChAT biomarkers. In this study, we have successfully utilised structure-based virtual screening approach and identified two ChAT inhibitors from a database of 1.4 million compounds. The compounds were then subjected to rigorous in vitro characterization. Compound V6 showed Ki value of 11 \u03bcM and IC50 value of 21.73 \u03bcM, while V15 showed Ki and IC50 values of 4.5 and 9.42 \u03bcM, respectively for ChAT enzyme. V6 and V15 showed good solubility of 0.21 mg/mL and 0.17 mg/mL respectively and cytotoxicity analysis indicated no toxicity. We also performed a 200 ns molecular dynamics simulation, which revealed the intricate interaction dynamics for V6 and V15 with ChAT binding pocket. Moreover, the Tanimoto similarity analysis indicated the novelty and structural diversity of the hits. In conclusion, these validated hits provide a platform to develop potent, selective, blood-brain barrier permeable small molecules as chemical probes of ChAT or as Positron Emission Tomography tracer for early diagnosis and/or in vivo monitoring of the effect of new therapeutic candidates in spectrum of neurodegenerative disorders, in which cholinergic deficit is one of the hallmarks.", "doi": "10.1016/j.ejphar.2025.177638", "pmid": "40252901", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-2999(25)00392-9"}], "notes": [], "created": "2025-11-28T10:43:04.096Z", "modified": "2025-11-28T10:43:04.146Z"}, {"entity": "publication", "iuid": "7fd1fb0bdc854b1b829c0dad9054ceb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fd1fb0bdc854b1b829c0dad9054ceb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fd1fb0bdc854b1b829c0dad9054ceb8"}}, "title": "Oat bran fiber protects against radiation-induced disruption of gut barrier dynamics and mucosal damage.", "authors": [{"family": "Patel", "given": "Piyush", "initials": "P"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Robeson", "given": "Michael", "initials": "M"}, {"family": "Malipatlolla", "given": "Dilip K", "initials": "DK"}, {"family": "Devarakonda", "given": "Sravani", "initials": "S"}, {"family": "Rasc\u00f3n", "given": "Ana", "initials": "A"}, {"family": "Nyman", "given": "Margareta", "initials": "M"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Wold", "given": "Agnes E", "initials": "AE"}, {"family": "Sj\u00f6berg", "given": "Fei", "initials": "F"}, {"family": "Bull", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2025-07-04", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "11", "issue": "1", "pages": "128", "issn-l": "2055-5008"}, "abstract": "Dietary fibers are recognized for their health benefits, yet cancer patients undergoing pelvic radiotherapy are often advised to reduce fiber intake. This may negatively impact their bowel health. To evaluate the effects of dietary fibers on bowel health post-irradiation, male C57BL/6 mice were fed diets containing either 0 or 15% fiber with varying proportions of readily fermentable bioprocessed oat bran fiber and/or poorly fermentable microcrystalline cellulose, and either irradiated or sham-irradiated. Irradiation triggered mucus degradation and depletion of short-chain fatty acids, and a fiber-free diet exacerbated radiation-induced mucosal damage. In contrast, mice fed oat bran fiber exhibited less mucosal damage, fewer dysbiotic and mucus-degrading bacteria, higher production of short-chain fatty acids, and improved bactericidal activity. These benefits were dose-dependent, with 15% oat bran fiber providing greater protection. Our findings suggest that fiber deprivation exacerbates radiation-induced intestinal damage, while supplementation with 15% highly fermentable oat bran fiber supports mucosal integrity and protects against radiation-induced injury.", "doi": "10.1038/s41522-025-00759-x", "pmid": "40615440", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12227613"}, {"db": "pii", "key": "10.1038/s41522-025-00759-x"}], "notes": [], "created": "2025-10-23T13:25:14.138Z", "modified": "2025-11-20T18:35:20.884Z"}, {"entity": "publication", "iuid": "43ff9ae2ee304005b3b75d388520674e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43ff9ae2ee304005b3b75d388520674e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43ff9ae2ee304005b3b75d388520674e"}}, "title": "From Recruitment to Retirement: Research Infrastructure Staff Views on the Diversification of Scientific Career Paths at Universities in Sweden in 2024.", "authors": [{"family": "Schroeder", "given": "Kristen", "initials": "K", "orcid": "0000-0002-6271-4530", "researcher": {"href": "https://publications.scilifelab.se/researcher/79f3c1b13a9844be86fdce0b7f425fb3.json"}}, {"family": "Fern\u00e1ndez-Rodr\u00edguez", "given": "Julia", "initials": "J"}, {"family": "Jenmalm-Jensen", "given": "Annika", "initials": "A"}, {"family": "Lundgren-Gawell", "given": "Josefin", "initials": "J"}, {"family": "Sandin", "given": "Sara", "initials": "S"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}], "type": "journal article", "published": "2025-07-04", "journal": {"title": "F1000Res", "issn": "2046-1402", "issn-l": "2046-1402", "volume": "14", "issue": null, "pages": "652"}, "abstract": "There is an ongoing need to develop diverse career paths that support the vital contributions of staff scientists, research engineers, scientific officers, and other knowledge professionals in scientific discovery. Research infrastructures and core facilities have a particular need to support sustainable and diverse careers, as they either employ - if being a legal entity - or daily manage research professionals in a broad variety of roles to enable resources, services, and innovation.\r\n\r\nIn 2019, a survey of the facility staff at SciLifeLab, a large national research infrastructure in Sweden, led to a recommendation for universities to develop career paths for their staff scientists. Five years later, we have conducted a survey and workshop to determine current views of infrastructure staff on career path diversity in Sweden.\r\n\r\nOur results indicate there is a strong need for clarity and communication about planning and implementation of career path structures at Swedish universities, as well as opportunities to foster excellence in infrastructure staff. While the workshop participants ranked Sweden as a stable and attractive place to work and reported continuous development of their technical and service skills, the lack of recognition of this expertise presents a barrier to a sustainable career.\r\n\r\nWe conclude that there is a need to continue advocating for increased clarity and diversity in career paths for staff scientists in Sweden, and raise the views presented by infrastructure staff on the challenges and opportunities unique to their roles.", "doi": "10.12688/f1000research.164794.1", "pmid": "40904623", "labels": {"Integrated Microscopy Technologies Gothenburg": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12402762"}], "notes": [], "created": "2025-11-05T14:09:53.317Z", "modified": "2025-11-05T14:10:39.124Z"}, {"entity": "publication", "iuid": "d086ca68d3ff42dc9c2f5eaa0834b478", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d086ca68d3ff42dc9c2f5eaa0834b478.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d086ca68d3ff42dc9c2f5eaa0834b478"}}, "title": "Droplet microfluidics-based detection of rare antibiotic-resistant subpopulations in Escherichia coli from bloodstream infections.", "authors": [{"family": "Agnihotri", "given": "Sagar N", "initials": "SN", "orcid": "0000-0003-0943-6751", "researcher": {"href": "https://publications.scilifelab.se/researcher/c42c1834bf5247a38d98b8bab8b4914d.json"}}, {"family": "Fatsis-Kavalopoulos", "given": "Nikos", "initials": "N", "orcid": "0000-0002-5081-0138", "researcher": {"href": "https://publications.scilifelab.se/researcher/c173faa59bde4b908da82e02a23d4b70.json"}}, {"family": "Windhager", "given": "Jonas", "initials": "J", "orcid": "0000-0002-2111-5291", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbdf2ef632c740cdaba02c8ee61f2b62.json"}}, {"family": "Tenje", "given": "Maria", "initials": "M", "orcid": "0000-0002-1264-1337", "researcher": {"href": "https://publications.scilifelab.se/researcher/18affd576ee84f62a7a40f678a600058.json"}}, {"family": "Andersson", "given": "Dan I", "initials": "DI", "orcid": "0000-0001-6640-2174", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb042b3dfa21450e862a29951ea0c1eb.json"}}], "type": "journal article", "published": "2025-07-04", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "27", "pages": "eadv4558", "issn-l": "2375-2548"}, "abstract": "Population heterogeneity in bacterial phenotypes, such as antibiotic resistance, is increasingly recognized as a medical concern. Heteroresistance occurs when a predominantly susceptible bacterial population harbors a rare resistant subpopulation. During antibiotic exposure, these resistant bacteria can be selected and lead to treatment failure. Standard antibiotic susceptibility testing methods often fail to reliably detect these subpopulations due to their low frequency, highlighting the need for improved diagnostic approaches. Here, we present a droplet microfluidics method where bacteria are encapsulated in droplets containing growth medium and antibiotics. The growth of rare resistant cells is detected by observing droplet shrinkage under microscopy. We validated this method for three clinically important antibiotics in Escherichia coli isolates obtained from bloodstream infections and showed that it can detect resistant subpopulations as infrequent as 10-6 using only 200 to 300 droplets. In addition, we designed a multiplex microfluidic chip to increase the throughput of the assay.", "doi": "10.1126/sciadv.adv4558", "pmid": "40614180", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12227044"}], "notes": [], "created": "2025-11-25T12:57:58.095Z", "modified": "2025-11-25T12:57:58.278Z"}, {"entity": "publication", "iuid": "5a86b071f2d442cdbad028b7b1279a77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a86b071f2d442cdbad028b7b1279a77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a86b071f2d442cdbad028b7b1279a77"}}, "title": "Identification of proliferating neural progenitors in the adult human hippocampus", "authors": [{"family": "Dumitru", "given": "Ionut", "initials": "I", "orcid": "0000-0001-6358-8049", "researcher": {"href": "https://publications.scilifelab.se/researcher/3887e761bcdc4812acf5d497ada9b72d.json"}}, {"family": "Paterlini", "given": "Marta", "initials": "M", "orcid": "0009-0009-8844-483X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a3e4310ae5455bb1583db6845ef761.json"}}, {"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f196173b40b4819a5fcd11bf76a4e6e.json"}}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "researcher": {"href": "https://publications.scilifelab.se/researcher/3297f21f1a174cd388ac586eda2b5177.json"}}, {"family": "Giatrellis", "given": "Sarantis", "initials": "S", "orcid": "0009-0002-6412-0530", "researcher": {"href": "https://publications.scilifelab.se/researcher/9554fd11c5a649a88d9d3cb51776012a.json"}}, {"family": "Saghaleyni", "given": "Rasool", "initials": "R", "orcid": "0000-0003-0956-039X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebd08b713a894a6986d9101453f5ecd9.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Tata", "given": "Mathew", "initials": "M", "orcid": "0000-0002-0960-5677", "researcher": {"href": "https://publications.scilifelab.se/researcher/b55d49cf14534ad4bd1655a7fea9484b.json"}}, {"family": "Druid", "given": "Henrik", "initials": "H", "orcid": "0000-0002-9198-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bb7f9c706b451f9813bae017e0fad7.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}], "type": "journal-article", "published": "2025-07-03", "journal": {"title": "Science", "issn": "0036-8075", "volume": "389", "issue": "6755", "pages": "58-63", "issn-l": null}, "abstract": null, "doi": "10.1126/science.adu9575", "pmid": null, "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-17T17:13:00.484Z", "modified": "2025-11-17T17:13:01.219Z"}, {"entity": "publication", "iuid": "36236e6be0ce4b17b39f3a3841e121fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36236e6be0ce4b17b39f3a3841e121fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36236e6be0ce4b17b39f3a3841e121fb"}}, "title": "Dissecting FAP+ Cell Diversity in Pancreatic Cancer Uncovers an Interferon-Response Subtype of Cancer-Associated Fibroblasts with Tumor-Restraining Properties.", "authors": [{"family": "Cumming", "given": "Joshua", "initials": "J", "orcid": "0000-0003-3661-7443", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd0f3e688ff047ef8e814134c0446774.json"}}, {"family": "Maneshi", "given": "Parniyan", "initials": "P", "orcid": "0000-0002-2180-4097", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c23ae21a4df4f319d2395580aa4fb2e.json"}}, {"family": "Dongre", "given": "Mitesh", "initials": "M", "orcid": "0000-0002-7151-1137", "researcher": {"href": "https://publications.scilifelab.se/researcher/6acd00be909d41399277be66d9600d41.json"}}, {"family": "Alsaed", "given": "Tala", "initials": "T", "orcid": "0009-0009-5690-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/58e2e9329f714da7ad4892b11a3c726d.json"}}, {"family": "Dehghan-Nayeri", "given": "Mohammad Javad", "initials": "MJ", "orcid": "0009-0002-1538-4871", "researcher": {"href": "https://publications.scilifelab.se/researcher/8399aab605474070a84399a52d4befe2.json"}}, {"family": "Ling", "given": "Agnes", "initials": "A", "orcid": "0000-0002-9503-0784", "researcher": {"href": "https://publications.scilifelab.se/researcher/acb1fab24b604772bf2bb07fc10c056d.json"}}, {"family": "Pietras", "given": "Kristian", "initials": "K", "orcid": "0000-0001-6738-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/5be0a3ec07654822a91df964eab1d6e4.json"}}, {"family": "Patthey", "given": "Cedric", "initials": "C", "orcid": "0000-0002-2627-9578", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b7707e8bd3d4e029fb1e1f43df86ad4.json"}}, {"family": "\u00d6hlund", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5847-2778", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e9e473f68c460098a37e22d0a41369.json"}}], "type": "journal article", "published": "2025-07-02", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "85", "issue": "13", "pages": "2388-2411", "issn-l": "0008-5472"}, "abstract": "Within the stroma of pancreatic ductal adenocarcinoma (PDAC), mesenchymal cells differentiate into cancer-associated fibroblast (CAF) subtypes that differentially mediate disease progression. Defining the regulatory mechanism and diversity of CAF subtypes could identify potential therapeutic strategies to harness the tumor-suppressive activities of CAFs. To address this, we utilized single-cell RNA sequencing to profile fibroblast activation protein-\u03b1 (FAP)-expressing mesenchymal cells in human PDAC. The mesenchymal subpopulations in PDAC reflected mesenchymal cell heterogeneity found in the normal developing pancreas. In addition to characterizing inflammatory CAF and myofibroblastic CAF subpopulations in detail, the analysis uncovered a previously undescribed interferon-response CAF (ifCAF) subtype. Tumor-derived signals induced specific CAF subtypes from pancreatic stellate cells in an organoid-based coculture model, and time-course experiments revealed regulatory mechanisms that govern subtype formation. STING agonists promoted an ifCAF phenotype in vivo and in vitro. Importantly, induction of an ifCAF phenotype suppressed tumor cell invasiveness and induced an antitumor phenotype in tumor-associated neutrophils. Together, this study resolves FAP+ stromal cell heterogeneity in PDAC and identifies an ifCAF subtype that can be induced to suppress protumorigenic features of PDAC.\n\nCharacterization of FAP+ mesenchymal cell heterogeneity in pancreatic cancer identifies a tumor-suppressive interferon-response cancer-associated fibroblast subtype that can be induced by stimulating type I interferon signaling using STING agonists.", "doi": "10.1158/0008-5472.CAN-23-3252", "pmid": "40215177", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Clinical Genomics": "Service", "Clinical Genomics Ume\u00e5": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12214878"}, {"db": "pii", "key": "757349"}], "notes": [], "created": "2025-11-21T18:45:35.492Z", "modified": "2025-11-28T10:52:09.338Z"}, {"entity": "publication", "iuid": "0711daac3c544b8fb60416da8e9cb152", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0711daac3c544b8fb60416da8e9cb152.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0711daac3c544b8fb60416da8e9cb152"}}, "title": "Bladder cancer subtypes exhibit limited plasticity across different microenvironments and in metastases.", "authors": [{"family": "Bernardo", "given": "Carina", "initials": "C"}, {"family": "Chattopadhyay", "given": "Subhayan", "initials": "S"}, {"family": "Andersson", "given": "Natalie", "initials": "N"}, {"family": "Eriksson", "given": "Pontus", "initials": "P"}, {"family": "Medle", "given": "Benjamin", "initials": "B"}, {"family": "Tran", "given": "Lena", "initials": "L"}, {"family": "Dain Marzouka", "given": "Nour Al", "initials": "NA"}, {"family": "Mattsson", "given": "Adam", "initials": "A"}, {"family": "Zadoroznyj", "given": "Aymeric", "initials": "A"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Liedberg", "given": "Fredrik", "initials": "F"}, {"family": "H\u00f6glund", "given": "Mattias", "initials": "M"}, {"family": "Sj\u00f6dahl", "given": "Gottfrid", "initials": "G"}], "type": "journal article", "published": "2025-07-02", "journal": {"title": "Exp Hematol Oncol", "issn": "2162-3619", "volume": "14", "issue": "1", "pages": "91", "issn-l": null}, "abstract": "Transcriptomic and genomic analyses of bladder cancer (BC) reveal a highly diverse disease stratified into molecular subtypes with distinct molecular features and biological behaviors. Intratumor heterogeneity (ITH) and plasticity can significantly impact diagnosis and patient management, yet their extent in BC remains highly debated. Here, we investigated whether the three main bladder cancer subtypes maintain or alter their identity in response to changes in the microenvironment and during metastatic colonization.\n\nSeven patient-derived xenograft (PDX) models representing the major BC subtypes were propagated into three distinct tissue microenvironments: subcutaneous, mammary fat pad and under the kidney capsule. Metastatic lesions were generated via systemic injection of tumor cells. Tumor samples were analysed using RNA- and exome sequencing, SNP-arrays and histopathology to assess subtype fidelity, genomic evolution, and clonal dynamics.\n\nA comprehensive, longitudinal multiomics analysis showed that tumors consistently maintain their molecular subtype, as well as their transcriptomic and genomic profiles, across different environments. No evidence of emerging ITH or subtype transitions was observed, regardless of the microenvironment. The transcriptomic adaptations observed in metastases and different implantation sites are limited and are associated primarily with hypoxia, epithelial-mesenchymal transition (EMT), and invasion.\n\nOur results suggest that invasive bladder cancers have a strong intrinsic tumor identity that is not easily reprogrammed by the microenvironment.", "doi": "10.1186/s40164-025-00682-z", "pmid": "40605119", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12225047"}, {"db": "pii", "key": "10.1186/s40164-025-00682-z"}], "notes": [], "created": "2025-08-22T08:26:48.445Z", "modified": "2025-11-12T06:56:23.529Z"}, {"entity": "publication", "iuid": "a934d3358dd642a89a636f574a2204fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a934d3358dd642a89a636f574a2204fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a934d3358dd642a89a636f574a2204fb"}}, "title": "Associations between carotid artery intima-media thickness, traditional risk factors and proteins", "authors": [{"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Zheng", "given": "Rui", "initials": "R"}], "type": "journal-article", "published": "2025-07-02", "journal": {"title": "npj Cardiovasc Health", "issn": "2948-2836", "issn-l": null, "volume": "2", "issue": "1", "pages": null}, "abstract": null, "doi": "10.1038/s44325-025-00073-7", "pmid": null, "labels": {"Affinity Proteomics Uppsala": "Service", "National Genomics Infrastructure": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-25T19:18:59.510Z", "modified": "2025-11-26T11:05:15.077Z"}, {"entity": "publication", "iuid": "936a7690dbce49328330eb645143c8cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/936a7690dbce49328330eb645143c8cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/936a7690dbce49328330eb645143c8cf"}}, "title": "Transcriptomic Patterns in Adult and Pediatric Patients with IgA Nephropathy or IgA Vasculitis with Nephropathy.", "authors": [{"family": "Levin", "given": "Anna", "initials": "A", "orcid": "0000-0002-1299-6920", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff22b37b69144ccc899c5e50be3abc5f.json"}}, {"family": "Schwarz", "given": "Angelina", "initials": "A", "orcid": "0009-0000-7828-9260", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee209747d3c64713a3aad7b1ff6c5748.json"}}, {"family": "van Hoef", "given": "Vincent", "initials": "V", "orcid": "0000-0003-1707-7066", "researcher": {"href": "https://publications.scilifelab.se/researcher/05c9836d67fa498381e8ee228464bada.json"}}, {"family": "Wijkstr\u00f6m", "given": "Julia", "initials": "J", "orcid": "0000-0001-6183-5878", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c20445221e242689b8473bdc2cc7a4b.json"}}, {"family": "Bruchfeld", "given": "Annette", "initials": "A", "orcid": "0000-0002-9752-9941", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc6ee3e8a4124c5f8d6506ab762949ae.json"}}, {"family": "Herthelius", "given": "Maria", "initials": "M", "orcid": "0000-0003-3306-2235", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe439528adab4cf6988826204b3a2929.json"}}, {"family": "Wennberg", "given": "Lars", "initials": "L", "orcid": "0000-0002-3313-3374", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d7c30072ecb4c70b53bb1abc7f072f3.json"}}, {"family": "B\u00e1r\u00e1ny", "given": "Peter", "initials": "P", "orcid": "0000-0001-6501-8293", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1694c39562e4675bc23cbf9366a0e18.json"}}, {"family": "Witasp", "given": "Anna", "initials": "A"}, {"family": "Wernerson", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "J. Am. Soc. Nephrol.", "issn": "1533-3450", "issn-l": "1046-6673", "volume": null, "issue": null, "pages": null}, "abstract": "Disease manifestations and progression of IgA Nephropathy vary widely between individuals, particularly between children and adults. To further understand these differences, we examined the transcriptional profiles in kidney biopsies from both adult and paediatric IgA nephropathy patients in relation to normal kidneys.\r\n\r\nKidney biopsies from 95 participants, 71 adults and 13 children with histopathologically verified IgA nephropathy or IgA vasculitis with nephropathy as well as 11 living donors, were microdissected into glomerular and tubulointerstitial fractions and subjected to RNA sequencing. Differential gene expression analysis was performed across groups, and functional enrichment analyses were conducted using Gene ontology and Kyoto Encyclopedia of Genes and Genomes. Histopathological grading (Oxford and part of the Banff classifications) and clinical data (at time of biopsy and up to five years of follow-up) were analysed in relation to normalized RNA counts.\r\n\r\nDifferentially expressed genes obtained from all patients versus living donors, both glomerular and tubulointerstitial fractions, were enriched for immune system and complement activation pathways. When comparing of adults to children within the IgA nephropathy/IgA vasculitis with nephropathy group, 5562 and 3539 differentially expressed genes in each fraction were identified with pathway enrichment of including processes related to the endoplasmic reticulum and mitochondrial activity (glomeruli), as well as T cell activation (tubulointerstitium).\r\n\r\nDistinct transcriptional profiles with enrichment of inflammation and immune response pathways were revealed in patients compared to living donors. However, the transcriptomic signatures across adult and paediatric patients were not consistent, highlighting differences in pathways involved in endoplasmic reticular, mitochondrial and T cell activity when comparing adults and children.", "doi": "10.1681/ASN.0000000787", "pmid": "40591410", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "00001751-990000000-00696"}], "notes": [], "created": "2025-11-20T15:20:22.134Z", "modified": "2025-11-21T12:59:19.906Z"}, {"entity": "publication", "iuid": "cc07bc3e7dbc4945b766931b0ee2f31a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc07bc3e7dbc4945b766931b0ee2f31a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc07bc3e7dbc4945b766931b0ee2f31a"}}, "title": "The interplay of genetics and fatty acid metabolism: exploring their impact on metabolic syndrome in Swedish men.", "authors": [{"family": "Oskarsdottir", "given": "Harpa", "initials": "H"}, {"family": "Palsson", "given": "Arnar", "initials": "A"}, {"family": "Olafsdottir", "given": "Erla B", "initials": "EB"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Mohammad", "given": "Salahuddin", "initials": "S"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Skuladottir", "given": "Gudrun V", "initials": "GV"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "Nutr J", "issn": "1475-2891", "volume": "24", "issue": "1", "pages": "99", "issn-l": "1475-2891"}, "abstract": "Genetic risk variants for obesity and metabolic syndrome (MetS) have been identified, but their link to relevant metabolic health parameters warrants further attention. This study aimed to investigate the extent to which single-nucleotide polymorphisms (SNPs) associated with obesity are linked to changes in fatty acid (FA) profiles in serum cholesteryl esters, lipid metabolism, and MetS risk.\n\nData from the Uppsala Longitudinal Study of Adult Men (ULSAM), conducted in men at age 50 (N = 1973) and age 70 (N = 982), were used to investigate SNPs associated with body mass index (BMI) in genome-wide association studies with metabolic parameters at age 50. The significant SNPs and associated lipid parameters were then used as predictors of MetS over a 20-year follow-up period, at age 70 in binary regression models.\n\nThe two genes, the brain-derived neurotrophic factor gene (BDNF) (rs7103411) and the fat mass and obesity-associated gene (FTO) (rs1558902), together with delta-5-desaturase (D5D) activity, 20:5n-3 in serum cholesteryl esters (CE), fasting blood glucose, abdominal skinfold thickness, apolipoprotein-B, and high-density lipoprotein cholesterol (HDL-C) at age 50, significantly predicted the risk of MetS at age 70.\n\nThe findings suggest a considerable contribution of the SNPs BDNF rs7103411, FTO rs1558902, and ETV5 rs9816226, along with low D5D activities and serum levels of HDL-C in men at age 50, to the risk for MetS 20 years later.", "doi": "10.1186/s12937-025-01168-8", "pmid": "40598589", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12210471"}, {"db": "pii", "key": "10.1186/s12937-025-01168-8"}], "notes": [], "created": "2025-09-08T07:04:09.137Z", "modified": "2025-09-08T07:04:09.166Z"}, {"entity": "publication", "iuid": "6e95ba5c190e4167a9c6aaa5aaea5a48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e95ba5c190e4167a9c6aaa5aaea5a48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e95ba5c190e4167a9c6aaa5aaea5a48"}}, "title": "Semaglutide effects on energy balance are mediated by Adcyap1+ neurons in the dorsal vagal complex.", "authors": [{"family": "Teixidor-Deulofeu", "given": "J\u00falia", "initials": "J"}, {"family": "Blid Sk\u00f6ldheden", "given": "Sebastian", "initials": "S"}, {"family": "Font-Giron\u00e8s", "given": "Ferran", "initials": "F"}, {"family": "Feje\u0161", "given": "Andrej", "initials": "A"}, {"family": "Ruud", "given": "Johan", "initials": "J"}, {"family": "Engstr\u00f6m Ruud", "given": "Linda", "initials": "L"}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "Cell Metab.", "issn": "1932-7420", "volume": "37", "issue": "7", "pages": "1530-1546.e6", "issn-l": "1550-4131"}, "abstract": "The use of the GLP-1R agonist semaglutide is revolutionizing the treatment of obesity, yet its mechanistic effects on energy balance remain elusive. Here, we demonstrate that reactivation of semaglutide-responsive dorsal vagal complex neurons mimics the drug's effects of reducing food intake and body weight and promoting fat utilization and conditioned taste aversion. We observe that many of the semaglutide-activated area postrema (AP) and nucleus of the solitary tract (NTS) neurons express Adcyap1 mRNA, and ablation of AP/NTS Adcyap1+ neurons largely reverses semaglutide's effects on energy balance acutely in lean mice and in subchronically treated obese mice. Semaglutide-activated AP/NTS Adcyap1+ neurons promote the loss of fat rather than lean mass, with only a modest effect on conditioned taste aversion. Furthermore, NTS Adcyap1+ neurons are engaged by GLP-1R-expressing AP neurons and are necessary for semaglutide-induced activation of several downstream satiety-related structures. Selective targeting of semaglutide-responsive Adcyap1+ neurons holds potential for improved future anti-obesity treatments.", "doi": "10.1016/j.cmet.2025.04.018", "pmid": "40409256", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S1550-4131(25)00256-6"}], "notes": [], "created": "2025-11-05T14:09:55.539Z", "modified": "2025-11-05T14:09:55.543Z"}, {"entity": "publication", "iuid": "3b583a77d8b3461e8235d388087a4736", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b583a77d8b3461e8235d388087a4736.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b583a77d8b3461e8235d388087a4736"}}, "title": "Proteomic analysis of Down syndrome cerebrospinal fluid compared to late-onset and autosomal dominant Alzheimer\u00b4s disease.", "authors": [{"family": "Montoliu-Gaya", "given": "Laia", "initials": "L", "orcid": "0000-0001-7684-6318", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddcfba9a14f14ba7ad912dcfd5fe92d9.json"}}, {"family": "Bian", "given": "Shijia", "initials": "S"}, {"family": "Dammer", "given": "Eric B", "initials": "EB", "orcid": "0000-0003-2947-7606", "researcher": {"href": "https://publications.scilifelab.se/researcher/026547f280c8451586bf92ab028090f7.json"}}, {"family": "Alcolea", "given": "Daniel", "initials": "D", "orcid": "0000-0002-3819-3245", "researcher": {"href": "https://publications.scilifelab.se/researcher/57c67b243f6a4ea38023ea8ae4f35e88.json"}}, {"family": "Sauer", "given": "Mathias", "initials": "M"}, {"family": "Mart\u00e1-Ariza", "given": "Mitchell", "initials": "M", "orcid": "0000-0002-2121-7685", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbbcf516eead45b0999f29a79d94afe1.json"}}, {"family": "Ashton", "given": "Nicholas J", "initials": "NJ"}, {"family": "Belbin", "given": "Olivia", "initials": "O", "orcid": "0000-0002-6109-6371", "researcher": {"href": "https://publications.scilifelab.se/researcher/24e4b78f7fe8416596794fd2da2d3b4b.json"}}, {"family": "Fuchs", "given": "Johannes", "initials": "J", "orcid": "0000-0001-9317-6969", "researcher": {"href": "https://publications.scilifelab.se/researcher/65bf045dd14e45a4b61b4eb36e979bc0.json"}}, {"family": "Watson", "given": "Caroline M", "initials": "CM", "orcid": "0000-0001-6574-0833", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab9107bdd4b246718df18654ffa1f67e.json"}}, {"family": "Ping", "given": "Lingyan", "initials": "L"}, {"family": "Duong", "given": "Duc M", "initials": "DM"}, {"family": "Nilsson", "given": "Johanna", "initials": "J", "orcid": "0000-0002-2856-6060", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbfa9ce69cde46568cc315f0af089d2b.json"}}, {"family": "Barroeta", "given": "Isabel", "initials": "I"}, {"family": "Lantero-Rodriguez", "given": "Juan", "initials": "J", "orcid": "0000-0002-7426-678X", "researcher": {"href": "https://publications.scilifelab.se/researcher/492e19dc85914831bad0cefe5b7eb613.json"}}, {"family": "Videla", "given": "Laura", "initials": "L", "orcid": "0000-0002-9748-8465", "researcher": {"href": "https://publications.scilifelab.se/researcher/be25e716385448deb9741619b60b91bd.json"}}, {"family": "Benejam", "given": "Bessy", "initials": "B"}, {"family": "Roberts", "given": "Blaine R", "initials": "BR", "orcid": "0000-0001-5466-0053", "researcher": {"href": "https://publications.scilifelab.se/researcher/558f53068f1e45f1a828e9fcf8d905c6.json"}}, {"family": "Blennow", "given": "Kaj", "initials": "K", "orcid": "0000-0002-1890-4193", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e646be026ce42ecbfd4d62eca3f9bce.json"}}, {"family": "Seyfried", "given": "Nicholas T", "initials": "NT", "orcid": "0000-0002-4507-624X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c940f8678724c38b1c6e98ea1b335e4.json"}}, {"family": "Levey", "given": "Allan I", "initials": "AI", "orcid": "0000-0002-3153-502X", "researcher": {"href": "https://publications.scilifelab.se/researcher/290c68791bfe4999b7a68ec208ea952b.json"}}, {"family": "Carmona-Iragui", "given": "Mar\u00eda", "initials": "M"}, {"family": "Gobom", "given": "Johan", "initials": "J", "orcid": "0000-0001-6193-6193", "researcher": {"href": "https://publications.scilifelab.se/researcher/add4c0c68cff447383c1f0184e2be943.json"}}, {"family": "Lle\u00f3", "given": "Alberto", "initials": "A", "orcid": "0000-0002-2568-5478", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f93b0e1f2b0458ea41339b0935e892b.json"}}, {"family": "Wisniewski", "given": "Thomas", "initials": "T", "orcid": "0000-0002-3379-8966", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c220af79d5a424f8bfe4e8d7c294276.json"}}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}, {"family": "Fortea", "given": "Juan", "initials": "J", "orcid": "0000-0002-1340-638X", "researcher": {"href": "https://publications.scilifelab.se/researcher/339f94b3044b4d8b82167c6968085be2.json"}}, {"family": "Johnson", "given": "Erik C B", "initials": "ECB", "orcid": "0000-0002-0604-2944", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e9903bd257a439b9a8072f0d478a558.json"}}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "6003", "issn-l": "2041-1723"}, "abstract": "Almost all individuals with Down Syndrome (DS) develop Alzheimer's disease (AD) by mid to late life. However, the degree to which AD in DS shares pathological changes with sporadic late-onset AD (LOAD) and autosomal dominant AD (ADAD) beyond core AD biomarkers such as amyloid-\u03b2 (A\u03b2) and tau is unknown. Here, we used proteomics of cerebrospinal fluid from individuals with DS (n = 229) in the Down Alzheimer Barcelona Neuroimaging Initiative (DABNI) cohort to assess the evolution of AD pathophysiology from asymptomatic to dementia stages and compared the proteomic biomarker changes in DS to those observed in LOAD and ADAD. Although many proteomic alterations were shared across DS, LOAD, and ADAD, DS demonstrated more severe changes in immune-related proteins, extracellular matrix pathways, and plasma proteins likely related to blood-brain barrier dysfunction compared to LOAD. These changes were present in young adults with DS prior to the onset of A\u03b2 or tau pathology, suggesting they are associated with trisomy 21 and may serve as risk factors for DSAD. DSAD showed an earlier increase in markers of axonal and white matter pathology and earlier changes in markers potentially associated with cerebral amyloid angiopathy compared to ADAD. The unique features of DSAD may have important implications for treatment strategies in this population.", "doi": "10.1038/s41467-025-61054-z", "pmid": "40595720", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12214755"}, {"db": "pii", "key": "10.1038/s41467-025-61054-z"}], "notes": [], "created": "2025-10-23T13:09:26.368Z", "modified": "2025-10-23T13:09:27.449Z"}, {"entity": "publication", "iuid": "f8373abc0f9c463fbd2dc37473ef4129", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8373abc0f9c463fbd2dc37473ef4129.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8373abc0f9c463fbd2dc37473ef4129"}}, "title": "NAD depletion in skeletal muscle does not compromise muscle function or accelerate aging.", "authors": [{"family": "Chubanava", "given": "Sabina", "initials": "S"}, {"family": "Karavaeva", "given": "Iuliia", "initials": "I"}, {"family": "Ehrlich", "given": "Amy M", "initials": "AM"}, {"family": "Justicia", "given": "Roger M", "initials": "RM"}, {"family": "Basse", "given": "Astrid L", "initials": "AL"}, {"family": "Kulik", "given": "Ivan", "initials": "I"}, {"family": "Dalbram", "given": "Emilie", "initials": "E"}, {"family": "Ahwazi", "given": "Danial", "initials": "D"}, {"family": "Heaselgrave", "given": "Samuel R", "initials": "SR"}, {"family": "Tro\u0161t", "given": "Kajetan", "initials": "K"}, {"family": "Stocks", "given": "Ben", "initials": "B"}, {"family": "Hodek", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Rodrigues", "given": "Raissa N", "initials": "RN"}, {"family": "Havelund", "given": "Jesper F", "initials": "JF"}, {"family": "Schlabs", "given": "Farina L", "initials": "FL"}, {"family": "Larsen", "given": "Steen", "initials": "S"}, {"family": "Yonamine", "given": "Caio Y", "initials": "CY"}, {"family": "Henriquez-Olgu\u00edn", "given": "Carlos", "initials": "C"}, {"family": "Giustarini", "given": "Daniela", "initials": "D"}, {"family": "Rossi", "given": "Ranieri", "initials": "R"}, {"family": "Gerhart-Hines", "given": "Zachary", "initials": "Z"}, {"family": "Moritz", "given": "Thomas", "initials": "T"}, {"family": "Zierath", "given": "Juleen R", "initials": "JR"}, {"family": "Sakamoto", "given": "Kei", "initials": "K"}, {"family": "Jensen", "given": "Thomas E", "initials": "TE"}, {"family": "F\u00e6rgeman", "given": "Nils J", "initials": "NJ"}, {"family": "Lavery", "given": "Gareth G", "initials": "GG"}, {"family": "Deshmukh", "given": "Atul S", "initials": "AS"}, {"family": "Treebak", "given": "Jonas T", "initials": "JT"}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "Cell Metab.", "issn": "1932-7420", "volume": "37", "issue": "7", "pages": "1460-1481.e17", "issn-l": "1550-4131"}, "abstract": "Nicotinamide adenine dinucleotide (NAD) is a ubiquitous electron carrier essential for energy metabolism and post-translational modification of numerous regulatory proteins. Dysregulations of NAD metabolism are widely regarded as detrimental to health, with NAD depletion commonly implicated in aging. However, the extent to which cellular NAD concentration can decline without adverse consequences remains unclear. To investigate this, we generated a mouse model in which nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis was disrupted in adult skeletal muscle. The intervention resulted in an 85% reduction in muscle NAD+ abundance while maintaining tissue integrity and functionality, as demonstrated by preserved muscle morphology, contractility, and exercise tolerance. This absence of functional impairments was further supported by intact mitochondrial respiratory capacity and unaltered muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings suggest that NAD depletion does not contribute to age-related decline in skeletal muscle function.", "doi": "10.1016/j.cmet.2025.04.002", "pmid": "40311622", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1550-4131(25)00212-8"}], "notes": [], "created": "2025-11-18T12:03:31.339Z", "modified": "2025-11-18T12:03:31.344Z"}, {"entity": "publication", "iuid": "1402afcac4d540aca64003dddf86e9be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1402afcac4d540aca64003dddf86e9be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1402afcac4d540aca64003dddf86e9be"}}, "title": "A high polygenic risk score is associated with SSA/SSB antibody positivity and early onset in primary Sj\u00f6gren's disease.", "authors": [{"family": "Fugmann", "given": "Cecilia", "initials": "C", "orcid": "0009-0005-6078-8826", "researcher": {"href": "https://publications.scilifelab.se/researcher/afc6666ee2204df6b3f8f84f58f89c81.json"}}, {"family": "Reid", "given": "Sarah", "initials": "S"}, {"family": "Pucholt", "given": "Pascal", "initials": "P", "orcid": "0000-0003-3342-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/61a214ff2d494b568cb6da944e858acf.json"}}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Bj\u00f6rk", "given": "Albin", "initials": "A"}, {"family": "Mofors", "given": "Johannes", "initials": "J", "orcid": "0000-0003-1873-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/4db00a3d9a5b49e9b86cec83a76bbfe2.json"}}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Olsson", "given": "Peter", "initials": "P"}, {"family": "Mandl", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7143-7088", "researcher": {"href": "https://publications.scilifelab.se/researcher/b72a91b349c148c9b9b59028d079217d.json"}}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H", "orcid": "0000-0001-7871-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a0765b2c9d64087bd9ad36bd473968e.json"}}, {"family": "Magnusson Bucher", "given": "Sara", "initials": "S"}, {"family": "Johnsen", "given": "Svein Joar", "initials": "SJ", "orcid": "0000-0002-1591-9250", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fcaa1c5f1164f9d87e856a6eafb9e2c.json"}}, {"family": "Norheim", "given": "Katrine Br\u00e6kke", "initials": "KB"}, {"family": "Appel", "given": "Silke", "initials": "S", "orcid": "0000-0002-2199-2315", "researcher": {"href": "https://publications.scilifelab.se/researcher/eebec3871f18492b9f5047fd5add422b.json"}}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Jensen", "given": "Janicke Liaaen", "initials": "JL", "orcid": "0000-0003-4276-9611", "researcher": {"href": "https://publications.scilifelab.se/researcher/773434ab6d4845d187376dd8cc972d8b.json"}}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R", "orcid": "0000-0002-9588-0260", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6edb43a7da34bf9af85c876b1b8974a.json"}}, {"family": "Baecklund", "given": "Eva", "initials": "E", "orcid": "0000-0001-5033-0188", "researcher": {"href": "https://publications.scilifelab.se/researcher/203b156cd5b3427aac72efeb47a89c96.json"}}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "volume": "64", "issue": "7", "pages": "4341-4346", "issn-l": "1462-0324"}, "abstract": "To calculate a polygenic risk score (PRS) based on single nucleotide variants (SNVs) previously associated with primary Sj\u00f6gren's disease (SjD) with genome-wide significance and determine the genetic risk for SjD stratified by antibodies, sex and age at diagnosis.\n\nPatients with SjD (n = 1065) were genotyped using Illumina OmniExpressExome chip. Control genotype data were available (n = 7742). Two PRSs were constructed, one including HLA gene variants (n = 21 SNVs), and one without HLA (n = 18 SNVs). High PRS quartile (Q4) individuals were compared with low PRS (Q1-3).\n\nA high PRS was associated with SSA antibody-positive SjD (OR 9.16, 95% CI 7.75-10.85, P = 3.7 \u00d7 10-146), and strengthened in SjD positive for both SSA/SSB antibodies (OR 13.67, 95% CI 10.88-17.32, P = 4.6 \u00d7 10-108). High PRS classified SSA/SSB antibody-positive SjD with very good accuracy (AUC 0.86). PRS without HLA showed a weaker association with SSA/SSB positive SjD (OR 2.09, 95% CI 1.71-2.55, P = 6.4 \u00d7 10-13). Antibody negative SjD displayed a PRS similar to controls. Patients in the high PRS quartile were significantly younger at diagnosis, 48.9 \u00b1 14.9 vs 53.4 \u00b1 13.4 years in the low PRS quartiles (Q1-3), P = 2.2 \u00d7 10-6, and presented higher frequencies of ANA, SSA and SSA/SSB antibodies, P < 1 \u00d7 10-5.\n\nA high PRS is associated with SSA/SSB antibody positivity and early disease onset, both largely attributed to the weight of the HLA alleles. Integration of PRS with other biomarkers applied to clinical phenotypes could be a useful tool for disease risk stratification and treatment decisions.", "doi": "10.1093/rheumatology/keae693", "pmid": "39693120", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12212914"}, {"db": "pii", "key": "7927842"}], "notes": [], "created": "2025-07-02T12:44:52.822Z", "modified": "2025-11-14T11:07:58.575Z"}, {"entity": "publication", "iuid": "4f31e8206ab542c7a81fb00a1819e982", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f31e8206ab542c7a81fb00a1819e982.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f31e8206ab542c7a81fb00a1819e982"}}, "title": "Uncemented hip arthroplasty and denosumab: increased postoperative dipeptide concentrations and identification of potential new bone turnover biomarkers.", "authors": [{"family": "Kultima", "given": "Kim", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}, {"family": "Ashtiani", "given": "Saman Hosseini", "initials": "SH"}, {"family": "Erngren", "given": "Ida", "initials": "I"}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "Carlsson", "given": "Henrik", "initials": "H"}, {"family": "Herman", "given": "Stephanie", "initials": "S"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Mallmin", "given": "Hans", "initials": "H"}, {"family": "Hailer", "given": "Nils P", "initials": "NP"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "JBMR Plus", "issn": "2473-4039", "volume": "9", "issue": "7", "pages": "ziaf091", "issn-l": null}, "abstract": "Denosumab is a potent antagonist of RANKL and is widely used to treat severe postmenopausal osteoporosis. Using high-resolution mass spectrometry (HRMS), we aimed to identify molecular mediators associated with the rapid reactivation of osteoclasts following discontinuation of denosumab. In a previously reported randomized controlled trial, 64 patients undergoing uncemented total hip arthroplasty were randomized to receive 2 doses of 60 mg denosumab or placebo, administered 1-3 d and 6 mo postoperatively. Serum samples were analyzed using untargeted HRMS coupled with liquid chromatography, and bone turnover markers were assessed. Data were evaluated using linear mixed-effects models and machine learning techniques. After surgery, 83 metabolite features showed significant concentration changes (p < .0001). Denosumab-treated patients exhibited increased levels of the dipeptides di-L-phenylalanine, phenylalanylleucine, and alpha-Asp-Phe, and decreased levels of fibrinopeptide A and related peptides 24 mo after surgery. The oxidized peptide AP(Ox)GDRGEP(Ox)GPP(Ox)GP, derived from the collagen type I alpha 1 chain (COL1A1) and referred to as COL1A1-OxP, showed a strong correlation with the bone formation marker procollagen type 1 amino-terminal propeptide (P1NP) (p = 4.4E-83). Similarly, the tripeptide DL-alpha-aspartyl-DL-valyl-DL-proline (DVP) correlated highly with the bone resorption marker carboxy-terminal telopeptide of type 1 collagen (CTX) (p = 1.1E-222). P1NP and CTX levels were suppressed at 3, 6, and 12 mo postoperatively but exceeded baseline levels by 24 mo. Global metabolic shifts were observed postoperatively, with distinct profiles between treatment groups. The observed increase in specific dipeptides may reflect mechanisms contributing to rebound bone loss following denosumab withdrawal. Fibrinopeptide A and its analogs may play a protective role, while COL1A1-OxP and DVP represent potential new markers of bone turnover. These findings suggest metabolomics-based biomarkers could aid clinical decision-making by allowing earlier detection of rebound effects and guiding individualized treatment strategies after denosumab therapy. Clinical trial registration number: ClinicalTrials.gov, NCT01630941 (URL: https://clinicaltrials.gov/); European Union Clinical Trials Register (EU CTR), EudraCT No. 2011-001481-18 (https://www.clinicaltrialsregister.eu/).", "doi": "10.1093/jbmrpl/ziaf091", "pmid": "40584156", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12202150"}, {"db": "pii", "key": "ziaf091"}, {"db": "ClinicalTrials.gov", "key": "NCT01630941"}], "notes": [], "created": "2025-11-21T12:10:46.965Z", "modified": "2025-11-21T12:10:47.024Z"}, {"entity": "publication", "iuid": "fc2e7d5d9c71484a92eb5a8c6ae44616", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc2e7d5d9c71484a92eb5a8c6ae44616.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc2e7d5d9c71484a92eb5a8c6ae44616"}}, "title": "UYSD: a novel data repository accessible via public website for worldwide population frequencies of Y-SNP haplogroups.", "authors": [{"family": "Ralf", "given": "Arwin", "initials": "A", "orcid": "0000-0001-6052-0807", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d150af894044707baff5f5e9b70b556.json"}}, {"family": "Zandstra", "given": "Dion", "initials": "D", "orcid": "0000-0002-2197-6315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f58e22ae5aaf4049a605267f970f7334.json"}}, {"family": "van Wersch", "given": "Bram", "initials": "B"}, {"family": "K\u00f6ksal", "given": "Zehra", "initials": "Z", "orcid": "0000-0002-0914-9384", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb480dc4583d4dd893cc6d9efc1094ed.json"}}, {"family": "Larmuseau", "given": "Maarten H D", "initials": "MHD", "orcid": "0000-0002-5974-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/98a3deba601b4b31b0cda42fe888e30a.json"}}, {"family": "Rosa", "given": "Alexandra", "initials": "A"}, {"family": "Jobling", "given": "Mark A", "initials": "MA"}, {"family": "D'Amato", "given": "Maria E", "initials": "ME"}, {"family": "Courts", "given": "Cornelius", "initials": "C", "orcid": "0000-0002-9811-8482", "researcher": {"href": "https://publications.scilifelab.se/researcher/066aed6d98534e1b9a4a3cf860c13083.json"}}, {"family": "Gysi", "given": "Mario", "initials": "M"}, {"family": "Haas", "given": "Cordula", "initials": "C", "orcid": "0000-0001-8122-1427", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea35da82d5b143a89ace9e4a2aec1d64.json"}}, {"family": "Flores", "given": "Rodrigo", "initials": "R"}, {"family": "Neis", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8817-8668", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef17ea28f26d4e788df7d01737be765a.json"}}, {"family": "Wetton", "given": "Jon H", "initials": "JH", "orcid": "0000-0001-8337-4654", "researcher": {"href": "https://publications.scilifelab.se/researcher/877cefdb3bf04df6b0fb80b5f54a0f7a.json"}}, {"family": "Kiesler", "given": "Kevin", "initials": "K"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Azonbakin", "given": "Simon", "initials": "S"}, {"family": "B\u00f4\u017eikov\u00e1", "given": "Alexandra", "initials": "A"}, {"family": "Choma", "given": "Andrej", "initials": "A"}, {"family": "De Ungria", "given": "Maria Corazon", "initials": "MC"}, {"family": "Corradini", "given": "Beatrice", "initials": "B"}, {"family": "Cruz", "given": "Catarina", "initials": "C"}, {"family": "Dunkelmann", "given": "Bettina", "initials": "B"}, {"family": "Ferri", "given": "Gianmarco", "initials": "G"}, {"family": "Fleckhaus", "given": "Jan", "initials": "J"}, {"family": "Fragou", "given": "Domniki", "initials": "D"}, {"family": "Gaens", "given": "Noah", "initials": "N", "orcid": "0009-0006-4871-2287", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2d331932b3b475bb6cce4b090a6fc4b.json"}}, {"family": "Gon\u00e7alves", "given": "Rita", "initials": "R"}, {"family": "Hava\u0161 Augu\u0161tin", "given": "Dubravka", "initials": "D"}, {"family": "Helm", "given": "Katharina", "initials": "K"}, {"family": "H\u00f6lzl-M\u00fcller", "given": "Petra", "initials": "P"}, {"family": "Kaliszan", "given": "Micha\u0142", "initials": "M"}, {"family": "Kasu", "given": "Mohaimin", "initials": "M"}, {"family": "Kovatsi", "given": "Leda", "initials": "L"}, {"family": "Lesaoana", "given": "Mpasi", "initials": "M"}, {"family": "Mizuno", "given": "Natsuko", "initials": "N"}, {"family": "Neuhuber", "given": "Franz", "initials": "F"}, {"family": "Nov\u00e1\u010dkov\u00e1", "given": "Jana", "initials": "J"}, {"family": "\u0147u\u0148ukov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Pamjav", "given": "Horolma", "initials": "H"}, {"family": "Parson", "given": "Walther", "initials": "W", "orcid": "0000-0002-5692-2392", "researcher": {"href": "https://publications.scilifelab.se/researcher/84574a9a6f03419ea3a37a6dd0470082.json"}}, {"family": "Ramankulov", "given": "Yerlan", "initials": "Y"}, {"family": "Rangel Villalobos", "given": "H\u00e9ctor", "initials": "H"}, {"family": "R\u0119ba\u0142a", "given": "Krzysztof", "initials": "K"}, {"family": "Rootsi", "given": "Siiri", "initials": "S"}, {"family": "Salvador", "given": "Jazelyn", "initials": "J", "orcid": "0000-0003-0223-4532", "researcher": {"href": "https://publications.scilifelab.se/researcher/146e5af0a5f7419fab85f5a8cb41c40e.json"}}, {"family": "\u0160arac", "given": "Jelena", "initials": "J"}, {"family": "Steffen", "given": "Carolyn R", "initials": "CR"}, {"family": "Stenzl", "given": "Vlastimil", "initials": "V"}, {"family": "T\u00f6r\u00f6k", "given": "Tibor", "initials": "T"}, {"family": "Villems", "given": "Richard", "initials": "R"}, {"family": "Watahiki", "given": "Haruhiko", "initials": "H"}, {"family": "Zhabagin", "given": "Maxat", "initials": "M", "orcid": "0000-0003-3414-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/62105b830a024d5487243c2de9221778.json"}}, {"family": "Schneider", "given": "Peter M", "initials": "PM"}, {"family": "Kayser", "given": "Manfred", "initials": "M", "orcid": "0000-0002-4958-847X", "researcher": {"href": "https://publications.scilifelab.se/researcher/17043e6d1c884aaab77836046954459d.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "volume": "33", "issue": "7", "pages": "904-912", "issn-l": "1018-4813"}, "abstract": "For decades, there has been scientific interest in the variation and geographic distribution of paternal lineages associated with the human Y chromosome. However, the relevant data have been dispersed across numerous publications, making it difficult to consolidate. Additionally, understanding the relationships between different variants, and the tools used to analyze them, have evolved over time, further complicating efforts to harmonize this information. The Universal Y-SNP Database (UYSD) marks a substantial advancement by providing a comprehensive and accessible platform for Y-SNP and haplogroup data from populations around the world. UYSD harmonizes diverse datasets into a unified repository, facilitating the exploration of global Y-chromosomal variation. The platform handles data generated with both high- and low-throughput technology and is compatible with the automated analysis software tool, Yleaf v3. Key functionalities include the ability to: i) visualize haplogroup distributions on an interactive world map, ii) estimate haplogroup frequencies in geographic regions with sparse data through interpolation, and iii) display detailed phylogenetic trees of Y-chromosomal haplogroups. Currently, UYSD encompasses data from over 6,600 males across 27 populations. This dataset largely aligns with known global Y-haplogroup patterns, but also reveals unexplored finer-scale geographic variations. While the present dataset is largely European-centered, UYSD is designed for ongoing expansion by the scientific community, aiming to include more global data and higher-resolution population sequencing data. The platform thus offers valuable insights into human genetic diversity and migration patterns, serving several fields of research such as: human population genetics, genetic anthropology, ancient DNA analysis and forensic genetics.", "doi": "10.1038/s41431-025-01854-5", "pmid": "40341774", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12229683"}, {"db": "pii", "key": "10.1038/s41431-025-01854-5"}], "notes": [], "created": "2025-08-19T14:00:52.158Z", "modified": "2025-08-19T14:00:52.819Z"}, {"entity": "publication", "iuid": "0a9eb063435d44b8b5aaa1d5222991bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a9eb063435d44b8b5aaa1d5222991bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a9eb063435d44b8b5aaa1d5222991bf"}}, "title": "The spatiotemporal distribution of human pathogens in ancient Eurasia.", "authors": [{"family": "Sikora", "given": "Martin", "initials": "M", "orcid": "0000-0003-2818-8319", "researcher": {"href": "https://publications.scilifelab.se/researcher/a55c0205eb8c4673b75ce6b3f5d8f061.json"}}, {"family": "Canteri", "given": "Elisabetta", "initials": "E", "orcid": "0000-0001-9867-8247", "researcher": {"href": "https://publications.scilifelab.se/researcher/6396a091e3434959ab086de16d7c2004.json"}}, {"family": "Fernandez-Guerra", "given": "Antonio", "initials": "A", "orcid": "0000-0002-8679-490X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9dae21b2abe4de6947cd132f9948819.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "\u00c5gren", "given": "Rasmus", "initials": "R"}, {"family": "Hansson", "given": "Lena", "initials": "L"}, {"family": "Irving-Pease", "given": "Evan K", "initials": "EK", "orcid": "0000-0003-1940-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/02e144af5864412baa97c9fa5defbfd5.json"}}, {"family": "M\u00fchlemann", "given": "Barbara", "initials": "B", "orcid": "0000-0002-5314-8530", "researcher": {"href": "https://publications.scilifelab.se/researcher/50e4d63a643241dda76febe2c017ba17.json"}}, {"family": "Holtsmark Nielsen", "given": "Sofie", "initials": "S", "orcid": "0000-0001-7463-360X", "researcher": {"href": "https://publications.scilifelab.se/researcher/429c378d6a3c4701831cbe8f7de4d8c3.json"}}, {"family": "Scorrano", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-0887-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce84de79eddb4dcfae112d976ac424d3.json"}}, {"family": "Allentoft", "given": "Morten E", "initials": "ME", "orcid": "0000-0003-4424-3568", "researcher": {"href": "https://publications.scilifelab.se/researcher/561280c38047471c9797eb18af77b701.json"}}, {"family": "Valeur Seersholm", "given": "Frederik", "initials": "F"}, {"family": "Schroeder", "given": "Hannes", "initials": "H", "orcid": "0000-0002-6743-0270", "researcher": {"href": "https://publications.scilifelab.se/researcher/42fd7d83095f4b849b4f3f774632581d.json"}}, {"family": "Gaunitz", "given": "Charleen", "initials": "C"}, {"family": "Stenderup", "given": "Jesper", "initials": "J", "orcid": "0000-0002-6916-106X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dc81abfa4244623a43209c510a22f33.json"}}, {"family": "Vinner", "given": "Lasse", "initials": "L"}, {"family": "Jones", "given": "Terry C", "initials": "TC", "orcid": "0000-0003-1120-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9b36b89964bf5a57076d0bf5f8f52.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Sj\u00f6gren", "given": "Karl-G\u00f6ran", "initials": "KG"}, {"family": "Parkhill", "given": "Julian", "initials": "J", "orcid": "0000-0002-7069-5958", "researcher": {"href": "https://publications.scilifelab.se/researcher/29c1551bb9e84080b2a0078966487128.json"}}, {"family": "Fugger", "given": "Lars", "initials": "L", "orcid": "0000-0003-2883-3226", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa5f367384c4e8a954a2a80510da69d.json"}}, {"family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcd12137b4184a72a81c48d2926c5280.json"}}, {"family": "Kristiansen", "given": "Kristian", "initials": "K", "orcid": "0000-0003-2423-308X", "researcher": {"href": "https://publications.scilifelab.se/researcher/949ec2cfb14c4fae8d63de611b7456f7.json"}}, {"family": "Iversen", "given": "Astrid K N", "initials": "AKN", "orcid": "0000-0002-3507-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7fb936cc43444d6a3d2d51fb6c5417a.json"}}, {"family": "Willerslev", "given": "Eske", "initials": "E", "orcid": "0000-0002-7081-6748", "researcher": {"href": "https://publications.scilifelab.se/researcher/da0055841300427e85d9af38b1863ef1.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "643", "issue": "8073", "pages": "1011-1019", "issn-l": "0028-0836"}, "abstract": "Infectious diseases have had devastating effects on human populations throughout history, but important questions about their origins and past dynamics remain1. To create an archaeogenetic-based spatiotemporal map of human pathogens, we screened shotgun-sequencing data from 1,313 ancient humans covering 37,000 years of Eurasian history. We demonstrate the widespread presence of ancient bacterial, viral and parasite DNA, identifying 5,486 individual hits against 492 species from 136 genera. Among those hits, 3,384 involve known human pathogens2, many of which had not previously been identified in ancient human remains. Grouping the ancient microbial species according to their likely reservoir and type of transmission, we find that most groups are identified throughout the entire sampling period. Zoonotic pathogens are only detected from around 6,500 years ago, peaking roughly 5,000 years ago, coinciding with the widespread domestication of livestock3. Our findings provide direct evidence that this lifestyle change resulted in an increased infectious disease burden. They also indicate that the spread of these pathogens increased substantially during subsequent millennia, coinciding with the pastoralist migrations from the Eurasian Steppe4,5.", "doi": "10.1038/s41586-025-09192-8", "pmid": "40634616", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12286840"}, {"db": "pii", "key": "10.1038/s41586-025-09192-8"}], "notes": [], "created": "2025-07-29T06:47:03.177Z", "modified": "2025-07-29T06:47:05.159Z"}, {"entity": "publication", "iuid": "d9e41b0ebd4d4c0f863ca1f45ef267cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9e41b0ebd4d4c0f863ca1f45ef267cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9e41b0ebd4d4c0f863ca1f45ef267cd"}}, "title": "Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort.", "authors": [{"family": "Song", "given": "Xiya", "initials": "X"}, {"family": "Jin", "given": "Han", "initials": "H"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yuan", "given": "Meng", "initials": "M"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Sato", "given": "Yusuke", "initials": "Y"}, {"family": "Kume", "given": "Haruki", "initials": "H"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "21", "issue": "7", "pages": "e1011770", "issn-l": "1553-7390"}, "abstract": "Clear cell renal carcinoma (ccRCC) is the predominant form of kidney cancer, but the prognostic value of expression quantitative trait loci (eQTLs) remains underexplored, particularly in Asian populations.\n\nWe analyzed whole-exome sequencing and RNA sequencing data from 100 Japanese ccRCC patients to identify eQTLs. Multiple Cox proportional hazard models assessed survival associations, with validation in the Cancer Genome Atlas ccRCC cohort (n = 287).\n\nWe identified 805 eGenes and 4,558 cis-eQTLs in the Japanese cohort. Survival analysis revealed a total of 9 eGenes significantly associated with overall survival (FDR < 0.05). Further exploratory analysis were performed using 158 eGenes and 711 eQTLs (p-value <0.05) as potential prognostic signals. Among these, 223 eQTLs regulating 54 eGenes showed consistent prognostic effects at both expression and genetic levels. Cross-population validation identified eight eQTLs regulating 11 eGenes with reproducible survival associations across ethnicities, including a missense mutation in ERV3-1 and regulatory variants near ANKRD20A7P. These variants demonstrated consistent allelic effects on both gene expression and patient survival in both cohorts.", "doi": "10.1371/journal.pgen.1011770", "pmid": "40622919", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12233309"}, {"db": "pii", "key": "PGENETICS-D-25-00018"}], "notes": [], "created": "2025-11-28T10:53:53.218Z", "modified": "2025-11-28T10:53:53.295Z"}, {"entity": "publication", "iuid": "ef64425174314a07beeabf70289268e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef64425174314a07beeabf70289268e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef64425174314a07beeabf70289268e4"}}, "title": "Stepwise ATP translocation into the endoplasmic reticulum by human SLC35B1.", "authors": [{"family": "Gulati", "given": "Ashutosh", "initials": "A", "orcid": "0000-0003-0960-994X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b2b0aa7260492c8141083762e08125.json"}}, {"family": "Ahn", "given": "Do-Hwan", "initials": "DH", "orcid": "0009-0007-1596-5621", "researcher": {"href": "https://publications.scilifelab.se/researcher/e261a6911b7441259e69545e2dfa2d1f.json"}}, {"family": "Suades", "given": "Albert", "initials": "A"}, {"family": "Hult", "given": "Yurie", "initials": "Y"}, {"family": "Wolf", "given": "Gernot", "initials": "G"}, {"family": "Iwata", "given": "So", "initials": "S"}, {"family": "Superti-Furga", "given": "Giulio", "initials": "G", "orcid": "0000-0002-0570-1768", "researcher": {"href": "https://publications.scilifelab.se/researcher/792572f495f9444d8051c9767b601349.json"}}, {"family": "Nomura", "given": "Norimichi", "initials": "N", "orcid": "0000-0002-6330-2239", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b604af54f4a49f8a7884fbd70d99101.json"}}, {"family": "Drew", "given": "David", "initials": "D", "orcid": "0000-0001-8866-6349", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc19844f8147480fb0af2e437744131b.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "643", "issue": "8072", "pages": "855-864", "issn-l": "0028-0836"}, "abstract": "ATP generated in the mitochondria is exported by an ADP/ATP carrier of the SLC25 family1. The endoplasmic reticulum (ER) cannot synthesize ATP but must import cytoplasmic ATP to energize protein folding, quality control and trafficking2,3. It was recently proposed that a member of the nucleotide sugar transporter family, termed SLC35B1 (also known as AXER), is not a nucleotide sugar transporter but a long-sought-after ER importer of ATP4. Here we report that human SLC35B1 does not bind nucleotide sugars but indeed executes strict ATP/ADP exchange with uptake kinetics consistent with the import of ATP into crude ER microsomes. A CRISPR-Cas9 cell-line knockout demonstrated that SLC35B1 clusters with the most essential SLC transporters for cell growth, consistent with its proposed physiological function. We have further determined seven cryogenic electron microscopy structures of human SLC35B1 in complex with an Fv fragment and either bound to an ATP analogue or ADP in all major conformations of the transport cycle. We observed that nucleotides were vertically repositioned up to approximately 6.5 \u00c5 during translocation while retaining key interactions with a flexible substrate-binding site. We conclude that SLC35B1 operates by a stepwise ATP translocation mechanism, which is a previously undescribed model for substrate translocation by an SLC transporter.", "doi": "10.1038/s41586-025-09069-w", "pmid": "40399679", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12267056"}, {"db": "pii", "key": "10.1038/s41586-025-09069-w"}], "notes": [], "created": "2025-11-23T22:21:14.741Z", "modified": "2025-11-23T22:21:15.218Z"}, {"entity": "publication", "iuid": "3629fbdd20714549bab70ec73d783648", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3629fbdd20714549bab70ec73d783648.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3629fbdd20714549bab70ec73d783648"}}, "title": "Staphylococcus aureus From Prosthetic Joint Infections and Blood Cultures Display the Same Genetic Background.", "authors": [{"family": "S\u00f6derquist", "given": "Bo", "initials": "B", "orcid": "0000-0001-5939-2932", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc4111ee338c4c52a17efbd0cfbab766.json"}}, {"family": "Wildeman", "given": "Peter", "initials": "P"}, {"family": "Stegger", "given": "Marc", "initials": "M"}, {"family": "Stenmark", "given": "Bianca", "initials": "B"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "APMIS", "issn": "1600-0463", "volume": "133", "issue": "7", "pages": "e70038", "issn-l": "0903-4641"}, "abstract": "Hematogenous prosthetic joint infections (PJIs) are primarily associated with Staphylococcus aureus, and there is a 30%-40% risk of contracting a hematogenous PJI following an S. aureus bacteremia. The aim of this study was to investigate whether identical strains of S. aureus were present in each patient from a cohort with both bacteremia and PJI and to explore the genomic differences between paired isolates obtained from blood cultures and tissue biopsies. All patients with a PJI and a temporally concomitant bacteremia due to S. aureus from 2005 to 2020 were included. Paired isolates of S. aureus from tissue biopsies and blood cultures were subjected to whole-genome sequencing. Twenty-four episodes of PJI were identified in 23 patients. All pairwise isolates from individual patients belonged to the same multilocus sequence type, clonal complex, and core genome multilocus sequence typing (cgMLST) complex type. The median number of single nucleotide polymorphisms (SNPs) in the conserved core genomes between the pairwise isolates was 3. In conclusion, identical cgMLST complex types and low levels of SNP differences between paired isolates of S. aureus from blood cultures and tissue biopsies suggest hematogenous seeding in all cases of PJI in this cohort.", "doi": "10.1111/apm.70038", "pmid": "40611607", "labels": {"Clinical Genomics": "Service", "Clinical Genomics \u00d6rebro": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12232108"}], "notes": [], "created": "2025-11-19T15:14:27.699Z", "modified": "2025-11-19T15:18:10.169Z"}, {"entity": "publication", "iuid": "c80bf1b852f04e6292b1e46a6eda7dde", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c80bf1b852f04e6292b1e46a6eda7dde.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c80bf1b852f04e6292b1e46a6eda7dde"}}, "title": "Small and Large Extracellular Vesicles From Human Preovulatory Follicular Fluid Display Distinct ncRNA Cargo Profiles and Differential Effects on KGN Granulosa Cells.", "authors": [{"family": "Varik", "given": "Inge", "initials": "I", "orcid": "0000-0003-1740-1022", "researcher": {"href": "https://publications.scilifelab.se/researcher/1528edffe440442f917a1e9b8d4f7309.json"}}, {"family": "Saretok", "given": "Katariina Johanna", "initials": "KJ", "orcid": "0009-0004-7370-5463", "researcher": {"href": "https://publications.scilifelab.se/researcher/a899d8117b0744aeb4c7675aa59aa64e.json"}}, {"family": "Rosenberg", "given": "Kristine", "initials": "K", "orcid": "0009-0006-0504-2818", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1bebda565f44bf897594d984ab023d2.json"}}, {"family": "Quintero", "given": "Ileana", "initials": "I", "orcid": "0000-0001-7040-1289", "researcher": {"href": "https://publications.scilifelab.se/researcher/208e9727fc004f10acca1e3ed3244366.json"}}, {"family": "Puhka", "given": "Maija", "initials": "M", "orcid": "0000-0002-6445-1017", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2506b7c86d543ed9c6b7309d7eaab59.json"}}, {"family": "Volkova", "given": "Nataliia", "initials": "N", "orcid": "0000-0003-1832-6116", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba8529d8ed54a239bcaa34490cd99a3.json"}}, {"family": "Tro\u0161in", "given": "Aleksander", "initials": "A"}, {"family": "Guazzi", "given": "Paolo", "initials": "P"}, {"family": "Velthut-Meikas", "given": "Agne", "initials": "A", "orcid": "0000-0003-1927-9016", "researcher": {"href": "https://publications.scilifelab.se/researcher/3371af7256714f478d42af5cf868134d.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "J Extracell Vesicles", "issn": "2001-3078", "volume": "14", "issue": "7", "pages": "e70119", "issn-l": "2001-3078"}, "abstract": "Follicular fluid extracellular vesicles (FF EVs) facilitate communication between oocytes and somatic cells within the ovarian follicle, playing a pivotal role in follicular development. This study highlights the molecular and functional distinctions between small (SEV) and large (LEV) FF EV subpopulations, revealing their specialised regulatory roles in granulosa cell (GC) biology and their consequential impact on ovarian function. Single-EV profiling uncovered distinct tetraspanin distributions, with LEVs containing a lower proportion of CD9/CD63/CD81-positive particles compared to SEVs. Fluorescent labelling confirmed uptake of both SEVs and LEVs by GCs, supporting their capacity to impact cellular behaviour. Functionally, LEVs increased testosterone production by GCs, whilst SEVs had no effect on steroid hormone secretion, suggesting a specific role for LEVs in androgen biosynthesis. Transcriptomic analysis revealed extensive SEV-induced changes in GC gene expression, affecting pathways involved in transcription, TGF-\u03b2 signalling, extracellular matrix (ECM) remodelling and cell cycle regulation. In contrast, LEVs elicited minimal transcriptional changes, primarily modulating genes associated with immune regulation and oxidative stress defence. Small RNA sequencing further revealed distinct non-coding RNA (ncRNA) profiles, with SEVs enriched in miRNAs targeting pathways critical for GC differentiation, whilst LEVs carried higher levels of piRNAs implicated in maintaining genomic stability. These findings advance our understanding of FF EV-mediated intercellular communication and underscore the importance of investigating EV subpopulations independently.", "doi": "10.1002/jev2.70119", "pmid": "40620085", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12230353"}], "notes": [], "created": "2025-11-28T10:40:26.293Z", "modified": "2025-11-28T10:40:26.691Z"}, {"entity": "publication", "iuid": "f2093e58779b4746bef0e24ae100356e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2093e58779b4746bef0e24ae100356e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2093e58779b4746bef0e24ae100356e"}}, "title": "Significant Associations Between Blood Cell Counts and a Large Number of Salivary Cytokines, Chemokines, and Growth Factors.", "authors": [{"family": "Eriksson", "given": "Lars B", "initials": "LB", "orcid": "0009-0002-1818-7347", "researcher": {"href": "https://publications.scilifelab.se/researcher/44d17c21be93409fb4d5bc5de121b497.json"}}, {"family": "Eriksson", "given": "Mats", "initials": "M", "orcid": "0000-0002-3178-4210", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfcf6caaeeea422997c259d802e7e6f8.json"}}, {"family": "Gordh", "given": "Torsten", "initials": "T", "orcid": "0000-0003-1454-3148", "researcher": {"href": "https://publications.scilifelab.se/researcher/de40b19a854f4dda88986d2e00e8f091.json"}}, {"family": "Larsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-3161-0402", "researcher": {"href": "https://publications.scilifelab.se/researcher/2276de26382b402aa384ac231f30f156.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Journal of Interferon & Cytokine Research", "issn": "1557-7465", "volume": "45", "issue": "7", "pages": "254-262", "issn-l": "1079-9907"}, "abstract": "The association between local oral inflammation and cardiovascular risk has been extensively studied, with results indicating a bidirectional relationship. The aim of the present study was to investigate the associations between blood cells and a large number of salivary cytokines, chemokines, and growth factors. The study consisted of 165 individuals who were referred to the Oral and Maxillofacial Surgery clinic at Falun County hospital, Sweden, for surgical removal of impacted lower third molar. The study subjects did not have any known inflammatory disorders. Complete blood cell counts were analyzed using the routine laboratory at Falun Hospital, Falun, Sweden. Proteomic analysis of 92 inflammation-related protein biomarkers in saliva was performed using a multiplex proximity extension assay. After adjustment for multiplicity testing using the false discovery rate approach, there remained significant association between several saliva cytokines, chemokines, and growth factors and white blood cell counts (n = 19), neutrophil counts (n = 18), erythrocyte counts (n = 13), hemoglobin concentrations (n = 20), erythrocyte volume fractions (n = 22), and platelet counts (n = 12). There are several significant associations between local inflammatory cytokines in the oral cavity and blood cell parameters indicating a relationship between local and systemic inflammatory activity.", "doi": "10.1089/jir.2025.0048", "pmid": "40392700", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-25T19:22:32.201Z", "modified": "2026-02-11T12:57:18.356Z"}, {"entity": "publication", "iuid": "e0be7d4528ff466fb50acb46d72fb250", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0be7d4528ff466fb50acb46d72fb250.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0be7d4528ff466fb50acb46d72fb250"}}, "title": "STING Agonist Drug Delivery by Bacterial Extracellular Vesicles Induces Synergistic Immuno-Oncology Responses and Efficient Inhibition of Tumour Growth.", "authors": [{"family": "L\u00f6tvall", "given": "Jan", "initials": "J"}, {"family": "Ordouzadeh", "given": "Negar", "initials": "N"}, {"family": "Crescitelli", "given": "Rossella", "initials": "R", "orcid": "0000-0002-1714-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d4b955f26ca4a679deb090e30d0ccf1.json"}}, {"family": "Deshmukh", "given": "Meghshree", "initials": "M"}, {"family": "Jin", "given": "Tao", "initials": "T"}, {"family": "Park", "given": "Kyong-Su", "initials": "KS", "orcid": "0000-0003-0902-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e308b29fe144b49f4db27f4b819c18.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "J Extracell Vesicles", "issn": "2001-3078", "volume": "14", "issue": "7", "pages": "e70117", "issn-l": "2001-3078"}, "abstract": "Bacterial extracellular vesicles are spherical, nanosized structures with lipid bilayer membranes and can suppress tumour growth in cancer models. However, the efficacy of some of these models is limited. One potential way to enhance their effects is by loading the bacterial vesicles with immunostimulatory molecules. We have here utilised synthetic bacterial vesicles (SyBV), previously shown to have anti-tumour effects but with reduced side effects. We hypothesized that loading SyBV with a STimulator of InterferoN Genes (STING) agonist can enhance anti-tumour effects. SyBV were generated from Escherichia coli membranes through cell breakdown induced by lysozyme and ionic stress. The produced nanovesicles encapsulated the STING agonist (SyBVSTING). SyBVSTING synergistically activated dendritic cells, leading to enhanced production of Interferon-\u03b2. Furthermore, in vivo experiments showed that immunisation with SyBVSTING synergistically suppresses melanoma and colon cancer growth by increasing the tumour infiltration of T cells. Intratumoural or subcutaneous injection of the SyBV resulted in retention in the tumour tissue over 24 h, but with some distribution to local lymph nodes. A toxicology experiment resulted in no histopathological concerns with SyBVSTING. These findings show that SyBV loaded with a STING agonist synergistically enhance anti-tumour immunity and may be a promising clinical immuno-oncology tool.", "doi": "10.1002/jev2.70117", "pmid": "40620049", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12230345"}], "notes": [], "created": "2025-11-05T13:54:01.033Z", "modified": "2025-11-05T13:54:01.099Z"}, {"entity": "publication", "iuid": "b5b7416273ac451f87d00bf6e94d1d70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5b7416273ac451f87d00bf6e94d1d70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5b7416273ac451f87d00bf6e94d1d70"}}, "title": "Rescue of loss-of-function long QT syndrome-associated mutations in KV7.1/KCNE1 by the endocannabinoid N-arachidonoyl-L-serine (ARA-S).", "authors": [{"family": "Hiniesto-I\u00f1igo", "given": "Irene", "initials": "I"}, {"family": "Sridhar", "given": "Akshay", "initials": "A"}, {"family": "Louradour", "given": "Julien", "initials": "J", "orcid": "0000-0002-0649-4975", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f26502cc6a74826b18e6b0b44ce711b.json"}}, {"family": "De la Cruz", "given": "Alicia", "initials": "A"}, {"family": "Lundholm", "given": "Siri", "initials": "S"}, {"family": "Jauregi-Miguel", "given": "Amaia", "initials": "A"}, {"family": "Giannetti", "given": "Federica", "initials": "F", "orcid": "0000-0002-1785-5529", "researcher": {"href": "https://publications.scilifelab.se/researcher/090b646375e94881b957c9ded9320cb2.json"}}, {"family": "Sala", "given": "Luca", "initials": "L", "orcid": "0000-0002-4129-6632", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bdf4fd6470c46f1be65535eae085f44.json"}}, {"family": "Odening", "given": "Katja E", "initials": "KE", "orcid": "0000-0001-6999-841X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa57ed2bc334eebada9236568f3ce81.json"}}, {"family": "Larsson", "given": "H Peter", "initials": "HP", "orcid": "0000-0002-1688-2525", "researcher": {"href": "https://publications.scilifelab.se/researcher/56340cab3dcd434ab18c86a949206e16.json"}}, {"family": "Ottosson", "given": "Nina E", "initials": "NE", "orcid": "0000-0003-2159-6731", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e54acedff4e45bbaa661096b33f8f7c.json"}}, {"family": "Liin", "given": "Sara I", "initials": "SI", "orcid": "0000-0001-8493-0114", "researcher": {"href": "https://publications.scilifelab.se/researcher/e82a591108f24dcabf50779d88fc8844.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "British Journal of Pharmacology", "issn": "1476-5381", "issn-l": "0007-1188", "volume": "182", "issue": "13", "pages": "2861-2877"}, "abstract": "Congenital long QT syndrome (LQTS) involves genetic mutations affecting ion channels, leading to a prolonged QT interval and increased risk of potentially lethal ventricular arrhythmias. Mutations in the genes encoding KV7.1/KCNE1 are the most frequent, with channel loss-of-function contributing to LQTS. The endocannabinoid N-arachidonoyl-L-serine (ARA-S) has been shown to facilitate activation of wild type KV7.1/KCNE1 channels and to counteract a prolonged QT interval in isolated guinea pig hearts. In this study, we examine the ability of ARA-S to facilitate activation of LQTS-associated mutations, in various regions of the channel, and hence to counteract loss-of-function.\n\nThe two-electrode voltage clamp technique on Xenopus oocytes expressing human KV7.1/KCNE1 channels was used to investigate the effects of ARA-S in 20 LQTS type 1-associated mutations distributed across the channel. Thereafter, different electrophysiology was used to assess ARA-S effects in mammalian cells.\n\nARA-S enhanced the function of all mutated channels by shifting V50 and increasing current amplitude. However, the magnitude of effect varied, related to whether mutations were in one of the two putative ARA-S binding sites on the channel as suggested by molecular dynamics simulations. ARA-S displayed translational potential by facilitating channel opening in mammalian cells and shortening the action potential duration in cardiomyocytes.\n\nThis study demonstrates the rescuing capability of ARA-S on a diverse set of LQTS mutants. These insights may aid in developing drug compounds using ARA-S sites and mechanisms and guide interpretation of which LQTS mutants respond well to such compounds.", "doi": "10.1111/bph.70008", "pmid": "40083204", "labels": {"Chemical Biology Consortium Sweden": "Collaborative", "Clinical Genomics": "Service", "Clinical Genomics Link\u00f6ping": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-18T09:19:04.181Z", "modified": "2025-11-28T11:33:53.532Z"}, {"entity": "publication", "iuid": "e581c7c77c5240b2877e994a10432e7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e581c7c77c5240b2877e994a10432e7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e581c7c77c5240b2877e994a10432e7d"}}, "title": "Refolding of the Deinococcus Radiodurans phytochrome photosensory module and an extended backbone resonance assignment by solution NMR", "authors": [{"family": "Vrhovac", "given": "Lidija S", "initials": "LS"}, {"family": "Levkovets", "given": "Maria", "initials": "M"}, {"family": "Orekhov", "given": "Vladislav Y", "initials": "VY"}, {"family": "Westenhoff", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-6961-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1519bb234b43c6a13833b04e6720b8.json"}}], "type": "journal-article", "published": "2025-07-00", "journal": {"title": "Protein Expression and Purification", "issn": "1046-5928", "volume": "231", "pages": "106699", "issn-l": null}, "abstract": null, "doi": "10.1016/j.pep.2025.106699", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:01:41.229Z", "modified": "2025-11-27T08:01:41.319Z"}, {"entity": "publication", "iuid": "86407d846e3944b5a9f63453e0d17e22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86407d846e3944b5a9f63453e0d17e22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86407d846e3944b5a9f63453e0d17e22"}}, "title": "Position-Specific Substitution in Cellulose Ethers Studied by DNP Enhanced Solid-State NMR Spectroscopy.", "authors": [{"family": "Karlsson", "given": "Hampus", "initials": "H"}, {"family": "Pinon", "given": "Arthur C", "initials": "AC"}, {"family": "Karlson", "given": "Leif", "initials": "L"}, {"family": "Wassenius", "given": "Helena", "initials": "H"}, {"family": "Iselau", "given": "Frida", "initials": "F"}, {"family": "Schantz", "given": "Staffan", "initials": "S", "orcid": "0000-0002-0136-4856", "researcher": {"href": "https://publications.scilifelab.se/researcher/d80e21a364f4412db2e0b837853e870c.json"}}, {"family": "Even\u00e4s", "given": "Lars", "initials": "L", "orcid": "0000-0002-6580-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d5546ed87b0480aae72d8574db96911.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Magn Reson Chem", "issn": "0749-1581", "volume": "63", "issue": "8", "pages": "560-568", "issn-l": null}, "abstract": "Ethyl hydroxyethyl cellulose (EHEC) and methyl ethyl hydroxyethyl cellulose (MEHEC) are hydrophilic cellulose ethers commonly employed as rheology modifiers in diverse industrial applications. The performance of these polymers, and their resistance to degradation by various cellulase enzymes, depends on their intricate molecular structure. Distribution of the etherifying groups, within the anhydroglucose units and along the polymer chain, is the key property to control. However, characterizing such structural properties is challenging, necessitating the development of novel analysis methods. In this study, we demonstrate the application of solid-state nuclear magnetic resonance (NMR) spectroscopy, enhanced by dynamic nuclear polarization (DNP), for this purpose. We prove that the hydrophilic EHEC and MEHEC samples are homogenously swelled in D2O/H2O-based radical solutions, a necessity to ensure uniform DNP enhancement throughout the material. And we illustrate how the high sensitivity enhancements obtained can be used to perform selective, J-coupling-based C1 to C2 transfer experiments to measure the fraction of substituted C2 positions in these cellulose ethers. Moreover, with further refinement, the methodology outlined in this work holds promise for elucidating C3-specific substitution patterns.", "doi": "10.1002/mrc.5535", "pmid": "40404341", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12223920"}], "notes": [], "created": "2025-11-27T08:01:55.917Z", "modified": "2025-11-27T13:37:28.616Z"}, {"entity": "publication", "iuid": "9fa3893f925743b0b5f018566f37b870", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fa3893f925743b0b5f018566f37b870.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fa3893f925743b0b5f018566f37b870"}}, "title": "Plasma metabolite profiles of meat intake and their association with cardiovascular disease risk: A population-based study in Swedish cohorts.", "authors": [{"family": "Arage", "given": "Getachew", "initials": "G"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF"}, {"family": "Ra\u0161o", "given": "Luka Marko", "initials": "LM"}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Ericson", "given": "Ulrika", "initials": "U"}, {"family": "Larsson", "given": "Susanna C", "initials": "SC"}, {"family": "Engel", "given": "Hanna", "initials": "H"}, {"family": "Baldanzi", "given": "Gabriel", "initials": "G"}, {"family": "Pertiwi", "given": "Kamalita", "initials": "K"}, {"family": "Sayols-Baixeras", "given": "Sergi", "initials": "S"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Ahmad", "given": "Shafqat", "initials": "S"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Metabolism", "issn": "1532-8600", "volume": "168", "pages": "156188", "issn-l": "0026-0495"}, "abstract": "Higher meat intake has been associated with adverse health outcomes, including cardiovascular disease (CVD). This study investigated plasma metabolites associated with meat intake and their relation with cardiometabolic biomarkers, subclinical CVD markers, and incident CVD.\n\nAssociations between self-reported meat intake and 1272 plasma metabolites were investigated in the SCAPIS cohort (n = 8,819; ages 50-64). Meat-associated metabolites were further examined for relation with subclinical CVD markers in the POEM cohort (n = 502; age 50) and incident CVD in the EpiHealth cohort (n = 2,278; ages 45-75; 107 incident cases over 9.6 years follow-up). Meat intake was categorized into white, unprocessed red, and processed red meat. Linear regression analyzed associations between meat intake, metabolites and cardiometabolic biomarkers, and subclinical CVD markers, while Cox models evaluated association between meat-associated metabolites and incident CVD.\n\nAfter correction for multiple testing, 458, 368, and 403 metabolites were associated with white, unprocessed red, and processed red meat, respectively. Processed red meat-associated metabolites were associated with higher levels of fasting insulin, hemoglobin A1c, and lipoprotein(a), and were inversely associated with maximal oxygen consumption. Two metabolites, 1-palmitoyl-2-linoleoyl-GPE (16:0/18:2) (hazard ratios (HR: 1.32; 95 % CI: 1.08, 1.62)) and glutamine degradant (HR: 1.35; 95 % CI: 1.07, 1.72), that were inversely associated with intake of all meat types, were also associated with a higher risk of incident CVD.\n\nThis study provides comprehensive analysis of self-reported meat intake and plasma metabolites. The findings may enhance our understanding of the relationship between meat intake and CVD, and provide insights into underlying mechanisms.", "doi": "10.1016/j.metabol.2025.156188", "pmid": "40081615", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0026-0495(25)00057-5"}], "notes": [], "created": "2025-11-28T10:44:10.272Z", "modified": "2025-11-28T10:44:10.282Z"}, {"entity": "publication", "iuid": "aff8eefa55834c5dbf68ed03a5ce4737", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aff8eefa55834c5dbf68ed03a5ce4737.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aff8eefa55834c5dbf68ed03a5ce4737"}}, "title": "Music style preferences and well-being: A genetic perspective", "authors": [{"family": "Bratchenko", "given": "Anastasiia", "initials": "A"}, {"family": "Xia", "given": "Penghao", "initials": "P"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Mosing", "given": "Miriam A", "initials": "MA"}, {"family": "Ull\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Wesseldijk", "given": "Laura W", "initials": "LW"}], "type": "journal-article", "published": "2025-07-00", "journal": {"title": "Personality and Individual Differences", "issn": "0191-8869", "volume": "241", "pages": "113162", "issn-l": null}, "abstract": null, "doi": "10.1016/j.paid.2025.113162", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:44:25.633Z", "modified": "2025-11-28T10:44:25.665Z"}, {"entity": "publication", "iuid": "3e287d397db04ea4a121c1a2cbd8a106", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e287d397db04ea4a121c1a2cbd8a106.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e287d397db04ea4a121c1a2cbd8a106"}}, "title": "Museomics unravels cryptic diversity in an endemic group of New Guinean songbirds.", "authors": [{"family": "Blom", "given": "Mozes Pil Kyu", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Bloom-Quinn", "given": "Saphira", "initials": "S", "orcid": "0009-0000-6457-8264", "researcher": {"href": "https://publications.scilifelab.se/researcher/766f9c58f99a4263a464c1138001ab83.json"}}, {"family": "Marki", "given": "Petter Zahl", "initials": "PZ", "orcid": "0000-0001-6990-9915", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ac768b5d0d540988dfeca8f83cf41cf.json"}}, {"family": "Koane", "given": "Bonny", "initials": "B", "orcid": "0000-0001-6770-5126", "researcher": {"href": "https://publications.scilifelab.se/researcher/966dc22dd4ca456294f7f2ed0a853c87.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "21", "issue": "7", "pages": "20240611", "issn-l": "1744-9561"}, "abstract": "Deciphering cryptic diversity can have substantial implications for our understanding of evolutionary processes and species conservation. Birds are arguably among the best studied organismal groups, but even in avian clades there are some genera that have not been thoroughly surveyed. This is particularly true for taxa that occur in hyperdiverse biogeographic regions. In this study, we focus on an endemic group of New Guinean birds, the jewel-babblers (genus: Ptilorrhoa), and study the diversification history of all known taxa. We assemble a de novo genome using linked-read sequencing and genomic data for 40 historical specimens. Both phylogenomic and population-genomic analyses strongly support the recovery of a cryptic species and shed new light on the diversification history of this group. The blue jewel-babbler (Ptilorrhoa caerulescens) is a paraphyletic species complex and P. c. nigricrissus is more closely related to the phenotypically distinct and sexually dimorphic P. geislerorum, than to other P. caerulescens subspecies. These findings demonstrate that even in well-studied groups such as birds, cryptic diversity can still be a prevalent reality. Moreover, by deciphering cryptic diversity, we shed new light on the processes driving speciation within Ptilorrhoa and the need to potentially revise the taxonomic status of all subspecies.", "doi": "10.1098/rsbl.2024.0611", "pmid": "40664242", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2025-07-18T10:24:09.986Z", "modified": "2025-07-18T10:24:10.511Z"}, {"entity": "publication", "iuid": "85abd43001ea47faba9f42368da29448", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85abd43001ea47faba9f42368da29448.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85abd43001ea47faba9f42368da29448"}}, "title": "Idiopathic inflammatory myopathies lack neutralising autoantibodies to type- I, II and III interferons", "authors": [{"family": "Behere", "given": "Anish", "initials": "A", "orcid": "0000-0002-2424-3475", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c155029e86d458cad39ed4c2670c880.json"}}, {"family": "Mildner", "given": "Hedvig", "initials": "H"}, {"family": "Peralta Garcia", "given": "Irene", "initials": "I"}, {"family": "P\u00e9rez Bucio", "given": "C\u00e9sar", "initials": "C"}, {"family": "Lundberg", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}, {"family": "Horuluoglu", "given": "Begum", "initials": "B"}, {"family": "Landegren", "given": "Nils", "initials": "N"}], "type": "journal-article", "published": "2025-07-00", "journal": {"title": "RMD Open", "issn": "2056-5933", "volume": "11", "issue": "3", "pages": "e005836", "issn-l": "2056-5933"}, "abstract": null, "doi": "10.1136/rmdopen-2025-005836", "pmid": null, "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-03T09:44:26.353Z", "modified": "2025-12-03T09:44:26.437Z"}, {"entity": "publication", "iuid": "816528b47a0d4fec91f70570d313e5bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/816528b47a0d4fec91f70570d313e5bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/816528b47a0d4fec91f70570d313e5bc"}}, "title": "Gut microbiota mediates SREBP-1c-driven hepatic lipogenesis and steatosis in response to zero-fat high-sucrose diet.", "authors": [{"family": "Bergentall", "given": "Mattias", "initials": "M"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Sun", "given": "Chuqing", "initials": "C"}, {"family": "Henricsson", "given": "Marcus", "initials": "M"}, {"family": "Khan", "given": "Muhammad Tanweer", "initials": "MT"}, {"family": "Manner\u00e5s Holm", "given": "Louise", "initials": "L"}, {"family": "Olsson", "given": "Lisa", "initials": "L"}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO"}, {"family": "Molinaro", "given": "Antonio", "initials": "A"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Caesar", "given": "Robert", "initials": "R"}, {"family": "Nieuwdorp", "given": "Max", "initials": "M"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Mol Metab", "issn": "2212-8778", "volume": "97", "pages": "102162", "issn-l": "2212-8778"}, "abstract": "Sucrose-rich diets promote hepatic de novo lipogenesis (DNL) and steatosis through interactions with the gut microbiota. However, the role of sugar-microbiota dynamics in the absence of dietary fat remains unclear. This study aimed to investigate the effects of a high-sucrose, zero-fat diet (ZFD) on hepatic steatosis and host metabolism in conventionally raised (CONVR) and germ-free (GF) mice.\n\nCONVR and GF mice were fed a ZFD, and hepatic lipid accumulation, gene expression, and metabolite levels were analyzed. DNL activity was assessed by measuring malonyl-CoA levels, expression of key DNL enzymes, and activation of the transcription factor SREBP-1c. Metabolomic analyses of portal vein plasma identified microbiota-derived metabolites linked to hepatic steatosis. To further examine the role of SREBP-1c, its hepatic expression was knocked down using antisense oligonucleotides in CONVR ZFD-fed mice.\n\nThe gut microbiota was essential for sucrose-induced DNL and hepatic steatosis. In CONVR ZFD-fed mice, hepatic fat accumulation increased alongside elevated expression of genes encoding DNL enzymes, higher malonyl-CoA levels, and upregulation of SREBP-1c. Regardless of microbiota status, ZFD induced fatty acid elongase and desaturase gene expression and increased hepatic monounsaturated fatty acids. Metabolomic analyses identified microbiota-derived metabolites associated with hepatic steatosis. SREBP-1c knockdown in CONVR ZFD-fed mice reduced hepatic steatosis and suppressed fatty acid synthase expression.\n\nSucrose-microbiota interactions and SREBP-1c are required for DNL and hepatic steatosis in the absence of dietary fat. These findings provide new insights into the complex interplay between diet, gut microbiota, and metabolic regulation.", "doi": "10.1016/j.molmet.2025.102162", "pmid": "40345386", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12145984"}, {"db": "pii", "key": "S2212-8778(25)00069-9"}], "notes": [], "created": "2025-05-26T07:51:16.266Z", "modified": "2025-11-14T11:06:18.789Z"}, {"entity": "publication", "iuid": "e43fd2012d994dabbae3508be896f740", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e43fd2012d994dabbae3508be896f740.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e43fd2012d994dabbae3508be896f740"}}, "title": "Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors.", "authors": [{"family": "Zheng", "given": "Zejia", "initials": "Z"}, {"family": "Gustavsson", "given": "David J I", "initials": "DJI"}, {"family": "Zheng", "given": "Dan", "initials": "D"}, {"family": "Holmin", "given": "Felix", "initials": "F"}, {"family": "Fal\u00e5s", "given": "Per", "initials": "P"}, {"family": "Wil\u00e9n", "given": "Britt-Marie", "initials": "BM"}, {"family": "Modin", "given": "Oskar", "initials": "O"}, {"family": "Persson", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "J Environ Manage", "issn": "1095-8630", "volume": "388", "pages": "125972", "issn-l": null}, "abstract": "Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m2\u00b7d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m2\u00b7d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.", "doi": "10.1016/j.jenvman.2025.125972", "pmid": "40449445", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0301-4797(25)01948-6"}], "notes": [], "created": "2025-11-28T10:44:00.290Z", "modified": "2025-11-28T10:44:00.301Z"}, {"entity": "publication", "iuid": "74bc759fdf384e7095a0514342639673", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74bc759fdf384e7095a0514342639673.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74bc759fdf384e7095a0514342639673"}}, "title": "Genome-Wide Adaptation to a Complex Environmental Gradient in a Keystone Phytoplankton Species.", "authors": [{"family": "Pinseel", "given": "Eveline", "initials": "E", "orcid": "0000-0002-1801-2187", "researcher": {"href": "https://publications.scilifelab.se/researcher/9abc32586e93470797e0b832287d5d8d.json"}}, {"family": "Ruck", "given": "Elizabeth C", "initials": "EC"}, {"family": "Nakov", "given": "Teofil", "initials": "T"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Kourtchenko", "given": "Olga", "initials": "O"}, {"family": "Kremp", "given": "Anke", "initials": "A"}, {"family": "Pinder", "given": "Matthew I M", "initials": "MIM", "orcid": "0000-0003-4407-0214", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6d9f52178249f3995c3d276fbc2728.json"}}, {"family": "Roberts", "given": "Wade R", "initials": "WR"}, {"family": "Sj\u00f6qvist", "given": "Conny", "initials": "C"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M", "orcid": "0000-0001-7989-696X", "researcher": {"href": "https://publications.scilifelab.se/researcher/278d2a953da240aa8dd58062eb8f8ff3.json"}}, {"family": "Godhe", "given": "Anna", "initials": "A"}, {"family": "Hahn", "given": "Matthew W", "initials": "MW"}, {"family": "Alverson", "given": "Andrew J", "initials": "AJ", "orcid": "0000-0003-1241-2654", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cfcd9fbf6d349d9b9a26579b6c112c3.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "13", "pages": "e17817", "issn-l": "0962-1083"}, "abstract": "Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experiment that has played out over the past 8000 years in one of the world's largest brackish water bodies: the colonisation of the Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To this end, we combined target capture of the entire nuclear genome with pooled shotgun sequencing, and showed that the method performs well on both cultures and single cells. Genotype-environment association analyses identified > 1000 genes with signals of selection in response to major environmental gradients in the Baltic Sea, which apart from salinity, include marked differences in temperature and nutrient supply. Locally adapted genes were related to diverse metabolic processes, including signal transduction, cell cycle, DNA methylation and maintenance of homeostasis. The locally adapted genes showed significant overlap with salinity-responsive genes identified in a laboratory common garden experiment, suggesting the Baltic salinity gradient contributes to local adaptation of S. marinoi. Taken together, our data show that local adaptation of phytoplankton to complex coastal environments, which are characterised by a multitude of environmental gradients, is driven by widespread changes in diverse metabolic pathways and functions.", "doi": "10.1111/mec.17817", "pmid": "40491268", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12186713"}], "notes": [], "created": "2025-11-05T13:58:54.365Z", "modified": "2025-11-05T13:58:54.571Z"}, {"entity": "publication", "iuid": "109d08b7139947779a648f3aea19ed7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/109d08b7139947779a648f3aea19ed7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/109d08b7139947779a648f3aea19ed7a"}}, "title": "Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management", "authors": [{"family": "S\u00f6derquist", "given": "Linus", "initials": "L", "orcid": "0000-0002-9894-4119", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a0c370d6402423284ea40a2f51179ae.json"}}, {"family": "Joffard", "given": "Nina", "initials": "N", "orcid": "0000-0003-3712-6080", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae9d351d1d14a129908a73c37ff5728.json"}}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a8063a48a446a7947d55f9900894a6.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P", "orcid": "0000-0001-8580-4291", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59e048cc6a4159a1829885b370d978.json"}}, {"family": "Karrenberg", "given": "Sophie", "initials": "S", "orcid": "0000-0002-7146-588X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a982636b44f4b93b7ec0bd64e5d6bfb.json"}}, {"family": "Sletvold", "given": "Nina", "initials": "N", "orcid": "0000-0002-9868-3449", "researcher": {"href": "https://publications.scilifelab.se/researcher/e342483c6e3f44c29453f9bc5ce5bb05.json"}}], "type": "journal-article", "published": "2025-07-00", "journal": {"title": "Ecography", "issn": "0906-7590", "volume": "2025", "issue": "7", "issn-l": null}, "abstract": null, "doi": "10.1111/ecog.07628", "pmid": null, "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:33:58.539Z", "modified": "2025-11-28T10:51:06.434Z"}, {"entity": "publication", "iuid": "3f5a358c368e430a9e7513509782e6dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f5a358c368e430a9e7513509782e6dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f5a358c368e430a9e7513509782e6dd"}}, "title": "Genetic markers associated with bone strength and density in Rhode Island Red laying hens.", "authors": [{"family": "Yue", "given": "Qiaoxian", "initials": "Q"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Wilson", "given": "Peter W", "initials": "PW"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Schmutz", "given": "Matthias", "initials": "M"}, {"family": "Benavides", "given": "Cristina", "initials": "C"}, {"family": "Dominguez-Gasca", "given": "Nazaret", "initials": "N"}, {"family": "Sanchez-Rodriguez", "given": "Estefania", "initials": "E"}, {"family": "Rodriguez-Navarro", "given": "Alejandro B", "initials": "AB"}, {"family": "Dunn", "given": "Ian C", "initials": "IC"}, {"family": "de Koning", "given": "Dirk-Jan", "initials": "DJ"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Poult. Sci.", "issn": "1525-3171", "volume": "104", "issue": "7", "pages": "105246", "issn-l": "0032-5791"}, "abstract": "Damage to the keel bone in commercial laying hens represent one of the greatest welfare issues in laying hens. This study aims to identify the DNA markers and candidate genes for bone strength and density traits in a Rhode Island Red laying hen population. We conducted genome-wide association studies (GWAS) on bone quality traits using a sample of 925 Rhode Island Red laying hens genotyped with a genotyping array consisting of 60 000 DNA markers. With a univariate linear mixed model, we identified 52 suggestive genetic markers located within 28 candidate genes that are associated with the humerus, keel, and tibia strength and density. We also found overlaps between the GWAS results for medullary bone score and tibia strength and density with published quantitative trait loci (QTL) for eggshell effective layer thickness and abdominal fat weight, respectively. Heritability estimates for the humerus stiffness, tibia stiffness, medullary bone score and minor bone diameter ranged from 0.21 to 0.34. Annotation term enrichment analysis of genes within 2 Megabases of suggestive markers found that mTOR signalling pathway, tryptophan metabolism, TGF-\u03b2 signalling pathway, and apoptosis were significantly enriched. These loci do not overlap previously published associations, and thus appear to be novel.", "doi": "10.1016/j.psj.2025.105246", "pmid": "40339236", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12138422"}, {"db": "pii", "key": "S0032-5791(25)00488-2"}], "notes": [], "created": "2025-09-08T07:15:20.568Z", "modified": "2025-09-08T07:15:20.576Z"}, {"entity": "publication", "iuid": "e5847a1ccb154e33b092ebbb525beec4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5847a1ccb154e33b092ebbb525beec4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5847a1ccb154e33b092ebbb525beec4"}}, "title": "Genetic and Environmental Effects on Parent-Rated Adaptive Behaviour in Infancy.", "authors": [{"family": "Halkola", "given": "Hanna", "initials": "H", "orcid": "0000-0002-2474-0682", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7f3e7c9f77645678b82928153a60bd1.json"}}, {"family": "Viktorsson", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-2727-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/465e2969410c4109aaa466735d26002b.json"}}, {"family": "Jones", "given": "Emily J H", "initials": "EJH"}, {"family": "Charman", "given": "Tony", "initials": "T", "orcid": "0000-0003-1993-6549", "researcher": {"href": "https://publications.scilifelab.se/researcher/bec55e31a33d40f688e58a0436ae92c9.json"}}, {"family": "Falck-Ytter", "given": "Terje", "initials": "T"}, {"family": "Bussu", "given": "Giorgia", "initials": "G"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Dev Sci", "issn": "1467-7687", "volume": "28", "issue": "4", "pages": "e70041", "issn-l": null}, "abstract": "Adaptive behaviour refers to the everyday skills that individuals are expected to have to function independently, based on their age and societal norms. Currently, we know little about the role of genetic and environmental factors in parent-rated adaptive behaviours in early infancy. The aim of this study was to investigate the aetiological factors that influence individual variability in different adaptive behaviour domains at 5 months, and the degree of genetic and environmental influences that are unique and shared across these domains. We analysed data from the Vineland Adaptive Behaviour Scale (VABS-II) motor domain and combined domain of socialization and communication (social-communication) using a multivariate twin modelling approach. Participants were a community sample of monozygotic and dizygotic twins assessed at 5 months of age (n = 594). The results show high shared environmental influence on both motor (0.67) and social-communication (0.78) domains with 45% shared variance. Both had low, but significant heritability estimates (0.21 and 0.12, respectively) but did not share genetic variance. No statistically significant associations were found between polygenic scores for autism, ADHD, schizophrenia, depression, and bipolar disorder, and either of the adaptive behaviours measured here. Our results highlight the importance of shared environmental factors in the development of social-communication and motor skills in infancy, whether it is through social interaction with caregivers, or the stimuli and opportunities presented at home. SUMMARY: During development structural arm length representation is underestimated, while the functional arm length representation is overestimated. Underestimation of structural arm length is driven by an underestimation of hand length, as forearm length is accurate. Structural hand length is underestimated, supporting that underestimation of hand length is a characteristic of human body representation. The opposite pattern of results between structural and functional arm representation suggests the existence of multiple independent representations of the body.", "doi": "10.1111/desc.70041", "pmid": "40537989", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12179425"}], "notes": [], "created": "2025-09-08T11:34:03.298Z", "modified": "2025-09-08T11:34:03.476Z"}, {"entity": "publication", "iuid": "e0d1dc8451a44076825e43da0bc8506c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0d1dc8451a44076825e43da0bc8506c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0d1dc8451a44076825e43da0bc8506c"}}, "title": "Ex vivo drug responses and molecular profiles of 597 pediatric acute lymphoblastic leukemia patients.", "authors": [{"family": "Enblad", "given": "Anna Pia", "initials": "AP"}, {"family": "Krali", "given": "Olga", "initials": "O"}, {"family": "Gezelius", "given": "Henrik", "initials": "H"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "Frost", "given": "Britt-Marie", "initials": "BM"}, {"family": "Ryh\u00e4nen", "given": "Samppa", "initials": "S"}, {"family": "Fl\u00e6gstad", "given": "Trond", "initials": "T"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur G", "initials": "\u00d3G"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Hemasphere", "issn": "2572-9241", "volume": "9", "issue": "7", "pages": "e70176", "issn-l": null}, "abstract": "Ex vivo drug response profiling is emerging as a valuable tool for identifying drug resistance mechanisms and advancing precision medicine in hematological cancers. However, the functional impact of dysregulation of the epigenome and transcriptome in this context remains poorly understood. In this study, we combined ex vivo drug sensitivity profiling with transcriptomic and epigenomic analyses in diagnostic samples from 597 pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. Ex vivo resistance to antimetabolites (e.g., cytarabine, thioguanine), glucocorticoids (e.g., dexamethasone, prednisolone), and doxorubicin was independently associated with reduced relapse-free survival (P < 0.05). Molecular profiling identified pretreatment DNA methylation and gene expression patterns distinguishing resistant from sensitive cases, revealing key drug resistance signatures. These included aberrant expression of genes related to heme metabolism (e.g., ATPV06A) and KRAS signaling (e.g., GS02). Notably, we also observed atypical expression of genes usually restricted to T cells and other immune cells (e.g., ITK) in resistant BCP-ALL cells. Our findings demonstrate that ex vivo drug response patterns are predictive of clinical outcomes and reflect intrinsic molecular states associated with drug tolerance. This integrative multi-omics approach highlights potential therapeutic targets and underscores the value of functional precision medicine in identifying treatment vulnerabilities in pediatric ALL.", "doi": "10.1002/hem3.70176", "pmid": "40727946", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12301861"}, {"db": "pii", "key": "HEM370176"}], "notes": [], "created": "2025-09-08T07:17:19.785Z", "modified": "2025-11-28T10:40:21.057Z"}, {"entity": "publication", "iuid": "fcdd1bf8581f4524b781381b94a66ef9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcdd1bf8581f4524b781381b94a66ef9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcdd1bf8581f4524b781381b94a66ef9"}}, "title": "Evaluating IL1RA-Autoantibodies Across SARS-CoV-2-Related Diseases.", "authors": [{"family": "Behere", "given": "Anish", "initials": "A", "orcid": "0000-0002-2424-3475", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c155029e86d458cad39ed4c2670c880.json"}}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Cederholm", "given": "Axel", "initials": "A"}, {"family": "Cavalli", "given": "Marco", "initials": "M", "orcid": "0000-0003-1143-1431", "researcher": {"href": "https://publications.scilifelab.se/researcher/e35211c06385459baee12101121d2a15.json"}}, {"family": "Yalcinkaya", "given": "Ahmet", "initials": "A"}, {"family": "COVID\u2010HGE", "given": "", "initials": ""}, {"family": "Bastard", "given": "Paul", "initials": "P"}, {"family": "Puel", "given": "Anne", "initials": "A", "orcid": "0000-0003-2603-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bcef4c205904e5db9e36f3aadaa13bb.json"}}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Landegren", "given": "Nils", "initials": "N"}], "type": "letter", "published": "2025-07-00", "journal": {"title": "Scand. J. Immunol.", "issn": "1365-3083", "volume": "102", "issue": "1", "pages": "e70039", "issn-l": "0300-9475"}, "abstract": null, "doi": "10.1111/sji.70039", "pmid": "40556349", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12188108"}], "notes": [], "created": "2025-09-10T08:20:51.920Z", "modified": "2025-09-10T08:20:52.252Z"}, {"entity": "publication", "iuid": "cbe37784889b4f2fa20d782492f9f6d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbe37784889b4f2fa20d782492f9f6d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbe37784889b4f2fa20d782492f9f6d6"}}, "title": "Chemical exposomics in biobanked plasma samples and associations with breast cancer risk factors", "authors": [{"family": "Edlund", "given": "Jessica", "initials": "J"}, {"family": "Sdougkou", "given": "Kalliroi", "initials": "K", "orcid": "0000-0001-9463-655X", "researcher": {"href": "https://publications.scilifelab.se/researcher/975451f91bf44300a7e4b0dbb91ea401.json"}}, {"family": "Papazian", "given": "Stefano", "initials": "S", "orcid": "0000-0003-2538-8702", "researcher": {"href": "https://publications.scilifelab.se/researcher/5de990c59ec4460e92c414dbc0ed0b16.json"}}, {"family": "Wu", "given": "Wendy Yi Ying", "initials": "WYY"}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications.scilifelab.se/researcher/f275a68856cb459ebbc933b18c3e315d.json"}}, {"family": "Harlid", "given": "Sophia", "initials": "S", "orcid": "0000-0001-8540-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a824f2687b460890ae6d9ef40d97c9.json"}}], "type": "journal-article", "published": "2025-07-00", "journal": {"title": "J Expo Sci Environ Epidemiol", "issn": "1559-064X", "issn-l": null, "volume": "35", "issue": "4", "pages": "567-577"}, "abstract": "The chemical exposome includes exposure to numerous environmental and endogenous molecules, many of which have been linked to reproductive outcomes due to their endocrine-disrupting properties. As several breast cancer risk factors, including age and parity, are related to reproduction, it is imperative to investigate the interplay between such factors and the chemical exposome prior to conducting large scale exposome-based breast cancer studies.\n\nThis pilot study aimed to provide an overview of the chemical exposome in plasma samples from healthy women and identify associations between environmental exposures and three risk factors for breast cancer: age, parity, and age at menarche.\n\nPlasma samples (n = 161), were selected based on reproductive history from 100 women participating in the Northern Sweden Health and Disease Study, between 1987 and 2006. Samples were analyzed by liquid chromatography high-resolution mass spectrometry (LC-HRMS) for 77 priority target analytes including contaminants and hormones, with simultaneous untargeted profiling of the chemical exposome and metabolome. Linear mixed effects models were applied to test associations between risk factors and chemical levels.\n\nFifty-five target analytes were detected in at least one individual and over 94,000 untargeted features were detected across all samples. Among untargeted features, 430 could be annotated and were broadly classified as environmental (246), endogenous (167) or ambiguous (17). Applying mixed effect models to features detected in at least 70% of the samples (16,778), we found seven targeted analytes (including caffeine and various per- and poly-fluoroalkyl substances) and 38 untargeted features, positively associated with age. The directionality of these associations reversed for parity, decreasing with increasing births. Seven separate targeted analytes were associated with age at menarche.\n\nThis study demonstrates how a comprehensive chemical exposome approach can be used to inform future research prioritization regarding associations between known and unknown substances, reproduction, and breast cancer risk.\n\nThis study illustrates how chemical exposomics of long-term stored blood samples offers valuable insights to discover chemical exposures and their potential links to disease in humans, particularly those related to reproduction and breast cancer risk factors.", "doi": "10.1038/s41370-024-00736-0", "pmid": "39643621", "labels": {"Exposomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41370-024-00736-0"}], "notes": [], "created": "2024-12-09T08:15:03.382Z", "modified": "2025-09-12T11:18:28.103Z"}, {"entity": "publication", "iuid": "8da9f8bb7e024de5b9d404a6ed360d99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8da9f8bb7e024de5b9d404a6ed360d99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8da9f8bb7e024de5b9d404a6ed360d99"}}, "title": "Angiopoietin-TIE2 feedforward circuit promotes PIK3CA-driven venous malformations.", "authors": [{"family": "Kraft", "given": "Marle", "initials": "M", "orcid": "0000-0002-3523-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bac6d144f4143b7ad9ad0a9058d95a0.json"}}, {"family": "Schoofs", "given": "Hans", "initials": "H", "orcid": "0000-0003-3429-912X", "researcher": {"href": "https://publications.scilifelab.se/researcher/32c662013aae42298c0776802f3628fa.json"}}, {"family": "Petkova", "given": "Milena", "initials": "M", "orcid": "0000-0002-7186-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/458b9dbc408c4118b97be343da8b3b49.json"}}, {"family": "Andrade", "given": "Jorge", "initials": "J", "orcid": "0000-0002-4577-8620", "researcher": {"href": "https://publications.scilifelab.se/researcher/477b341b9d0048dab408f6106fc5b915.json"}}, {"family": "Grosso", "given": "Ana Rita", "initials": "AR", "orcid": "0000-0001-6974-4209", "researcher": {"href": "https://publications.scilifelab.se/researcher/07a33297431f417eaabbdbe477c06c4f.json"}}, {"family": "Benedito", "given": "Rui", "initials": "R", "orcid": "0000-0003-2458-3055", "researcher": {"href": "https://publications.scilifelab.se/researcher/e15242bf49384c309118be8db7abe19a.json"}}, {"family": "De Roo", "given": "An-Katrien", "initials": "AK", "orcid": "0000-0002-0000-1260", "researcher": {"href": "https://publications.scilifelab.se/researcher/108ee3be589741e28c1e676b248ec20f.json"}}, {"family": "Boon", "given": "Laurence M", "initials": "LM", "orcid": "0000-0001-8273-3328", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bdedae62ce74bd08d22df3bd007e76a.json"}}, {"family": "Vikkula", "given": "Miikka", "initials": "M", "orcid": "0000-0002-6236-338X", "researcher": {"href": "https://publications.scilifelab.se/researcher/14ec2db8cf364aa383bcac2ebf64cc39.json"}}, {"family": "Kapp", "given": "Friedrich G", "initials": "FG", "orcid": "0000-0002-2729-6177", "researcher": {"href": "https://publications.scilifelab.se/researcher/392ca5f5f1914e0585da18619bda2c00.json"}}, {"family": "H\u00e4gerling", "given": "Ren\u00e9", "initials": "R", "orcid": "0000-0002-6830-2043", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc9254578d4a4ee8b7d24b2e4a3025ab.json"}}, {"family": "Potente", "given": "Michael", "initials": "M", "orcid": "0000-0002-5689-0036", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2fbc439106a4708b03a324aa5499f47.json"}}, {"family": "M\u00e4kinen", "given": "Taija", "initials": "T", "orcid": "0000-0002-9338-1257", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf99a0589d1f4532b532bfc575edaada.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Nat Cardiovasc Res", "issn": "2731-0590", "volume": "4", "issue": "7", "pages": "801-820", "issn-l": null}, "abstract": "Venous malformations (VMs) are vascular anomalies lacking curative treatments, often caused by somatic PIK3CA mutations that hyperactivate the PI3K\u03b1-AKT-mTOR signaling pathway. Here, we identify a venous-specific signaling circuit driving disease progression, where excessive PI3K\u03b1 activity amplifies upstream TIE2 receptor signaling through autocrine and paracrine mechanisms. In Pik3caH1047R-driven VM mouse models, single-cell transcriptomics and lineage tracking revealed clonal expansion of mutant endothelial cells with a post-capillary venous phenotype, characterized by suppression of the AKT-inhibited FOXO1 and its target genes, including the TIE2 antagonist ANGPT2. An imbalance in TIE2 ligands, likely exacerbated by aberrant recruitment of smooth muscle cells producing the agonist ANGPT1, increased TIE2 activity in both mouse and human VMs. While mTOR blockade had limited effects on advanced VMs in mice, inhibiting TIE2 or ANGPT effectively suppressed their growth. These findings uncover a PI3K-FOXO1-ANGPT-TIE2 circuit as a core driver of PIK3CA-related VMs and highlight TIE2 as a promising therapeutic target.", "doi": "10.1038/s44161-025-00655-9", "pmid": "40410415", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12259471"}, {"db": "pii", "key": "10.1038/s44161-025-00655-9"}], "notes": [], "created": "2025-11-18T11:56:53.465Z", "modified": "2025-11-28T10:48:02.845Z"}, {"entity": "publication", "iuid": "25984d72fd804514b958fd6c22e02cf3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25984d72fd804514b958fd6c22e02cf3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25984d72fd804514b958fd6c22e02cf3"}}, "title": "Pretreatment with estrogen enhances the therapeutic efficacy of cardiac progenitor cells and improves cardiac recovery in a failing heart model", "authors": [{"family": "Aydos", "given": "Dunya", "initials": "D"}, {"family": "Basak", "given": "Neslihan", "initials": "N"}, {"family": "Olgar", "given": "Yusuf", "initials": "Y"}, {"family": "Genc", "given": "Kardelen", "initials": "K"}, {"family": "Uyar", "given": "Recep", "initials": "R"}, {"family": "Ekim", "given": "Okan", "initials": "O"}, {"family": "Sych", "given": "Taras", "initials": "T", "orcid": "0000-0002-7330-9063", "researcher": {"href": "https://publications.scilifelab.se/researcher/d104a7d8096b4a4ab2a9fe618489fc7e.json"}}, {"family": "Aksoy", "given": "Zeynep Busra", "initials": "ZB"}, {"family": "Kosker", "given": "Tugba Aktan", "initials": "TA"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Bitirim", "given": "Ceylan Verda", "initials": "CV", "orcid": "0000-0002-7979-0679", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d725c869b534c469501b6b7e629ab50.json"}}], "type": "posted-content", "published": "2025-06-28", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.06.25.661574", "pmid": null, "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:49:13.818Z", "modified": "2025-12-18T19:13:38.397Z"}, {"entity": "publication", "iuid": "5c24b2e6125b42d29feff583fc4f1da4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c24b2e6125b42d29feff583fc4f1da4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c24b2e6125b42d29feff583fc4f1da4"}}, "title": "Mosaic loss of chromosome Y in blood is associated with male susceptibility for idiopathic pulmonary fibrosis.", "authors": [{"family": "Bjurling", "given": "Josefin", "initials": "J", "orcid": "0009-0006-7675-429X", "researcher": {"href": "https://publications.scilifelab.se/researcher/442f42e953684bab8d50784c29c6e151.json"}}, {"family": "Chavkin", "given": "Nicholas W", "initials": "NW"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Thel", "given": "Mark C", "initials": "MC"}, {"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Kim", "given": "John S", "initials": "JS"}, {"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Ma", "given": "Shwu-Fan", "initials": "SF", "orcid": "0000-0002-3058-9480", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2346407b4814a0abe0415d60ec2b9fe.json"}}, {"family": "Martinez", "given": "Fernando J", "initials": "FJ", "orcid": "0000-0002-2412-3182", "researcher": {"href": "https://publications.scilifelab.se/researcher/81b4019b58504b3e84a228b7419d90a4.json"}}, {"family": "Anstrom", "given": "Kevin", "initials": "K"}, {"family": "Noth", "given": "Imre", "initials": "I"}, {"family": "Walsh", "given": "Kenneth", "initials": "K", "orcid": "0000-0001-7580-2276", "researcher": {"href": "https://publications.scilifelab.se/researcher/f06edcdf9ef24a1d9cadcb8ea3a30fff.json"}}, {"family": "Forsberg", "given": "Lars A", "initials": "LA", "orcid": "0000-0002-1701-755X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac2d8e983764a82982118b6db84029e.json"}}], "type": "journal article", "published": "2025-06-28", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "246", "issn-l": null}, "abstract": "The prevalence of idiopathic pulmonary fibrosis (IPF) is higher in men, a previously not well-understood sex bias that extends across severity and mortality. Mosaic loss of chromosome Y (mLOY) in blood is male-specific and associated with adverse outcomes, including IPF. In mLOY-mice, enhanced TGF-\u03b2 signaling has been reported to contribute to fibrosis of internal organs, but it is not known if such mLOY-driven disease mechanism exists in humans.\n\nWe focused here on IPF in men to investigate if mLOY contributes to fibrotic disease processes in humans, as demonstrated in mouse models. To this end, we investigated mLOY as a risk factor for male IPF in epidemiological and clinical datasets, as well as by re-analyses of published single-cell RNA sequencing (scRNAseq) datasets.\n\nWe find that men with mLOY in blood display an increased risk for IPF diagnosis and death caused by IPF in UK Biobank, and that mLOY is associated with reduced lung functions in two cohorts. Approximately 80% of the male excess in IPF prevalence occurs in the group of men with mLOY in blood leukocytes. Notably, scRNAseq analyses support that pulmonary leukocytes with Y loss exacerbate IPF by upregulating profibrotic genes and enhancing TGF-\u03b2 signaling.\n\nOur results contribute to explaining the profound sex bias in IPF and replicate a mLOY-driven profibrotic disease mechanism first identified in mice. Male IPF patients with mLOY represent a subgroup that may benefit from treatment with TGF-\u03b2 inhibitors.", "doi": "10.1038/s43856-025-00966-9", "pmid": "40581694", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12206232"}, {"db": "pii", "key": "10.1038/s43856-025-00966-9"}], "notes": [], "created": "2025-11-28T10:47:51.945Z", "modified": "2025-11-28T10:47:52.216Z"}, {"entity": "publication", "iuid": "eee4ee4c42964130a2cc8776b8228c33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eee4ee4c42964130a2cc8776b8228c33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eee4ee4c42964130a2cc8776b8228c33"}}, "title": "Out-of-Anatolia: Cultural and genetic interactions during the Neolithic expansion in the Aegean.", "authors": [{"family": "Koptekin", "given": "Dilek", "initials": "D", "orcid": "0000-0003-2664-5774", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e95decb115f488ca913d25d1174711a.json"}}, {"family": "Aydo\u011fan", "given": "Ay\u00e7a", "initials": "A", "orcid": "0000-0003-0171-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/191b5ce05f6343e4825ef86d5703f8df.json"}}, {"family": "Karamurat", "given": "Cansu", "initials": "C", "orcid": "0000-0002-3596-9036", "researcher": {"href": "https://publications.scilifelab.se/researcher/04c6c312d10a4d5a8c806b8550709016.json"}}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE", "orcid": "0000-0003-0653-4292", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0ad7b1c36784c0092fd82f6d792c4bb.json"}}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB", "orcid": "0000-0003-3964-3065", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d3f195bbd4998b69ca678f1ff9fb7.json"}}, {"family": "Kazanc\u0131", "given": "D Deniz", "initials": "DD", "orcid": "0000-0002-8333-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f28aea0bd7e4bb7b6ac3d8843cae17f.json"}}, {"family": "Do\u011fu", "given": "Ay\u00e7a K\u00fc\u00e7\u00fckakda\u011f", "initials": "AK", "orcid": "0000-0001-6208-4092", "researcher": {"href": "https://publications.scilifelab.se/researcher/5599e1dd0d34404cb490ae2da3213b17.json"}}, {"family": "Kaptan", "given": "Damla", "initials": "D", "orcid": "0000-0001-7953-1354", "researcher": {"href": "https://publications.scilifelab.se/researcher/d969faa7d65045298f3ef289d849dfe8.json"}}, {"family": "Gemici", "given": "Hasan Can", "initials": "HC", "orcid": "0000-0003-4424-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/e57ecd0264874105bb04cf9eb0cfce25.json"}}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E", "orcid": "0000-0002-8194-0277", "researcher": {"href": "https://publications.scilifelab.se/researcher/c319bee9c36a4e6a88dee29c8edc9d0d.json"}}, {"family": "Moots", "given": "Hannah M", "initials": "HM", "orcid": "0000-0002-6637-6321", "researcher": {"href": "https://publications.scilifelab.se/researcher/5105354f578c480ba144061ffbb49bf5.json"}}, {"family": "Umurtak", "given": "G\u00fcls\u00fcn", "initials": "G", "orcid": "0000-0003-0493-1868", "researcher": {"href": "https://publications.scilifelab.se/researcher/797ff752aeb54d4f9ea67dc624e25380.json"}}, {"family": "Duru", "given": "Refik", "initials": "R"}, {"family": "Fidan", "given": "Erkan", "initials": "E", "orcid": "0000-0002-6777-927X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cfca389b2f9421391c08cac15b6577b.json"}}, {"family": "\u00c7evik", "given": "\u00d6zlem", "initials": "\u00d6", "orcid": "0000-0001-5442-3744", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecbb50dfe46c4ed4b3a2894df441dee4.json"}}, {"family": "Erdo\u011fu", "given": "Bur\u00e7in", "initials": "B"}, {"family": "Korkut", "given": "Taner", "initials": "T", "orcid": "0000-0001-9810-231X", "researcher": {"href": "https://publications.scilifelab.se/researcher/50588d8226e34cb6a6572eecdb51690d.json"}}, {"family": "Kn\u00fcsel", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-2506-3652", "researcher": {"href": "https://publications.scilifelab.se/researcher/02d89a57c7ef4d7a8681d49fb13b9b97.json"}}, {"family": "Haddow", "given": "Scott", "initials": "S", "orcid": "0000-0002-3970-7447", "researcher": {"href": "https://publications.scilifelab.se/researcher/433ccd36adc742fc984c9db5f0bc5c25.json"}}, {"family": "Larsen", "given": "Clark Spencer", "initials": "CS", "orcid": "0000-0002-6905-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/9319177bbfe04b6d8c491ee0083c807f.json"}}, {"family": "\u00d6zbal", "given": "Rana", "initials": "R", "orcid": "0000-0001-6765-2765", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ad960fa098e477eac6f367ce0e659c9.json"}}, {"family": "Gerritsen", "given": "Fokke", "initials": "F", "orcid": "0000-0002-6665-1928", "researcher": {"href": "https://publications.scilifelab.se/researcher/d447abfa3d8b42bd85d56693a1c9cbb0.json"}}, {"family": "\u00d6zdo\u011fan", "given": "Eylem", "initials": "E", "orcid": "0000-0003-1314-3695", "researcher": {"href": "https://publications.scilifelab.se/researcher/501515d068784d6b8d38c053e6860ae5.json"}}, {"family": "Akbaba", "given": "Ali", "initials": "A", "orcid": "0000-0001-6755-6546", "researcher": {"href": "https://publications.scilifelab.se/researcher/757adfca411c4168a0a51c5765852aa9.json"}}, {"family": "Usanmaz", "given": "Uygar Ozan", "initials": "UO", "orcid": "0000-0002-7013-3023", "researcher": {"href": "https://publications.scilifelab.se/researcher/b125bb77ca0e4b4d8a91c7a0a0c1706b.json"}}, {"family": "Derici", "given": "Yasin Cemre", "initials": "YC", "orcid": "0000-0001-5631-9588", "researcher": {"href": "https://publications.scilifelab.se/researcher/548691e4be8e416ba6b7ba0ef06f6910.json"}}, {"family": "U\u00e7mazo\u011flu", "given": "Mine", "initials": "M", "orcid": "0009-0000-9101-6929", "researcher": {"href": "https://publications.scilifelab.se/researcher/79197c3193164647b40444bf386d0c6d.json"}}, {"family": "Jay", "given": "Flora", "initials": "F", "orcid": "0000-0001-5884-4730", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8c74aed5a8a4976be210b133fb905f5.json"}}, {"family": "\u00d6zdo\u011fan", "given": "Mehmet", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "Erdal", "given": "Y\u0131lmaz Selim", "initials": "YS", "orcid": "0000-0001-8143-8159", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f77cf0f580409f98004f71cf99c001.json"}}, {"family": "Malaspinas", "given": "Anna-Sapfo", "initials": "AS", "orcid": "0000-0003-1001-7511", "researcher": {"href": "https://publications.scilifelab.se/researcher/883d44be08be42188c3423a3498ef898.json"}}, {"family": "Atakuman", "given": "\u00c7i\u011fdem", "initials": "\u00c7", "orcid": "0000-0001-8675-6236", "researcher": {"href": "https://publications.scilifelab.se/researcher/acefd01d35f04a0b99350ec4828adfcb.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F", "orcid": "0000-0003-0443-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/676b684e50e04c7686e5ddfd1b9c41a1.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}], "type": "journal article", "published": "2025-06-26", "journal": {"title": "Science", "issn": "1095-9203", "volume": "388", "issue": "6754", "pages": "eadr3326", "issn-l": "0036-8075"}, "abstract": "West Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. In this work, we describe the changing genetic and cultural landscapes of early Holocene West Anatolia using 30 new paleogenomes. We show that Neolithization in West Anatolia was a multifaceted process, characterized by the assimilation of Neolithic practices by local foragers, the influx of eastern populations, and their admixture, with their descendants subsequently establishing Neolithic Southeast Europe. We then coanalyzed genetic and cultural similarities across early Holocene Anatolian and Aegean Neolithic villages using 58 material culture elements. Cultural distances among villages correlate with their spatial distances but not with their genetic distances after controlling for geography. This suggests that cultural change was often decoupled from genetically visible mobility.", "doi": "10.1126/science.adr3326", "pmid": "40570102", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-24T10:40:50.203Z", "modified": "2025-11-24T10:40:52.334Z"}, {"entity": "publication", "iuid": "366b9dcbbd5948908195760c17d29905", "links": {"self": {"href": "https://publications.scilifelab.se/publication/366b9dcbbd5948908195760c17d29905.json"}, "display": {"href": "https://publications.scilifelab.se/publication/366b9dcbbd5948908195760c17d29905"}}, "title": "Doublet decoding of tRNASer3 demonstrates plasticity of ribosomal decoding center.", "authors": [{"family": "Krishnaswamy", "given": "Shruthi", "initials": "S", "orcid": "0009-0004-3486-4939", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3419361bb4d468997ff52ecd38dfc51.json"}}, {"family": "Akbar", "given": "Shirin", "initials": "S", "orcid": "0000-0003-2437-9679", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4fff2c547b64e3c81e0c935f911028a.json"}}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e2b9321c1064208b9c0a1b11dde571d.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Selmer", "given": "Maria", "initials": "M", "orcid": "0000-0001-9079-2774", "researcher": {"href": "https://publications.scilifelab.se/researcher/860221451df4451b8c035ff4cf25c812.json"}}], "type": "journal article", "published": "2025-06-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "5402", "issn-l": "2041-1723"}, "abstract": "Frameshifts can be caused by specific combinations of tRNA and mRNA. The wildtype AGC-decoding E. coli tRNASer3GCU has been shown to induce -1 ribosomal frameshifting on GCA alanine codons, and proposed to read a two-base codon instead of a canonical triplet. However, it has remained unclear whether this type of non-cognate decoding can be accommodated by the ribosome. Here, we perform single-particle cryo-EM reconstructions on E. coli 70S ribosomes with the frameshift-inducing tRNASer3 bound to the non-cognate GCA codon or the cognate AGC codon in the ribosomal A site. The structures demonstrate that doublet decoding is made possible when A1493, the conserved monitoring base in 16S rRNA, mimics a first codon base, forming a Hoogsteen base pair with U36 from the anticodon and stacking with the mRNA. This interaction pushes the first two bases of the A-site codon in position for base pairing with C35 and G34 of the anticodon.", "doi": "10.1038/s41467-025-61016-5", "pmid": "40571681", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12202706"}, {"db": "pii", "key": "10.1038/s41467-025-61016-5"}], "notes": [], "created": "2025-10-29T14:57:32.646Z", "modified": "2025-10-29T14:57:53.989Z"}, {"entity": "publication", "iuid": "245f01038cc64bee8160e4ba13f4a037", "links": {"self": {"href": "https://publications.scilifelab.se/publication/245f01038cc64bee8160e4ba13f4a037.json"}, "display": {"href": "https://publications.scilifelab.se/publication/245f01038cc64bee8160e4ba13f4a037"}}, "title": "Unveiling the Structure of Anhydrous Sodium Valproate with 3D Electron Diffraction and a Facile Sample Preparation Workflow.", "authors": [{"family": "Xu", "given": "Jiaoyan", "initials": "J"}, {"family": "Srinivas", "given": "Vivek", "initials": "V", "orcid": "0000-0002-0265-1873", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6a2692ce1ff4d07ba13f6a180e9232e.json"}}, {"family": "Kumar", "given": "Rohit", "initials": "R"}, {"family": "Pacoste", "given": "Laura", "initials": "L"}, {"family": "Guo", "given": "Yiwang", "initials": "Y"}, {"family": "Yang", "given": "Taimin", "initials": "T", "orcid": "0000-0003-4318-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/1705d217df9c44c98a8be4fa607527fb.json"}}, {"family": "Sun", "given": "Changquan Calvin", "initials": "CC", "orcid": "0000-0001-7284-5334", "researcher": {"href": "https://publications.scilifelab.se/researcher/19052e47349e4a608ec1b11bb1f4388e.json"}}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M"}, {"family": "Zou", "given": "Xiaodong", "initials": "X"}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}], "type": "journal article", "published": "2025-06-25", "journal": {"title": "ACS Cent Sci", "issn": "2374-7943", "volume": "11", "issue": "6", "pages": "960-966", "issn-l": null}, "abstract": "Understanding the structure of an active pharmaceutical ingredient is essential for gaining insights into its physicochemical properties. Sodium valproate, one of the most effective antiepileptic drugs, was first approved for medical use in 1967. However, the structure of its anhydrous form has remained unresolved. This is because it was difficult to grow crystals of sufficient size for single-crystal X-ray diffraction (SCXRD). Although 3D electron diffraction (3D ED) can be used for studying crystals that are too small for SCXRD, the crystals of anhydrous sodium valproate are extremely sensitive to both humidity and electron beams. They degrade quickly both in air and under an electron beam at room temperature. In this study, we developed a glovebox-assisted cryo-transfer workflow for the preparation of EM grids in a protected atmosphere to overcome the current challenges for studying air- and beam-sensitive samples using 3D ED. Using this technique, we successfully determined the structure of anhydrous sodium valproate, revealing the formation of Na-valproate polyhedral chains. Our results provide a robust framework for the 3D ED analysis of air-sensitive crystals, greatly enhancing its utility across various scientific disciplines.", "doi": "10.1021/acscentsci.5c00412", "pmid": "40585805", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12203429"}], "notes": [], "created": "2025-11-25T15:58:49.665Z", "modified": "2025-11-25T15:58:50.127Z"}, {"entity": "publication", "iuid": "9f05d86339b84c169856faace9e38db9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f05d86339b84c169856faace9e38db9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f05d86339b84c169856faace9e38db9"}}, "title": "The mitochondrial methylation potential gates mitoribosome assembly.", "authors": [{"family": "Glasgow", "given": "Ruth I C", "initials": "RIC"}, {"family": "Singh", "given": "Vivek", "initials": "V", "orcid": "0000-0003-4656-3362", "researcher": {"href": "https://publications.scilifelab.se/researcher/0576b8ffc93d42f6b47d9d0d7d01bbd0.json"}}, {"family": "Pe\u00f1a-P\u00e9rez", "given": "Luc\u00eda", "initials": "L", "orcid": "0000-0002-5044-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/111f8a8c4c6d4d2ea60e5fc76831b7fa.json"}}, {"family": "Wilhalm", "given": "Alissa", "initials": "A"}, {"family": "Moedas", "given": "Marco F", "initials": "MF"}, {"family": "Moore", "given": "David", "initials": "D"}, {"family": "Rosenberger", "given": "Florian A", "initials": "FA", "orcid": "0000-0003-4604-6170", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9cd9d0742d40e3b5dc1abfde64d5c4.json"}}, {"family": "Li", "given": "Xinping", "initials": "X"}, {"family": "Atanassov", "given": "Ilian", "initials": "I", "orcid": "0000-0001-8259-2545", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d22eab41e44364be8966abaf693de1.json"}}, {"family": "Saba", "given": "Mira", "initials": "M"}, {"family": "Cipullo", "given": "Miriam", "initials": "M"}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Freyer", "given": "Christoph", "initials": "C", "orcid": "0000-0003-0418-1673", "researcher": {"href": "https://publications.scilifelab.se/researcher/888298d25fb94acca7639063d3592373.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Wredenberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-2500-6121", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ea9ee7305424cdb8c238ef569e5be03.json"}}], "type": "journal article", "published": "2025-06-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "5388"}, "abstract": "S-adenosylmethionine (SAM) is the principal methyl donor in cells and is essential for mitochondrial gene expression, influencing RNA modifications, translation, and ribosome biogenesis. Using direct long-read RNA sequencing in mouse tissues and embryonic fibroblasts, we show that processing of the mitochondrial ribosomal gene cluster fails in the absence of mitochondrial SAM, leading to an accumulation of unprocessed precursors. Proteomic analysis of ribosome fractions revealed these precursors associated with processing and assembly factors, indicating stalled biogenesis. Structural analysis by cryo-electron microscopy demonstrated that SAM-dependent methylation is required for peptidyl transferase centre formation during mitoribosome assembly. Our findings identify a critical role for SAM in coordinating mitoribosomal RNA processing and large subunit maturation, linking cellular methylation potential to mitochondrial translation capacity.", "doi": "10.1038/s41467-025-60977-x", "pmid": "40562754", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Applications)": null}, "xrefs": [{"db": "pmc", "key": "PMC12198368"}, {"db": "pii", "key": "10.1038/s41467-025-60977-x"}], "notes": [], "created": "2025-08-19T13:45:26.954Z", "modified": "2025-12-08T12:41:21.324Z"}, {"entity": "publication", "iuid": "1883c3293a9942b7bbff3df7e9c1d61b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1883c3293a9942b7bbff3df7e9c1d61b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1883c3293a9942b7bbff3df7e9c1d61b"}}, "title": "BMI during childhood and puberty - associations with blood pressure and hypertension.", "authors": [{"family": "Lilja", "given": "Lina", "initials": "L", "orcid": "0000-0003-2908-7456", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd8f5f9d6454648b700455cb1d64c91.json"}}, {"family": "Bygdell", "given": "Maria", "initials": "M", "orcid": "0000-0002-0737-8642", "researcher": {"href": "https://publications.scilifelab.se/researcher/b54e9b05bcb74e4a91a4e9cfcdf187aa.json"}}, {"family": "Martikainen", "given": "Jari", "initials": "J", "orcid": "0000-0003-0366-1683", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfd56b6dfb74494890131a51097996d8.json"}}, {"family": "Li", "given": "Huiqi", "initials": "H", "orcid": "0000-0002-1127-0829", "researcher": {"href": "https://publications.scilifelab.se/researcher/abcde2f8415b4c17971fcd44c25c3d50.json"}}, {"family": "Schmidt", "given": "Caroline", "initials": "C", "orcid": "0000-0001-8534-3237", "researcher": {"href": "https://publications.scilifelab.se/researcher/a80ef1ead9ec48bbbcdcd9a16724c716.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Rosengren", "given": "Annika", "initials": "A", "orcid": "0000-0002-5409-6605", "researcher": {"href": "https://publications.scilifelab.se/researcher/59e4c8b35336454ab5f74df9c6b9531b.json"}}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}, {"family": "Kindblom", "given": "Jenny M", "initials": "JM", "orcid": "0000-0001-8437-0639", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d338479632e48c0ba14bf948e4cc34f.json"}}], "type": "journal article", "published": "2025-06-25", "journal": {"title": "Eur J Prev Cardiol", "issn": "2047-4881", "issn-l": "2047-4873"}, "abstract": "The present study aimed to evaluate the association between BMI during childhood and puberty and blood pressure and hypertension in midlife, and to explore midlife BMI as a potential mediator of these associations.\n\nWe linked the BMI Epidemiology Study Gothenburg (BEST) with developmental BMI, with the Swedish CArdioPulmonary bioImage Study (SCAPIS) with blood pressure and hypertension in midlife (n= 2394). The associations between childhood BMI (7-8 years) and pubertal BMI change (young adult BMI minus childhood BMI), and blood pressure and hypertension in midlife, were evaluated using linear or logistic regression models. Mediation analysis was conducted to evaluate the indirect effect, via midlife BMI, and the direct effect on blood pressure and hypertension. The analyses were adjusted for birth year and smoking.\n\nThe pubertal BMI change was positively associated with systolic and diastolic blood pressure and hypertension in midlife, independent of childhood BMI, in both men and women (p<0.01). For men but not for women, childhood BMI was positively associated with systolic and diastolic blood pressure in midlife, independent of the pubertal BMI change (p<0.01). No significant independent association was observed for childhood BMI with hypertension. Mediation analyses for the association between the pubertal BMI change and blood pressure and hypertension in midlife indicate that these associations were largely mediated by BMI in midlife.\n\nThese findings indicate that high blood pressure may originate in early life. A life-course approach for targeted prevention, starting already during the developmental years, could reduce the risk of high blood pressure.", "doi": "10.1093/eurjpc/zwaf376", "pmid": "40561523", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Collaborative"}, "xrefs": [{"db": "pii", "key": "8173940"}], "notes": [], "created": "2025-07-08T13:55:21.859Z", "modified": "2025-11-04T11:36:37.987Z"}, {"entity": "publication", "iuid": "6364cb53a18c436d8ce6315496b97353", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6364cb53a18c436d8ce6315496b97353.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6364cb53a18c436d8ce6315496b97353"}}, "title": "Combined targeting of PRDX6 and GSTP1 as a potential differentiation strategy for neuroblastoma treatment.", "authors": [{"family": "Lia\u00f1o-Pons", "given": "Judit", "initials": "J", "orcid": "0000-0001-8097-4750", "researcher": {"href": "https://publications.scilifelab.se/researcher/8285ad3848b94349b5d603d817f82db6.json"}}, {"family": "Garde-Lapido", "given": "Elisa", "initials": "E", "orcid": "0009-0001-5321-1253", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb52703f9d1944e5bc91922727deb49c.json"}}, {"family": "Fahrig", "given": "Fenja L", "initials": "FL", "orcid": "0009-0008-9040-5752", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de91297944a444a9d866dd451806130.json"}}, {"family": "J\u00e4ckering", "given": "Merle", "initials": "M", "orcid": "0009-0003-9519-2120", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c3ca09ca6cd42aba02538439b46b63c.json"}}, {"family": "Yuan", "given": "Ye", "initials": "Y"}, {"family": "Andersson", "given": "Stina", "initials": "S", "orcid": "0000-0003-3226-4740", "researcher": {"href": "https://publications.scilifelab.se/researcher/13415a4a70654146ac1c56e009ee31c4.json"}}, {"family": "Schort", "given": "Lea", "initials": "L"}, {"family": "Esteve", "given": "Maria", "initials": "M", "orcid": "0000-0003-2299-9153", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ea254453baa4725a3fd36a5491a57cb.json"}}, {"family": "Mohlin", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2458-3963", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e095a99e2c84d52b13973c9d46d128a.json"}}, {"family": "Bedoya-Reina", "given": "Oscar C", "initials": "OC", "orcid": "0009-0001-1703-2258", "researcher": {"href": "https://publications.scilifelab.se/researcher/94abfc2a001941cb8c33b64271618be9.json"}}, {"family": "Arsenian-Henriksson", "given": "Marie", "initials": "M", "orcid": "0000-0001-6376-7792", "researcher": {"href": "https://publications.scilifelab.se/researcher/e78a2e958a7b4eaaa9aecad01f0e7c57.json"}}], "type": "journal article", "published": "2025-06-24", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "25", "pages": "e2427211122", "issn-l": "0027-8424"}, "abstract": "Neuroblastoma (NB) is a heterogeneous childhood cancer, characterized by the amplification of the MYCN oncogene in 40% of the high-risk cases. Our previous work demonstrated that MYCN drives metabolic reprogramming in NB, including upregulation of antioxidant enzymes. Here, we identify peroxiredoxin 6 (PRDX6) as a promising therapeutic target in NB. Pharmacological inhibition of PRDX6 reduces MYCN levels, induces apoptosis, and promotes neuronal differentiation accompanied by lipid droplet accumulation, essential for the phenotypic reprogramming. Moreover, combined inhibition of PRDX6 and glutathione S-transferase Pi 1 (GSTP1), a key antioxidant enzyme needed for PRDX6 activation, demonstrated synergistic effects both in vitro and in vivo. This strategy results in neuronal maturation as well as activity and initiates downstream pathways distinct from the ones triggered by retinoic acid, the differentiation-inducing agent currently used in clinical practice for NB. Notably, both PRDX6 and GSTP1 are highly expressed in the developing murine adrenal gland, as well as in high-risk, MYCN-amplified NB, correlating with an undifferentiated state and poor prognosis. Together, our results provide insights into the potential of PRDX6 and GSTP1 as therapeutic targets for differentiation induction for children with NB.", "doi": "10.1073/pnas.2427211122", "pmid": "40531876", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12207458"}], "notes": [], "created": "2025-11-28T10:48:18.601Z", "modified": "2025-11-28T10:48:18.946Z"}, {"entity": "publication", "iuid": "dea72700c25245e996b572c5f84a1692", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dea72700c25245e996b572c5f84a1692.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dea72700c25245e996b572c5f84a1692"}}, "title": "Development of empirical anti-inflammatory diet index: a cross-sectional study.", "authors": [{"family": "Kaluza", "given": "Joanna", "initials": "J"}, {"family": "Hellerstr\u00f6m", "given": "Lisa", "initials": "L"}, {"family": "Kaluza", "given": "Daniel", "initials": "D"}, {"family": "Chabok", "given": "Abbas", "initials": "A"}, {"family": "\u00c5kesson", "given": "Agneta", "initials": "A"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Wolk", "given": "Alicja", "initials": "A"}], "type": "journal article", "published": "2025-06-23", "journal": {"title": "Nutr J", "issn": "1475-2891", "volume": "24", "issue": "1", "pages": "97", "issn-l": "1475-2891"}, "abstract": "There is evidence that some foods and dietary patterns may influence low-grade inflammation status. We aimed to develop a user-friendly empirical Anti-inflammatory Diet Index (eADI) that predicts low-grade chronic inflammation.\n\nIn this cross-sectional study of 4,432 men (aged 74 \u00b1 6 years) from the Cohort of Swedish Men-Clinical, inflammatory status was assessed by high-sensitivity C-reactive protein (hsCRP), interleukin 6 (IL-6), tumor necrosis factor receptor 1 (TNF-R1), and tumor necrosis factor receptor 2 (TNF-R2). Dietary intake was assessed using a food frequency questionnaire. The eADI was developed in a randomly chosen Discovery group (n = 2,216) using a 10-fold feature selection with filtering (based on Lasso regression) to select food groups most correlated with inflammatory biomarkers. From the selected foods, the eADI was then constructed based on summed scores of the consumption tertiles (corresponding to 0, 0.5, and 1 point). Next, in the Replication group (n = 2,216), the association of eADI with inflammatory biomarkers was examined using multivariable-adjusted linear regression models.\n\neADI-17 included 17 food groups (11 with anti-inflammatory, 6 with pro-inflammatory potential). In the Replication group, the median of eADI-17 was 9 (range: 2-16) scores and the Spearman correlation coefficients for eADI-17 vs. hsCRP, IL-6, TNF-R1, and TNF-R2 were -0.17, -0.23, -0.28, and -0.26, respectively. Each increment by 4.5-point eADI-17 (2 SD) was associated with concentrations that were 12% lower for hsCRP, 6% lower for IL-6, 8% lower for TNF-R1, and 9% lower for TNF-R2. These results obtained for the Replication group were robust as they were essentially the same as those of the Discovery group.\n\nThe eADI-17 is a validated, robust and user-friendly anti-inflammatory diet index developed to predict low-grade chronic inflammation. This index has the potential to further refine future dietary guidelines and to be used in personalized nutrition. However, its predictive validity should be further evaluated in diverse populations.", "doi": "10.1186/s12937-025-01165-x", "pmid": "40551133", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12183828"}, {"db": "pii", "key": "10.1186/s12937-025-01165-x"}], "notes": [], "created": "2025-11-25T19:22:25.131Z", "modified": "2025-11-25T19:22:25.135Z"}, {"entity": "publication", "iuid": "216034feb18744a0a4b16eee84c50110", "links": {"self": {"href": "https://publications.scilifelab.se/publication/216034feb18744a0a4b16eee84c50110.json"}, "display": {"href": "https://publications.scilifelab.se/publication/216034feb18744a0a4b16eee84c50110"}}, "title": "Scalable single-cell metagenomic analysis with Bascet and Zorn", "authors": [{"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H", "orcid": "0000-0001-9807-1082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4143a879fa2043e7873be9e2aa72d051.json"}}, {"family": "Yakovenko", "given": "Iryna", "initials": "I", "orcid": "0009-0003-5235-2999", "researcher": {"href": "https://publications.scilifelab.se/researcher/36136ba9041945989f03f1cfdd3864ee.json"}}, {"family": "Verma", "given": "Jyoti", "initials": "J", "orcid": "0009-0005-5907-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/39af7a10e1f74ee1ab1c05fb85b301a5.json"}}, {"family": "Dicken", "given": "Julian", "initials": "J", "orcid": "0009-0009-8614-7321", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1949a292273482782597e58dee65804.json"}}, {"family": "Albrecht", "given": "Florian", "initials": "F", "orcid": "0009-0002-9253-5290", "researcher": {"href": "https://publications.scilifelab.se/researcher/5918af4c54344d548c4c03a0cc3e3f7a.json"}}, {"family": "Ma\u017eutis", "given": "Linas", "initials": "L", "orcid": "0000-0002-5552-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ef7493c863a406ebebf8937113a65e1.json"}}, {"family": "Normark", "given": "Johan", "initials": "J", "orcid": "0000-0001-5831-4369", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ff458cccc2a422ca28ba878e98afb9c.json"}}, {"family": "Sheng", "given": "Nongfei", "initials": "N", "orcid": "0009-0004-0642-3394", "researcher": {"href": "https://publications.scilifelab.se/researcher/c84842af60ed41daa4c616211724b135.json"}}, {"family": "Str\u00f6mberg", "given": "Nicklas", "initials": "N", "orcid": "0000-0002-8417-3560", "researcher": {"href": "https://publications.scilifelab.se/researcher/a218efc1db1848eca1a8f27f8a3973ff.json"}}, {"family": "L\u00f6fstedt", "given": "Tommy", "initials": "T", "orcid": "0000-0001-7119-7646", "researcher": {"href": "https://publications.scilifelab.se/researcher/e51b3354e15845e1ad6a29e40c8aac43.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bc122d4cd6e4a5aac6959827f824c91.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}], "type": "posted-content", "published": "2025-06-21", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.06.20.660799", "pmid": null, "labels": {"Clinical Genomics": "Service", "Clinical Genomics Ume\u00e5": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-26T09:15:47.785Z", "modified": "2025-12-18T19:13:56.331Z"}, {"entity": "publication", "iuid": "081d42ccc86240e9ba5bc5a2b40a7eec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/081d42ccc86240e9ba5bc5a2b40a7eec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/081d42ccc86240e9ba5bc5a2b40a7eec"}}, "title": "Real-time genome imaging of host interactions in adeno-associated virus genome release.", "authors": [{"family": "Bustamante-Jaramillo", "given": "Luisa F", "initials": "LF"}, {"family": "Yue", "given": "Lei", "initials": "L"}, {"family": "Fingal", "given": "Joshua", "initials": "J"}, {"family": "Rydell", "given": "Gustaf", "initials": "G"}, {"family": "Johansson", "given": "Maria", "initials": "M"}, {"family": "Edreira", "given": "Tomas", "initials": "T"}, {"family": "M\u00fcller", "given": "Oliver J", "initials": "OJ"}, {"family": "Hille", "given": "Susanne", "initials": "S"}, {"family": "M\u00fcller", "given": "Martin", "initials": "M"}, {"family": "Gallardo", "given": "Franck", "initials": "F"}, {"family": "Chen", "given": "Qingxin", "initials": "Q"}, {"family": "Blondot", "given": "Marie-Lise", "initials": "ML"}, {"family": "Kann", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2025-06-20", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "28", "issue": "6", "pages": "112624", "issn-l": "2589-0042"}, "abstract": "Adeno-associated virus (AAVs) with a self-complementary genome (sc) comprising a gene of interest are used in gene therapy. Their efficiency is limited but the molecular factors contributing to this restriction are poorly understood. We utilized scAAV2 containing a fluorescent protein-binding anchor sequence on its genome allowing visualization of released genomes by time-lapse microscopy. Pairing this technique with capsid staining, we showed that scAAV2 genome release was initiated by a partial genome exposure, triggered by elevated calcium levels while the capsids interacted with proteins of the nuclear pore. Genome release occurred subsequently requiring Rad52 decamerization in the vicinity of the host chromatin. A fraction of the released genomes was degraded by Mre11, an essential factor for chromatin stability, and cellular DNA double-strand breaks. These steps were key-factors limiting transduction, suggesting that temporary modulation of DNA damage-response-proteins is a promising way to increase scAAV efficiency in therapy.", "doi": "10.1016/j.isci.2025.112624", "pmid": "40546945", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12178803"}, {"db": "pii", "key": "S2589-0042(25)00885-5"}], "notes": [], "created": "2025-11-05T13:48:04.799Z", "modified": "2025-11-05T13:48:04.808Z"}, {"entity": "publication", "iuid": "2880e18d516e44c1953815d1ae7b27f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2880e18d516e44c1953815d1ae7b27f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2880e18d516e44c1953815d1ae7b27f5"}}, "title": "Diagnostic yield of 1000 trio analyses with exome and genome sequencing in a clinical setting.", "authors": [{"family": "Malmgren", "given": "Helena", "initials": "H"}, {"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Gustafsson", "given": "Peter", "initials": "P"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Arthur", "given": "Cecilia", "initials": "C"}, {"family": "Carlsten", "given": "Jonas", "initials": "J"}, {"family": "De Geer", "given": "Karl", "initials": "K"}, {"family": "Ehn", "given": "Emma", "initials": "E"}, {"family": "Grigelionien\u00e9", "given": "Giedre", "initials": "G"}, {"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A"}, {"family": "Helgadottir", "given": "Hafdis T", "initials": "HT"}, {"family": "Hellstr\u00f6m-Pigg", "given": "Maritta", "initials": "M"}, {"family": "Iwarsson", "given": "Erik", "initials": "E"}, {"family": "Kuchinskaya", "given": "Ekaterina", "initials": "E"}, {"family": "Lindel\u00f6f", "given": "Hillevi", "initials": "H"}, {"family": "Mannila", "given": "Maria", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Rudd", "given": "Eva", "initials": "E"}, {"family": "Sahlin", "given": "Ellika", "initials": "E"}, {"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Tham", "given": "Emma", "initials": "E"}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H"}, {"family": "Westenius", "given": "Eini", "initials": "E"}, {"family": "Winberg", "given": "Johanna", "initials": "J"}, {"family": "Winerdal", "given": "Max", "initials": "M"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Johansson-Soller", "given": "Maria", "initials": "M"}, {"family": "Wirta", "given": "Valtteri", "initials": "V"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2025-06-20", "journal": {"title": "Front Genet", "issn": "1664-8021", "volume": "16", "pages": "1580879", "issn-l": "1664-8021"}, "abstract": "A trio analysis refers to the strategy of exome or genome sequencing of DNA from a patient, as well as parents, in order to identify the genetic cause of a disorder or syndrome.\n\nDuring the last 10 years, we have successfully applied exome or genome sequencing and performed trio analysis for 1,000 patients.\n\nOverall, 39% of the patients were diagnosed, with the detection of causative variant(s). The variants were located in 308 different genes. Autosomal dominant de novo variants were detected in 46% of the solved cases. Detection rates were highest in patients with a syndromic neurodevelopmental disorder (46%) and in patients with known consanguinity (59%). Even for patients previously analyzed as singletons, using a pre-defined gene panel, a consecutive trio analysis resulted in the detection of a causative variant in 30%.\n\nA major advantage of trio analysis is the immediate identification of de novo variants as well as confirmation of compound heterozygosity. Additionally, inherited variants from a healthy parent can be dismissed as non-disease causing. The trio strategy enables analysis of a high number of genes-or even the whole genome-simultaneously. The strengths of a trio analysis, in combination with analysis of genome sequence data, allows for the detection of a wide range of genetic aberrations. This enables a high diagnostic yield, even in previously analyzed patients. Our current protocol for trio analysis is based on genome sequencing data, which allows for simultaneous detection of single nucleotide variants, insertion/deletions, structural variants, expanded short tandem repeats, as well as a copy number analysis corresponding to an array-CGH, and analysis regarding SMN1 gene copies.", "doi": "10.3389/fgene.2025.1580879", "pmid": "40620702", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12226303"}, {"db": "pii", "key": "1580879"}], "notes": [], "created": "2025-11-18T20:46:07.297Z", "modified": "2025-11-18T20:46:07.301Z"}, {"entity": "publication", "iuid": "237bc9b3ceaf4af580a4097b4ee55e08", "links": {"self": {"href": "https://publications.scilifelab.se/publication/237bc9b3ceaf4af580a4097b4ee55e08.json"}, "display": {"href": "https://publications.scilifelab.se/publication/237bc9b3ceaf4af580a4097b4ee55e08"}}, "title": "Cerebrospinal fluid protein profiling of inflammatory and neurobiological markers in Lyme neuroborreliosis.", "authors": [{"family": "Haglund", "given": "Sofie", "initials": "S"}, {"family": "Gyllemark", "given": "Paula", "initials": "P"}, {"family": "Forsberg", "given": "Pia", "initials": "P"}, {"family": "Brudin", "given": "Lars", "initials": "L"}, {"family": "Tjernberg", "given": "Ivar", "initials": "I"}, {"family": "Henningsson", "given": "Anna J", "initials": "AJ"}], "type": "journal article", "published": "2025-06-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "20190", "issn-l": "2045-2322"}, "abstract": "Lyme neuroborreliosis (LNB) is the most common form of disseminated Lyme borreliosis in Europe and North America. There are limitations in existing LNB diagnostics and a lack of reliable objective markers for disease-course. Here, extensive protein profiling with two panels of 184 proteins, was done in the search for new clinically useful diagnostic and prognostic candidate biomarkers. Cerebrospinal fluid (CSF) was collected from patients with definite LNB (n = 13) at the time of diagnosis before initiating antibiotic treatment, and at a follow-up one month later. When symptoms were evaluated at a six-month follow-up, six patients had recovered with no persistent symptoms (NPS), and seven experienced delayed recovery with persistent post-treatment symptoms (PS). Orthopedic patients (n = 60) served as controls. With the panels used, no protein biomarkers able to differentiate between PS and NPS were identified. However, from a diagnostic perspective, we identified multiple proteins that were differentially expressed between LNB and controls. The majority of them were downregulated following antibiotic treatment, at the one-month follow-up. IL10, TNF, and CCL8 were considered examples of potentially useful candidate biomarkers in both the early diagnostics and in monitoring of treatment response. These markers merit further investigation to understand their utility in relation to other neurological manifestations.", "doi": "10.1038/s41598-025-06146-y", "pmid": "40542080", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12181437"}, {"db": "pii", "key": "10.1038/s41598-025-06146-y"}], "notes": [], "created": "2025-11-25T19:22:23.103Z", "modified": "2025-11-25T19:22:23.107Z"}, {"entity": "publication", "iuid": "00ab4a882a5c45daaf75dcb38a32836b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00ab4a882a5c45daaf75dcb38a32836b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00ab4a882a5c45daaf75dcb38a32836b"}}, "title": "Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation.", "authors": [{"family": "Marsh", "given": "Audrey J", "initials": "AJ"}, {"family": "Pirogov", "given": "Sergei", "initials": "S"}, {"family": "Kaur", "given": "Yadwinder", "initials": "Y"}, {"family": "Ruffridge", "given": "Abby J", "initials": "AJ"}, {"family": "Sajwan", "given": "Suresh", "initials": "S"}, {"family": "Gibson", "given": "Tyler J", "initials": "TJ"}, {"family": "Hunt", "given": "George", "initials": "G"}, {"family": "Harrison", "given": "Melissa M", "initials": "MM"}, {"family": "Mannervik", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2025-06-19", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "volume": "85", "issue": "12", "pages": "2409-2424.e8", "issn-l": "1097-2765"}, "abstract": "Immediately after fertilization, the genome is transcriptionally quiescent. Maternally encoded pioneer factors reprogram the chromatin state and facilitate transcription of the zygotic genome. In Drosophila, transcription is initiated by the pioneer factor Zelda. While Zelda-occupied sites are enriched with histone acetylation, a post-translational mark associated with active cis-regulatory regions, the functional relationship between Zelda and histone acetylation remained unclear. We show that Zelda-mediated recruitment of the histone acetyltransferase CREB-binding protein (CBP) is essential for zygotic transcription. CBP catalytic activity is necessary for the release of RNA polymerase II (RNA Pol II) into elongation and for embryonic development. However, CBP also activates transcription independent of acetylation through RNA Pol II recruitment. Neither CBP-mediated acetylation nor CBP itself is required for the pioneering function of Zelda. Our data suggest that pioneer-factor-mediated recruitment of CBP is a conserved mechanism required to activate zygotic transcription but is separable from the function of pioneer factors in restructuring chromatin accessibility.", "doi": "10.1016/j.molcel.2025.05.009", "pmid": "40441155", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2081331"}, {"db": "pmc", "key": "PMC12181052"}, {"db": "pii", "key": "S1097-2765(25)00414-9"}], "notes": [], "created": "2025-07-18T10:23:07.052Z", "modified": "2025-07-18T10:23:07.057Z"}, {"entity": "publication", "iuid": "6e499e6478cc4696a5a0a6a7534b3c6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e499e6478cc4696a5a0a6a7534b3c6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e499e6478cc4696a5a0a6a7534b3c6c"}}, "title": "A cell-based degrader assessment platform facilitates discovery of functional NUDT5 PROTACs", "authors": [{"family": "Alam", "given": "Seher", "initials": "S", "orcid": "0000-0002-8494-832X", "researcher": {"href": "https://publications.scilifelab.se/researcher/034588861fbc437bafe9cf7074ecd7ab.json"}}, {"family": "Pires", "given": "Maria J", "initials": "MJ", "orcid": "0009-0007-0384-091X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e7a891756624e5583914ea7b2d3176e.json"}}, {"family": "Tidestav", "given": "Gabriel", "initials": "G"}, {"family": "Jemth", "given": "Ann Sofie", "initials": "AS", "orcid": "0000-0002-7550-1833", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd07c6c543544af1a904e039f73ba857.json"}}, {"family": "Eklund", "given": "Julia", "initials": "J", "orcid": "0009-0000-7449-2456", "researcher": {"href": "https://publications.scilifelab.se/researcher/96b04b6202964265b671901bcf4b66b4.json"}}, {"family": "Klingeg\u00e5rd", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-6280-3894", "researcher": {"href": "https://publications.scilifelab.se/researcher/87593a4ce9ba4b3d8d1e3bc6836d42af.json"}}, {"family": "Caraballo", "given": "R\u00e9mi", "initials": "R", "orcid": "0000-0001-5912-8429", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e3194cd076e4eac95e029cfe4adefbc.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Rotilli", "given": "Dante", "initials": "D", "orcid": "0000-0002-8428-8763", "researcher": {"href": "https://publications.scilifelab.se/researcher/4939561c24b14fbbbdd82aa08a9e1ab5.json"}}, {"family": "van den Elzen", "given": "Siebe", "initials": "S"}, {"family": "van Berkum", "given": "Eri", "initials": "E"}, {"family": "Wallner", "given": "Olov", "initials": "O", "orcid": "0000-0002-6481-237X", "researcher": {"href": "https://publications.scilifelab.se/researcher/83eb2f7ee2f34f2cbacaae2dadcd90e9.json"}}, {"family": "Malmstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Arvidsson", "given": "Per I", "initials": "PI", "orcid": "0000-0002-9453-6812", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae064b90b750457e80e974947f2dfc7a.json"}}, {"family": "Valerie", "given": "Nicholas C K", "initials": "NCK", "orcid": "0000-0002-9423-964X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d90c5a1f924c8b97409934dec74b0b.json"}}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}], "type": "posted-content", "published": "2025-06-19", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.06.13.659494", "pmid": null, "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T16:38:01.820Z", "modified": "2025-12-18T19:14:22.271Z"}, {"entity": "publication", "iuid": "36e900898c0248dc8966c275ca8cbf84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36e900898c0248dc8966c275ca8cbf84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36e900898c0248dc8966c275ca8cbf84"}}, "title": "A Combined Model-Based Meta-Analysis of Aggregated and Individual FEV1 Data From Randomized COPD Trials.", "authors": [{"family": "Yang", "given": "Liang", "initials": "L", "orcid": "0000-0001-9012-3669", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf9ecaa8808549108e6f2e98dde88375.json"}}, {"family": "Llanos-Paez", "given": "Carolina", "initials": "C"}, {"family": "Yang", "given": "Shuying", "initials": "S"}, {"family": "Ambery", "given": "Claire", "initials": "C"}, {"family": "Berges", "given": "Alienor", "initials": "A"}, {"family": "Kjellsson", "given": "Maria C", "initials": "MC", "orcid": "0000-0003-3531-9452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f141039b41a84acf9599dfee7dcc3396.json"}}, {"family": "Karlsson", "given": "Mats O", "initials": "MO", "orcid": "0000-0003-1258-8297", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b7ca3868f0b431799ea51c4641d1e5a.json"}}], "type": "journal article", "published": "2025-06-19", "journal": {"title": "CPT Pharmacometrics Syst Pharmacol", "issn": "2163-8306", "issn-l": null}, "abstract": "Model-based meta-analysis allows integration of aggregated-level data (AD) from different clinical trials in one model to assess population efficacy/safety. However, AD is limited in individual-level information, while individual-patient-level data (IPD) are hard to obtain. Combined modeling may take advantage of both sources. Chronic obstructive pulmonary disease (COPD) is a leading cause of poor health and death. This study established a combined ADIPD model of COPD clinical trials with forced expiratory volume in 1 s (FEV1) as an endpoint and explored methods for estimating interstudy variability (ISV), interindividual variability (IIV), and aggregation bias. Stochastic simulation and estimations (SSE) showed the best method in NONMEM to estimate ISV/IIV: using $LEVEL with equal weight of studies; for the AD part, ISVs from the AD model were fixed, estimating IIV with separate ETAs for each arm; the IPD part shared the fixed ISV and estimated IIV. An approximated normal distribution was derived for lognormal IIV to avoid aggregation bias. Covariate correlations were different at aggregated and individual levels, but did not introduce aggregation bias according to SSE. A separate AD model (published) and IPD model were built, then combined to form the ADIPD model. The ADIPD model included FEV1 baseline, disease progression, placebo effect, and Emax/constant dose-responses for 23 compounds. Identified covariate relationships: higher age, female, higher disease severity, non-current smoker related to lower baseline; higher baseline related to faster disease progression and higher drug effects. Covariate coefficients were estimated more precisely in the ADIPD model than the AD model. ADIPD modeling allows more informed clinical trial simulations for study design. Trial Registration: ClinicalTrials.gov identifier: NCT01053988 and NCT01054885.", "doi": "10.1002/psp4.70059", "pmid": "40536286", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "ClinicalTrials.gov", "key": "NCT01054885"}, {"db": "ClinicalTrials.gov", "key": "NCT01053988"}], "notes": [], "created": "2025-11-28T10:40:52.459Z", "modified": "2025-11-28T10:40:52.557Z"}, {"entity": "publication", "iuid": "e60c8cab27a24067b89de060bdcc92e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e60c8cab27a24067b89de060bdcc92e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e60c8cab27a24067b89de060bdcc92e4"}}, "title": "The plasma proteome reveals distinct signaling pathways associated with PR3-ANCA positive and MPO-ANCA positive vasculitis.", "authors": [{"family": "Hellbacher", "given": "Erik", "initials": "E"}, {"family": "van Hoef", "given": "Vincent", "initials": "V"}, {"family": "Johansson", "given": "Alina", "initials": "A"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J"}], "type": "journal article", "published": "2025-06-18", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1600754", "issn-l": "1664-3224"}, "abstract": "Despite recent advances, the pathophysiological mechanisms underlying anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV) remain incompletely understood, and comparative proteomic analyses of AAV subtypes are lacking. This study aimed to identify key molecular signaling pathways activated in AAV and to elucidate molecular distinctions between AAV with proteinase 3 ANCA (PR3-AAV) and AAV with myeloperoxidase ANCA (MPO-AAV).\n\nPlasma samples from 41 cases with active PR3-AAV, 24 with active MPO-AAV and 138 population controls were analyzed for 185 proteins using proximity extension assay and Luminex. Differential expression was assessed between PR3-AAV, MPO-AAV and controls using univariate and partial least squares discriminant analyses. Protein-protein interactions and pathway enrichment were explored using STRING and Cytoscape databases.\n\nCompared with controls, 31 proteins were significantly upregulated in PR3-AAV and 29 in MPO-AAV; 18 were shared, whereas 13 and 11 were specific to PR3-AAV and MPO-AAV, respectively. Shared proteins were enriched in general immune pathways, including IL-6 signaling. AAV subgroup-specific proteins were combined with proteins differentiating between PR3-AAV and MPO-AAV in a direct comparison. MMP-1, MMP-9, HGF, and OSM were uniquely upregulated in PR3-AAV, while TNF, TNF-R1/R2, TNFRSF14, and TNFRSF9 were prominent in MPO-AAV. Functional enrichment analyses underscored STAT3 signaling in PR3-AAV and TNF signaling in MPO-AAV.\n\nThis study identifies distinct and shared signaling pathways in PR3-AAV and MPO-AAV, highlighting STAT3 and TNF pathways as potential subtype-specific mechanisms. These findings offer insight into AAV pathogenesis and may guide the development of more targeted, less toxic treatments tailored to AAV subtypes.", "doi": "10.3389/fimmu.2025.1600754", "pmid": "40607391", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12213373"}], "notes": [], "created": "2025-11-18T17:41:37.997Z", "modified": "2025-11-18T17:41:38.003Z"}, {"entity": "publication", "iuid": "6a882e6f1a1b4223856db18d105468ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6a882e6f1a1b4223856db18d105468ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6a882e6f1a1b4223856db18d105468ea"}}, "title": "Advanced Microbiome Therapeutics Accelerate MASLD Recovery by Restoring Intestinal Microbiota Equilibrium and the Gut-Liver Axis in a Mouse Model.", "authors": [{"family": "Lok", "given": "Johnson", "initials": "J"}, {"family": "Chen", "given": "Congjia", "initials": "C", "orcid": "0009-0004-6800-3184", "researcher": {"href": "https://publications.scilifelab.se/researcher/119fd6649b3246d58f27178b96506865.json"}}, {"family": "Iannone", "given": "Valeria", "initials": "V"}, {"family": "Babu", "given": "Ambrin Farizah", "initials": "AF"}, {"family": "Lo", "given": "Emily Kwun Kwan", "initials": "EKK"}, {"family": "Vazquez-Uribe", "given": "Ruben", "initials": "R"}, {"family": "Vaaben", "given": "Troels Holger", "initials": "TH"}, {"family": "Kettunen", "given": "Mikko", "initials": "M"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Schwab", "given": "Ursula", "initials": "U"}, {"family": "Sommer", "given": "Morten Otto Alexander", "initials": "MOA", "orcid": "0000-0003-4005-5674", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae0481b087348b9867cedce834bf483.json"}}, {"family": "Hanhineva", "given": "Kati", "initials": "K"}, {"family": "Kolehmainen", "given": "Marjukka", "initials": "M"}, {"family": "El-Nezami", "given": "Hani", "initials": "H"}, {"family": "G\u00f3mez-Gallego", "given": "Carlos", "initials": "C", "orcid": "0000-0003-0219-1827", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8036c43a3b74d8f91614e5406ec93ca.json"}}], "type": "journal article", "published": "2025-06-18", "journal": {"title": "J. Agric. Food Chem.", "issn": "1520-5118", "volume": "73", "issue": "24", "pages": "15199-15214", "issn-l": "0021-8561"}, "abstract": "Gut microbiota dysbiosis and endocrine dysregulation are key players in metabolic dysfunction-associated steatotic liver disease (MASLD) development. This study evaluated whether advanced microbiome therapeutics can restore intestinal microbial equilibrium and gut-liver axis balance during MASLD recovery. MASLD was induced in mice using a high-fat, high-sugar diet, and then shifted to a standard diet, where intervention groups received engineered Escherichia coli Nissle 1917 expressing IGF1 (EcNI) or aldafermin (EcNA), and control groups received E. coli Nissle 1917 vehicle (EcN) or no microbial intervention (CTRL). EcNI and EcNA improved MASLD recovery compared to controls by lowering hepatic fat, plasma cholesterol, and body weight, while increasing bacterial diversity, plasma acetate, and propionate, and modulating particular microbial groups, potentially alleviating dysbiosis. Additionally, EcNI and EcNA downregulated acetyl-CoA, the steroid hormone biosynthesis pathway, and EcNA upregulated the pentose phosphate pathway and pyruvate, which are related to oxidative stress reduction. These results suggest that EcNI and EcNA are potential novel treatments for MASLD.", "doi": "10.1021/acs.jafc.5c01674", "pmid": "40480642", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12186743"}], "notes": [], "created": "2025-11-27T11:24:02.659Z", "modified": "2025-11-27T11:24:03.021Z"}, {"entity": "publication", "iuid": "af31c78497dd425b9e018282d774153b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af31c78497dd425b9e018282d774153b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af31c78497dd425b9e018282d774153b"}}, "title": "Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics.", "authors": [{"family": "An", "given": "Yueqing", "initials": "Y", "orcid": "0000-0003-0267-7106", "researcher": {"href": "https://publications.scilifelab.se/researcher/f83fa56252e649ffa3a39db8f3377932.json"}}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-6362-6199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddfc67c7c774583861a5ea3774eaa1a.json"}}], "type": "journal article", "published": "2025-06-17", "journal": {"title": "mSystems", "issn": "2379-5077", "pages": "e0172324", "volume": "10", "issue": "6", "issn-l": "2379-5077"}, "abstract": "Gut microbiomes of holometabolous insects can be strongly affected by metamorphosis. Previous studies suggest that microbiome colonization and community development often rely on specialized transmission routes between host life stages. However, there is a lack of comparative studies of microbial community dynamics from different transmission mechanisms. We compared the gut microbial community dynamics across life stages in five Galerucella species that differ in their potential microbial transfer mechanism by sequencing amplicons of the 16S rRNA gene. Females of three of the studied species place a fecal string on top of the egg, which may enhance the transfer of gut microbes, whereas females of the two other species do not. We found that the \u03b1-diversity was more stable between life stages in fecal string-placer species compared with the non-fecal string-placer species. Moreover, there were consistent microbiome differences between species, with multiple taxa in each species consistently appearing in all life stages. Fecal strings placed on eggs seem to play an important role in the diversity and dynamics of gut bacteria in Galerucella species, facilitating the vertical transfer of gut bacteria between host insect generations. Alternative, but less efficient, transmission routes appear to occur in non-fecal string-placer species.\n\nWe explore the consequences of having different mechanisms for transferring and establishing the gut microbiome between generations on gut microbial community dynamics. This process is often problematic in holometabolous insects, which have a complete metamorphosis between larval and adult stages. In our previous research, we found that females of some species within the genus Galerucella (Chrysomelidae) place a fecal string on the eggs, which is later consumed by the hatching larvae, whereas other species in the same genus do not have this behavior. In this paper, we therefore quantify the microbial community dynamics across all life stages in five Galerucella beetles (three with and two without fecal strings). Our results also indicate that the dynamics are much more stable in the species with fecal strings, particularly in the early life stages.", "doi": "10.1128/msystems.01723-24", "pmid": "40358205", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12172492"}], "notes": [], "created": "2025-05-26T07:50:58.503Z", "modified": "2025-11-14T11:08:35.746Z"}, {"entity": "publication", "iuid": "57c66b4fec014cb3a5e4976e7ce16789", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57c66b4fec014cb3a5e4976e7ce16789.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57c66b4fec014cb3a5e4976e7ce16789"}}, "title": "Fin Whale as a Sink of Legacy and Emerging Contaminants: First Integrated Chemical Exposomics and Gene Expression Analysis in Cetaceans", "authors": [{"family": "Fossi", "given": "Maria Cristina", "initials": "MC"}, {"family": "Limonta", "given": "Giacomo", "initials": "G", "orcid": "0000-0002-6634-3909", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a99061b9b54e94909135192408132e.json"}}, {"family": "Baini", "given": "Matteo", "initials": "M", "orcid": "0000-0003-2237-7688", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bee0fd6597646638c9fe8b6c60a4d0a.json"}}, {"family": "Urban R", "given": "Jorge", "initials": "J"}, {"family": "Athanassiadis", "given": "Ioannis", "initials": "I"}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications.scilifelab.se/researcher/f275a68856cb459ebbc933b18c3e315d.json"}}, {"family": "Papazian", "given": "Stefano", "initials": "S"}, {"family": "Rosso", "given": "Massimiliano", "initials": "M"}, {"family": "Panti", "given": "Cristina", "initials": "C"}], "type": "journal-article", "published": "2025-06-17", "journal": {"title": "Environ. Sci. Technol.", "issn": "0013-936X", "volume": "59", "issue": "23", "pages": "11477-11492", "issn-l": null}, "abstract": "Cetaceans face numerous anthropogenic chemical stressors in global oceans, yet there is a lack of studies that simultaneously assess their cumulative exposure to both legacy and emerging contaminants and their combined effects. To evaluate the susceptibility of fin whale (Balaenoptera physalus) to chemical pollution, this study employed for the first time a multidiagnostic molecular approach that integrates chemical exposomics and gene expression analysis in live-sampled skin and blubber biopsies from two distinct populations: the endangered Mediterranean subpopulation (Italy) and the vulnerable population from the Sea of Cortez (Mexico). Both marine regions are biodiversity hotspots characterized by different anthropogenic impacts, making them ideal for the assessment of heterogeneous contaminants exposure and their effects. Results revealed distinct exposure profiles in the two populations, with Mediterranean fin whales exhibiting higher concentrations of legacy pollutants such as polychlorinated biphenyls (PCBs), as well as plasticizers, perfluoroalkyl substances (PFAS), while both populations showed traces of pharmaceuticals and lifestyle-related chemicals (e.g., paracetamol, diclofenac, nicotine, UV filters) and other substances not previously reported in whales. Supported by 32 network correlations with gene expression relevant to transcriptional regulation, endocrine disruption, lipid homeostasis, and inflammation, our findings suggest that complex anthropogenic chemical exposures may compromise the health and reproductive viability of the endangered Mediterranean fin whales, affirming their importance as a global sentinel species, which reflects marine ecosystem integrity within the \"One Health\" framework.", "doi": "10.1021/acs.est.5c00844", "pmid": "40456520", "labels": {"Exposomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-06-03T12:28:03.619Z", "modified": "2025-09-12T11:18:06.902Z"}, {"entity": "publication", "iuid": "7c4997ed4db645119c39892493357126", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c4997ed4db645119c39892493357126.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c4997ed4db645119c39892493357126"}}, "title": "Cryo-Electron Microscopy Provides Mechanistic Insights into Solution-Dependent Polymorphism and Cross-Aggregation Phenomena of the Human and Rat Islet Amyloid Polypeptides.", "authors": [{"family": "Valli", "given": "Dylan", "initials": "D", "orcid": "0009-0005-6060-4169", "researcher": {"href": "https://publications.scilifelab.se/researcher/56aa1f7e1c77487a95cbe1070944dd3c.json"}}, {"family": "Ooi", "given": "Saik Ann", "initials": "SA"}, {"family": "Kaya", "given": "Ibrahim", "initials": "I"}, {"family": "Thomassen", "given": "Asger Berg", "initials": "AB", "orcid": "0009-0005-9503-5189", "researcher": {"href": "https://publications.scilifelab.se/researcher/3820df7bd16743738870314195f45e6b.json"}}, {"family": "Chaudhary", "given": "Himanshu", "initials": "H"}, {"family": "Weidner", "given": "Tobias", "initials": "T", "orcid": "0000-0002-7083-7004", "researcher": {"href": "https://publications.scilifelab.se/researcher/3387ad7c43da4e9b8535d7334ef0d40c.json"}}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}, {"family": "Maj", "given": "Micha\u0142", "initials": "M", "orcid": "0000-0003-1567-9514", "researcher": {"href": "https://publications.scilifelab.se/researcher/1be0f07d0c5f40adac62cf38f2244e79.json"}}], "type": "journal article", "published": "2025-06-17", "journal": {"title": "Biochemistry", "issn": "1520-4995", "volume": "64", "issue": "12", "pages": "2583-2595", "issn-l": "0006-2960"}, "abstract": "Inhibitors targeting amyloids formed by the human Islet Amyloid Polypeptide (hIAPP) are promising therapeutic candidates for type 2 diabetes. Peptide formulations derived from the nonamyloidogenic rat IAPP (rIAPP) sequence are currently used as hIAPP mimetics to support insulin therapy. rIAPP itself acts as a peptide inhibitor; yet, the structural-level consequences of such inhibition, particularly its impact on amyloid polymorphism, have not been studied in detail. Here, we conduct coaggregation experiments with varying rIAPP-to-hIAPP concentration ratios and employ high-resolution cryo-electron microscopy (Cryo-EM) to elucidate the polymorphism of the resulting fibril structures. Our results demonstrate that the polymorphism of hIAPP amyloids is highly sensitive to the electrostatic environment, which can be modulated by buffer composition, the concentration of the inhibitor, and cosolvents such as hexafluoroisopropanol (HFIP). Under native conditions, rIAPP associates with hIAPP but does not cross-aggregate, resulting in fibrils primarily composed of hIAPP. Significant inhibition is observed at relatively high concentrations of rIAPP. However, trace amounts of HFIP disrupt this inhibition, leading to increased fibril concentrations due to the formation of cross-seeded products composed of both hIAPP and rIAPP, as evidenced by mass spectrometry and two-dimensional infrared (2D IR) spectroscopy. These findings highlight the critical role of experimental conditions, particularly the electrostatic environment, in modulating amyloid polymorphism, cross-seeding, and inhibition. By providing structural insights into these processes, this study advances our understanding of peptide aggregation and offers valuable guidance for the rational design of more effective therapeutic inhibitors targeting hIAPP-related amyloidosis.", "doi": "10.1021/acs.biochem.5c00042", "pmid": "40417836", "labels": {"Spatial Mass Spectrometry": "Collaborative", "Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12177924"}], "notes": [], "created": "2025-11-21T09:46:23.350Z", "modified": "2025-11-24T16:05:13.234Z"}, {"entity": "publication", "iuid": "e423aa4f3d3743ffa8ead1c41ea5a808", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e423aa4f3d3743ffa8ead1c41ea5a808.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e423aa4f3d3743ffa8ead1c41ea5a808"}}, "title": "Beta-blockers prolong response to androgen deprivation therapy in prostate cancer through modulation of the neuro-immuno-oncology axis.", "authors": [{"family": "Thulin", "given": "Malin Hagberg", "initials": "MH"}, {"family": "Ramberg", "given": "H\u00e5kon", "initials": "H"}, {"family": "Nielsen", "given": "Heidi Kristin", "initials": "HK"}, {"family": "Grytli", "given": "Helene Hartvedt", "initials": "HH"}, {"family": "Sivanesan", "given": "Shivanthe", "initials": "S"}, {"family": "Pandya", "given": "Abhilash D", "initials": "AD"}, {"family": "Seip", "given": "Kotryna", "initials": "K"}, {"family": "Andressen", "given": "Kjetil Wessel", "initials": "KW"}, {"family": "Linder", "given": "Anna", "initials": "A", "orcid": "0000-0002-9444-1346", "researcher": {"href": "https://publications.scilifelab.se/researcher/38b4f1c441ff49b891db4d7fb8163491.json"}}, {"family": "\u00d8ijordsbakken", "given": "Miriam", "initials": "M"}, {"family": "Poutanen", "given": "Matti", "initials": "M"}, {"family": "Katz", "given": "Betina", "initials": "B"}, {"family": "Halvorsen", "given": "Bente", "initials": "B", "orcid": "0000-0002-6529-6485", "researcher": {"href": "https://publications.scilifelab.se/researcher/83218278a90c41609ea44fcd6315d395.json"}}, {"family": "M\u00e6landsmo", "given": "Gunhild Mari", "initials": "GM"}, {"family": "Task\u00e9n", "given": "Kristin Austlid", "initials": "KA", "orcid": "0000-0001-5530-4915", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c58b6542626483697216077c630309a.json"}}], "type": "journal article", "published": "2025-06-17", "journal": {"title": "J Transl Med", "issn": "1479-5876", "volume": "23", "issue": "1", "pages": "672", "issn-l": "1479-5876"}, "abstract": "The therapeutic impact of beta-blockers (BB), beta-adrenergic receptor antagonists, on prostate cancer remains controversial. The underlying health conditions of BB users complicate the ability to isolate and evaluate the specific effects of these drugs on the tumour cells. This study investigated whether BBs, by inhibiting sympathetic nerve signalling, extended the duration of androgen deprivation therapy (ADT) effectiveness in patients with de novo metastatic hormone sensitive prostate cancer and in prostate cancer xenograft models, while also uncovering the molecular mechanisms involved.\n\nAn analysis was conducted on prospectively collected data from the Cancer Registry of Norway, Norwegian Prescription Database, and Norwegian Cause of Death Registry focusing on patients with de novo metastatic prostate cancer undergoing ADT using the commencement of second-line treatment as the endpoint. In addition, the causal effect of BB treatment was studied in two different hormone-sensitive prostate cancer xenograft mouse models. Prior to treatment, mice were surgically castrated, to mimic ADT, and tumour progression was tracked by measuring serum PSA levels. RNA sequencing was performed on xenografted orthotopic tumours to investigate the underlying mechanisms, utilizing annotation based on human data and protein levels were validated by the Protein Simple Immunoassay. Immune-related effects were evaluated using immunohistochemistry on tumour tissue and measuring neopterin levels, along with 92 analytes, using the OLINK proximity extension assay on serum samples from xenografted mice and prostate cancer patients, both BB users and non-users.\n\nA competitive risk analysis indicated that BB treatment postponed the initiation of second-line treatment in prostate cancer patients on ADT. Additionally, in both prostate cancer xenograft models, BB treatment reduced tumour burden and delayed progression to castration-resistant prostate cancer. Mechanistically, BB treatment suppressed androgen receptor signalling and induced a metabolic shift by up-regulating oxidative phosphorylation transcripts and down-regulating those involved in fatty acid synthesis and the PI3K/AKT/mTOR pathway. Additionally, BB treatment increased serum pro-inflammatory cytokines, such as the IL23/IL17 axis, in both xenografted mice and in patient samples. Enhanced intra-tumoral CD68+ immune cell infiltration was also observed in the tumours.\n\nThe data suggest that BB combined with ADT delay the progression to castration-resistant prostate cancer. This may be achieved by influencing androgen receptor activity, adjusting energy metabolism and fostering a pro-inflammatory antitumoral microenvironment.", "doi": "10.1186/s12967-025-06644-7", "pmid": "40528241", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12175445"}, {"db": "pii", "key": "10.1186/s12967-025-06644-7"}], "notes": [], "created": "2025-07-08T13:57:28.735Z", "modified": "2025-11-04T11:53:28.029Z"}, {"entity": "publication", "iuid": "85bf454ae0ea47db840b8c216ce1dbd8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85bf454ae0ea47db840b8c216ce1dbd8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85bf454ae0ea47db840b8c216ce1dbd8"}}, "title": "Synthesis and Evaluation of Pseudoglucosinolates Releasing Isothiocyanates in the Presence of Azoreductases.", "authors": [{"family": "Chakrabarti", "given": "Aishi", "initials": "A", "orcid": "0009-0002-9704-0801", "researcher": {"href": "https://publications.scilifelab.se/researcher/74cbfb341f864b898bade9ee188639fe.json"}}, {"family": "Ganskow", "given": "Charity S G", "initials": "CSG", "orcid": "0000-0001-9779-4844", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c8663ca640e444ebf466126f4f0a592.json"}}, {"family": "Kagho", "given": "Mervic D", "initials": "MD", "orcid": "0000-0003-3714-7738", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0d7812a50e942f09ec2df8bb7d6e287.json"}}, {"family": "Jimidar", "given": "Claire C", "initials": "CC", "orcid": "0000-0002-2737-4374", "researcher": {"href": "https://publications.scilifelab.se/researcher/4edac4d70ce44a14b5fe8d79ddfa0eb0.json"}}, {"family": "Wiese", "given": "Lorenz", "initials": "L", "orcid": "0009-0002-1416-6231", "researcher": {"href": "https://publications.scilifelab.se/researcher/4182ca8b2ddf4d80a64df37d22e8b3a4.json"}}, {"family": "Beyazit", "given": "Neslihan", "initials": "N", "orcid": "0000-0002-5722-2400", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce21988b7734695ab1e80388c61faff.json"}}, {"family": "Beutling", "given": "Ulrike", "initials": "U"}, {"family": "Seeger", "given": "Margarita", "initials": "M", "orcid": "0000-0002-5609-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/d60b0512cc8647f68b9cf92db167fdca.json"}}, {"family": "Smits", "given": "Silvana", "initials": "S", "orcid": "0009-0006-0818-9006", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaa8fcc8ec794afa81c08f7517ba7fa5.json"}}, {"family": "Nystr\u00f6m", "given": "Stella", "initials": "S"}, {"family": "Farewell", "given": "Anne", "initials": "A", "orcid": "0000-0002-0841-4908", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3e0018041984a31b07fe5e75bf9a03b.json"}}, {"family": "Schallmey", "given": "Anett", "initials": "A", "orcid": "0000-0002-6670-0574", "researcher": {"href": "https://publications.scilifelab.se/researcher/4401c83d548c4946a13cbbfc80bc5aa5.json"}}, {"family": "Br\u00f6nstrup", "given": "Mark", "initials": "M", "orcid": "0000-0002-8971-7045", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1a6de4f8ba24330be8a7007aba5eab0.json"}}, {"family": "Klahn", "given": "Philipp", "initials": "P", "orcid": "0000-0003-4713-2345", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c6f067dc85a4e12b3593401e34e36d6.json"}}], "type": "journal article", "published": "2025-06-16", "journal": {"title": "ChemBioChem", "issn": "1439-7633", "volume": "26", "issue": "12", "pages": "e202500152", "issn-l": "1439-4227"}, "abstract": "Naturally occurring isothiocyanates (ITCs) display multiple interesting bioactivities, but their medicinal exploitation is very limited as ITCs are non-druglike compounds with problematic pharmacokinetic properties. The concept of pseudoglucosinolates provides a novel prodrug approach for the release of ITCs which can be adjusted to different triggers such as enzymatic and chemical microenvironments. Herein, the first adaptation of this concept toward the release of ITCs in the presence of azoreductases within a turn-on fluorescence probe is reported and its applicability in covalent protein labeling is underlined.", "doi": "10.1002/cbic.202500152", "pmid": "40345969", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12177692"}], "notes": [], "created": "2025-11-20T18:09:51.374Z", "modified": "2025-11-20T18:09:52.598Z"}, {"entity": "publication", "iuid": "a766e9c08ee74573bed64d1b46c492de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a766e9c08ee74573bed64d1b46c492de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a766e9c08ee74573bed64d1b46c492de"}}, "title": "Synthesis and Evaluation of Pseudo glucosinolates Releasing Isothiocyanates in the Presence of Azoreductases", "authors": [{"family": "Chakrabarti", "given": "Aishi", "initials": "A", "orcid": "0009-0002-9704-0801", "researcher": {"href": "https://publications.scilifelab.se/researcher/74cbfb341f864b898bade9ee188639fe.json"}}, {"family": "Ganskow", "given": "Charity S G", "initials": "CSG", "orcid": "0000-0001-9779-4844", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c8663ca640e444ebf466126f4f0a592.json"}}, {"family": "Kagho", "given": "Mervic D", "initials": "MD", "orcid": "0000-0003-3714-7738", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0d7812a50e942f09ec2df8bb7d6e287.json"}}, {"family": "Jimidar", "given": "Claire C", "initials": "CC", "orcid": "0000-0002-2737-4374", "researcher": {"href": "https://publications.scilifelab.se/researcher/4edac4d70ce44a14b5fe8d79ddfa0eb0.json"}}, {"family": "Wiese", "given": "Lorenz", "initials": "L", "orcid": "0009-0002-1416-6231", "researcher": {"href": "https://publications.scilifelab.se/researcher/4182ca8b2ddf4d80a64df37d22e8b3a4.json"}}, {"family": "Beyazit", "given": "Neslihan", "initials": "N", "orcid": "0000-0002-5722-2400", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce21988b7734695ab1e80388c61faff.json"}}, {"family": "Beutling", "given": "Ulrike", "initials": "U"}, {"family": "Seeger", "given": "Margarita", "initials": "M", "orcid": "0000-0002-5609-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/d60b0512cc8647f68b9cf92db167fdca.json"}}, {"family": "Smits", "given": "Silvana", "initials": "S", "orcid": "0009-0006-0818-9006", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaa8fcc8ec794afa81c08f7517ba7fa5.json"}}, {"family": "Nystr\u00f6m", "given": "Stella", "initials": "S"}, {"family": "Farewell", "given": "Anne", "initials": "A", "orcid": "0000-0002-0841-4908", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3e0018041984a31b07fe5e75bf9a03b.json"}}, {"family": "Schallmey", "given": "Anett", "initials": "A", "orcid": "0000-0002-6670-0574", "researcher": {"href": "https://publications.scilifelab.se/researcher/4401c83d548c4946a13cbbfc80bc5aa5.json"}}, {"family": "Br\u00f6nstrup", "given": "Mark", "initials": "M", "orcid": "0000-0002-8971-7045", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1a6de4f8ba24330be8a7007aba5eab0.json"}}, {"family": "Klahn", "given": "Philipp", "initials": "P", "orcid": "0000-0003-4713-2345", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c6f067dc85a4e12b3593401e34e36d6.json"}}], "type": "journal-article", "published": "2025-06-16", "journal": {"title": "ChemBioChem", "issn": "1439-4227", "volume": "26", "issue": "12", "issn-l": null}, "abstract": null, "doi": "10.1002/cbic.202500152", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:06:32.788Z", "modified": "2025-11-27T08:06:33.054Z"}, {"entity": "publication", "iuid": "6c6cbdbfe7064dcfb2e87e001b74625e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c6cbdbfe7064dcfb2e87e001b74625e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c6cbdbfe7064dcfb2e87e001b74625e"}}, "title": "Proteomic analysis of human kidney biopsies unveils emerging acute kidney injury very early after liver graft reperfusion.", "authors": [{"family": "Nor\u00e9n", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Boi", "given": "Roberto", "initials": "R"}, {"family": "Pullerits", "given": "Rille", "initials": "R"}, {"family": "M\u00f6lne", "given": "Johan", "initials": "J"}, {"family": "Ebefors", "given": "Kerstin", "initials": "K"}, {"family": "Friman", "given": "Styrbj\u00f6rn", "initials": "S"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Herlenius", "given": "Gustaf", "initials": "G"}, {"family": "Nystr\u00f6m", "given": "Jenny", "initials": "J"}, {"family": "Oltean", "given": "Mihai", "initials": "M", "orcid": "0000-0003-3783-5207", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a46e232d2644afbe9a4f3d89316a7a.json"}}], "type": "journal article", "published": "2025-06-16", "journal": {"title": "J Transl Med", "issn": "1479-5876", "volume": "23", "issue": "1", "pages": "658", "issn-l": "1479-5876"}, "abstract": "Acute kidney injury (AKI) is a frequent complication after liver transplantation (LT) and is associated with morbidity, mortality, and late development of chronic kidney disease. Risk factors for AKI after LT include patient, perioperative and graft-related factors. The exact renal molecular mechanisms behind AKI in LT are unclear.\n\nAlterations in the proteome were investigated in kidney biopsies from 21 patients undergoing LT using quantitative proteomics. The most upregulated protein was validated using immunohistochemistry. In addition, serum levels of interleukin (IL)-33, insulin-like growth factor binding protein (IGFBP)-7 and high-mobility group box (HMGB)-1 were analyzed. In silico data validation was performed using 14 recently published proteomics and transcriptomics datasets.\n\nIn post-reperfusion biopsies, we identified 731 differentially regulated proteins between patients with and without AKI. The most upregulated pathways were related to inflammation, integrin signaling and extracellular matrix (ECM) remodeling. The most downregulated pathways were traceable to a mitochondrial origin. HMGB-1 was found to be already upregulated (15%) 2 h after LT in patients who later developed AKI. The AKI group also showed upregulation of the alarmin IGFBP-7, caspases 1, 4 and 8, nuclear factor kappa B subunits, and the inflammasome adaptor protein PYCARD. Circulating IL-33 and HMGB-1 (but not IGFBP-7) increased during LT but returned to normal levels within 24 h. Altogether, these findings indicate ongoing inflammatory signaling activity in the kidneys of LT recipients who ultimately develop moderate or severe AKI shortly after liver graft reperfusion.\n\nLT induces extensive alarmin signaling and ECM remodeling in the kidneys of recipients who develop postoperative AKI. Further strategies to curtail this phenomenon are mandated. Trial registration https://www.researchweb.org/is/en/vgr/project/278585 , Registered 24 May 2022 (Retrospectively registered).", "doi": "10.1186/s12967-025-06695-w", "pmid": "40524147", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12172208"}, {"db": "pii", "key": "10.1186/s12967-025-06695-w"}], "notes": [], "created": "2025-10-23T09:39:17.958Z", "modified": "2025-10-23T09:39:18.049Z"}, {"entity": "publication", "iuid": "787108830f0c435ca9c7523b64600053", "links": {"self": {"href": "https://publications.scilifelab.se/publication/787108830f0c435ca9c7523b64600053.json"}, "display": {"href": "https://publications.scilifelab.se/publication/787108830f0c435ca9c7523b64600053"}}, "title": "Cardiovascular protein profiling in patients with first-episode psychosis.", "authors": [{"family": "Malmqvist", "given": "Anna", "initials": "A"}, {"family": "Eren", "given": "Feride", "initials": "F", "orcid": "0000-0001-6068-5329", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3d182fcac27441a8be3d8cec7f601d2.json"}}, {"family": "Schwieler", "given": "Lilly", "initials": "L"}, {"family": "Orhan", "given": "Funda", "initials": "F"}, {"family": "Fatouros-Bergman", "given": "Helena", "initials": "H"}, {"family": "Flyckt", "given": "Lena", "initials": "L", "orcid": "0000-0003-2680-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1639aee0337479499d2639e66fb4080.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Cervenka", "given": "Simon", "initials": "S"}, {"family": "B\u00e4ck", "given": "Magnus", "initials": "M"}, {"family": "Sellgren", "given": "Carl M", "initials": "CM", "orcid": "0000-0001-9103-2785", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c0740ddfd6d4c98988b2a19096a9814.json"}}, {"family": "Engberg", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-1659-5232", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c02408e77944e6b90c3b8fb81400191.json"}}, {"family": "Erhardt", "given": "Sophie", "initials": "S", "orcid": "0000-0001-7359-5250", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef85d6ecce13432c9b67192efa9b2567.json"}}], "type": "journal article", "published": "2025-06-14", "journal": {"title": "Schizophrenia (Heidelb)", "issn": "2754-6993", "volume": "11", "issue": "1", "pages": "88", "issn-l": null}, "abstract": "Patients with schizophrenia have a threefold higher mortality from cardiovascular disease than people in the general population. Atherosclerosis is linked to immune activation, a process tentatively entwined with the underlying pathophysiological mechanisms of schizophrenia. The aim of the present study was to investigate an extensive array of cardiovascular biomarkers in individuals experiencing their first episode of psychosis (FEP), either drug-na\u00efve or exposed to short-term antipsychotic treatment, alongside a group of healthy controls (HC). Using the OLINK Proximity Extension Assay, Cardiovascular II Panel, we analyzed plasma from 72 FEP patients, including 42 later diagnosed with schizophrenia and 54 HCs. Biomarker levels, that significantly differed between patients and controls, were correlated with symptom severity, cognitive performance and cardiovascular risk factors. Fifteen out of 92 cardiovascular biomarkers were higher in individuals with FEP compared to HC, and one biomarker was lower in FEP patients compared to HC. BMI, waist size, blood pressure, fp-glucose, HbA1c and serum lipid levels were similar between the groups. No correlations that held for multiple comparisons were seen between biomarker concentrations and symptom severity, cognitive performance or cardiovascular risk factors in FEP patients. Higher concentrations of several cardiovascular biomarkers were observed in individuals with FEP compared to in HC. This suggests that patients with FEP are at an increased risk of developing cardiovascular disease from the onset of psychosis, even before changes in traditional biomarkers are detectable. It underscores the need for innovative approaches to detect and monitor this risk early.", "doi": "10.1038/s41537-025-00633-x", "pmid": "40517141", "labels": {"Affinity Proteomics Uppsala": "Service", "Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12167380"}, {"db": "pii", "key": "10.1038/s41537-025-00633-x"}], "notes": [], "created": "2025-11-25T19:22:27.206Z", "modified": "2025-11-25T21:34:22.441Z"}, {"entity": "publication", "iuid": "d7516c3dcf1d40f885a03f6e3f2e3c26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7516c3dcf1d40f885a03f6e3f2e3c26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7516c3dcf1d40f885a03f6e3f2e3c26"}}, "title": "Genomic Analysis of Trichotillomania.", "authors": [{"family": "Halvorsen", "given": "Matthew W", "initials": "MW"}, {"family": "Garrett", "given": "Melanie E", "initials": "ME"}, {"family": "Cuccaro", "given": "Michael L", "initials": "ML"}, {"family": "Ashley-Koch", "given": "Allison E", "initials": "AE"}, {"family": "Crowley", "given": "James J", "initials": "JJ"}], "type": "journal article", "published": "2025-06-13", "journal": {"title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn": "1552-485X", "pages": "e33035", "issn-l": "1552-4841"}, "abstract": "Trichotillomania (TTM) is a psychiatric condition in which people feel an overwhelming urge to pull out their hair, resulting in noticeable hair loss and significant distress. Twin and family studies suggest that TTM is at least partly genetic, but no genome-wide analyses have been completed. To fill the gap in this field, we have conducted a case-control study of genotype array data from 101 European ancestry TTM cases and 488 ancestry-matched unaffected controls. TTM cases were ascertained in the United States through web-based recruitment, patient support groups, and conferences organized by the Trichotillomania Learning Center. Following clinical confirmation of a TTM diagnosis, patients completed self-report assessments of frequency and duration of hair pulling, other psychiatric symptoms, and family history. Unaffected controls were also ascertained in the United States and were matched to cases by ancestry. In the first formal genome-wide association study of TTM, we did not identify any common variants with a genome-wide significant (p < 5 \u00d7 10-8) association level with case status. We found that cases carry a higher load of common polygenic risk for psychiatric disorders (p = 0.008). We also detected copy number variants previously associated with neuropsychiatric disorders (specifically, deletions in NRXN1, CSMD1, and 15q11.2). These results further support genetics' role in the etiology of TTM and suggest that larger studies are likely to identify risk variation and, ultimately, specific risk genes associated with the condition.", "doi": "10.1002/ajmg.b.33035", "pmid": "40511557", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2090990"}, {"db": "pmc", "key": "PMC12354282"}], "notes": [], "created": "2025-09-08T07:02:43.198Z", "modified": "2025-09-08T07:02:43.211Z"}, {"entity": "publication", "iuid": "4ab36094824b49f9b5c0f08fa6ce17cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ab36094824b49f9b5c0f08fa6ce17cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ab36094824b49f9b5c0f08fa6ce17cb"}}, "title": "Early-Life Diet Diversity and the Subsequent Risk of Inflammatory Bowel Disease: Findings From Two Scandinavian Birth Cohorts.", "authors": [{"family": "Guo", "given": "Annie", "initials": "A", "orcid": "0000-0003-4635-1183", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cd6b08ddc81426aadf53933500955bf.json"}}, {"family": "Ludvigsson", "given": "Johnny", "initials": "J"}, {"family": "H\u00e5rd Af Segerstad", "given": "Elin M", "initials": "EM"}, {"family": "Brants\u00e6ter", "given": "Anne Lise", "initials": "AL"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "St\u00f8rdal", "given": "Ketil", "initials": "K"}, {"family": "M\u00e5rild", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2025-06-13", "journal": {"title": "Inflamm Bowel Dis", "issn": "1536-4844", "volume": "31", "issue": "6", "pages": "1493-1501", "issn-l": null}, "abstract": "Diet diversity in early childhood promotes microbial diversity, influences the developing immune system, and has been linked to a reduced risk of immune-mediated diseases. This study aimed to determine the association between childhood diet diversity and later inflammatory bowel disease (IBD), for which data are limited.\n\nQuestionnaire data from the population-based birth cohorts All Babies in Southeast Sweden (ABIS) and the Norwegian Mother, Father, and Child Cohort (MoBa), including participants from Southeast Sweden and Norway, were used to estimate a diet diversity score at ages 1 and 3 years. This score represents the diversity of intakes across 5 food groups comprising 11 subgroups. A higher score signifies higher diet diversity. We used linked health registry data to identify IBD diagnoses up to the year 2021. Cox regression and random-effect models were used to estimate pooled hazard ratios (aHRs) adjusted for sociodemographics, breastfeeding, and early-life antibiotic use.\n\nAmong 81 272 children with 1 304 325 person-years of follow-up, 307 developed IBD. Diet diversity at ages 1 and 3 years was in pooled analyses not associated with later IBD (per one-unit increase, aHR = 0.96 [95% CI = 0.81-1.14] and aHR = 0.96 [95% CI = 0.83-1.11]). In MoBa, but not ABIS, a higher diet diversity at 1 and 3 years of age was inversely associated with ulcerative colitis (UC) (per one-unit increase, aHR = 0.78 [95% CI = 0.66-0.94] and aHR = 0.78 [95% CI = 0.65-0.95]). Still, pooled aHRs for UC as well as Crohn's disease approximated one.\n\nIn this prospective study of 2 Scandinavian birth cohorts, no association was observed between early-life diet diversity and the subsequent risk of IBD.", "doi": "10.1093/ibd/izae210", "pmid": "39276084", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12166299"}, {"db": "pii", "key": "7758013"}], "notes": [], "created": "2024-11-01T08:23:03.766Z", "modified": "2025-11-04T11:35:47.152Z"}, {"entity": "publication", "iuid": "ead989ea22be400abf08c96a2de3f6c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ead989ea22be400abf08c96a2de3f6c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ead989ea22be400abf08c96a2de3f6c0"}}, "title": "RNA transcripts regulate G-quadruplex landscapes through G-loop formation.", "authors": [{"family": "Sato", "given": "Koichi", "initials": "K", "orcid": "0000-0002-0574-774X", "researcher": {"href": "https://publications.scilifelab.se/researcher/419db8b1c9a142d8994dc12727020ed4.json"}}, {"family": "Lyu", "given": "Jing", "initials": "J"}, {"family": "van den Berg", "given": "Jeroen", "initials": "J", "orcid": "0000-0002-9430-7155", "researcher": {"href": "https://publications.scilifelab.se/researcher/d81ddd6ecb4e4654aef53c4388448204.json"}}, {"family": "Braat", "given": "Diana", "initials": "D", "orcid": "0009-0003-1086-7185", "researcher": {"href": "https://publications.scilifelab.se/researcher/8028609fa976407c9f756fa4640b9012.json"}}, {"family": "Cruz", "given": "Victoria M", "initials": "VM", "orcid": "0000-0001-5385-1472", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8d30dbce78446cc8b327a0df98ce69c.json"}}, {"family": "Navarro Luz\u00f3n", "given": "Carmen", "initials": "C", "orcid": "0000-0001-5438-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}}, {"family": "Schimmel", "given": "Joost", "initials": "J", "orcid": "0000-0002-2620-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a37bb4f3de34d3c8c9fffab2d3a6d0c.json"}}, {"family": "Esteban-Jurado", "given": "Clara", "initials": "C"}, {"family": "Alemany", "given": "Ma\u00eblys", "initials": "M", "orcid": "0009-0004-3277-6206", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc9d305d46084a598ff3eeb47127d700.json"}}, {"family": "Dreyer", "given": "Jan", "initials": "J"}, {"family": "Hendrikx", "given": "Aiko", "initials": "A"}, {"family": "Mattiroli", "given": "Francesca", "initials": "F", "orcid": "0000-0002-1574-7217", "researcher": {"href": "https://publications.scilifelab.se/researcher/0afa3a260bfb4e49b2ed1ef9b3af3357.json"}}, {"family": "van Oudenaarden", "given": "Alexander", "initials": "A", "orcid": "0000-0002-9442-3551", "researcher": {"href": "https://publications.scilifelab.se/researcher/86e54078e6ea45949e7468b2653601d9.json"}}, {"family": "Tijsterman", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8465-9002", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1e816845f6048e2a2c7dc29e9a13cdf.json"}}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Knipscheer", "given": "Puck", "initials": "P", "orcid": "0000-0003-4198-0132", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0b1d8281b234a30b7e450f2759559c2.json"}}], "type": "journal article", "published": "2025-06-12", "journal": {"title": "Science", "issn": "1095-9203", "volume": "388", "issue": "6752", "pages": "1225-1231", "issn-l": "0036-8075"}, "abstract": "G-quadruplexes (G4s) are prevalent DNA structures that regulate transcription but also threaten genome stability. How G4 dynamics are controlled remains poorly understood. Here, we report that RNA transcripts govern G4 landscapes through coordinated G-loop assembly and disassembly. G-loop assembly involves activation of the ATM and ATR kinases, followed by homology-directed invasion of RNA opposite the G4 strand mediated by BRCA2 and RAD51. Disassembly of the G-loop resolves the G4 structure through DHX36-FANCJ-mediated G4 unwinding, which triggers nucleolytic incision and subsequent hybrid strand renewal by DNA synthesis. Inhibition of G-loop disassembly causes global G4 and R-loop accumulation, leading to transcriptome dysregulation, replication stress, and genome instability. These findings establish an intricate G-loop assembly-disassembly mechanism that controls G4 landscapes and is essential for cellular homeostasis and survival.", "doi": "10.1126/science.adr0493", "pmid": "40504899", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:51:58.676Z", "modified": "2025-11-28T10:51:59.081Z"}, {"entity": "publication", "iuid": "5993e1e4e51044008a8a228e19ce6f0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5993e1e4e51044008a8a228e19ce6f0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5993e1e4e51044008a8a228e19ce6f0b"}}, "title": "Deep plasma proteomics identifies and validates an eight-protein biomarker panel that separate benign from malignant tumors in ovarian cancer.", "authors": [{"family": "Moskov", "given": "Mikaela", "initials": "M"}, {"family": "Hedlund Lindberg", "given": "Julia", "initials": "J"}, {"family": "Lycke", "given": "Maria", "initials": "M"}, {"family": "Ivansson", "given": "Emma", "initials": "E", "orcid": "0000-0002-4630-1576", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d2acd6a50fe49178f424c55df0a6b51.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Sundfeldt", "given": "Karin", "initials": "K"}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}], "type": "journal article", "published": "2025-06-12", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "230", "issn-l": null}, "abstract": "Ovarian cancer has the highest mortality of all gynecological cancers and surgery is commonly used as final diagnostic. Available literature indicates that women with benign tumors could often be conservatively managed, but accurate molecular tests are needed for triaging when gold-standard imaging techniques are inconclusive or lacking.\n\nHere, we analyzed 5416 plasma proteins in two independent cohorts (N1 = 171, N2 = 233) with women surgically diagnosed with benign or malignant tumors. Using one cohort as discovery, we compared protein levels of benign tumors with early stage (I-II), late stage (III-IV) or any stage (I-IV) ovarian cancer and trained risk-score reporting multivariate models including a fixed cut-off for malignancy. Associations and model performance was then evaluated in the replication cohort.\n\nWe identify 327 biomarker associations, corresponding to 191 unique proteins, and replicate 326 (99.7%). By comparing the 191 proteins with their corresponding tumor gene expression we find that only 11% (21/191) have significant correlation. Through analyzes of protein-protein correlation networks, we find that 62 of the 191 proteins have high correlation with at least one other protein, suggesting that many of the associations are secondary effects. In the replication cohort, our model has areas under the curve (AUC = 0.96) corresponding to 97% sensitivity at 68% specificity. For early-stage tumors, we estimate the sensitivity to 91% at a specificity of 68% as compared to 85% and 54% for CA-125 alone.\n\nOur results indicates that up to one third of benign cases can be identified by molecular measures thereby reducing the need for diagnostic surgery.", "doi": "10.1038/s43856-025-00945-0", "pmid": "40506476", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12162877"}, {"db": "pii", "key": "10.1038/s43856-025-00945-0"}], "notes": [], "created": "2025-09-08T07:17:14.990Z", "modified": "2025-11-14T11:07:27.366Z"}, {"entity": "publication", "iuid": "7f700b3e5e634b2295705bc2ae62f3eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f700b3e5e634b2295705bc2ae62f3eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f700b3e5e634b2295705bc2ae62f3eb"}}, "title": "Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons.", "authors": [{"family": "Krauter", "given": "Doris", "initials": "D", "orcid": "0000-0002-1779-093X", "researcher": {"href": "https://publications.scilifelab.se/researcher/631f89b570c44663b8c6a29f0759aca2.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J", "orcid": "0000-0003-1540-5193", "researcher": {"href": "https://publications.scilifelab.se/researcher/96dfeacf7fe04bf099fbddf0c45ef693.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2025-06-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "908", "issn-l": "2399-3642"}, "abstract": "Heterogeneity among somatosensory neurons is necessary for internal and external sensation. Precise patterns of gene transcription orchestrated through enhancer activation maintain heterogeneity. Thus, high-resolution cell type classification, chromatin accessibility and its relation to enhancer activation can explain the governing principles for sensory neuron heterogeneity. Here, we present an integrated atlas from published high-quality scRNA-seq datasets and resequencing the dorsal root ganglion, including over 44,000 neurons. MERSCOPE spatial transcriptomics confirms cell types in situ, including previously unrecognized neuronal types, and a spatial zonation of both neurons and non-neuronal cells. We present a cell type specific open chromatin atlas revealing enhancer driven regulons and gene-regulatory networks organized into co-regulated gene-programs that together define sensory neuron diversity. Cell type complexity is shown to be generated by layered co-regulated transcriptional modules representing shared functions across different scales of the neuronal type hierarchy with cell type specific contribution as the exception.", "doi": "10.1038/s42003-025-08315-1", "pmid": "40500276", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12159162"}, {"db": "pii", "key": "10.1038/s42003-025-08315-1"}], "notes": [], "created": "2025-07-18T10:23:45.299Z", "modified": "2025-11-14T11:07:16.782Z"}, {"entity": "publication", "iuid": "347e692b0c264b76bcc65c0e8231ec83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/347e692b0c264b76bcc65c0e8231ec83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/347e692b0c264b76bcc65c0e8231ec83"}}, "title": "Exploring the O-glycomic Degradome Using Natural Mucin Libraries.", "authors": [{"family": "Tofthagen", "given": "Marthe", "initials": "M"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Patel", "given": "Piyush", "initials": "P"}, {"family": "Sj\u00f6berg", "given": "Fei", "initials": "F"}, {"family": "Luis", "given": "Ana S", "initials": "AS"}, {"family": "Maciej-Hulme", "given": "Marissa L", "initials": "ML"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal article", "published": "2025-06-11", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2942", "pages": "145-156", "issn-l": "1064-3745"}, "abstract": "The interactions between intestinal mucins and the gut microbiota significantly influence digestive processes, metabolic activities, and pathogen resistance in the gastrointestinal tract. To explore this dynamic relationship, this chapter describes a workflow for studying the degradation of mucin oligosaccharides from isolated mucins. The approach involves purifying mucins from intestinal tissues and then subjecting them to a mixture of fecal glycosidases originating from commensal bacteria. The remaining oligosaccharides attached to the mucins after glycosidase treatment are released and then characterized and quantified using liquid chromatography-mass spectrometry (LC-MS)2. This approach identifies relevant intestinal oligosaccharides that are degraded by commensal flora. By combining natural oligosaccharide characterization with measurement of their degradation, we expand the repertoire of glycan structures for studying the intestinal glycomic degradome. Few commercially available characterized glycans or glycoproteins exist that cover the unique type of glycan mixtures found in the intestines where most microbes in the gastrointestinal tract reside. The presented workflow uses relevant glyco-substrates to investigate mucus degradation patterns, which are crucial for discerning pathological conditions associated with intestinal dysbiosis.", "doi": "10.1007/978-1-0716-4627-4_12", "pmid": "40498313", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-23T13:27:11.477Z", "modified": "2025-11-20T18:35:23.766Z"}, {"entity": "publication", "iuid": "4ebe944497c84c018f0043418df03daa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ebe944497c84c018f0043418df03daa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ebe944497c84c018f0043418df03daa"}}, "title": "Daily profiles of plasma short-chain fatty acids after the intake of three different cereal fibers: a randomized controlled study.", "authors": [{"family": "Costabile", "given": "Giuseppina", "initials": "G", "orcid": "0000-0001-5761-8002", "researcher": {"href": "https://publications.scilifelab.se/researcher/098c45ceafa349ad854cb8ce6a37bc2a.json"}}, {"family": "Vitale", "given": "Marilena", "initials": "M"}, {"family": "Testa", "given": "Roberta", "initials": "R"}, {"family": "Rivieccio", "given": "Annamaria", "initials": "A"}, {"family": "Palmn\u00e4s", "given": "Marie", "initials": "M"}, {"family": "Lopez-Sanchez", "given": "Patricia", "initials": "P"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Riccardi", "given": "Gabriele", "initials": "G"}, {"family": "Giacco", "given": "Rosalba", "initials": "R"}], "type": "journal article", "published": "2025-06-11", "journal": {"title": "Eur J Nutr", "issn": "1436-6207", "volume": "64", "issue": "5", "pages": "217", "issn-l": null}, "abstract": "To evaluate plasma short-chain fatty acids (SCFA) profiles after the acute intake of cereal fibers in overweight individuals.\n\nIn a randomized, controlled cross-over study, twenty overweight/obese individuals, 30-75 years, consumed at one-week interval three products, each containing 11 g fiber (arabinoxylan (AX), wheat bran or cellulose) during a standard breakfast meal. Plasma samples were collected at fasting, for 8-h after breakfast and on the following morning. SCFAs were measured by LC-MS/MS.\n\nPlasma acetate, propionate and butyrate increased after the three test fibers (p = 0.0001, time effect). The acetate peak was observed between 300 and 360 min after all test fibers (p < 0.05-0.003). Propionate increased significantly by 60 min after AX (p = 0.017) and wheat bran (p = 0.036) while butyrate increased only after AX (p = 0.038). A second peak was observed for propionate at 390 min after AX (p = 0.065) and wheat bran (p = 0.037) and for butyrate only after wheat bran (p = 0.024), remaining above baseline until the morning after. No significant difference was observed between the average daily plasma concentrations of acetate, propionate and butyrate. A very high inter- and intra-subjects' variability of SCFA response was observed. Cluster analysis identified high and low SCFA producers after fiber ingestion among the study participants.\n\nAfter fiber ingestion plasma kinetics of acetate differ from those of butyrate and propionate. Among the tested fibers, AX and wheat bran show a better intestinal fermentation ability than cellulose. Heterogeneity in the fermentation ability exists among study participants, with half of them having a minimal SCFA increase after fiber ingestion.\n\nNCT05443828; https://classic.\n\ngov/ct2/show/NCT05443828.", "doi": "10.1007/s00394-025-03741-7", "pmid": "40498116", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s00394-025-03741-7"}, {"db": "ClinicalTrials.gov", "key": "NCT05443828"}], "notes": [], "created": "2025-12-01T05:42:37.763Z", "modified": "2025-12-01T05:42:37.874Z"}, {"entity": "publication", "iuid": "cab93e2072c94a28915de34b2869b27e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cab93e2072c94a28915de34b2869b27e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cab93e2072c94a28915de34b2869b27e"}}, "title": "Associations between physical activity and CVD-related metabolomic and proteomic biomarkers.", "authors": [{"family": "Ekblom", "given": "\u00d6rjan", "initials": "\u00d6", "orcid": "0000-0001-6058-4982", "researcher": {"href": "https://publications.scilifelab.se/researcher/8516b23568bd46d4beb6e50a7088d387.json"}}, {"family": "Bj\u00f6rkbacka", "given": "Harry", "initials": "H", "orcid": "0000-0003-3918-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f4c07bc840f491d843f67a9932d5f3a.json"}}, {"family": "B\u00f6rjesson", "given": "Mats", "initials": "M"}, {"family": "Ekblom-Bak", "given": "Elin", "initials": "E", "orcid": "0000-0002-3901-7833", "researcher": {"href": "https://publications.scilifelab.se/researcher/127054fb7e954e6c8dae39c39c6c63ba.json"}}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Caidahl", "given": "Kenneth", "initials": "K", "orcid": "0000-0002-5079-9696", "researcher": {"href": "https://publications.scilifelab.se/researcher/c54c79603a954f9e81d2b82470e3ec36.json"}}, {"family": "Ehrenborg", "given": "Ewa", "initials": "E", "orcid": "0000-0003-1993-2468", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b48ca2016954380a63df7ecbd09373b.json"}}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Engvall", "given": "Jan", "initials": "J", "orcid": "0000-0002-5716-5098", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dc825fc91ea40afa83516f8fd649b97.json"}}, {"family": "Erlinge", "given": "David", "initials": "D"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Jernberg", "given": "Tomas", "initials": "T", "orcid": "0000-0003-1695-379X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbe08775f7a047ffa46bf6e065c776c9.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Molnar", "given": "David", "initials": "D"}, {"family": "Oldgren", "given": "Jonas", "initials": "J"}, {"family": "Rawshani", "given": "Aidin", "initials": "A"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S"}, {"family": "Wennberg", "given": "Patrik", "initials": "P"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ"}], "type": "journal article", "published": "2025-06-11", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "6", "pages": "e0325720", "issn-l": "1932-6203"}, "abstract": "Habitual physical activity (PA) affects metabolism and homeostasis in various tissues and organs. However, detailed knowledge of associations between PA and cardiovascular disease (CVD) risk markers is limited. We sought to identify associations between accelerometer-assessed PA classes and 183 proteomic and 154 metabolomic CVD-related biomarkers.\n\nWe utilized cross-sectional data from the main SCAPIS cohort (n = 4647, median age: 57.5 yrs, 50.5% female) as a discovery sample and the SCAPIS pilot cohort (n = 910, median age: 57.5 yrs, 50.3% female) as a validation sample. PA was assessed via hip-worn accelerometers, while plasma concentrations of proteomic biomarkers were measured using Olink CVD II and III panels. Metabolomic markers were assessed using the Nightingale NMR platform. We evaluated associations between four PA classes (moderate-to-vigorous PA [MVPA], low-intensity PA [LIPA], sedentary [SED], and prolonged SED [prolSED]) and biomarkers, controlling for potential confounders and applying a false discovery rate of 5% using multiple linear regressions.\n\nA total of eighty-five metabolomic markers and forty-three proteomic markers were validated and found to be significantly associated with one or more PA classes. LIPA and SED markers demonstrated significant mirroring or opposing relations to biomarkers, while prolSED mainly shared relations with SED. Notably, HDL species were predominantly negatively associated with SED, whereas LDL species were positively associated with SED and negatively associated with MVPA. Among the proteomic markers, eighteen were uniquely associated with MVPA (among those Interleukin - 6 [IL6] and Growth/differentiation factor 15 [GDF15] both negatively related), seven with SED (among those Metalloproteinase inhibitor 4 [TIMP4] and Tumor necrosis factor receptor 2 [TNFR2], both positively related), and eight were related to both SED/prolSED (among those Lipoprotein lipase [LPL] negatively related to SED and leptin [LEP] positively related to SED) and MVPA (with LPL positively related to MVPA and LEP negatively related to MVPA).\n\nOur findings suggest the existence of specific associations between PA classes and metabolomic and cardiovascular protein biomarkers in a middle-aged population. Beyond validation of previous results, we identified new associations. This multitude of connections between PA and CVD-related markers may help elucidate the previously observed relationship between PA and CVD. The identified cross-sectional associations could inform the design of future experimental studies, serving as important outcome measures.", "doi": "10.1371/journal.pone.0325720", "pmid": "40498722", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12157240"}, {"db": "pii", "key": "PONE-D-24-56786"}], "notes": [], "created": "2025-11-25T19:22:29.643Z", "modified": "2025-11-25T19:22:29.858Z"}, {"entity": "publication", "iuid": "7e6fe197fa52413bbf069e2dd7171511", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e6fe197fa52413bbf069e2dd7171511.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e6fe197fa52413bbf069e2dd7171511"}}, "title": "Revised Diffusion Law Permits Quantitative Nanoscale Characterization of Membrane Organization.", "authors": [{"family": "Svobodov\u00e1", "given": "Barbora", "initials": "B"}, {"family": "\u0160t'astn\u00fd", "given": "David", "initials": "D"}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "Mikhalyov", "given": "Ilya", "initials": "I"}, {"family": "Gretskaya", "given": "Natalia", "initials": "N"}, {"family": "Ballekov\u00e1", "given": "Alena", "initials": "A", "orcid": "0000-0002-4969-8361", "researcher": {"href": "https://publications.scilifelab.se/researcher/4de2e94b6e464fe6b5740bf0c83a9170.json"}}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Hof", "given": "Martin", "initials": "M", "orcid": "0000-0003-2884-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ee7e14809ee4a579220428faa1cb058.json"}}, {"family": "\u0160achl", "given": "Radek", "initials": "R", "orcid": "0000-0002-0441-3908", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b156d9020064ad7badda162f54f7a6a.json"}}], "type": "journal article", "published": "2025-06-10", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "97", "issue": "22", "pages": "11478-11485", "issn-l": "0003-2700"}, "abstract": "The formation of functional nanoscopic domains is an inherent property of plasma membranes. Stimulated emission depletion combined with fluorescence correlation spectroscopy (STED-FCS) has been previously used to identify such domains; however, the information obtained by STED-FCS has been limited to the presence of such domains while crucial parameters have not been accessible, such as size (Rd), the fraction of occupied membrane surface (f), in-membrane lipid diffusion inside (Din) and outside (Dout) the nanodomains as well as their self-diffusion (Dd). Here, we introduce a quantitative approach based on a revised interpretation of the diffusion law. By analyzing experimentally recorded STED-FCS diffusion law plots using a comprehensive library of simulated diffusion law plots, we extract these five parameters from STED-FCS data. That approach is verified on ganglioside nanodomains in giant unilamellar vesicles, validating the Saffman-Delbr\u00fcck assumption for Dd. STED-FCS data in both plasma membranes of living PtK2 cells and giant plasma membrane vesicles are examined, and a quantitative framework for molecular diffusion modes in biological membranes is presented.", "doi": "10.1021/acs.analchem.5c00021", "pmid": "40437882", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-06-13T18:27:49.253Z", "modified": "2025-06-13T18:27:49.584Z"}, {"entity": "publication", "iuid": "ce713a21963c48ea9389dc8b6dbfa37f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce713a21963c48ea9389dc8b6dbfa37f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce713a21963c48ea9389dc8b6dbfa37f"}}, "title": "Melamine-Based Molecularly Imprinted Monoliths Targeting Glyphosate in Aqueous Media: Synthesis and Binding Mechanism Elucidation.", "authors": [{"family": "Huynh", "given": "Chau Minh", "initials": "CM"}, {"family": "Luong", "given": "N Tan", "initials": "NT"}, {"family": "Nguyen", "given": "Trung", "initials": "T"}, {"family": "Dinh", "given": "Ngoc Phuoc", "initials": "NP"}, {"family": "Boily", "given": "Jean-Fran\u00e7ois", "initials": "JF", "orcid": "0000-0003-4954-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a8cc96018014a97a0ab7e99b4fc0eb5.json"}}, {"family": "Irgum", "given": "Knut", "initials": "K", "orcid": "0000-0003-3457-7564", "researcher": {"href": "https://publications.scilifelab.se/researcher/a53af6b9ed8a45748869319a088b15bf.json"}}], "type": "journal article", "published": "2025-06-10", "journal": {"title": "ACS Omega", "issn": "2470-1343", "volume": "10", "issue": "22", "pages": "22412-22425", "issn-l": "2470-1343"}, "abstract": "Cross-linked melamine imprinted monoliths targeting glyphosate were synthesized using 4-phosphonobutanoic acid (PBA) and N-(phosphonomethyl)-iminodiacetic acid (PMIDA) as templates. The binding capacities, evaluated in an aqueous medium, showed that both PMIDA and PBA promoted selective binding sites with imprinting factors of 2.5 and 1.7, respectively. Despite a relatively low imprinting factor, the polymer imprinted with PMIDA showed a noticeably higher binding efficiency in the presence of sodium chloride compared to the nonimprinted reference, demonstrating an ability to selectively target the desired analytes in real sample matrices. Spectroscopic investigations using Fourier transform infrared and 1H nuclear magnetic resonance spectroscopy revealed the formation of \"memory pockets\" for glyphosate molecules in the imprinted melamine-formaldehyde scaffold promoted by simultaneous contributions from (i) hydrogen bonding with N-H/O-H moieties and (ii) electrostatic interaction toward the triazine ring.", "doi": "10.1021/acsomega.4c06690", "pmid": "40521448", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12163837"}], "notes": [], "created": "2025-09-10T14:22:11.304Z", "modified": "2025-10-17T13:03:52.271Z"}, {"entity": "publication", "iuid": "43c900f054f54ac892c881ee00972405", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43c900f054f54ac892c881ee00972405.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43c900f054f54ac892c881ee00972405"}}, "title": "Genomic insights into antimicrobial resistance and virulence of E. coli in central Ethiopia: a one health approach.", "authors": [{"family": "Chekole", "given": "Wagaw Sendeku", "initials": "WS"}, {"family": "Potgieter", "given": "Lizel", "initials": "L"}, {"family": "Adamu", "given": "Haileeyesus", "initials": "H"}, {"family": "Sternberg-Lewerin", "given": "Susanna", "initials": "S"}, {"family": "Tessema", "given": "Tesfaye Sisay", "initials": "TS"}, {"family": "Magnusson", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2025-06-10", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "16", "pages": "1597580", "issn-l": "1664-302X"}, "abstract": "Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among E. coli isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as E. coli, later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were bla-ampH (90.9%), bla-AmpC1 (89.6%), tet(A) (84.4%), mdf(A) (81.8%), aph(3\")-Ib (79%), sul2 (79%), aph(6)-Id (75%), and bla-PBP (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI \u2265 0.5). In eight isolates, mutations in the gyrA (3) and par-C/E (5) genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were Tn3 with bla-TEM-105 (34), Int1 with sul1 (13), and dhfr7 (11). Meanwhile, the most frequently detected VGs (n \u2265 71 isolates) included elfA-G, fimB-I, hcpA-C, espL, ibeC, entA, fepA-C, ompA, ecpA-E, fepD, fes, and ibeB. Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.", "doi": "10.3389/fmicb.2025.1597580", "pmid": "40556891", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12185407"}], "notes": [], "created": "2025-09-08T07:13:07.348Z", "modified": "2025-09-08T07:13:07.354Z"}, {"entity": "publication", "iuid": "cbd3115766d1403b90d47770ed1ebec6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbd3115766d1403b90d47770ed1ebec6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbd3115766d1403b90d47770ed1ebec6"}}, "title": "Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia.", "authors": [{"family": "Bergholm", "given": "Julia", "initials": "J"}, {"family": "Tessema", "given": "Tesfaye Sisay", "initials": "TS"}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "Berg", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2025-06-07", "journal": {"title": "Virol J", "issn": "1743-422X", "volume": "22", "issue": "1", "pages": "188", "issn-l": "1743-422X"}, "abstract": "Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia.\n\nFecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis.\n\nThe metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses.\n\nTo our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses.", "doi": "10.1186/s12985-025-02821-8", "pmid": "40483486", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12145588"}, {"db": "pii", "key": "10.1186/s12985-025-02821-8"}, {"db": "BioProject", "key": "PRJNA1224038"}, {"db": "SRA", "key": "PRJNA1224038"}, {"db": "GENBANK", "key": "PV076094-PV076105."}, {"db": "GENBANK", "key": "PV053516"}, {"db": "GENBANK", "key": "PV061389-PV061398"}], "notes": [], "created": "2025-06-09T05:48:13.273Z", "modified": "2025-11-14T11:08:51.197Z"}, {"entity": "publication", "iuid": "c88fc4c3f1e943478813ffc698da32c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c88fc4c3f1e943478813ffc698da32c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c88fc4c3f1e943478813ffc698da32c4"}}, "title": "Exploring Fungal Communities in the Needles of Marginal Conifer Tree Populations", "authors": [{"family": "Lazarevi\u0107", "given": "Jelena", "initials": "J", "orcid": "0000-0002-9460-7342", "researcher": {"href": "https://publications.scilifelab.se/researcher/68dde8362e4944388ee89bf5fa442512.json"}}, {"family": "Menkis", "given": "Audrius", "initials": "A", "orcid": "0000-0002-6545-8907", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d4d16d281344b9f9cf2c3c27fb40f06.json"}}], "type": "journal-article", "published": "2025-06-07", "journal": {"title": "Forests", "issn": "1999-4907", "volume": "16", "issue": "6", "pages": "968", "issn-l": "1999-4907"}, "abstract": null, "doi": "10.3390/f16060968", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-08-19T13:50:36.063Z", "modified": "2025-08-19T13:50:36.150Z"}, {"entity": "publication", "iuid": "674ed939c1a74109b72a53ce6576ea0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/674ed939c1a74109b72a53ce6576ea0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/674ed939c1a74109b72a53ce6576ea0d"}}, "title": "Unlocking novel T cell-based immunotherapy for hepatocellular carcinoma through neoantigen-driven T cell receptor isolation.", "authors": [{"family": "Maravelia", "given": "Panagiota", "initials": "P"}, {"family": "Yao", "given": "Haidong", "initials": "H", "orcid": "0009-0007-4791-5063", "researcher": {"href": "https://publications.scilifelab.se/researcher/03a40cff36064374912d40cc5a9c65db.json"}}, {"family": "Cai", "given": "Curtis", "initials": "C", "orcid": "0000-0002-3490-4361", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ea25e71e96246d89437270a12cc9e47.json"}}, {"family": "Nascimento Silva", "given": "Daniela", "initials": "D", "orcid": "0000-0003-2165-4989", "researcher": {"href": "https://publications.scilifelab.se/researcher/061bbf2c5a864c5c9e852fcab907d29e.json"}}, {"family": "Fransson", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-4762-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/30428cafc89647768f6c69eecf98efcf.json"}}, {"family": "Nilsson", "given": "Ola B", "initials": "OB", "orcid": "0000-0002-7516-1760", "researcher": {"href": "https://publications.scilifelab.se/researcher/096ce3bf888b4ad395d53bb3c11f6946.json"}}, {"family": "Lu", "given": "Yong-Chen William", "initials": "YW", "orcid": "0000-0002-0275-9825", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa8d7936625c42078b815953810ee136.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Gatto", "given": "Francesca", "initials": "F"}, {"family": "Rovesti", "given": "Giulia", "initials": "G", "orcid": "0000-0002-2761-9482", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd6c4824c71c44378a7f45649766f4cd.json"}}, {"family": "Carlsten", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9815-0012", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dadae83c2494c7abc65118f04e1b6b6.json"}}, {"family": "Sallberg", "given": "Matti", "initials": "M", "orcid": "0000-0002-8858-5132", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d4712be75441d6b49aca02c600bc70.json"}}, {"family": "St\u00e5l", "given": "Per", "initials": "P"}, {"family": "Jorns", "given": "Carl", "initials": "C", "orcid": "0000-0001-7727-8113", "researcher": {"href": "https://publications.scilifelab.se/researcher/59d387bd893f45bdb3663a0ef3aae88a.json"}}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Pasetto", "given": "Anna", "initials": "A", "orcid": "0000-0002-5254-2173", "researcher": {"href": "https://publications.scilifelab.se/researcher/781c8b467fa144e494d13c7a3e80b4fc.json"}}], "type": "journal article", "published": "2025-06-06", "journal": {"title": "Gut", "issn": "1468-3288", "volume": "74", "issue": "7", "pages": "1125-1136", "issn-l": "0017-5749"}, "abstract": "Tumour-infiltrating T cells can mediate both antitumour immunity and promote tumour progression by creating an immunosuppressive environment. This dual role is especially relevant in hepatocellular carcinoma (HCC), characterised by a unique microenvironment and limited success with current immunotherapy.\n\nWe evaluated T cell responses in patients with advanced HCC by analysing tumours, liver flushes and liver-draining lymph nodes, to understand whether reactive T cell populations could be identified despite the immunosuppressive environment.\n\nT cells isolated from clinical samples were tested for reactivity against predicted neoantigens. Single-cell RNA sequencing was employed to evaluate the transcriptomic and proteomic profiles of antigen-experienced T cells. Neoantigen-reactive T cells expressing 4-1BB were isolated and characterised through T-cell receptor (TCR)-sequencing.\n\nBioinformatic analysis identified 542 candidate neoantigens from seven patients. Of these, 78 neoantigens, along with 11 hotspot targets from HCC driver oncogenes, were selected for ex vivo T cell stimulation. Reactivity was confirmed in co-culture assays for 14 targets, with most reactive T cells derived from liver flushes and lymph nodes. Liver flush-derived T cells exhibited central memory and effector memory CD4+ with cytotoxic effector profiles. In contrast, tissue-resident memory CD4+ and CD8+ T cells with an exhausted profile were primarily identified in the draining lymph nodes.\n\nThese findings offer valuable insights into the functional profiles of neoantigen-reactive T cells within and surrounding the HCC microenvironment. T cells isolated from liver flushes and tumour-draining lymph nodes may serve as a promising source of reactive T cells and TCRs for further use in immunotherapy for HCC.", "doi": "10.1136/gutjnl-2024-334148", "pmid": "39832892", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12611799"}, {"db": "pii", "key": "gutjnl-2024-334148"}], "notes": [], "created": "2025-11-19T08:23:34.477Z", "modified": "2025-11-21T15:22:04.326Z"}, {"entity": "publication", "iuid": "5677316fa2684bbba44365a528fe26fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5677316fa2684bbba44365a528fe26fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5677316fa2684bbba44365a528fe26fb"}}, "title": "Three-dimensional cell-cell interactions promote direct reprogramming of patient fibroblasts into functional and transplantable neurons.", "authors": [{"family": "Kajtez", "given": "Janko", "initials": "J", "orcid": "0000-0001-9997-2325", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b3315d47d804d8cb1dc7f6ff2b31731.json"}}, {"family": "Laurin", "given": "Kerstin", "initials": "K", "orcid": "0000-0002-3267-1111", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fabb942c9c540de9e23f5e79018535c.json"}}, {"family": "Nilsson", "given": "Fredrik", "initials": "F"}, {"family": "Bruzelius", "given": "Andreas", "initials": "A"}, {"family": "Cepeda-Prado", "given": "Efrain", "initials": "E", "orcid": "0000-0001-9781-3742", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0ee87e59e144bd6b8a0cce5b1e29194.json"}}, {"family": "Birtele", "given": "Marcella", "initials": "M", "orcid": "0000-0003-2123-6453", "researcher": {"href": "https://publications.scilifelab.se/researcher/5597264e465b4396b0016336b46a7fb1.json"}}, {"family": "Barker", "given": "Roger A", "initials": "RA", "orcid": "0000-0001-8843-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/125769a66f77471da6266577717a6395.json"}}, {"family": "Herborg", "given": "Freja", "initials": "F", "orcid": "0000-0002-0159-4598", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab2173b0ed34bf48a77880e33146a05.json"}}, {"family": "Rylander Ottosson", "given": "Daniella", "initials": "D", "orcid": "0000-0002-9270-3576", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d5ebb28287f4725b41a4bbf981d0e40.json"}}, {"family": "Storm", "given": "Petter", "initials": "P", "orcid": "0000-0002-7655-3731", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5af5462a2c04920bb43120d429ac386.json"}}, {"family": "Fiorenzano", "given": "Alessandro", "initials": "A", "orcid": "0000-0003-2478-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a17c87028884ff8b5bf3da42a0d63fe.json"}}, {"family": "Habekost", "given": "Mette", "initials": "M", "orcid": "0000-0002-5987-2909", "researcher": {"href": "https://publications.scilifelab.se/researcher/f50503763ece48ba851a3031aade3256.json"}}, {"family": "Parmar", "given": "Malin", "initials": "M", "orcid": "0000-0001-5002-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48b5aaff3bc4832a96fda4f2cf127cb.json"}}], "type": "journal article", "published": "2025-06-06", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "23", "pages": "eadq7855", "issn-l": "2375-2548"}, "abstract": "Direct reprogramming of somatic cells into induced neurons (iNs) has become an attractive strategy for the generation of patient-specific neurons for disease modeling and regenerative neuroscience. To this end, adult human dermal fibroblasts (hDFs) present one of the most relevant cell sources. However, iNs generated from adult hDFs using two-dimensional cultures are difficult to maintain in vitro and face challenges in survival upon transplantation into the adult brain, thus imposing constraints on biomedical applications of iN technology. Here, we present a platform for direct in vitro reprogramming of adult hDFs inside three-dimensional suspension microcultures (3D-iNs). We show that the 3D environment favors neuronal over fibroblast cellular identity to yield more robust conversion into functional neurons with extended culturing span. The 3D reprogramming approach also provides a platform for fusion into induced assembloids. 3D-iNs can be gently harvested and transplanted into the adult rodent brain to reproducibly generate neuron-rich grafts, thus eliminating a major bottleneck in the direct reprogramming field.", "doi": "10.1126/sciadv.adq7855", "pmid": "40479059", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12143395"}], "notes": [], "created": "2025-09-08T07:10:49.448Z", "modified": "2025-09-08T07:10:50.125Z"}, {"entity": "publication", "iuid": "122b967ba2574093834d76cc77fc72ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/122b967ba2574093834d76cc77fc72ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/122b967ba2574093834d76cc77fc72ee"}}, "title": "The low endoribonuclease activity and lack of rNMP preference of human mitochondrial topoisomerase 1 protect against ribonucleotide-dependent deletions", "authors": [{"family": "Bader", "given": "Cyrielle P J", "initials": "CPJ"}, {"family": "Miyazaki-Kasho", "given": "Erika", "initials": "E"}, {"family": "Forslund", "given": "Josefin M E", "initials": "JME"}, {"family": "Dash", "given": "Aiswarya", "initials": "A"}, {"family": "Wessels", "given": "Malgorzata", "initials": "M"}, {"family": "Wanrooij", "given": "Paulina H", "initials": "PH", "orcid": "0000-0002-8607-7564", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac6d0c050c9d47698f5123b935c4068b.json"}}], "type": "journal-article", "published": "2025-06-06", "journal": {"issn": "0305-1048", "volume": "53", "issue": "11", "issn-l": null}, "abstract": null, "doi": "10.1093/nar/gkaf475", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-04T09:06:04.693Z", "modified": "2025-10-17T13:04:26.558Z"}, {"entity": "publication", "iuid": "0f073501935845a496a3ad4c5b006c61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f073501935845a496a3ad4c5b006c61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f073501935845a496a3ad4c5b006c61"}}, "title": "Sex-biased Migration and Demographic History of the Big European Firefly Lampyris noctiluca.", "authors": [{"family": "Catal\u00e1n", "given": "Ana", "initials": "A", "orcid": "0000-0002-4543-748X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5edac0f763941e29cbe9595b998023b.json"}}, {"family": "Gygax", "given": "Daniel", "initials": "D", "orcid": "0009-0005-2362-0063", "researcher": {"href": "https://publications.scilifelab.se/researcher/09e144aa221d456b9074cb3209f3dcdf.json"}}, {"family": "Candolin", "given": "Ulrika", "initials": "U", "orcid": "0000-0001-8736-7793", "researcher": {"href": "https://publications.scilifelab.se/researcher/be6522db87e249a0b5d7dc6d41de6973.json"}}, {"family": "Tusso", "given": "Sergio", "initials": "S", "orcid": "0000-0002-0612-9230", "researcher": {"href": "https://publications.scilifelab.se/researcher/027fc05d9bd843afaa82aeecce0747e8.json"}}, {"family": "Duchen", "given": "Pablo", "initials": "P", "orcid": "0000-0002-9318-5002", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fe957e35f6a4c1296171b837d465ee9.json"}}, {"family": "H\u00f6hna", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-6519-6292", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f5fbb4f78854a67979096ececa410b8.json"}}], "type": "journal article", "published": "2025-06-04", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "42", "issue": "6", "issn-l": "0737-4038"}, "abstract": "Differential dispersion between the sexes can impact the colonization process and demographic history of a species. Here, we explored the demographic history of the big European firefly, Lampyris noctiluca, which exhibits female neoteny. Distribution of L. noctiluca extends throughout Europe, but nothing is known about its colonization process. To investigate its demographic history, we produced the first Lampyris genome (653 Mb), including an IsoSeq annotation and the identification of the X chromosome. We collected 115 individuals from six populations of L. noctiluca (Finland to Italy) and generated whole-genome re-sequencing data for each individual. We inferred several population expansions and bottlenecks throughout the Pleistocene that correlate with glaciation events. Surprisingly, we uncovered strong population structure and low gene flow. We reject a stepwise, south to north, colonization history scenario and instead uncovered a complex demographic history with a putative eastern European origin. Analyzing the evolutionary history of the mitochondrial genome as well as X-linked and autosomal loci, we found evidence of a maternal colonialization of Germany, putatively from a farther western European population, followed by a male-only migration from south of the Alps (Italy). Overall, investigating the demographic history and colonization patterns of a species should form part of an integrative approach of biodiversity research. Our results provide evidence of sex-biased migration which is important to consider for demographic, biogeographic and species delimitation studies.", "doi": "10.1093/molbev/msaf123", "pmid": "40542536", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12204758"}, {"db": "pii", "key": "8170119"}], "notes": [], "created": "2025-08-19T13:56:39.426Z", "modified": "2025-08-19T13:56:39.667Z"}, {"entity": "publication", "iuid": "0576cf154a2a400882560447fb8f649c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0576cf154a2a400882560447fb8f649c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0576cf154a2a400882560447fb8f649c"}}, "title": "Quantitative Mass Spectrometry Imaging Protocols for Spatially Heterogeneous Samples.", "authors": [{"family": "Shariatgorji", "given": "Reza", "initials": "R", "orcid": "0000-0001-9484-0921", "researcher": {"href": "https://publications.scilifelab.se/researcher/7762e9f6779c4780a4077c557eb7a3b6.json"}}, {"family": "Niehues", "given": "Michael", "initials": "M"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Angerer", "given": "Tina", "initials": "T", "orcid": "0000-0003-3852-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3f5ed541c9f4e2bb6c7c7519d6ad36b.json"}}, {"family": "Stroth", "given": "Nikolas", "initials": "N"}, {"family": "Paslawski", "given": "Wojciech", "initials": "W"}, {"family": "Jabre", "given": "Sandra", "initials": "S"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}], "type": "journal article", "published": "2025-06-03", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "97", "issue": "21", "pages": "10957-10961", "issn-l": "0003-2700"}, "abstract": "Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a promising tool for the spatial quantitation of endogenous and exogenous compounds directly in biological tissue sections. However, precise quantitation may be hampered due to matrix effects and variations in ionization efficiency, especially in spatially heterogeneous samples such as brain tissue. In this study, we developed and implemented two advanced MALDI-MSI protocols to address these limitations by employing a standard addition approach. The protocols involved the homogeneous spraying of standard solutions onto tissue sections to minimize the matrix effects associated with heterogeneous samples. The first method utilized spraying of deuterated analogues of neurotransmitters across all tissue sections for normalization, while calibration standards were applied in a quantitative manner to consecutive tissue sections. The second method employed two stable isotope-labeled compounds: one for calibration and the other for normalization. Both methods were applied to quantify neurotransmitters and their metabolites, e.g., dopamine, norepinephrine, and 3-methoxytyramine, in rodent brain tissue. The results showed strong linearity between signal intensities and analyte concentrations across brain tissue sections with values comparable to those obtained using high-performance liquid chromatography-electrochemical detection. The standard addition approach significantly enhanced the quantitation accuracy by accounting for tissue-specific matrix effects, providing a robust method for the spatial quantification of neurotransmitters in complex brain tissue environments.", "doi": "10.1021/acs.analchem.5c00677", "pmid": "40404577", "labels": {"Spatial Mass Spectrometry": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12138873"}], "notes": [], "created": "2025-11-21T09:59:52.122Z", "modified": "2025-11-21T09:59:52.198Z"}, {"entity": "publication", "iuid": "87a87989503945b7842ab3f695a22318", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87a87989503945b7842ab3f695a22318.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87a87989503945b7842ab3f695a22318"}}, "title": "Pooled optical screening in bacteria using chromosomally expressed barcodes.", "authors": [{"family": "Soares", "given": "Ruben R G", "initials": "RRG", "orcid": "0000-0001-5958-5232", "researcher": {"href": "https://publications.scilifelab.se/researcher/88ea8e0d81284c35a271f05187289390.json"}}, {"family": "Garc\u00eda-Soriano", "given": "Daniela A", "initials": "DA", "orcid": "0000-0003-2849-8528", "researcher": {"href": "https://publications.scilifelab.se/researcher/2aeeed6de99647a1878352e0da2220af.json"}}, {"family": "Larsson", "given": "Jimmy", "initials": "J"}, {"family": "Fange", "given": "David", "initials": "D", "orcid": "0009-0006-3981-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/195ab3e1f94e4ad39b4aa32da6b3e217.json"}}, {"family": "Schirman", "given": "Dvir", "initials": "D", "orcid": "0000-0001-5175-0176", "researcher": {"href": "https://publications.scilifelab.se/researcher/02550d8122ed486fb67691b456926aed.json"}}, {"family": "Grillo", "given": "Marco", "initials": "M", "orcid": "0000-0003-2155-0645", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd8bec6567444558acbcbd1b3d28f7a.json"}}, {"family": "Kn\u00f6ppel", "given": "Anna", "initials": "A"}, {"family": "Sen", "given": "Beer Chakra", "initials": "BC"}, {"family": "Svahn", "given": "Fabian", "initials": "F", "orcid": "0000-0002-5914-520X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f015b5855854d40b853c17a31d3d632.json"}}, {"family": "Zikrin", "given": "Spartak", "initials": "S", "orcid": "0000-0002-7802-8869", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a82f27ea7bf43deaded33d359270820.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.json"}}], "type": "journal article", "published": "2025-06-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "851", "issn-l": "2399-3642"}, "abstract": "Optical pooled screening is an important tool to study dynamic phenotypes for libraries of genetically engineered cells. However, the desired engineering often requires that the barcodes used for in situ genotyping are expressed from the chromosome. This has not previously been achieved in bacteria. Here we describe a method for in situ genotyping of libraries with genomic barcodes in Escherichia coli. The method is applied to measure the intracellular maturation time of 84 red fluorescent proteins.", "doi": "10.1038/s42003-025-08268-5", "pmid": "40461651", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12134211"}, {"db": "pii", "key": "10.1038/s42003-025-08268-5"}], "notes": [], "created": "2025-11-28T10:47:35.410Z", "modified": "2025-11-28T10:47:35.689Z"}, {"entity": "publication", "iuid": "5753418da8414fd289afbad0fb47aa21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5753418da8414fd289afbad0fb47aa21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5753418da8414fd289afbad0fb47aa21"}}, "title": "Pathway activation model for personalized prediction of drug synergy.", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications.scilifelab.se/researcher/043294bad46e4ccaa3d0d7cd43ebdccd.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "Osterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R"}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Backvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas", "initials": "L"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Lehmann", "given": "Soren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90993bc42694d969a24a50f21393b76.json"}}], "type": "journal article", "published": "2025-06-03", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "13", "issn-l": "2050-084X"}, "abstract": "Targeted monotherapies for cancer often fail due to inherent or acquired drug resistance. By aiming at multiple targets simultaneously, drug combinations can produce synergistic interactions that increase drug effectiveness and reduce resistance. Computational models based on the integration of omics data have been used to identify synergistic combinations, but predicting drug synergy remains a challenge. Here, we introduce Drug synergy Interaction Prediction (DIPx), an algorithm for personalized prediction of drug synergy based on biologically motivated tumor- and drug-specific pathway activation scores (PASs). We trained and validated DIPx in the AstraZeneca-Sanger (AZS) DREAM Challenge human cell-line dataset using two separate test sets: Test Set 1 comprised the combinations already present in the training set, while Test Set 2 contained combinations absent from the training set, thus indicating the model's ability to handle novel combinations. The Spearman's correlation coefficients between predicted and observed drug synergy were 0.50 (95% CI: 0.47-0.53) in Test Set 1 and 0.26 (95% CI: 0.22-0.30) in Test Set 2, compared to 0.38 (95% CI: 0.34-0.42) and 0.18 (95% CI: 0.16-0.20), respectively, for the best performing method in the Challenge. We show evidence that higher synergy is associated with higher functional interaction between the drug targets, and this functional interaction information is captured by PAS. We illustrate the use of PAS to provide a potential biological explanation in terms of activated pathways that mediate the synergistic effects of combined drugs. In summary, DIPx can be a useful tool for personalized prediction of drug synergy and exploration of activated pathways related to the effects of combined drugs.", "doi": "10.7554/eLife.100071", "pmid": "40459126", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12133153"}, {"db": "pii", "key": "100071"}], "notes": [], "created": "2025-11-28T10:54:44.321Z", "modified": "2025-11-28T10:54:44.431Z"}, {"entity": "publication", "iuid": "649fc3eb5a4345c08df63ed4ea1bd9d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/649fc3eb5a4345c08df63ed4ea1bd9d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/649fc3eb5a4345c08df63ed4ea1bd9d8"}}, "title": "Wastewater surveillance of SARS-CoV-2 from aircraft to citywide monitoring.", "authors": [{"family": "Perez-Zabaleta", "given": "Mariel", "initials": "M"}, {"family": "Berg", "given": "Carlo", "initials": "C", "orcid": "0000-0001-7815-1077", "researcher": {"href": "https://publications.scilifelab.se/researcher/3665efd3f7e04e5f9bebff32085aac8a.json"}}, {"family": "Latorre-Margalef", "given": "Neus", "initials": "N"}, {"family": "Owusu-Agyeman", "given": "Isaac", "initials": "I"}, {"family": "Kiyar", "given": "Ayda", "initials": "A"}, {"family": "Botnen", "given": "Helene", "initials": "H", "orcid": "0009-0008-1027-0676", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ad9bceb481948d3b7aa41540f1756e1.json"}}, {"family": "Sch\u00f6nning", "given": "Caroline", "initials": "C"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dfdcf0109a942228d35d8dbfdede585.json"}}, {"family": "Cetecioglu", "given": "Zeynep", "initials": "Z", "orcid": "0000-0002-8170-379X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9d8df50bf824688a0149bff5fb1853a.json"}}], "type": "journal article", "published": "2025-06-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "5125", "issn-l": "2041-1723"}, "abstract": "Wastewater monitoring is highly efficient in SARS-CoV-2 surveillance for tracking virus spread through travel, surpassing traditional airport passenger testing. This study explored the links between SARS-CoV-2 contents and variants from aircraft to city, assessing the impact of detected variants from international travellers versus the local population. A total of 969 variants using next-generation sequencing (NGS) were examined to understand the links between-aircraft, Arlanda airport, wastewater treatment plants (WWTPs), and Stockholm city-and compared these to variants detected in Stockholm hospitals from January to May 2023. SARS-CoV-2 contents in WWTPs reflected local infection rates, requiring analysis from multiple plants for an accurate city-wide infection assessment. Variants initially detected in aircraft arriving from China did not spread widely during the study period. RT-qPCR is adequate for the detection of specific variants in wastewater, including Variants Under Monitoring. However, NGS remains a powerful method for identifying novel variants. Wastewater monitoring was more effective than clinical testing in the early detection of specific variants, with notable delays observed in clinical surveillance. Furthermore, a broad range of variants are detected in wastewater that surpasses clinical tests. This underscores the vital role of wastewater-based epidemiology in managing future outbreaks and enhancing global health security.", "doi": "10.1038/s41467-025-60490-1", "pmid": "40456842", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12130461"}, {"db": "pii", "key": "10.1038/s41467-025-60490-1"}], "notes": [], "created": "2025-11-04T15:30:58.937Z", "modified": "2025-11-04T15:30:59.626Z"}, {"entity": "publication", "iuid": "f64e4dcded1240568e175d59318ecd68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f64e4dcded1240568e175d59318ecd68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f64e4dcded1240568e175d59318ecd68"}}, "title": "The genome sequence of the Eurasian Curlew, Numenius arquata (Linnaeus, 1758).", "authors": [{"family": "Walsh", "given": "Grace", "initials": "G"}, {"family": "Donoghue", "given": "Barry O'", "initials": "BO"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "McMahon", "given": "Barry John", "initials": "BJ", "orcid": "0000-0003-3143-8075", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ba44012f4b040ae918c7cabfdbb49ec.json"}}, {"family": "Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team", "given": "", "initials": ""}, {"family": "WellcomeSanger Institute Scientific Operations: Sequencing Operations", "given": "", "initials": ""}, {"family": "Wellcome Sanger Institute Tree of Life Core Informatics team", "given": "", "initials": ""}, {"family": "Tree of Life Core Informatics collective", "given": "", "initials": ""}, {"family": "Darwin Tree of Life Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2025-06-02", "journal": {"title": "Wellcome Open Res", "issn": "2398-502X", "volume": "10", "pages": "298", "issn-l": "2398-502X"}, "abstract": "We present a genome assembly from a female specimen of Numenius arquata (Eurasian Curlew; Chordata; Aves; Charadriiformes; Scolopacidae). The assembly contains two haplotypes with total lengths of 1,348.86 megabases and 1,198.36 megabases. Most of haplotype 1 (89.99%) is scaffolded into 41 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.13 kilobases. Gene annotation of this assembly on Ensembl identified 15,412 protein-coding genes.", "doi": "10.12688/wellcomeopenres.24272.1", "pmid": "40880729", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12381557"}], "notes": [], "created": "2025-11-21T09:17:11.591Z", "modified": "2025-11-21T09:17:11.682Z"}, {"entity": "publication", "iuid": "f953007cda72485fa1bb4c6dca244705", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f953007cda72485fa1bb4c6dca244705.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f953007cda72485fa1bb4c6dca244705"}}, "title": "Referenceless 4D flow cardiovascular magnetic resonance with deep learning.", "authors": [{"family": "Trenti", "given": "Chiara", "initials": "C"}, {"family": "Ylip\u00e4\u00e4", "given": "Erik", "initials": "E"}, {"family": "Ebbers", "given": "Tino", "initials": "T"}, {"family": "Carlh\u00e4ll", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Engvall", "given": "Jan", "initials": "J"}, {"family": "Dyverfeldt", "given": "Petter", "initials": "P"}], "type": "journal article", "published": "2025-06-02", "journal": {"title": "J Cardiovasc Magn Reson", "issn": "1532-429X", "volume": "27", "issue": "2", "pages": "101920", "issn-l": null}, "abstract": "Despite its potential to improve the assessment of cardiovascular diseases, four-dimensional (4D) flow cardiovascular magnetic resonance (CMR) is hampered by long scan times. 4D flow CMR is conventionally acquired with three motion encodings and one reference encoding, as the three-dimensional velocity data are obtained by subtracting the phase of the reference from the phase of the motion encodings. In this study, we aim to use deep learning to predict the reference encoding from the three motion encodings for cardiovascular 4D flow.\n\nA U-Net was trained with adversarial learning (U-NetADV) and with a velocity frequency-weighted loss function (U-NetVEL) to predict the reference encoding from the three motion encodings obtained with a non-symmetric velocity-encoding scheme. Whole-heart 4D flow datasets from 126 patients with different types of cardiomyopathies were retrospectively included. The models were trained on 113 patients with a 5-fold cross-validation, and tested on 13 patients. Flow volumes in the aorta and pulmonary artery, mean and maximum velocity, total and maximum turbulent kinetic energy at peak systole in the cardiac chambers and main vessels were assessed.\n\nThree-dimensional velocity data reconstructed with the reference encoding predicted by deep learning agreed well with the velocities obtained with the reference encoding acquired at the scanner for both models. U-NetADV performed more consistently throughout the cardiac cycle and across the test subjects, while U-NetVEL performed better for systolic velocities. Comprehensively, the largest error for flow volumes, maximum and mean velocities was -6.031% for maximum velocities in the right ventricle for the U-NetADV, and -6.92% for mean velocities in the right ventricle for U-NetVEL. For total turbulent kinetic energy, the highest errors were in the left ventricle (-77.17%) for the U-NetADV, and in the right ventricle (24.96%) for the U-NetVEL, while for maximum turbulent kinetic energy were in the pulmonary artery for both models, with a value of -15.5% for U-NetADV and 15.38% for the U-NetVEL.\n\nDeep learning-enabled referenceless 4D flow CMR permits velocities and flow volumes quantification comparable to conventional 4D flow. Omitting the reference encoding reduces the amount of acquired data by 25%, thus allowing shorter scan times or improved resolution, which is valuable for utilization in the clinical routine.", "doi": "10.1016/j.jocmr.2025.101920", "pmid": "40467036", "labels": {"AIDA Data Hub": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12270065"}, {"db": "pii", "key": "S1097-6647(25)00082-1"}], "notes": [], "created": "2025-11-25T13:10:43.341Z", "modified": "2025-11-25T13:10:43.364Z"}, {"entity": "publication", "iuid": "b5fbc4b85dea4d92ba07db4892a0f3f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5fbc4b85dea4d92ba07db4892a0f3f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5fbc4b85dea4d92ba07db4892a0f3f5"}}, "title": "Integrating Cell Painting and Thermal Proteome Profiling for Inference of Targets and Mechanism of Action", "authors": [{"family": "Johansson", "given": "Camilla", "initials": "C", "orcid": "0000-0002-2685-5715", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fb85fc7f3e44ad1ae5ab810d7d177d0.json"}}, {"family": "Johansson", "given": "Martin", "initials": "M", "orcid": "0000-0002-3733-8975", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1fdb7ed5e7047f3963ada15a0f8d48e.json"}}, {"family": "Carreras Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications.scilifelab.se/researcher/28ad5f6a1a064e52aca72780adc4bb96.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Jansson", "given": "Erik T", "initials": "ET", "orcid": "0000-0002-0675-3412", "researcher": {"href": "https://publications.scilifelab.se/researcher/b896baf96b99439b941fcb6b5c53802e.json"}}], "type": "posted-content", "published": "2025-06-02", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.05.30.657006", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-03T08:44:57.191Z", "modified": "2025-12-19T07:57:28.071Z"}, {"entity": "publication", "iuid": "aeb9fc21fabb4b8f8b5a91ef25b0c7a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aeb9fc21fabb4b8f8b5a91ef25b0c7a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aeb9fc21fabb4b8f8b5a91ef25b0c7a8"}}, "title": "Antimicrobial resistance and serotype distribution of Salmonella spp. isolated from fresh foods in Cambodia.", "authors": [{"family": "Huoy", "given": "Laingshun", "initials": "L", "orcid": "0000-0002-0194-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/6683581dbb2448008f33711ca1ada131.json"}}, {"family": "Nasirzadeh", "given": "Leila", "initials": "L", "orcid": "0000-0003-0282-1227", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9465e8d872740a083579657d96bb431.json"}}, {"family": "Phan", "given": "Kongkea", "initials": "K", "orcid": "0000-0003-2965-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/0826a7f731ac490b84b1e6823b9cedb5.json"}}, {"family": "Tieng", "given": "Siteng", "initials": "S", "orcid": "0000-0002-9037-6671", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd94295461f642cca1a44b46e4b923a2.json"}}, {"family": "Sternberg-Lewerin", "given": "Susanna", "initials": "S", "orcid": "0000-0001-7907-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/41bff7b199434422b316875f399f5ebe.json"}}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Boqvist", "given": "Sofia", "initials": "S", "orcid": "0000-0002-8072-7132", "researcher": {"href": "https://publications.scilifelab.se/researcher/04e91c7a79164ce88c1a2aeaed836ca7.json"}}], "type": "journal article", "published": "2025-06-02", "journal": {"title": "J Appl Microbiol", "issn": "1365-2672", "volume": "136", "issue": "6", "issn-l": "1364-5072"}, "abstract": "To determine the Salmonella serotype distribution, antimicrobial resistance profiles, and antimicrobial resistance genes (ARGs) in food samples obtained from local markets in a low-income urban setting and nearby farms in Cambodia.\n\nOne hundred and thirty-nine Salmonella isolates from various food sources were tested for antibiotic susceptibility using a panel of 12 antibiotics, and 81 selected Salmonella isolates were further sequenced for serotype distribution and ARG identification. The results showed that 71% (99/139) of the isolates exhibited resistance to at least one antibiotic, with 39% (39/99) classified as multidrug-resistant (MDR). The highest resistance was observed against azithromycin (37%), followed by oxytetracycline (35%). A total of 32 serotypes were identified, with the six most common being S. Corvallis (7%), S. Haifa (6%), S. Weltevreden (6%), S. Agona (5%), S. Kentucky (5%), and S. Livingstone (5%). A broad range of ARGs was observed across multiple antibiotic classes, including macrolides, aminoglycosides, tetracyclines, phenicols, fluoroquinolones, sulfonamide-trimethoprim, beta-lactams, and MDR genes.\n\nThe results highlight the potential role of fresh food products in the widespread dissemination of Salmonella strains resistant to multiple antibiotics.", "doi": "10.1093/jambio/lxaf137", "pmid": "40459912", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "8155881"}], "notes": [], "created": "2025-06-04T12:59:02.555Z", "modified": "2025-09-08T06:59:27.016Z"}, {"entity": "publication", "iuid": "d93e5fccf3bb4b2587ad6d172e92b485", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d93e5fccf3bb4b2587ad6d172e92b485.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d93e5fccf3bb4b2587ad6d172e92b485"}}, "title": "The acute effects of neuromuscular electrical stimulation on coagulation and cardiovascular factors.", "authors": [{"family": "Flodin", "given": "Johanna", "initials": "J", "orcid": "0000-0003-0095-064X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcf4a01b5e794e989f43c8a79157f0ed.json"}}, {"family": "Reitzner", "given": "Stefan M", "initials": "SM", "orcid": "0000-0003-0151-2780", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ca59c30b2e45459eb3638c65b452b3.json"}}, {"family": "Mahmoud Hourani Soutari", "given": "Nida", "initials": "N"}, {"family": "Ahmed", "given": "Aisha S", "initials": "AS"}, {"family": "Guo", "given": "Li", "initials": "L"}, {"family": "Persson", "given": "Nils-Krister", "initials": "NK"}, {"family": "Antovic", "given": "Jovan P", "initials": "JP"}, {"family": "Ackermann", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-5520-169X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbb35e677dc240c788d765ea42f89cfd.json"}}], "type": "journal article", "published": "2025-06-01", "journal": {"title": "Physiol. Genomics", "issn": "1531-2267", "volume": "57", "issue": "6", "pages": "391-402", "issn-l": "1094-8341"}, "abstract": "Neuromuscular electrical stimulation (NMES) can potentially be used to prevent venous thromboembolism; however, its impact on coagulation-related factors remains poorly understood. We aimed to investigate the acute effects on coagulation- and cardiovascular factors immediately after a 2-h NMES session. Levels of overall hemostatic potential (OHP), fibrinogen, factor VIII, and Olink proteomic cardiovascular factors were assessed before and after the NMES session in 36 healthy participants (20 males and 16 females) with a mean age of 31.9 yr. NMES was administered using integrated textile electrodes in pants (NMES pants). Mean intensities during the quadriceps, hamstrings, and gluteus muscle stimulation were 16.5, 20.5, and 25.4 mA, respectively, corresponding to submaximal intensity levels with acceptable discomfort (just below 4 on the visual analogue scale [VAS], 0-10). The NMES session resulted in a significant increase in mean (SD) OHP [94.4 (28.3) to 103 (31.0)], and overall coagulation potential [292 (50.4) to 307(49.8)], and a decrease in overall fibrinolytic potential [68.2 (5.46) to 67.1 (5.20)]. These changes were highly correlated with the increase in fibrinogen (all R > 0.7, P \u2264 0.001), but not with the increase in factor VIII. In addition, 18 of 92 cardiovascular proteins, specifically those involved in regulating inflammation and extracellular matrix remodeling, were influenced by NMES; however, low correlations were found between the changes in these proteins and OHP analyses. In conclusion, the NMES session resulted in a slight increase in the coagulative state, mirroring that seen after a bout of regular exercise. The changes observed in cardiovascular factors, which are mostly not directly related to coagulation, suggest that NMES may subsequently modulate inflammatory responses, warranting further investigation.NEW & NOTEWORTHY The immediate response to a 2-h neuromuscular electrical stimulation (NMES) session, delivered at an acceptable level of discomfort using NMES-pants, marginally increases the coagulative state, similar to what is observed after regular physical exercise. This change is not expected to significantly increase the risk of blood clotting, as all factors remain within the normal reference range. Interestingly, NMES simultaneously appears to affect proteins that regulate the transition of inflammation into an anti-inflammatory response.", "doi": "10.1152/physiolgenomics.00172.2024", "pmid": "40240321", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-25T19:24:15.746Z", "modified": "2025-11-25T19:24:15.816Z"}, {"entity": "publication", "iuid": "20721b382c4c48ff8b6b7a83b0867e34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20721b382c4c48ff8b6b7a83b0867e34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20721b382c4c48ff8b6b7a83b0867e34"}}, "title": "Transcriptomic characterization of maturing neurons from human neural stem cells across developmental time points.", "authors": [{"family": "Hosseini", "given": "Kimia", "initials": "K"}, {"family": "Philippot", "given": "Ga\u00ebtan", "initials": "G"}, {"family": "Salomonsson", "given": "Sara B", "initials": "SB"}, {"family": "Cediel-Ulloa", "given": "Andrea", "initials": "A"}, {"family": "Gholizadeh", "given": "Elnaz", "initials": "E"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "IBRO Neurosci Rep", "issn": "2667-2421", "volume": "18", "pages": "679-689", "issn-l": null}, "abstract": "Neurodevelopmental studies employing animal models encounter challenges due to interspecies differences and ethical concerns. Maturing neurons of human origin, undergoing several developmental stages, present a powerful alternative. In this study, human embryonic stem cell (H9 cell line) was differentiated into neural stem cells and subsequently matured into neurons over 30 days. Ion AmpliSeq\u2122 was used for transcriptomic characterization of human stem cell-derived neurons at multiple time points. Data analysis revealed a progressive increase of markers associated with neuronal development and astrocyte markers, indicating the establishment of a co-culture accommodating both glial and neurons. Transcriptomic and pathway enrichment analysis also revealed a more pronounced GABAergic phenotype in the neurons, signifying their specialization toward this cell type. The findings confirm the robustness of these cells across different passages and demonstrate detailed progression through stages of development. The model is intended for neurodevelopmental applications and can be adapted to investigate how genetic modifications or exposure to chemicals, pharmaceuticals, and other environmental factors influence neurons and glial maturation.", "doi": "10.1016/j.ibneur.2025.04.013", "pmid": "40336753", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12056963"}, {"db": "pii", "key": "S2667-2421(25)00061-2"}], "notes": [], "created": "2025-11-04T15:29:22.984Z", "modified": "2025-11-28T10:43:24.432Z"}, {"entity": "publication", "iuid": "e5b95af37d844d26a7b55ddc098747cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5b95af37d844d26a7b55ddc098747cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5b95af37d844d26a7b55ddc098747cd"}}, "title": "Trajectories and dimensional phenotypes of depressive symptoms throughout pregnancy and postpartum in relation to prior premenstrual symptoms.", "authors": [{"family": "Schleimann-Jensen", "given": "Ella", "initials": "E"}, {"family": "Sundstr\u00f6m-Poromaa", "given": "Inger", "initials": "I"}, {"family": "Meltzer-Brody", "given": "Samantha", "initials": "S"}, {"family": "Eisenlohr-Moul", "given": "Tory A", "initials": "TA"}, {"family": "Papadopoulos", "given": "Fotis C", "initials": "FC"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}, {"family": "Comasco", "given": "Erika", "initials": "E", "orcid": "0000-0002-2174-2068", "researcher": {"href": "https://publications.scilifelab.se/researcher/83fe689667824167ac7cf6a058b5e150.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Br J Psychiatry", "issn": "1472-1465", "volume": "226", "issue": "6", "pages": "401-409", "issn-l": null}, "abstract": "Sensitivity to ovarian hormone fluctuations can lead to mental distress during the luteal phase of the menstrual cycle, such as in premenstrual syndrome (PMS) and premenstrual dysphoric disorder (PMDD), and also during pregnancy and postpartum, as in perinatal depression (PND).\n\nIn two cohorts, we investigated the relationship between history of PMS/PMDD and PND symptoms. We also examined how premenstrual symptoms are associated with perinatal symptom trajectories and dimensional phenotypes of PND symptoms, which remains unidentified.\n\nFrom early pregnancy until 6 months postpartum, participants of two large longitudinal cohorts were followed using the Edinburgh Postnatal Depression Scale (EPDS). Premenstrual symptoms were self-reported retrospectively.\n\nBoth pre-pregnancy PMS and PMDD were associated with higher EPDS scores across pregnancy and postpartum, even after adjustment for confounders. The odds of developing PND were higher among those reporting PMS and PMDD, ranging up to 1.68 (95% CI 1.25-2.29) (6-13 weeks postpartum) and 3.05 (95% CI 2.26-4.10) (late pregnancy) respectively for PMS and PMDD, throughout the perinatal period. Premenstrual symptomatology was associated more with certain PND trajectories based on the time of occurrence and persistence of symptoms. However, PND symptom severity did not differ depending on premenstrual symptomatology in any trajectory. Prior PMS/PMDD was associated with underlying dimensions of symptom constructs of PND, including severe and moderate symptoms of depressed mood, anxiety and anhedonia.\n\nWomen with a history of PMS/PMDD require coordinated care by psychiatrists, other mental health clinicians, midwives and gynaecologists during pregnancy as well as postpartum.", "doi": "10.1192/bjp.2025.38", "pmid": "40538355", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12257281"}, {"db": "pii", "key": "S0007125025000388"}], "notes": [], "created": "2025-11-28T10:53:32.763Z", "modified": "2025-11-28T10:53:32.856Z"}, {"entity": "publication", "iuid": "c466edad3243407ba07ae58843066301", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c466edad3243407ba07ae58843066301.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c466edad3243407ba07ae58843066301"}}, "title": "Small molecules restore mutant mitochondrial DNA polymerase activity.", "authors": [{"family": "Valenzuela", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-5153-8431", "researcher": {"href": "https://publications.scilifelab.se/researcher/16c5cd1a4e8a4d9389514f33049240a5.json"}}, {"family": "Zhu", "given": "Xuefeng", "initials": "X"}, {"family": "Macao", "given": "Bertil", "initials": "B"}, {"family": "Stamgren", "given": "Mattias", "initials": "M"}, {"family": "Geukens", "given": "Carol", "initials": "C"}, {"family": "Charifson", "given": "Paul S", "initials": "PS"}, {"family": "Kern", "given": "Gunther", "initials": "G"}, {"family": "Hoberg", "given": "Emily", "initials": "E"}, {"family": "Jenninger", "given": "Louise", "initials": "L"}, {"family": "Gruszczyk", "given": "Anja V", "initials": "AV", "orcid": "0000-0003-3060-4107", "researcher": {"href": "https://publications.scilifelab.se/researcher/57299dfd50ed45219e6d9f9765f6cd12.json"}}, {"family": "Lee", "given": "Seoeun", "initials": "S"}, {"family": "Johansson", "given": "Katarina A S", "initials": "KAS", "orcid": "0009-0005-8992-7631", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3bac3ed243c4f0493e0d494f79a7ca2.json"}}, {"family": "Miralles Fust\u00e9", "given": "Javier", "initials": "J", "orcid": "0000-0001-8818-9650", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dcf35ce5b204221b2167f281ce219b3.json"}}, {"family": "Shi", "given": "Yonghong", "initials": "Y"}, {"family": "Kerns", "given": "S Jordan", "initials": "SJ"}, {"family": "Arabanian", "given": "Laleh", "initials": "L"}, {"family": "Martinez Botella", "given": "Gabriel", "initials": "G"}, {"family": "Ekstr\u00f6m", "given": "Sofie", "initials": "S"}, {"family": "Green", "given": "Jeremy", "initials": "J", "orcid": "0000-0003-4544-6412", "researcher": {"href": "https://publications.scilifelab.se/researcher/91088e7b066944c7b415aa1b18632c44.json"}}, {"family": "Griffin", "given": "Andrew M", "initials": "AM"}, {"family": "Pardo-Hern\u00e1ndez", "given": "Carlos", "initials": "C"}, {"family": "Keating", "given": "Thomas A", "initials": "TA", "orcid": "0009-0009-1386-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/52c4d61c63fe4129b9d06c0758c6cef9.json"}}, {"family": "K\u00fcppers-Munther", "given": "Barbara", "initials": "B"}, {"family": "Larsson", "given": "Nils-G\u00f6ran", "initials": "NG", "orcid": "0000-0001-5100-996X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc68aa2893a4ab8845fc32d8d6bc59a.json"}}, {"family": "Phan", "given": "Cindy", "initials": "C"}, {"family": "Posse", "given": "Viktor", "initials": "V", "orcid": "0000-0003-4936-4967", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd6a8d4e0f94ea090d12a376b17876a.json"}}, {"family": "Jones", "given": "Juli E", "initials": "JE"}, {"family": "Xie", "given": "Xie", "initials": "X"}, {"family": "Giroux", "given": "Simon", "initials": "S", "orcid": "0000-0003-1499-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dbcb75a94a24eff8dd3737366bb3423.json"}}, {"family": "Gustafsson", "given": "Claes M", "initials": "CM", "orcid": "0000-0003-3531-8468", "researcher": {"href": "https://publications.scilifelab.se/researcher/2851656430d147dab7a8a32e50fee7b7.json"}}, {"family": "Falkenberg", "given": "Maria", "initials": "M", "orcid": "0000-0001-8713-173X", "researcher": {"href": "https://publications.scilifelab.se/researcher/562109b99a5c4eb3bd8b92f30014828b.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "642", "issue": "8067", "pages": "501-507", "issn-l": "0028-0836"}, "abstract": "Mammalian mitochondrial DNA (mtDNA) is replicated by DNA polymerase \u03b3 (POL\u03b3), a heterotrimeric complex consisting of a catalytic POL\u03b3A subunit and two accessory POL\u03b3B subunits1. More than 300 mutations in POLG, the gene encoding the catalytic subunit, have been linked to severe, progressive conditions with high rates of morbidity and mortality, for which no treatment exists2. Here we report on the discovery and characterization of PZL-A, a first-in-class small-molecule activator of mtDNA synthesis that is capable of restoring function to the most common mutant variants of POL\u03b3. PZL-A binds to an allosteric site at the interface between the catalytic POL\u03b3A subunit and the proximal POL\u03b3B subunit, a region that is unaffected by nearly all disease-causing mutations. The compound restores wild-type-like activity to mutant forms of POL\u03b3 in vitro and activates mtDNA synthesis in cells from paediatric patients with lethal POLG disease, thereby enhancing biogenesis of the oxidative phosphorylation machinery and cellular respiration. Our work demonstrates that a small molecule can restore function to mutant DNA polymerases, offering a promising avenue for treating POLG disorders and other severe conditions linked to depletion of mtDNA.", "doi": "10.1038/s41586-025-08856-9", "pmid": "40205042", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12158775"}, {"db": "pii", "key": "10.1038/s41586-025-08856-9"}], "notes": [], "created": "2025-11-05T14:10:00.381Z", "modified": "2025-11-13T12:50:07.085Z"}, {"entity": "publication", "iuid": "2c7db473960c4c7fa52c676e6bfc84e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c7db473960c4c7fa52c676e6bfc84e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c7db473960c4c7fa52c676e6bfc84e0"}}, "title": "Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer.", "authors": [{"family": "Sur", "given": "Inderpreet", "initials": "I"}, {"family": "Zhao", "given": "Wenshuo", "initials": "W"}, {"family": "Zhang", "given": "Jilin", "initials": "J", "orcid": "0000-0002-9976-1605", "researcher": {"href": "https://publications.scilifelab.se/researcher/b595931cc9c045dbbeb2dba7f3913d05.json"}}, {"family": "Kling Pilstr\u00f6m", "given": "Margareta", "initials": "M"}, {"family": "Webb", "given": "Anna T", "initials": "AT", "orcid": "0000-0001-6045-415X", "researcher": {"href": "https://publications.scilifelab.se/researcher/909754226aa04eb0824fc87c9efc628a.json"}}, {"family": "Cheng", "given": "Huaitao", "initials": "H"}, {"family": "Ristim\u00e4ki", "given": "Ari", "initials": "A"}, {"family": "Katajisto", "given": "Pekka", "initials": "P", "orcid": "0000-0002-3033-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/68045c70bad544b68bbe913e7bf0ded8.json"}}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Rannikmae", "given": "Helena", "initials": "H"}, {"family": "de la Roche", "given": "Marc", "initials": "M"}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "8", "issue": "6", "issn-l": "2575-1077"}, "abstract": "Cancer has been characterized as a wound that does not heal. Malignant cells are morphologically distinct from normal proliferating cells but have extensive similarities to tissues undergoing wound healing and/or regeneration. The mechanistic basis of this similarity has, however, remained enigmatic. Here, we show that the genomic region upstream of Myc, which carries more cancer susceptibility in humans than any other genomic region, is required for intestinal regeneration after radiation damage. Failure to regenerate is associated with inefficient Ly6a/Sca1+ stem/progenitor cell mobilization, and almost complete failure to re-establish Lgr5+ cell compartment in the intestinal crypts. The Myc upstream region is also critical for growth of adult intestinal cells in 3D organoid culture. We show that culture conditions recapitulating most aspects of adult normal tissue architecture still reprogram normal cells to proliferate using a mechanism similar to that employed by cancer cells. Our results establish a function for the Myc super-enhancer region as the genetic link between tissue regeneration and tumorigenesis, and demonstrates that normal tissue renewal and regeneration of tissues after severe damage are mechanistically distinct.2-540", "doi": "10.26508/lsa.202403090", "pmid": "40180576", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11969384"}, {"db": "pii", "key": "8/6/e202403090"}], "notes": [], "created": "2025-04-07T08:30:27.159Z", "modified": "2025-04-07T08:30:27.535Z"}, {"entity": "publication", "iuid": "9666dfe7453c4a56a722421336a9dd97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9666dfe7453c4a56a722421336a9dd97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9666dfe7453c4a56a722421336a9dd97"}}, "title": "Repeatability of evolution and genomic predictions of temperature adaptation in seed beetles.", "authors": [{"family": "R\u00eago", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-2737-1859", "researcher": {"href": "https://publications.scilifelab.se/researcher/648746555fc7437d8560ca5be086baea.json"}}, {"family": "Baur", "given": "Julian", "initials": "J", "orcid": "0000-0002-4739-2756", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e69e394b67145188a77f90365f3fe15.json"}}, {"family": "Girard-Tercieux", "given": "Camille", "initials": "C"}, {"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abfa65f99b44f1ba6f8f0e6f3d7d8a4.json"}}, {"family": "Stelkens", "given": "Rike", "initials": "R", "orcid": "0000-0002-8530-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3449c244a4c13b8610e401f4cbef4.json"}}, {"family": "Berger", "given": "David", "initials": "D", "orcid": "0000-0003-0196-6109", "researcher": {"href": "https://publications.scilifelab.se/researcher/c788f99e9df4435587f7e991eae4311e.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "9", "issue": "6", "pages": "1061-1074", "issn-l": "2397-334X"}, "abstract": "Climate warming is threatening biodiversity by increasing temperatures beyond the optima of many ectotherms. Owing to the inherent non-linear relationship between temperature and the rate of cellular processes, such shifts towards hot temperature are predicted to impose stronger selection compared with corresponding shifts towards cold temperature. This suggests that when adaptation to warming occurs, it should be relatively rapid and predictable. Here we tested this hypothesis from the level of single-nucleotide polymorphisms to life-history traits in the beetle Callosobruchus maculatus. We conducted an evolve-and-resequence experiment on three genetic backgrounds of the beetle reared at hot or cold temperature. Indeed, we find that phenotypic evolution was faster and more repeatable at hot temperature. However, at the genomic level, adaptation to heat was less repeatable when compared across genetic backgrounds. As a result, genomic predictions of phenotypic adaptation in populations exposed to hot temperature were accurate within, but not between, backgrounds. These results seem best explained by genetic redundancy and an increased importance of epistasis during adaptation to heat, and imply that the same mechanisms that exert strong selection and increase repeatability of phenotypic evolution at hot temperature reduce repeatability at the genomic level. Thus, predictions of adaptation in key phenotypes from genomic data may become increasingly difficult as climates warm.", "doi": "10.1038/s41559-025-02716-5", "pmid": "40379980", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12148939"}, {"db": "pii", "key": "10.1038/s41559-025-02716-5"}], "notes": [], "created": "2025-11-28T10:46:21.586Z", "modified": "2025-11-28T10:46:21.757Z"}, {"entity": "publication", "iuid": "3b2a02d67f144ff88bea2f6a5a15421b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b2a02d67f144ff88bea2f6a5a15421b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b2a02d67f144ff88bea2f6a5a15421b"}}, "title": "Proteomic signatures for fibrosis in MASLD: a biopsy-proven dual-cohort study.", "authors": [{"family": "Blomdahl", "given": "Julia", "initials": "J", "orcid": "0000-0002-6364-8758", "researcher": {"href": "https://publications.scilifelab.se/researcher/73da360e98674266bec90264c3063c69.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Frid\u00e9n", "given": "Michael", "initials": "M", "orcid": "0000-0002-6545-4439", "researcher": {"href": "https://publications.scilifelab.se/researcher/51e5a97ff89243cdb1bacc10c258638d.json"}}, {"family": "Ahlstr\u00f6m", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-8701-969X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e4a209929642ceaadf3e0aed6b8c69.json"}}, {"family": "Hockings", "given": "Paul", "initials": "P", "orcid": "0000-0002-7154-9047", "researcher": {"href": "https://publications.scilifelab.se/researcher/9361c9d64c2441d1b2466093a328a1dc.json"}}, {"family": "Hulthe", "given": "Johannes", "initials": "J"}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Gabrysch", "given": "Katja", "initials": "K", "orcid": "0009-0003-4234-8814", "researcher": {"href": "https://publications.scilifelab.se/researcher/837ace5843754a7092e87a38c040950c.json"}}, {"family": "Nasr", "given": "Patrik", "initials": "P", "orcid": "0000-0002-2928-4188", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c50e5ee47e24bb1aea2118a99fa870d.json"}}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U", "orcid": "0000-0002-8620-4586", "researcher": {"href": "https://publications.scilifelab.se/researcher/cca577a7bfc942ccbf5284e4b82995f4.json"}}, {"family": "Kechagias", "given": "Stergios", "initials": "S", "orcid": "0000-0001-7614-739X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c68083028c74ec19620787550e769b5.json"}}, {"family": "Rorsman", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-4023-9617", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fa2976e78ac4486a4edaef33f144d7d.json"}}, {"family": "Ekstedt", "given": "Mattias", "initials": "M", "orcid": "0000-0002-5590-8601", "researcher": {"href": "https://publications.scilifelab.se/researcher/423ba88447d045acb91cf6578a848299.json"}}, {"family": "Vessby", "given": "Johan", "initials": "J", "orcid": "0000-0003-1832-6386", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa93020464454653b142d9951e23a0bb.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Scand. J. Gastroenterol.", "issn": "1502-7708", "volume": "60", "issue": "6", "pages": "597-605", "issn-l": "0036-5521"}, "abstract": "Predicting disease progression in metabolic dysfunction-associated steatotic liver disease (MASLD) is challenging, and current non-invasive tests (NITs) lack the precision to replace liver biopsy. This study aimed to identify plasma biomarkers for different stages of fibrosis using affinity-based proteomics in two biopsy-proven cohorts. The primary objective was to identify biomarkers capable of distinguishing between low-to-no fibrosis (F0-1) and significant fibrosis (F2-4) in MASLD.\n\nParticipants in the discovery cohort were recruited from Uppsala University Hospital and Swedish CArdioPulmonary bioImage Study (SCAPIS), while the validation cohort was included from Link\u00f6ping University Hospital. All participants diagnosed with MASLD underwent liver biopsy and were categorized by fibrosis stage (F0-1 or F2-4). A total of 276 plasma proteins were analyzed using Olink\u00ae panels, with biomarkers identified through ordinal logistic regression, random forest (RF) analysis and the Boruta algorithm.\n\nThe discovery cohort included 60 participants, with 60% having fibrosis stage F0-1 and 40% having F2-4. The validation cohort had 59 participants, of whom 35 had fibrosis stage F0-1 (59.3%) and 24 had stage F2-4 (40.7%). Five biomarkers were significantly associated with fibrosis stage in the discovery cohort, with four confirmed in the validation cohort. A model combining angiotensin converting enzyme-2 (ACE2), hepatocyte growth factor (HGF) and insulin-like growth factor-binding protein-7 (IGFBP-7) demonstrated strong predictive performance for significant fibrosis (c-statistics 0.82-0.83), outperforming fibrosis-4 (FIB-4) (c-statistics 0.61-0.72).\n\nA biomarker model including ACE2, HGF and IGFBP7 shows promise in distinguishing between low-stage and significant fibrosis.", "doi": "10.1080/00365521.2025.2490996", "pmid": "40237197", "labels": {"Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T19:16:23.507Z", "modified": "2025-11-25T19:19:33.192Z"}, {"entity": "publication", "iuid": "4525a2586b724ec19984cd16fbb4d237", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4525a2586b724ec19984cd16fbb4d237.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4525a2586b724ec19984cd16fbb4d237"}}, "title": "Preserving Neuronal Chemical Messengers: Heat Stabilization Versus Snap Freezing for Improved MALDI Mass Spectrometry Imaging of Brain Tissues.", "authors": [{"family": "Salviati", "given": "Emanuela", "initials": "E"}, {"family": "Lupt\u00e1kov\u00e1", "given": "Dominika", "initials": "D"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Shariatgorji", "given": "Reza", "initials": "R"}, {"family": "Campiglia", "given": "Pietro", "initials": "P"}, {"family": "Tjernstr\u00f6m", "given": "Nikita", "initials": "N"}, {"family": "Roman", "given": "Erika", "initials": "E"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "J. Neurochem.", "issn": "1471-4159", "volume": "169", "issue": "6", "pages": "e70122", "issn-l": "0022-3042"}, "abstract": "One of the main challenges in analyzing chemical messengers in the brain is the optimization of tissue sampling and preparation protocols. Limiting postmortem time and terminating enzyme activity is critical to identify low-abundance neurotransmitters and neuropeptides. Here, we used a rapid and uniform conductive heat transfer stabilization method that was compared with a conventional fresh freezing protocol. Together with a selective chemical derivatization method and an optimized quantitation approach using deuterated internal standards, we spatially mapped neurotransmitters and their related metabolites by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) in rat brain tissue sections. Although the heat stabilization did not show differences in the levels of dopamine, norepinephrine, and serotonin, their related metabolites 3,4-dihydroxyphenylacetaldehyde, 3,4-dihydroxyphenylacetic acid, homovanillic acid, 3-methoxy-4-hydroxyphenylacetaldehyde, dihydroxyphenylethyleneglycol, and 5-hydroxyindoleacetic acid were all significantly lower, indicating reduced neurotransmitter postmortem turnover ratios. Heat stabilization enabled detection of an increased number and higher levels of prodynorphin, proenkephalin, and tachykinin-derived bioactive neuropeptides. The low-abundant C-terminal flanking peptide, neuropeptide-\u03b3, and nociceptin remained intact and were exclusively imaged in heat-stabilized brains. Without heat stabilization, degradation fragments of full-length peptides occurred in the fresh frozen tissues. The sample preparation protocols were furthermore tested on rat brains affected by acute anesthesia induced by isoflurane and medetomidine, showing comparable results to non-anesthetized animals on the neurotransmitters level without significant changes. Our data provide evidence for the potential use of heat stabilization prior to MALDI-MSI analyses to improve the examination of the in vivo state of neuronal chemical messengers in brain tissues not impacted by prior acute anesthesia.", "doi": "10.1111/jnc.70122", "pmid": "40522155", "labels": {"Spatial Mass Spectrometry": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12169076"}], "notes": [], "created": "2025-11-21T09:59:53.638Z", "modified": "2025-11-21T09:59:53.691Z"}, {"entity": "publication", "iuid": "b5cadf33662a43ba963d6e97bfa96d3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5cadf33662a43ba963d6e97bfa96d3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5cadf33662a43ba963d6e97bfa96d3a"}}, "title": "Precision Omics Initiative Sweden (PROMISE) will integrate research with healthcare.", "authors": [{"family": "K\u00e4mpe", "given": "Anders", "initials": "A", "orcid": "0000-0002-1829-3855", "researcher": {"href": "https://publications.scilifelab.se/researcher/0785e17b57384962a0ff9bc7ecaa80c8.json"}}, {"family": "Gudmundsson", "given": "Sanna", "initials": "S"}, {"family": "Walsh", "given": "Colum P", "initials": "CP"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}, {"family": "Clareborn", "given": "Anna", "initials": "A"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Edsj\u00f6", "given": "Anders", "initials": "A", "orcid": "0000-0001-8783-8284", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fae25d88855440194b9bb11b3d18bf8.json"}}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Ehrencrona", "given": "Hans", "initials": "H", "orcid": "0000-0002-5589-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b89608a8ce941c3b9911630b4ff9720.json"}}, {"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Franks", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-0520-7604", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebbf40c0f7e49dd8c75a2b6cbf27276.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Haag", "given": "Margareta", "initials": "M"}, {"family": "Hagwall", "given": "Anna", "initials": "A"}, {"family": "Johansson Soller", "given": "Maria", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Lu", "given": "Yi", "initials": "Y", "orcid": "0000-0001-9933-3654", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a73eafe0b0e4221a77b96800883413d.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}, {"family": "Melin", "given": "Beatrice", "initials": "B"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Saal", "given": "Lao H", "initials": "LH", "orcid": "0000-0002-0815-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a1ec17a1d2e46e78f483f8e43f5e5f2.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sikora", "given": "Per", "initials": "P"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Van Guelpen", "given": "Bethany", "initials": "B", "orcid": "0000-0002-9692-101X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ea901d796bc4f3fbc53f930c5021118.json"}}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Jacobsson", "given": "Bo", "initials": "B", "orcid": "0000-0001-5079-2374", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6968816ded4a50b1029ee3f4afbeed.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Persson", "given": "Bengt", "initials": "B"}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Lappalainen", "given": "Tuuli", "initials": "T"}], "type": "letter", "published": "2025-06-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "issn-l": "1078-8956", "volume": "31", "issue": "6", "pages": "1730-1732"}, "abstract": null, "doi": "10.1038/s41591-025-03631-9", "pmid": "40186080", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Clinical Genomics Lund": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41591-025-03631-9"}], "notes": [], "created": "2025-07-08T13:55:07.435Z", "modified": "2025-11-21T13:21:42.346Z"}, {"entity": "publication", "iuid": "f0769cf27b0a4d2db77bc3cfe4f6f8d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0769cf27b0a4d2db77bc3cfe4f6f8d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0769cf27b0a4d2db77bc3cfe4f6f8d1"}}, "title": "Phylogenetic relationships and the identification of allopolyploidy in circumpolar Silene sect. Physolychnis.", "authors": [{"family": "Quatela", "given": "Anne-Sophie", "initials": "AS", "orcid": "0009-0009-1449-2281", "researcher": {"href": "https://publications.scilifelab.se/researcher/abdbdd63913b492c808ef0f1d9b2a639.json"}}, {"family": "Cangren", "given": "Patrik", "initials": "P"}, {"family": "de Lima Ferreira", "given": "Paola", "initials": "P", "orcid": "0000-0002-6957-4243", "researcher": {"href": "https://publications.scilifelab.se/researcher/71143c335a5c4c21954e2730e8e7c528.json"}}, {"family": "Woudstra", "given": "Yannick", "initials": "Y", "orcid": "0000-0001-8861-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/424f227ccfbd44ed9c52387faa30269a.json"}}, {"family": "Zsoldos-Skahjem", "given": "Andreas", "initials": "A"}, {"family": "Bacon", "given": "Christine D", "initials": "CD", "orcid": "0000-0003-2341-2705", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4e957ca1d6049418d276fcc44e077fc.json"}}, {"family": "de Boer", "given": "Hugo J", "initials": "HJ", "orcid": "0000-0003-1985-7859", "researcher": {"href": "https://publications.scilifelab.se/researcher/a232c69265cb41c9980512b4a30c19f6.json"}}, {"family": "Oxelman", "given": "Bengt", "initials": "B", "orcid": "0000-0002-6104-4264", "researcher": {"href": "https://publications.scilifelab.se/researcher/516997145fcf40eb8a777d82d5f1dca1.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Am. J. Bot.", "issn": "1537-2197", "volume": "112", "issue": "6", "pages": "e70051", "issn-l": "0002-9122"}, "abstract": "Species complexes are groups of closely related species with ambiguous delimitation, often composed of recently diverged lineages. Polyploidization and uniparental reproduction (i.e., selfing and apomixis) can play important roles in the origin of species complexes. These complexes pose challenges for species-based scientific questions, such as the estimation of species richness or conservation prioritization.\n\nWe determined the potential of resolving taxonomically complex groups using target enrichment in the circumpolar Silene uralensis complex (Caryophyllaceae). We proposed a metric using genetic distances between phased alleles to distinguish diploids from allopolyploids.\n\nOur results identified geographic structure of populations, with the northern American and Greenlandic samples having a common ancestor. We found little phylogenetic support for the most recent taxonomic treatment of the Silene uralensis complex.\n\nThe study highlights the use of target enrichment in testing taxonomic hypotheses in diploids and the challenges of studying recently diverged lineages.", "doi": "10.1002/ajb2.70051", "pmid": "40405418", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12189834"}], "notes": [], "created": "2025-11-24T11:06:01.819Z", "modified": "2025-11-24T11:06:02.169Z"}, {"entity": "publication", "iuid": "ba1cfe4ddcce4dd29b0d2cb2fbae1912", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba1cfe4ddcce4dd29b0d2cb2fbae1912.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba1cfe4ddcce4dd29b0d2cb2fbae1912"}}, "title": "Multimorbidity patterns and blood biomarkers of Alzheimer's disease in community-dwelling cognitively unimpaired older adults.", "authors": [{"family": "Marengoni", "given": "Alessandra", "initials": "A"}, {"family": "Grande", "given": "Giulia", "initials": "G"}, {"family": "Valletta", "given": "Martina", "initials": "M"}, {"family": "Gregorio", "given": "Caterina", "initials": "C"}, {"family": "Calder\u00f3n-Larra\u00f1aga", "given": "Amaia", "initials": "A"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Winblad", "given": "Bengt", "initials": "B"}, {"family": "Vetrano", "given": "Davide Liborio", "initials": "DL"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Alzheimers Dement", "issn": "1552-5279", "volume": "21", "issue": "6", "pages": "e70411", "issn-l": null}, "abstract": "Alzheimer's disease (AD) blood biomarkers hold clinical potential but their concentration may vary with somatic conditions.\n\nWe investigated the concentration of six AD blood biomarkers in relation to multimorbidity as disease count and four multimorbidity patterns in 2290 cognitively unimpaired older adults.\n\nLevels of phosphorylated tau (p-tau)181, p-tau217, neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) increased with increasing number of diseases. In multi-adjusted regressions, compared to individuals without multimorbidity, the anemia/sensory impairment pattern was associated with altered levels of all biomarkers except amyloid beta (A\u03b2)42/40, GFAP, and total tau (p-tau181: \u03b2 = 0.18, 95% confidence interval [CI]: 0.08, 0.28; p-tau217: \u03b2 = 0.11, 95% CI: 0.03, 0.18; NfL: \u03b2 = 0.14, 95% CI: 0.06, 0.21) and the cardiometabolic/inflammatory pattern was associated with altered levels of all biomarkers except A\u03b242/40 and GFAP (p-tau181: \u03b2 = 0.24, 95% CI: 0.12, 0.36; p-tau217: \u03b2 = 0.23, 95% CI: 0.14, 0.32; NfL: \u03b2 = 0.32, 95% CI: 0.23, 0.40; total tau: \u03b2 = 0.23, 95% CI: 0.07, 0.39). Results remained unchanged after excluding those who developed dementia in 15 years.\n\nMore diseases and specific multimorbidity patterns altered the levels of several AD blood biomarkers, highlighting caution when using them in adults with complex health profiles.\n\nIn cognitively unimpaired older adults blood biomarkers of Alzheimer's disease varied depending on the number of chronic diseases and specific patterns of multimorbidity. Phosphorylated tau (p-tau)181, p-tau217, neurofilament light chain (NfL), and glial fibrillary acidic protein levels increased along with increasing numbers of chronic diseases. P-tau181, p-tau217, and NfL levels were significantly higher in individuals in the anemia/sensory impairment and cardiometabolic/inflammatory multimorbidity patterns compared to those without multimorbidity. Results remained unchanged after excluding participants who developed dementia during 15-year follow-up.", "doi": "10.1002/alz.70411", "pmid": "40545553", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12183106"}], "notes": [], "created": "2025-09-21T09:52:35.744Z", "modified": "2025-09-21T09:52:35.748Z"}, {"entity": "publication", "iuid": "63fb5b675de44aedaf3eb7c0432be9e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63fb5b675de44aedaf3eb7c0432be9e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63fb5b675de44aedaf3eb7c0432be9e7"}}, "title": "Implications of Breeding for Growth on Drought Tolerance in Scots Pine (Pinus sylvestris L.)-Insights From Metabolomics and High-Throughput Plant Architecture Analysis.", "authors": [{"family": "Gil-Mu\u00f1oz", "given": "Francisco", "initials": "F"}, {"family": "Ranade", "given": "Sonali Sachin", "initials": "SS"}, {"family": "Hayatgheibi", "given": "Haleh", "initials": "H", "orcid": "0009-0000-8867-9369", "researcher": {"href": "https://publications.scilifelab.se/researcher/323aa70939f14ecd91aea226521a367d.json"}}, {"family": "Niemi", "given": "Juha", "initials": "J"}, {"family": "\u00d6stlund", "given": "Lars", "initials": "L"}, {"family": "Garc\u00eda-Gil", "given": "Mar\u00eda Rosario", "initials": "MR", "orcid": "0000-0002-6834-6708", "researcher": {"href": "https://publications.scilifelab.se/researcher/774898d2b46f44cb8475be89ecd8b79d.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "18", "issue": "6", "pages": "e70122", "issn-l": "1752-4571"}, "abstract": "Drought has been identified as one of the important environmental factors in the context of climate change due to its interaction with other biotic and abiotic stresses. However, only a few studies have reported the effect of breeding on forest adaptability to climate change. Using a common garden experiment with seedlings from families of Scots pine (Pinus sylvestris L.) from northern Sweden, we have found differences in drought tolerance between seedlings from breeding stands and those from natural forests. We performed a genetic analysis including high-throughput image-based phenotyping of seedling canopy and root traits and conducted metabolomic and hormone analyses with the aerial parts of the seedlings. Our results indicate that root architecture traits associated with drought tolerance exhibit moderate to high heritability. Analyses of seedling architecture reveal that families from breeding stands have higher drought resistance but lower genetic variation than the ones from natural forests, especially in the case of canopy traits. Metabolomic and hormone analyses of the aerial parts of the seedlings also support that the breeding stands may have a higher capacity to withstand or deal with drought conditions as compared to the natural forests. For example, increase in abscisic acid along with increase in tryptophan and auxin conjugates in the breeding stands compared to the natural forests under drought conditions may contribute to alleviation of drought response in the breeding stands. The methodology employed to evaluate drought tolerance and plant architecture in this study might be useful for future research and forest management focused on climate change adaptability.", "doi": "10.1111/eva.70122", "pmid": "40557245", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12185384"}, {"db": "pii", "key": "EVA70122"}], "notes": [], "created": "2025-11-18T12:07:40.988Z", "modified": "2025-11-18T12:07:41.072Z"}, {"entity": "publication", "iuid": "0cf514f45b5e4d7fac663132f0139fab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cf514f45b5e4d7fac663132f0139fab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cf514f45b5e4d7fac663132f0139fab"}}, "title": "Green Listed v2.0: A Web Application for Streamlined Design of Custom CRISPR Screens.", "authors": [{"family": "Henkel", "given": "Esbj\u00f6rn", "initials": "E"}, {"family": "Li", "given": "Zhaojun", "initials": "Z"}, {"family": "Uvehag", "given": "Daniel", "initials": "D"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B"}, {"family": "Henkel", "given": "Martin", "initials": "M"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9633-677X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a34df8186ba24df3b14fe9743cf546b4.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "CRISPR J", "issn": "2573-1602", "issn-l": null, "volume": "8", "issue": "3", "pages": "216-223"}, "abstract": "Custom CRISPR screens are powerful tools for rapid, hypothesis-driven discovery, but their design is often complex and time-consuming. Green Listed v2.0 simplifies this process with an intuitive workflow for designing custom CRISPR spacer libraries and supports downstream analysis for all users, irrespective of their computational experience. The web application features a user-friendly graphical interface freely accessible at https://greenlisted.cmm.se. Version 2.0 includes significant upgrades to the original 2016 version that were implemented based on user feedback. This includes a new gene synonym tool, expanded library options, optimized output lists, performance improvements, and linked scripts for the rational design of custom CRISPR screen gene sets.", "doi": "10.1089/crispr.2025.0023", "pmid": "40329823", "labels": {"CRISPR Functional Genomics": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2025-05-09T09:28:25.653Z", "modified": "2025-09-05T13:57:58.831Z"}, {"entity": "publication", "iuid": "19d4f0ca29364061b137e9116162d5d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19d4f0ca29364061b137e9116162d5d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19d4f0ca29364061b137e9116162d5d2"}}, "title": "Genetically Determined Inflammation-Related Proteins in Asthma and Type-2 Signatures.", "authors": [{"family": "Hernandez-Pacheco", "given": "Natalia", "initials": "N", "orcid": "0000-0002-6313-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/833e75515e024830b827806684d61126.json"}}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK", "orcid": "0000-0001-5974-7676", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7a04c6538814b089994c7a822ecf07f.json"}}, {"family": "Kere", "given": "Maura", "initials": "M", "orcid": "0000-0002-5725-2773", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d213ed52d084d79a7a87e09a3688d01.json"}}, {"family": "Kumar", "given": "Ashish", "initials": "A", "orcid": "0000-0002-7075-5930", "researcher": {"href": "https://publications.scilifelab.se/researcher/de86e6bb6d154c2db787a769da96323b.json"}}, {"family": "Klevebro", "given": "Susanna", "initials": "S", "orcid": "0000-0002-1261-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cace10c20c847f6a04259937e74891e.json"}}, {"family": "Mogensen", "given": "Ida", "initials": "I", "orcid": "0000-0002-0198-2718", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e3b914932c4470ba02ff73278972c8.json"}}, {"family": "Ekstr\u00f6m", "given": "Sandra", "initials": "S", "orcid": "0000-0002-2060-8190", "researcher": {"href": "https://publications.scilifelab.se/researcher/d813a2fda4fc410cb5db71c62af9d0ea.json"}}, {"family": "Janson", "given": "Christer", "initials": "C", "orcid": "0000-0001-5093-6980", "researcher": {"href": "https://publications.scilifelab.se/researcher/bae457d633714159a73704f9ebe7bfa6.json"}}, {"family": "Palmberg", "given": "Lena", "initials": "L", "orcid": "0000-0001-5650-4484", "researcher": {"href": "https://publications.scilifelab.se/researcher/c77734a210e146dbaadc33363eaaaa6f.json"}}, {"family": "van Hage", "given": "Marianne", "initials": "M", "orcid": "0000-0003-3091-1596", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e9a55cd378c46d5a1fc6b4694423849.json"}}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A", "orcid": "0000-0003-2608-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70c845d32264b448e0b4631b826be6d.json"}}, {"family": "Merritt", "given": "Anne-Sophie", "initials": "AS", "orcid": "0000-0002-4497-1779", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a96b69dc76435a83ea3dc089a5b657.json"}}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-9701-1130", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d97eee1803d4ce3a85c1fcb423c75d9.json"}}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0002-7981-6314", "researcher": {"href": "https://publications.scilifelab.se/researcher/70d058e4d5bc49d7a3c958950c9d4e6d.json"}}, {"family": "Kull", "given": "Inger", "initials": "I", "orcid": "0000-0001-6096-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f248045358c4711b1d10d7b9fe9649c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Allergy", "issn": "1398-9995", "volume": "80", "issue": "6", "pages": "1702-1714", "issn-l": "0105-4538"}, "abstract": "Protein quantitative trait loci (pQTLs) remain underexplored in asthma but might provide valuable insights into the underlying molecular mechanisms. This study aimed to investigate associations between genetic variation and inflammation-related plasma proteins and to assess differences in the levels of genetically determined proteins in subjects with signatures of type-2 inflammation and/or asthma.\n\nA pQTL mapping of 92 inflammation-related plasma proteins was conducted in young adults from the Swedish BAMSE cohort (n = 1538). Replication of sentinel pQTLs was attempted, and the overlap and colocalization of pQTLs with expression quantitative trait loci (eQTLs) were investigated using publicly available data. Proteins with significant pQTLs were tested for association with type-2 signatures defined as high levels of fractional exhaled nitric oxide, blood eosinophils, and/or sensitization to airborne allergens in subjects with or without asthma in BAMSE.\n\nForty-five sentinel pQTLs (33 cis, 12 trans) for 39 inflammation-related proteins were identified (p \u2264 7.14 \u00d7 10-11), and a high proportion of these were validated in independent populations. A high likelihood for colocalization of cis-pQTLs and cis-eQTLs was observed for 19 proteins in different tissues. Six of the 39 circulating proteins with significant pQTLs were associated with type-2 signatures and/or asthma, and matrix metalloproteinase-10 (MMP-10) showed the most significant associations.\n\nThese findings underscore the existence of a genetic component influencing the plasma levels of proteins involved in inflammatory processes, including MMP-10, which is suggested to have a role in high type-2 inflammation in asthma subjects.", "doi": "10.1111/all.16608", "pmid": "40464643", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12186602"}], "notes": [], "created": "2025-09-08T07:17:11.553Z", "modified": "2025-11-25T19:21:03.863Z"}, {"entity": "publication", "iuid": "dbbacfc5e2734fc19c98ec14dd081705", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbbacfc5e2734fc19c98ec14dd081705.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbbacfc5e2734fc19c98ec14dd081705"}}, "title": "Frequent Hybridisation Between Parapatric Lekking Bird-of-Paradise Species.", "authors": [{"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "Nagombi", "given": "Elizah", "initials": "E"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "11", "pages": "e17780", "issn-l": "0962-1083"}, "abstract": "Hybridisation is known to occur between a wide range of taxa, including species for which strong sexual selection has led to markedly different sexual phenotypes and lek-mating behaviours. To what extent occasional hybridisation can overcome the reproductive barriers in such systems and, for example, lead to the establishment of hybrid zones is poorly known. In this study, we address this question by focusing on one of the most well-known avian radiations in which sexual selection has resulted in an extraordinary assemblage of phenotypic diversity and lek-mating behaviours: the birds-of-paradise (Paradisaeidae). We quantify the genome-wide distribution of introgression and find multiple signals of recent and historical gene flow between and within two genera of birds-of-paradise, Astrapia and Paradigalla. In addition, we present the first empirical genomic indication of a putative hybrid zone between two lekking bird-of-paradise species that differ substantially in their sexually selected traits and behaviours. Our findings are consistent with the idea that behavioural and phenotypic traits may constitute weaker pre- and post-zygotic barriers to gene flow than generally thought in lek-mating species.", "doi": "10.1111/mec.17780", "pmid": "40298045", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12100584"}], "notes": [], "created": "2025-05-26T07:50:33.961Z", "modified": "2025-11-28T10:51:32.111Z"}, {"entity": "publication", "iuid": "20eb2f2bbb1c422eaa580402cd480382", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20eb2f2bbb1c422eaa580402cd480382.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20eb2f2bbb1c422eaa580402cd480382"}}, "title": "Fermentative Yeast Diversity at the Northern Range Limit of Their Oak Tree Hosts.", "authors": [{"family": "Pinto", "given": "Javier", "initials": "J"}, {"family": "Haberkorn", "given": "Chlo\u00e9", "initials": "C", "orcid": "0000-0002-7371-9177", "researcher": {"href": "https://publications.scilifelab.se/researcher/099838e4d3b94ee1af5cdfbf8ffea5d2.json"}}, {"family": "Franz\u00e9n", "given": "Markus", "initials": "M"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}, {"family": "Stelkens", "given": "Rike", "initials": "R", "orcid": "0000-0002-8530-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3449c244a4c13b8610e401f4cbef4.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "17", "issue": "3", "pages": "e70110", "issn-l": "1758-2229"}, "abstract": "Fermentative yeasts play important roles in both ecological and industrial processes, but their distribution and abundance in natural environments are not well understood. We investigated the diversity of yeasts at the northern range limit of their oak tree hosts (Quercus spp.) in Sweden, and identified climatic and ecological conditions governing their distribution. Yeasts were isolated from bark samples from 28 forests and identified to the species level using DNA metabarcoding. Most communities were dominated by species in the Saccharomycetaceae family, especially by species of Saccharomyces, Kluyveromyces and Pichia. Each genus showed a distinct latitudinal and longitudinal distribution, and both temperature and precipitation metrics predicted significant variation in their abundance. Consistent with this, laboratory assays revealed significant effects of temperature on the growth of strains collected from different longitudes and latitudes. We found that older trees harbour more diverse and more balanced fermentative yeast communities with more evenly distributed species abundances. Communities across trees were more similar when sharing a common dominant species. This work provides a baseline for future studies on the impact of climate change on the fermentative yeast biodiversity of temperate forests in northern latitudes and contributes to a growing collection of wild isolates for potential biotechnological applications.", "doi": "10.1111/1758-2229.70110", "pmid": "40410946", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12102073"}], "notes": [], "created": "2025-11-28T10:50:51.200Z", "modified": "2025-12-05T11:26:12.741Z"}, {"entity": "publication", "iuid": "8e11b542333346ebbaae93123f6e533c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e11b542333346ebbaae93123f6e533c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e11b542333346ebbaae93123f6e533c"}}, "title": "Excitatory and inhibitory neurotransmitter alterations with advancing age and injury in the mouse retina.", "authors": [{"family": "Bell", "given": "Katharina C", "initials": "KC"}, {"family": "Chrysostomou", "given": "Vicki", "initials": "V"}, {"family": "Karlsson", "given": "Markus", "initials": "M"}, {"family": "Jones", "given": "Bryan W", "initials": "BW"}, {"family": "Williams", "given": "Pete A", "initials": "PA"}, {"family": "Crowston", "given": "Jonathan G", "initials": "JG"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Neurobiol. Aging", "issn": "1558-1497", "volume": "150", "pages": "69-79", "issn-l": "0197-4580"}, "abstract": "Increasing age and elevated intraocular pressure (IOP) are the two major risk factors for glaucoma, the most common cause of irreversible blindness worldwide. Accumulating evidence is pointing to metabolic failure predisposing to neuronal loss with advancing age and IOP injury. Many neurotransmitters are synthesized from endogenous metabolites and are essential for correct cell to cell signaling along the visual pathways. We performed detailed, small molecule metabolomic profiling of the aging mouse retina and further explored the impact of IOP elevation at different ages. The resultant metabolomic profiles showed clear discrimination between young and middle-aged retinas and these changes are accentuated following eye pressure elevation. Alterations in glutamate and Gamma-aminobutyric acid (GABA) related metabolites were the most apparent changes with advancing age with further reductions in GABA and related pathways after IOP elevation. These changes were further confirmed using immunohistochemistry and patch-clamp electrophysiological recording experiments.", "doi": "10.1016/j.neurobiolaging.2025.03.004", "pmid": "40073716", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S0197-4580(25)00044-2"}], "notes": [], "created": "2025-11-18T12:06:44.381Z", "modified": "2025-11-18T12:06:44.397Z"}, {"entity": "publication", "iuid": "769397eccc3044d2b50395eaade60782", "links": {"self": {"href": "https://publications.scilifelab.se/publication/769397eccc3044d2b50395eaade60782.json"}, "display": {"href": "https://publications.scilifelab.se/publication/769397eccc3044d2b50395eaade60782"}}, "title": "Enduring modulation of dorsal raphe nuclei regulates (R,S)-ketamine-mediated resilient stress-coping behavior.", "authors": [{"family": "Camargo", "given": "Anderson", "initials": "A"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Shariatgorji", "given": "Reza", "initials": "R"}, {"family": "Appleton", "given": "Ellen", "initials": "E"}, {"family": "Branzell", "given": "Niclas", "initials": "N"}, {"family": "Doyon", "given": "Daniel", "initials": "D"}, {"family": "Giovenzana", "given": "Mattia", "initials": "M", "orcid": "0009-0002-1384-3413", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2cd71f47b7a40d7b996da916888798b.json"}}, {"family": "Zhang", "given": "Xiaoqun", "initials": "X", "orcid": "0000-0002-9461-8682", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f307c88103d43b1b0b893fa59a8e828.json"}}, {"family": "Dautan", "given": "Daniel", "initials": "D"}, {"family": "Andren", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Mol. Psychiatry", "issn": "1476-5578", "volume": "30", "issue": "6", "pages": "2504-2516", "issn-l": "1359-4184"}, "abstract": "Ketamine may be a novel pharmacologic approach to enhance resilience and protect against stress-related disorders, but the molecular targets underlying this response remain to be fully characterized. The multifunctional protein p11 is crucial in the pathophysiology of depression and antidepressant responses. However, it is still unclear whether p11 plays a role in the pro-resilience effects induced by ketamine. Here, we demonstrated that prophylactic administration of ketamine buffers passive stress-induced maladaptive phenotypes induced by chronic stress exposure. Spatial neurotransmitter and metabolite analysis revealed that prophylactic ketamine was also effective in blunting stress-induced disturbances of tryptophan metabolism in dorsal raphe nuclei (DRN). Additionally, we demonstrated that ketamine prevented chronic restraint stress-induced p11 reduction in DRN, a highly p11-enriched region. Furthermore, we provide novel evidence indicating that p11 deficiency regulates susceptibility to stress-induced depression-related phenotypes, and these behavioral maladaptations are dependent, at least in part, on p11 function in serotonergic neurons. Spatial neurotransmitter and metabolite analysis also showed a reduction of tryptophan and dopamine metabolism in DRN of serotonergic p11-deficient mice. Viral-mediated downregulation of p11 within DRN induced a stress-susceptible phenotype. Finally, our results also unveiled that the ability of ketamine to elicit a pro-resilience response against stress-induced maladaptive phenotypes was occluded when p11 was selectively deleted in serotonergic neurons. Altogether, we showed a previously unexplored role of the DRN circuit in regulating stress susceptibility and resilience-enhancing actions of ketamine.", "doi": "10.1038/s41380-024-02853-6", "pmid": "39592824", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12092261"}, {"db": "pii", "key": "10.1038/s41380-024-02853-6"}], "notes": [], "created": "2025-11-21T09:46:25.178Z", "modified": "2025-11-21T09:46:25.384Z"}, {"entity": "publication", "iuid": "721cdb8f88d04033a4d1712ca70be216", "links": {"self": {"href": "https://publications.scilifelab.se/publication/721cdb8f88d04033a4d1712ca70be216.json"}, "display": {"href": "https://publications.scilifelab.se/publication/721cdb8f88d04033a4d1712ca70be216"}}, "title": "EMD missense variant causes X-linked isolated dilated cardiomyopathy with myocardial emerin deficiency.", "authors": [{"family": "Bulmer", "given": "Linda", "initials": "L", "orcid": "0009-0001-5119-1156", "researcher": {"href": "https://publications.scilifelab.se/researcher/147a202ba3f14c4e9063c6a2feaddeb6.json"}}, {"family": "Ljungman", "given": "Charlotta", "initials": "C", "orcid": "0000-0002-2785-1919", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f1722548cf24b6fb76bbfd196c63408.json"}}, {"family": "Hallin", "given": "Johan", "initials": "J"}, {"family": "Dahlberg", "given": "Pia", "initials": "P"}, {"family": "Polte", "given": "Christian L", "initials": "CL", "orcid": "0000-0001-7125-9747", "researcher": {"href": "https://publications.scilifelab.se/researcher/20a7519ac50d4ac8bd4fc7c986eefcd0.json"}}, {"family": "Hedberg-Oldfors", "given": "Carola", "initials": "C", "orcid": "0000-0002-7141-4185", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc67028bf0c04f1b9a73bac5e72f9897.json"}}, {"family": "Oldfors", "given": "Anders", "initials": "A"}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "volume": "33", "issue": "6", "pages": "775-783", "issn-l": "1018-4813"}, "abstract": "Pathogenic variants in the EMD gene cause X-linked Emery-Dreifuss muscular dystrophy type 1 (EDMD1), typically presenting with joint contractures and skeletal muscle atrophy, followed by atrial arrhythmias, cardiac conduction defects, and atrial dilatation. Although an association with isolated dilated cardiomyopathy (DCM) has been suggested, evidence is currently insufficient to verify the gene-disease association. We investigated the causality of a missense variant, c.23C>G, p.Ser8Trp, in EMD in a large family with a history of DCM and suspected sudden cardiac death (SCD) in males. DCM was diagnosed in six hemizygous males aged 36-50 and detailed phenotyping identified end-stage heart failure, cardiac conduction defects, and ventricular arrhythmias as prominent features. Cardiac magnetic resonance imaging showed late gadolinium enhancement with mixed ischemic and non-ischemic patterns. Muscular dystrophy was absent in all six males, of whom five underwent neuromuscular examination including serum-creatine kinase measurement. Immunohistochemical analysis showed greatly reduced levels of emerin in both cardiac and skeletal muscle samples. The EMD variant c.23C>G co-segregated with DCM, with an estimated LOD score of 3.9 and full-likelihood Bayes factor of >2500:1 in favor of causality. Among the 17 heterozygous females, ages 20-87, one developed DCM at age 72. We concluded that the EMD c.23C>G missense variant is associated with DCM in the absence of muscular dystrophy, thereby providing new evidence of isolated DCM as a distinct cardiac EMD-phenotype, separate from EDMD1. The phenotypic similarities with LMNA-DCM, with a high risk of cardiac conduction defects and ventricular arrhythmias, might warrant early interventions to prevent SCD.", "doi": "10.1038/s41431-025-01827-8", "pmid": "40065010", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12185710"}, {"db": "pii", "key": "10.1038/s41431-025-01827-8"}], "notes": [], "created": "2025-07-08T13:52:10.967Z", "modified": "2025-11-04T11:32:46.724Z"}, {"entity": "publication", "iuid": "12010dd55a294967a7bec8f110ff6836", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12010dd55a294967a7bec8f110ff6836.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12010dd55a294967a7bec8f110ff6836"}}, "title": "Direct and indirect pathways linking the Lon protease to motility behaviors in the pathogen Pseudomonas aeruginosa.", "authors": [{"family": "Kallazhi", "given": "Aswathy", "initials": "A"}, {"family": "Rahman", "given": "Anamika", "initials": "A"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}, {"family": "Jonas", "given": "Kristina", "initials": "K", "orcid": "0000-0002-1469-4424", "researcher": {"href": "https://publications.scilifelab.se/researcher/3351b638c7904141b4ae20dd41929e26.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "PLoS Pathog.", "issn": "1553-7374", "volume": "21", "issue": "6", "pages": "e1013288", "issn-l": "1553-7366"}, "abstract": "The ATP-dependent cytoplasmic protease Lon has critical functions in protein quality control and cellular regulation in organisms across the three domains of life. In the opportunistic pathogen Pseudomonas aeruginosa, lon loss-of-function mutants exhibit multiple phenotypic defects in motility, virulence, antibiotic tolerance and biofilm formation. However, only a couple of native substrate proteins of Lon are described in P. aeruginosa until now and most of the phenotypes associated with Lon remain unexplained. Here, we searched for novel Lon substrates in P. aeruginosa by analyzing proteome-wide changes in protein levels and stabilities following lon overexpression. Our search yielded a large number of putative Lon substrates with diverse cellular functions, including metabolic enzymes, stress proteins and a significant fraction of motility-related proteins. In vitro degradation assays confirmed the metabolic protein SpeH, the heat shock protein IbpA as well as seven proteins involved in flagella- and type IV pilus-mediated motility as novel substrates of Lon. The new motility-associated substrates include both key regulators of motility (FliA, RpoN, AmrZ) as well as structural flagellar components (FliG, FliS and FlgE). Further, by isolating suppressor mutations bypassing the motility defect of lon- cells, we reveal that Lon-dependent degradation of the specific substrate SulA, a cell division inhibitor, is crucial for ensuring proper cell division and motility under optimal conditions. In sum, our work highlights Lon's regulatory role in degrading functional proteins involved in critical cellular processes and contributes to a better molecular understanding of the pathways underlying Pseudomonas pathogenicity.", "doi": "10.1371/journal.ppat.1013288", "pmid": "40561152", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12221181"}, {"db": "pii", "key": "PPATHOGENS-D-25-00035"}], "notes": [], "created": "2025-11-27T13:03:21.073Z", "modified": "2025-11-27T13:03:21.261Z"}, {"entity": "publication", "iuid": "14f1504c9c7c4920969417300aea155d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14f1504c9c7c4920969417300aea155d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14f1504c9c7c4920969417300aea155d"}}, "title": "Diffuse large B cell lymphoma in rheumatoid arthritis patients is associated with elevated B-cell driving factors including CXCL13.", "authors": [{"family": "Euler", "given": "Nora", "initials": "N"}, {"family": "Hellbacher", "given": "Erik", "initials": "E"}, {"family": "Klint", "given": "Erik Af", "initials": "EA"}, {"family": "Hansson", "given": "Monika", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Gr\u00f6nwall", "given": "Caroline", "initials": "C"}, {"family": "AUTO-LYMPHOMA study group", "given": "", "initials": ""}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Clin. Immunol.", "issn": "1521-7035", "volume": "275", "pages": "110476", "issn-l": "1521-6616"}, "abstract": "Patients with rheumatoid arthritis (RA) are at increased risk of diffuse large B cell lymphoma (DLBCL) compared to the general population. Here, we explored the inflammatory profiles in the blood of RA patients who had developed DLBCL. RA-DLBCL patients had significantly higher levels of the pro-inflammatory markers TNF, IL-8, CXCL9, APRIL, and particularly CXCL13 (median 796 vs. 206 pg/mL, p = 0.001), compared to RA controls. By including an extensive autoantibody panel of rheumatoid factor, IgG anti-CCP2, anti-citrullinated protein antibodies (ACPA) fine-specificities, and other anti-modified protein antibodies, all RA-DLBCL patients were autoantibody seropositive. Yet, RA-DLBCL patients did not display significantly different autoantibody signatures compared to RA controls. The levels of immunoglobulin free light chains and C-reactive protein were similar in RA-DLBCL patients and RA controls. In conclusion, RA-DLBCL patients exhibit pro-inflammatory signatures with elevated markers that are important for B cells and may contribute to enhanced B-cell activation and promote lymphoma development.", "doi": "10.1016/j.clim.2025.110476", "pmid": "40118130", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "S1521-6616(25)00051-8"}], "notes": [], "created": "2025-04-30T12:27:52.440Z", "modified": "2025-04-30T12:27:52.444Z"}, {"entity": "publication", "iuid": "2a2ca50ec2b44ca99ee63649522c4aaf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a2ca50ec2b44ca99ee63649522c4aaf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a2ca50ec2b44ca99ee63649522c4aaf"}}, "title": "Diel Bacterioplankton Community Dynamics Under Contrasting Light Regimes.", "authors": [{"family": "Papadopoulou", "given": "Sofia", "initials": "S", "orcid": "0000-0001-7315-3671", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f6cb7f8c28f4e0fbc030ee7311c6078.json"}}, {"family": "Linkhorst", "given": "Annika", "initials": "A", "orcid": "0000-0002-3609-5107", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba8c037d8ba4defbfa03364e2e264e7.json"}}, {"family": "Balmonte", "given": "John Paul", "initials": "JP", "orcid": "0000-0001-5571-4893", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3949f1396414e15a27c85460886d7ac.json"}}, {"family": "Csit\u00e1ri", "given": "Bianka", "initials": "B", "orcid": "0000-0002-5219-5829", "researcher": {"href": "https://publications.scilifelab.se/researcher/72ae1be693ac4900987f70a21a271494.json"}}, {"family": "Felf\u00f6ldi", "given": "Tam\u00e1s", "initials": "T", "orcid": "0000-0003-2009-2478", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a452e1d353649bc860f59485fc8bf03.json"}}, {"family": "M\u00e1rton", "given": "Zsuzsanna", "initials": "Z", "orcid": "0000-0002-7420-5039", "researcher": {"href": "https://publications.scilifelab.se/researcher/631b674f8b91403e95b1bbc8383fd8a8.json"}}, {"family": "Mershad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Szab\u00f3", "given": "Attila", "initials": "A", "orcid": "0000-0002-7777-8166", "researcher": {"href": "https://publications.scilifelab.se/researcher/78425c54e73b4bc1bf8c8b900224d41d.json"}}, {"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "issn-l": "1758-2229", "volume": "17", "issue": "3", "pages": "e70099"}, "abstract": "In the Boreal region, extreme seasonal variations in day-night length expose communities to dynamic light and temperature fluctuations. Freshwater bacterioplankton, representing key ecosystem components, faces climate-driven shifts; yet the fixed day-length patterns determined by latitude underscore the importance of studying light's role in predicting ecosystem responses. We investigated bacterial community composition in a brown peat bog and a clear oligotrophic lake across seasons with contrasting light regimes: the summer solstice (> 20 h of daylight) and the autumn equinox (equal day-night length). Using amplicon sequencing of 16S rRNA transcripts, alongside measurements of physicochemical parameters, organic matter characterisation and dissolved carbon dioxide and methane gas measurements, we found no diel cycling in the lake during either period or in the peat bog near the summer solstice. However, the structure of bacterial peat bog communities exhibited cyclic changes over diel cycles at the autumn equinox. Twelve amplicon sequence variants, including both phototrophic and heterotrophic taxa, increased in abundance at all measured morning sampling times. These findings provide valuable insights into the diel patterns of boreal lentic habitats and their bacterioplankton communities, highlighting the absence of diel fluctuations in some systems and seasons, while revealing cyclic dynamics in others, driven by conditionally rare taxa.", "doi": "10.1111/1758-2229.70099", "pmid": "40344486", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12061850"}], "notes": [], "created": "2025-05-12T05:46:12.949Z", "modified": "2025-11-28T10:50:46.010Z"}, {"entity": "publication", "iuid": "3cba993176914d9489704b83ceb80532", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3cba993176914d9489704b83ceb80532.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3cba993176914d9489704b83ceb80532"}}, "title": "Defining short linear motif binding determinants by phage display-based deep mutational scanning.", "authors": [{"family": "Benz", "given": "Caroline", "initials": "C"}, {"family": "Maassen", "given": "Lars", "initials": "L"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Mihalic", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Tsitsa", "given": "Ifigenia", "initials": "I", "orcid": "0000-0001-8154-5528", "researcher": {"href": "https://publications.scilifelab.se/researcher/9afb0faf7a4c435cbba2b4aa63b99b51.json"}}, {"family": "Konstantinou", "given": "Aimiliani", "initials": "A"}, {"family": "Jemth", "given": "Per", "initials": "P", "orcid": "0000-0003-1516-7228", "researcher": {"href": "https://publications.scilifelab.se/researcher/91bb46ceba74462498354a328886b982.json"}}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "34", "issue": "6", "pages": "e70174", "issn-l": "0961-8368"}, "abstract": "Deep mutational scanning (DMS) has emerged as a powerful approach for evaluating the effects of mutations on binding or function. Here, we developed a DMS by phage display protocol to define the specificity determinants of short linear motifs (SLiMs) binding to peptide-binding domains. We first designed a benchmarking DMS library to evaluate the performance of the approach on well-known ligands for 11 different peptide-binding domains, including the talin-1 PTB domain, the G3BP1 NTF2 domain, and the MDM2 SWIB domain. Comparison with a set of reference motifs from the eukaryotic linear motif (ELM) database confirmed that the DMS by phage display analysis correctly identifies known motif binding determinants and provides novel insights into specificity determinants, including defining a non-canonical talin-1 PTB binding motif with a putative extended conformation. A second DMS library was designed, aiming to provide information on the binding determinants for 19 SLiM-based interactions between human and SARS-CoV-2 proteins. The analysis confirmed the affinity determining residues of viral peptides binding to host proteins and refined the consensus motifs in human peptides binding to five domains from SARS-CoV-2 proteins, including the non-structural protein (NSP) 9. The DMS analysis further pinpointed mutations that increased the affinity of ligands for NSP3 and NSP9. An affinity-improved cell-permeable NSP9-binding peptide was found to exert stronger antiviral effects than the wild-type peptide. Our study demonstrates that DMS by phage display can efficiently be multiplexed and applied to refine binding determinants and shows how the results can guide peptide-engineering efforts.", "doi": "10.1002/pro.70174", "pmid": "40411416", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12102759"}], "notes": [], "created": "2025-09-08T11:37:16.206Z", "modified": "2025-11-21T18:30:05.510Z"}, {"entity": "publication", "iuid": "e9951e493ce143e8977c1f7de3cc015c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9951e493ce143e8977c1f7de3cc015c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9951e493ce143e8977c1f7de3cc015c"}}, "title": "Basal and exercise-induced expression of NLRP3 inflammasome-related components is increased in patients with chronic coronary syndrome.", "authors": [{"family": "Mahmood", "given": "Zeid", "initials": "Z"}, {"family": "B\u00e4ck", "given": "Maria", "initials": "M"}, {"family": "Leanderson", "given": "Per", "initials": "P"}, {"family": "Thune", "given": "Rebecka", "initials": "R"}, {"family": "Skoglund", "given": "Camilla", "initials": "C"}, {"family": "Jonasson", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Atherosclerosis", "issn": "1879-1484", "volume": "405", "pages": "119227", "issn-l": "0021-9150"}, "abstract": "NLRP3 inflammasome is considered a critical actor in the inflammatory process of coronary artery disease. Increased expression of NLRP3 inflammasome components has been reported in patients with acute coronary syndrome, but whether this persists beyond the acute phase is less known. We performed a prospective study to investigate whether basal and/or exercise-induced NLRP3 inflammasome components were elevated in patients with chronic coronary syndrome (CCS).\n\nPatients (n = 81) underwent exercise stress tests twice: 3-4 weeks and 3-6 months after a major coronary event, whereas controls (n = 30) performed it once. Concentrations of interleukin(IL)-18, IL-1Ra and IL-6 were measured before and 30 min after exercise. Genes related to NLRP3 inflammasome and NF\u03baB signaling pathways were measured in blood mononuclear cells before and after exercise. On the first visit, patients were prescribed an exercise-based cardiac rehabilitation program. Physical activity levels were reported on both visits.\n\nPatients were clinically stable and exhibited increased exercise capacity as well as increased self-reported physical activity between visits. Basal plasma levels of IL-18, as well as exercise-induced levels of IL-18 and IL-1Ra, were higher in patients compared with controls on both visits. Also, basal gene expression of NLRP3 was higher in patients, as were several NF\u03baB-related genes. After exercise, gene expression related to NLRP3 inflammasome activation, in particular P2RX7, was higher in patients on both visits.\n\nUp to 6 months after a coronary event, patients exhibited an increase in NLRP3 inflammasome-related components that was even more pronounced after acute exercise, compared with controls. The results indicate that a primed NLRP3 inflammasome system is maintained despite clinical stability and best available therapy, highlighting the need to further combat inflammation in patients with CCS.", "doi": "10.1016/j.atherosclerosis.2025.119227", "pmid": "40339359", "labels": {"Clinical Genomics Link\u00f6ping": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9150(25)00125-X"}], "notes": [], "created": "2025-08-11T10:12:24.434Z", "modified": "2025-08-11T10:12:24.438Z"}, {"entity": "publication", "iuid": "df0652c365514257b768c4ffb776a3f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df0652c365514257b768c4ffb776a3f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df0652c365514257b768c4ffb776a3f3"}}, "title": "Bacterial transcriptional repressor NrdR - a flexible multifactorial nucleotide sensor.", "authors": [{"family": "Rozman Grinberg", "given": "Inna", "initials": "I"}, {"family": "Bima\u00ef", "given": "Ornella", "initials": "O"}, {"family": "Shahid", "given": "Saher", "initials": "S"}, {"family": "Philipp", "given": "Lena", "initials": "L"}, {"family": "Mart\u00ednez-Carranza", "given": "Markel", "initials": "M"}, {"family": "Banerjee", "given": "Ipsita", "initials": "I"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Sj\u00f6berg", "given": "Britt-Marie", "initials": "BM"}, {"family": "Logan", "given": "Derek T", "initials": "DT", "orcid": "0000-0002-0098-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/da2734243cdb4142be696e5a82e788ae.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "FEBS J.", "issn": "1742-4658", "volume": "292", "issue": "12", "pages": "3091-3112", "issn-l": "1742-464X"}, "abstract": "NrdR is a bacterial transcriptional repressor consisting of a zinc (Zn)-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel antibacterials. NrdR binds specifically to two \"NrdR boxes\" upstream of ribonucleotide reductase operons, of which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, in the last of which we identified a new box. We show that E. coli NrdR (EcoNrdR) has similar binding strength to all three sites when loaded with ATP plus deoxyadenosine triphosphate (dATP) or equivalent diphosphate combinations. No other combination of adenine nucleotides promotes binding to DNA. We present crystal structures of EcoNrdR-ATP-dATP and EcoNrdR-ADP-dATP, which are the first high-resolution crystal structures of an NrdR. We have also determined cryo-electron microscopy structures of DNA-bound EcoNrdR-ATP-dATP and novel filaments of EcoNrdR-ATP. Tetrameric forms of EcoNrdR involve alternating interactions between pairs of Zn-ribbon domains and ATP-cones. The structures reveal considerable flexibility in relative orientation of ATP-cones vs Zn-ribbon domains. The structure of DNA-bound EcoNrdR-ATP-dATP shows that significant conformational rearrangements between ATP-cones and Zn-ribbons accompany DNA binding while the ATP-cones retain the same relative orientation. In contrast, ATP-loaded EcoNrdR filaments show rearrangements of the ATP-cone pairs and sequester the DNA-binding residues of NrdR such that they are unable to bind to DNA. Our results, in combination with a previous structural and biochemical study, point to highly flexible EcoNrdR structures that, when loaded with the correct nucleotides, adapt to an optimal promoter-binding conformation.", "doi": "10.1111/febs.70037", "pmid": "40029022", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12176259"}, {"db": "RefSeq", "key": "NP_414947.1"}], "notes": [], "created": "2025-11-24T10:53:44.358Z", "modified": "2025-11-24T10:53:44.475Z"}, {"entity": "publication", "iuid": "12e31be46bf649a1be2593342dedea99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12e31be46bf649a1be2593342dedea99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12e31be46bf649a1be2593342dedea99"}}, "title": "An optimised Bcl\u20103 inhibitor for melanoma treatment", "authors": [{"family": "Saamarthy", "given": "Karunakar", "initials": "K"}, {"family": "Daams", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Sime", "given": "Wondossen", "initials": "W"}, {"family": "Persson", "given": "Cecilia", "initials": "C"}, {"family": "Chygorin", "given": "Eduard", "initials": "E"}, {"family": "Ahlqvist", "given": "Kristofer", "initials": "K"}, {"family": "Evans\u2010Axelsson", "given": "Susan", "initials": "S"}, {"family": "Strand", "given": "Daniel", "initials": "D"}, {"family": "Massoumi", "given": "Ramin", "initials": "R"}], "type": "journal-article", "published": "2025-06-00", "journal": {"title": "British Journal of Pharmacology", "issn": "0007-1188", "volume": "182", "issue": "11", "pages": "2426-2446", "issn-l": null}, "abstract": null, "doi": "10.1111/bph.17467", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:01:50.285Z", "modified": "2025-11-27T08:01:50.306Z"}, {"entity": "publication", "iuid": "8d0fd70d87f34c9889e699292e0734c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d0fd70d87f34c9889e699292e0734c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d0fd70d87f34c9889e699292e0734c2"}}, "title": "An Investigation of TDA1 Deficiency in Saccharomyces cerevisiae During Diauxic Growth.", "authors": [{"family": "Bjurstr\u00f6m", "given": "Erik Y", "initials": "EY", "orcid": "0000-0002-8863-1207", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a4311020e2f4d64be784512c7a889a6.json"}}, {"family": "Lasin", "given": "Praphapan", "initials": "P"}, {"family": "Brunns\u00e5ker", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5167-0536", "researcher": {"href": "https://publications.scilifelab.se/researcher/648a5362be334826ab3778d40fe2730b.json"}}, {"family": "Tiukova", "given": "Ievgeniia A", "initials": "IA"}, {"family": "King", "given": "Ross D", "initials": "RD"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Yeast", "issn": "1097-0061", "volume": "42", "issue": "5-7", "pages": "142-156", "issn-l": null}, "abstract": "Tda1p is a protein kinase in Saccharomyces cerevisiae. Here we investigate the function of TDA1 during the diauxic shift using transcriptomics. We compared the gene expression in the deletion mutant tda1\u2206 and the reference strain (BY4741) during both the aerobic fermentation phase (log phase), and the respiratory phase (post-diauxic shift phase, PDS) in three separate independent experiments. We found: Differential gene expression analysis showed that compared to the reference strain, the tda1\u2206 mutant exhibited an upregulation of the glucose repressed hexose transporter HXT6 during the log phase, and upregulation of mitochondrial proteins and genes related to mitochondrial translation during the PDS phase. Gene set enrichment analysis showed an enrichment in mitochondrial translation in the PDS phase for the deletion mutant tda1\u2206, but not for the reference strain. Transcription factor analysis showed that the enrichment of Mig1p repressed genes was not statistically significant in TDA1 deletion mutants for neither log-phase nor PDS-phase. This conflicted with the previously suggested model that argued for an interaction between Tda1p and Mig1p. Instead, transcription factor analysis showed an enrichment of genes regulated by the HAP-complex, which regulates mitochondrial translation, during the PDS-phase in the tda1\u2206 mutant. The combined evidence from this study indicates that Tda1p does not participate in Mig1p-mediated glucose repression. Instead, we propose that it is involved in the regulation of mitochondrial translation by repressing the expression of HAP complex subunits.", "doi": "10.1002/yea.4004", "pmid": "40568959", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12232523"}], "notes": [], "created": "2025-11-27T11:29:01.431Z", "modified": "2025-11-27T11:29:01.515Z"}, {"entity": "publication", "iuid": "7d263670b0c24bf98f24eaca72b02833", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d263670b0c24bf98f24eaca72b02833.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d263670b0c24bf98f24eaca72b02833"}}, "title": "Abundance of dopamine and its receptors in the brain and adipose tissue following diet-induced obesity or caloric restriction.", "authors": [{"family": "Hukema", "given": "Fleur W", "initials": "FW"}, {"family": "Hetty", "given": "Susanne", "initials": "S"}, {"family": "Kagios", "given": "Christakis", "initials": "C"}, {"family": "Zelleroth", "given": "Sofia", "initials": "S"}, {"family": "Fanni", "given": "Giovanni", "initials": "G"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ"}, {"family": "Svensson", "given": "Maria K", "initials": "MK"}, {"family": "Sundbom", "given": "Magnus", "initials": "M"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "Roman", "given": "Erika", "initials": "E"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Translational Research", "issn": "1878-1810", "volume": "280", "pages": "41-54", "issn-l": null}, "abstract": "While obesity and type 2 diabetes (T2D) are associated with altered dopaminergic activity in the central nervous system and in adipose tissue (AT), the directions and underlying mechanisms remain inconclusive. Therefore, we characterized changes in the abundance of dopamine, its metabolites, and receptors DRD1 and DRD2 in the brain and AT upon dietary intervention or obesity. Male Wistar rats were fed either a standard pellet diet, a cafeteria diet inducing obesity and insulin resistance, or a calorie-restricted diet for 12 weeks. Abundance of dopamine and its receptors DRD1 and DRD2 were examined in brain regions relevant for feeding behavior and energy homeostasis. Furthermore, DRD1 and DRD2 protein levels were analyzed in rat inguinal and epidydimal AT and in human subcutaneous and omental AT from individuals with or without obesity. Rats with diet-induced obesity displayed higher dopamine levels, as well as DRD1 or DRD2 receptor levels in the caudate putamen and the nucleus accumbens core. Surprisingly, caloric restriction induced similar changes in DRD1 and DRD2, but not in dopamine levels, in the brain. Both diets reduced DRD1 abundance in inguinal and epidydimal AT, but upregulated DRD2 levels in inguinal AT. Furthermore, in human obesity, DRD1 protein levels were elevated only in omental AT, while DRD2 was upregulated in both omental and subcutaneous AT. These findings highlight dopaminergic responses to changes in energy balance, occurring both in the brain and AT. We propose that dopaminergic pathways are involved in tissue crosstalk during the development of obesity and T2D.", "doi": "10.1016/j.trsl.2025.05.001", "pmid": "40345434", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1931-5244(25)00050-7"}], "notes": [], "created": "2025-11-21T09:46:21.825Z", "modified": "2025-11-21T09:46:21.835Z"}, {"entity": "publication", "iuid": "a853b1443cee4b79835aa5a9bc6e26fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a853b1443cee4b79835aa5a9bc6e26fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a853b1443cee4b79835aa5a9bc6e26fb"}}, "title": "A marine and salt marsh sediment organic carbon database for European regional seas (EURO-CARBON).", "authors": [{"family": "Graversen", "given": "Anna Elizabeth L\u00f8vgren", "initials": "AEL"}, {"family": "L\u00f8nborg", "given": "Christian", "initials": "C"}, {"family": "Addamo", "given": "Anna Maria", "initials": "AM"}, {"family": "Pedersen", "given": "Sidsel Gurholt", "initials": "SG"}, {"family": "Chemello", "given": "Silvia", "initials": "S"}, {"family": "Alejo", "given": "Irene", "initials": "I"}, {"family": "Apostolaki", "given": "Eugenia T", "initials": "ET"}, {"family": "Asplund", "given": "Maria E", "initials": "ME"}, {"family": "Austin", "given": "William E N", "initials": "WEN"}, {"family": "Berov", "given": "Dimitar", "initials": "D"}, {"family": "Berto", "given": "Daniela", "initials": "D"}, {"family": "Bj\u00f6rk", "given": "Mats", "initials": "M"}, {"family": "Black", "given": "Kirsty", "initials": "K"}, {"family": "Bobchev", "given": "Nikola", "initials": "N"}, {"family": "Bonaglia", "given": "Stefano", "initials": "S"}, {"family": "Borgersen", "given": "Gunhild", "initials": "G"}, {"family": "Bouma", "given": "Tjeerd", "initials": "T"}, {"family": "Costello", "given": "Mark J", "initials": "MJ"}, {"family": "Dahl", "given": "Martin", "initials": "M"}, {"family": "Diaz-Almela", "given": "Elena", "initials": "E"}, {"family": "Dimitriou", "given": "Panagiotis D", "initials": "PD"}, {"family": "Duarte", "given": "Carlos M", "initials": "CM"}, {"family": "Due\u00f1as", "given": "Carmen Leiva", "initials": "CL"}, {"family": "Efthymiadis", "given": "Pavlos T", "initials": "PT"}, {"family": "Elosegui", "given": "Ines Mazarrasa", "initials": "IM"}, {"family": "Espinosa", "given": "Maria Recio", "initials": "MR"}, {"family": "Filipsson", "given": "Helena L", "initials": "HL"}, {"family": "Fontela", "given": "Marcos", "initials": "M"}, {"family": "Fredriksen", "given": "Stein", "initials": "S"}, {"family": "Frigstad", "given": "Helene", "initials": "H"}, {"family": "Gagnon", "given": "Karine", "initials": "K"}, {"family": "Garcia-Escudero", "given": "Catalina A", "initials": "CA"}, {"family": "Giani", "given": "Michele", "initials": "M"}, {"family": "Grouhel-Pellouin", "given": "Anne", "initials": "A"}, {"family": "Guerra", "given": "Roberta", "initials": "R"}, {"family": "Gullstr\u00f6m", "given": "Martin", "initials": "M"}, {"family": "Gundersen", "given": "Hege", "initials": "H"}, {"family": "Hancke", "given": "Kasper", "initials": "K"}, {"family": "Majt\u00e9nyi-Hill", "given": "Claudia", "initials": "C"}, {"family": "Hunt", "given": "Corallie", "initials": "C"}, {"family": "Inostroza", "given": "Karina", "initials": "K"}, {"family": "Karakassis", "given": "Ioannis", "initials": "I"}, {"family": "Karamfilov", "given": "Ventzislav", "initials": "V"}, {"family": "Klayn", "given": "Stefania", "initials": "S"}, {"family": "Koziorowska", "given": "Katarzyna", "initials": "K"}, {"family": "Kuli\u0144ski", "given": "Karol", "initials": "K"}, {"family": "Lavery", "given": "Paul", "initials": "P"}, {"family": "Lenstra", "given": "Wytze K", "initials": "WK"}, {"family": "Lilleb\u00f8", "given": "Ana I", "initials": "AI"}, {"family": "Logemann", "given": "Ella", "initials": "E"}, {"family": "Magni", "given": "Paolo", "initials": "P"}, {"family": "Marb\u00e0", "given": "N\u00faria", "initials": "N"}, {"family": "Marco-Mendez", "given": "Candela", "initials": "C"}, {"family": "Martins", "given": "Marcio", "initials": "M"}, {"family": "Mateo", "given": "Miguel Angel", "initials": "MA"}, {"family": "Monnier", "given": "Briac", "initials": "B"}, {"family": "Mueller", "given": "Peter", "initials": "P"}, {"family": "Neto", "given": "Joao M", "initials": "JM"}, {"family": "Papageorgiou", "given": "Nafsika", "initials": "N"}, {"family": "de Rezende", "given": "Carlos Eduardo", "initials": "CE"}, {"family": "Pardo", "given": "Juan Carlos Farias", "initials": "JCF"}, {"family": "Pe\u00f1a", "given": "Jose Antonio Juanes De La", "initials": "JAJ"}, {"family": "Pergent", "given": "G\u00e9rard", "initials": "G"}, {"family": "Pi\u00f1eiro-Juncal", "given": "Nerea", "initials": "N"}, {"family": "Preston", "given": "Joanne", "initials": "J"}, {"family": "Rampazzo", "given": "Federico", "initials": "F"}, {"family": "Reithmaier", "given": "Gloria", "initials": "G"}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH"}, {"family": "Reynolds", "given": "Sarah", "initials": "S"}, {"family": "Ricart", "given": "Aurora M", "initials": "AM"}, {"family": "Santos", "given": "Rui", "initials": "R"}, {"family": "de Los Santos", "given": "Carmen B", "initials": "CB"}, {"family": "Santos", "given": "Isaac R", "initials": "IR"}, {"family": "Serrano", "given": "Eduard", "initials": "E"}, {"family": "Serrano", "given": "Oscar", "initials": "O"}, {"family": "Slomp", "given": "Caroline P", "initials": "CP"}, {"family": "Smeaton", "given": "Craig", "initials": "C"}, {"family": "Soler", "given": "Montserrar", "initials": "M"}, {"family": "Sousa", "given": "Ana I", "initials": "AI"}, {"family": "Spiegel", "given": "Timo", "initials": "T"}, {"family": "Stevenson", "given": "Angela", "initials": "A"}, {"family": "Thormar", "given": "Jonas", "initials": "J"}, {"family": "Trannum", "given": "Hilde Cecilie", "initials": "HC"}, {"family": "van Helmond", "given": "Niels A G M", "initials": "NAGM"}, {"family": "Paradis", "given": "Sarah", "initials": "S"}, {"family": "Vizzini", "given": "Salvatrice", "initials": "S"}, {"family": "Ward", "given": "Emma A", "initials": "EA"}, {"family": "Yau", "given": "Yvonne Y Y", "initials": "YYY"}, {"family": "Zakhama-Sraieb", "given": "Rym", "initials": "R"}, {"family": "Zribi", "given": "Imen", "initials": "I"}, {"family": "Zygadlowska", "given": "Olga M", "initials": "OM"}, {"family": "Jensen", "given": "Dorte Krause", "initials": "DK"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Data Brief", "issn": "2352-3409", "volume": "60", "pages": "111595", "issn-l": "2352-3409"}, "abstract": "Marine and salt marsh sediments contain large amounts of organic carbon (OC) and are therefore important in the global carbon cycle. Here, we collated previously published and unpublished measurements of sediment OC in marine and salt marsh sediments in European regional seas (EURO-CARBON; available at https://doi.org/10.5281/zenodo.14905489). To the extent possible the OC data were complemented by variables such as sediment porosity and dry bulk density. The EURO-CARBON dataset holds 61306 individual data entries of sediment OC content from different regions of European regional seas. Around three quarters (76%) were collected in coastal and deep sea bare sediments, 18% from salt marshes, 7% from seagrass habitats, and 0.03% from macroalgal habitats. For all habitats and sediment depth layers the OC content varied between <0.1 and 41.56 % (avg.: 2.47 \u00b1 3.37 %; median: 1.39 %), with the content generally decreasing in the following sequence: salt marsh (5.01 \u00b1 5.96 %; 3.03 %) > seagrass (2.37 \u00b1 5.96 %; 3.03 %) > bare sediment (1.88 \u00b1 2.03 %; 1.20 %). The EURO-CARBON dataset will serve as a basis for future work, and it will be an important resource for researchers, managers, and policymakers working towards protecting sediment OC pools.", "doi": "10.1016/j.dib.2025.111595", "pmid": "40496737", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12149566"}, {"db": "pii", "key": "S2352-3409(25)00327-0"}], "notes": [], "created": "2025-11-21T16:03:18.981Z", "modified": "2025-11-21T17:39:04.259Z"}, {"entity": "publication", "iuid": "d68819db6d2b4972833ed77bcff28ccc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d68819db6d2b4972833ed77bcff28ccc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d68819db6d2b4972833ed77bcff28ccc"}}, "title": "Human LY9 governs CD4+ T cell IFN-\u03b3 immunity to Mycobacterium tuberculosis.", "authors": [{"family": "Ogishi", "given": "Masato", "initials": "M", "orcid": "0000-0003-2421-7389", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9205246af72422f993f696135d03d00.json"}}, {"family": "Puchan", "given": "Julia", "initials": "J", "orcid": "0000-0003-0284-3629", "researcher": {"href": "https://publications.scilifelab.se/researcher/6067f38c03114b40981e92d0337479b0.json"}}, {"family": "Yang", "given": "Rui", "initials": "R", "orcid": "0000-0003-4427-2158", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e4faa40d4b94755a28e630d6e26c918.json"}}, {"family": "Arias", "given": "Andr\u00e9s Augusto", "initials": "AA"}, {"family": "Han", "given": "Ji Eun", "initials": "JE", "orcid": "0000-0003-1112-9320", "researcher": {"href": "https://publications.scilifelab.se/researcher/c81e24eb454147e1b68e642748424c0d.json"}}, {"family": "Nguyen", "given": "Tina", "initials": "T", "orcid": "0000-0003-0709-3636", "researcher": {"href": "https://publications.scilifelab.se/researcher/28a78707a08d4614bba6392434635526.json"}}, {"family": "Guti\u00e9rrez-C\u00f3zar", "given": "Rebeca", "initials": "R", "orcid": "0000-0003-0348-3223", "researcher": {"href": "https://publications.scilifelab.se/researcher/0042df6ba0b74d4aae8b17e7785b33ce.json"}}, {"family": "Conil", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Seeleuthner", "given": "Yoann", "initials": "Y"}, {"family": "Rinchai", "given": "Darawan", "initials": "D", "orcid": "0000-0001-8851-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/83435aa472e94885bf67a8cad09737fd.json"}}, {"family": "Zhang", "given": "Peng", "initials": "P", "orcid": "0000-0002-6129-567X", "researcher": {"href": "https://publications.scilifelab.se/researcher/20fcd31c47a940e8b72a8eb8d6e2a63b.json"}}, {"family": "Ponsin", "given": "Khoren", "initials": "K"}, {"family": "Chaldebas", "given": "Matthieu", "initials": "M", "orcid": "0000-0002-4920-3947", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ade171e91a94d3eac168e79443b954b.json"}}, {"family": "Feng", "given": "Yi", "initials": "Y", "orcid": "0000-0002-2393-1700", "researcher": {"href": "https://publications.scilifelab.se/researcher/779f0d6a0fda42e99f58a2f09f17b2d2.json"}}, {"family": "Neehus", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0002-8573-6820", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d78343f97c469cb88a2d38fd4945ec.json"}}, {"family": "Delmonte", "given": "Ottavia M", "initials": "OM", "orcid": "0000-0002-4772-0799", "researcher": {"href": "https://publications.scilifelab.se/researcher/8036b2ad257e4aa680127162020b0c28.json"}}, {"family": "Khan", "given": "Taushif", "initials": "T", "orcid": "0000-0002-7917-8965", "researcher": {"href": "https://publications.scilifelab.se/researcher/c19c3e42c4e9403eb5e37f3257ef1c04.json"}}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "Bohlen", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-0458-9484", "researcher": {"href": "https://publications.scilifelab.se/researcher/a740e67ef67a4958961dc5fbbf27c95f.json"}}, {"family": "Peel", "given": "Jessica N", "initials": "JN"}, {"family": "Fagniez", "given": "Iris", "initials": "I", "orcid": "0009-0009-9900-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea0a500efb1b48abac039da065cd95d8.json"}}, {"family": "Pelham", "given": "Simon J", "initials": "SJ", "orcid": "0000-0002-3119-662X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee668998ba674af5b89a2a8fb2d1e49d.json"}}, {"family": "Lei", "given": "Wei-Te", "initials": "WT", "orcid": "0000-0003-1677-8901", "researcher": {"href": "https://publications.scilifelab.se/researcher/84ba1115d51941bba83fdcab614d6005.json"}}, {"family": "Chrabieh", "given": "Maya", "initials": "M"}, {"family": "Laine", "given": "Candice", "initials": "C", "orcid": "0000-0003-3258-6969", "researcher": {"href": "https://publications.scilifelab.se/researcher/29a0e7587c494ae68155085ee0a1a1cd.json"}}, {"family": "Ouair", "given": "Hind", "initials": "H"}, {"family": "Benhsaien", "given": "Ibtihal", "initials": "I", "orcid": "0000-0001-5727-9629", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a7e07f8530c4d2482f60f8e60df5d46.json"}}, {"family": "Abid", "given": "Ahmed", "initials": "A", "orcid": "0000-0003-4885-6572", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b1708390385407cae181952bdcde860.json"}}, {"family": "Abderrhamani Ghorfi", "given": "Ismail", "initials": "I", "orcid": "0000-0001-6403-0098", "researcher": {"href": "https://publications.scilifelab.se/researcher/f040661497c2440da7a6f6687863df63.json"}}, {"family": "Souhi", "given": "Hicham", "initials": "H", "orcid": "0000-0003-3183-1627", "researcher": {"href": "https://publications.scilifelab.se/researcher/93ebbf18946842a3ada75998b5a95df9.json"}}, {"family": "Ouazzani", "given": "Hanane", "initials": "H"}, {"family": "Aniss", "given": "Rafik", "initials": "R"}, {"family": "Riminton", "given": "D Sean", "initials": "DS", "orcid": "0000-0002-9953-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f500629c8194268b99b12b9d6ce2970.json"}}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}, {"family": "Turvey", "given": "Stuart E", "initials": "SE", "orcid": "0000-0003-1599-1065", "researcher": {"href": "https://publications.scilifelab.se/researcher/55c5b74659bf4f9dac9e02826a9d6cec.json"}}, {"family": "Marr", "given": "Nico", "initials": "N", "orcid": "0000-0002-1927-7072", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cc63695a4ca4553ae5ed703ea6bdcf8.json"}}, {"family": "Notarangelo", "given": "Luigi D", "initials": "LD", "orcid": "0000-0002-8335-0262", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8d346e44c2d443ba3da3fcf2725b96c.json"}}, {"family": "Hatipoglu", "given": "Nevin", "initials": "N", "orcid": "0000-0003-2858-0150", "researcher": {"href": "https://publications.scilifelab.se/researcher/d396fdc46870452697c42b889866e40e.json"}}, {"family": "Bousfiha", "given": "Aziz", "initials": "A", "orcid": "0000-0002-5011-9873", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0206681da8543a39287d5b5d22f71fb.json"}}, {"family": "Ozcelik", "given": "Tayfun", "initials": "T", "orcid": "0000-0001-5937-1082", "researcher": {"href": "https://publications.scilifelab.se/researcher/251a5fd386594151b80b5a3a71f6ab58.json"}}, {"family": "El Baghdadi", "given": "Jamila", "initials": "J", "orcid": "0000-0002-1920-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9f21356552345c8a7f1085e5dc92d35.json"}}, {"family": "Cobat", "given": "Aurelie", "initials": "A", "orcid": "0000-0001-7209-6257", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaba2f9452294eec89161b589d96ff29.json"}}, {"family": "Ma", "given": "Cindy S", "initials": "CS", "orcid": "0000-0001-5387-8413", "researcher": {"href": "https://publications.scilifelab.se/researcher/398f17ef657242a1a091b04d05388cf9.json"}}, {"family": "Abel", "given": "Laurent", "initials": "L", "orcid": "0000-0001-7016-6493", "researcher": {"href": "https://publications.scilifelab.se/researcher/24ef4ca1eb3a4b1bbee73f07cd64fe92.json"}}, {"family": "Puel", "given": "Anne", "initials": "A", "orcid": "0000-0003-2603-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bcef4c205904e5db9e36f3aadaa13bb.json"}}, {"family": "Bustamante", "given": "Jacinta", "initials": "J", "orcid": "0000-0002-3439-2482", "researcher": {"href": "https://publications.scilifelab.se/researcher/152dc8084c1d4ba89ace373889bea81e.json"}}, {"family": "Engel", "given": "Pablo", "initials": "P", "orcid": "0000-0001-8410-252X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce0386cfa7d4851bfd8d16f2b0b8f71.json"}}, {"family": "Gros", "given": "Philippe", "initials": "P", "orcid": "0000-0002-0114-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0012dd9120a421ebdda3f5da528ec16.json"}}, {"family": "Tangye", "given": "Stuart G", "initials": "SG", "orcid": "0000-0002-5360-5180", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e3fa03cfc304a8aa0262e5f8c51665d.json"}}, {"family": "Sallusto", "given": "Federica", "initials": "F", "orcid": "0000-0003-3750-2752", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdca95394616420ba260e86d35809977.json"}}, {"family": "Boisson-Dupuis", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0002-7115-116X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5584eef132004c55a120c70d9a9f9eee.json"}}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL", "orcid": "0000-0002-7782-4169", "researcher": {"href": "https://publications.scilifelab.se/researcher/009e2306468648c08fb1eea319f0c488.json"}}], "type": "journal article", "published": "2025-05-30", "journal": {"title": "Sci Immunol", "issn": "2470-9468", "volume": "10", "issue": "107", "pages": "eads7377", "issn-l": null}, "abstract": "CD4+ T cells are indispensable for optimal immunity to Mycobacterium tuberculosis (M.tb), a pathogen that triggers tuberculosis (TB) in humans. M.tb-specific human CD4+ T cells are known to polarize toward an interferon-\u03b3 (IFN-\u03b3)-producing, CCR4-CCR6+CXCR3+T-bet+ROR\u03b3T+ T helper 1* cell (TH1*cell) memory phenotype. We report that autosomal recessive deficiency of the human lymphocytic surface receptor LY9 (SLAMF3 and CD229), which is found in less than 10-5 individuals in the general population, underlies TB in three unrelated patients due to selective impairment in IFN-\u03b3 production by TH1* cells. TH1* cells express higher levels of LY9 than other CD4+ T cells. Mechanistically, LY9 polarizes na\u00efve CD4+ T cells toward memory TH1* cells by inducing T-bet via signaling lymphocytic activation molecule (SLAM)-associated protein (SAP) and ROR\u03b3T (thymus-specific retinoid-related orphan receptor \u03b3) without SAP. LY9 costimulation enhances TCR-driven IFN-\u03b3 production of memory TH1*, but not TH1, cells in a T cell-intrinsic manner via NFAT1 (nuclear factor of activated T cells 1) and ROR\u03b3T. LY9 is likely to govern an optimal TH1* cell- and IFN-\u03b3-dependent protective immunity to M.tb in humans.", "doi": "10.1126/sciimmunol.ads7377", "pmid": "40446017", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2092213"}, {"db": "pmc", "key": "PMC12242830"}], "notes": [], "created": "2025-09-10T08:24:54.248Z", "modified": "2025-09-10T08:24:55.981Z"}, {"entity": "publication", "iuid": "92e3372715cf4361b696885f895c9243", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92e3372715cf4361b696885f895c9243.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92e3372715cf4361b696885f895c9243"}}, "title": "Comprehensive transcriptome assessment in PBMCs of post-COVID patients at a median follow-up of 28 months after a mild COVID infection reveals upregulation of JAK/STAT signaling and a prolonged immune response.", "authors": [{"family": "Fineschi", "given": "Serena", "initials": "S"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Lopez Egido", "given": "Juan Ramon", "initials": "JR"}, {"family": "Schuster", "given": "Jens", "initials": "J"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Kaden", "given": "Ren\u00e9", "initials": "R"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2025-05-30", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1589589", "issn-l": "1664-3224"}, "abstract": "Post-acute sequelae of SARS-CoV-2 infection (PASC), also known as post-COVID-19 condition (here abbreviated as post-COVID) is an escalating global health issue. The aim of our study was to investigate the mechanisms and clinical manifestations of post-COVID following a mild SARS-CoV-2 infection.\n\nWe analyzed the gene expression profile in PBMCs from 60 middle-aged post-COVID patients and 50 age-matched controls at a median time of 28 months following a mild SARS-CoV-2 infection. The clinical assessments included intensity of post-COVID symptoms, physical and mental fatigue, depression and anxiety. Sixty-seven participants performed a mild exertion ergometer test with assessment of lactate concentrations. Transcriptome analysis was performed on mRNA selected by poly-A enrichment and SARS-CoV-2 RNA fragments were analyzed using the ARTIC protocol.\n\nWe identified 463 differentially expressed transcripts in PBMCs, of which 324 were upregulated and 129 downregulated in post-COVID patients. Upregulated genes in post-COVID individuals were enriched for processes involving JAK-STAT signaling, negative regulation of ubiquitination, IL9 signaling, and negative regulation of viral process, suggesting chronic inflammation. Downregulated genes were enriched for processes involving mitochondrial ATP synthesis, and oxidative phosphorylation, suggesting mitochondrial dysfunction. No SARS-CoV-2 gene fragments were detected in PBMCs of patients with post-COVID and no IFN genes were found differentially expressed in post-COVID patients. Post-COVID was associated with elevated lactate levels in blood, both at rest and after a short recovery phase following exertion, suggesting increased anaerobic activity in skeletal muscles. We did not find differences in the transcriptional profiles or clinical manifestations when comparing patients who contracted the infection from early SARS-CoV-2 variants with those who contracted the infection during the period when the Omicron variant was prevalent.\n\nOur findings highlight molecular changes compatible with a persistent immune response in PBMCs of post-COVID subjects at a median follow-up of 28 months after a mild infection, supporting the hypothesis that post-COVID is a chronic inflammatory condition. The upregulation of JAK/STAT signaling suggests a potential therapeutic target in post-COVID.", "doi": "10.3389/fimmu.2025.1589589", "pmid": "40519915", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12162955"}], "notes": [], "created": "2025-06-18T07:32:51.275Z", "modified": "2025-11-26T14:14:30.711Z"}, {"entity": "publication", "iuid": "4511a6759a1f496e8c06555aa49190df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4511a6759a1f496e8c06555aa49190df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4511a6759a1f496e8c06555aa49190df"}}, "title": "Design of a Streptolysin O Epitope-Centric Nanoparticle Vaccine Against Streptococcus pyogenes", "authors": [{"family": "Tang", "given": "Di", "initials": "D", "orcid": "0000-0001-6323-9375", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2a27467c4094d9f8d8f8402efa333f4.json"}}, {"family": "Chao", "given": "Yashuan", "initials": "Y", "orcid": "0000-0002-0295-3142", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed7bd7c821754977ba516c3e1c04eceb.json"}}, {"family": "Hjortswang", "given": "Elisabeth", "initials": "E", "orcid": "0009-0003-9932-1751", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fcf5002d49b458f81cea775594e63fb.json"}}, {"family": "Str\u00f6baek", "given": "Joel", "initials": "J", "orcid": "0000-0003-1231-0420", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8d9f6cfe0e845d0a4208d442e4b652c.json"}}, {"family": "Hultgren", "given": "Lucas", "initials": "L"}, {"family": "Mohanty", "given": "Tirthankar", "initials": "T", "orcid": "0000-0003-4593-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a9c51697d33414f8197c7833d9dcc04.json"}}, {"family": "Karlsson", "given": "Christofer", "initials": "C", "orcid": "0000-0002-7099-0092", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef353abbc90943218c194ccdd2bbdb52.json"}}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S", "orcid": "0000-0002-7694-285X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6416b323664f4126b70067193d7b8347.json"}}, {"family": "Happonen", "given": "Lotta", "initials": "L", "orcid": "0000-0002-5922-4549", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7af0a6faf6a48e7937a644be472edbe.json"}}, {"family": "Shannon", "given": "Oonagh", "initials": "O", "orcid": "0000-0001-8291-8189", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed4685bab7584028a070fc5a829bd386.json"}}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad3c999da10c41e4a3afda2718815083.json"}}], "type": "posted-content", "published": "2025-05-28", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.05.25.655993", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-13T14:22:08.439Z", "modified": "2025-12-18T19:15:21.994Z"}, {"entity": "publication", "iuid": "dc00b746f211426db5e81bd6815bf3c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc00b746f211426db5e81bd6815bf3c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc00b746f211426db5e81bd6815bf3c5"}}, "title": "Rab7 inhibitor enhances stem cell differentiation into keratinocyte-like cells with anti-inflammatory properties.", "authors": [{"family": "Alghazali", "given": "Raghad", "initials": "R"}, {"family": "Tabebi", "given": "Mouna", "initials": "M"}, {"family": "Elmasry", "given": "Moustafa", "initials": "M"}, {"family": "El-Serafi", "given": "Ahmed", "initials": "A"}], "type": "journal article", "published": "2025-05-26", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1503007", "issn-l": "1664-3224"}, "abstract": "Management of difficult-to-heal skin wounds presents a significant clinical challenge, particularly when associated with inflammatory skin disorders. The differentiation of stem cells into keratinocyte-like cells has been explored as a potential regenerative therapy. Ras-related protein (Rab) 7, a key regulator of membrane trafficking, influences the activity of several growth factors. In this study, the competitive Rab7 inhibitor, CID-1067700, was investigated for the differentiation of adipose-derived stem cell into keratinocyte-like cells. This treatment upregulated several epidermal markers, including P63, cytokeratin 5 and 14 and filaggrin, while downregulated the stem cell marker, vimentin. Microarray data showed upregulation of the anti-inflammatory gene HMOX-1, coupled with the downregulation of various inflammation-related pathways, such as TNF, chemokine, AGE-RAGE and IL-17 signalling cascades, as well as cytokine-cytokine receptor interaction pathways. Gene set enrichment analysis predicted Ehmt2, an epigenetic regulator, to be the top activated upstream regulator, enhancing the transcriptional activity. Protein array analysis showed reduced secretion of several inflammatory cytokines, including IL-1\u03b1, IL-8, IL-17A, and IL-32, while enhancing the secretion of the epidermal growth factor. Our findings provide preliminary evidence that CID-1067700, as an additive to the differentiation media, not only enhances stem cell differentiation into keratinocyte-like cells, but also improves their anti-inflammatory properties. These combined regenerative and anti-inflammatory properties may offer significant therapeutic potential for patients with chronic skin wounds, particularly those with underlying inflammatory conditions.", "doi": "10.3389/fimmu.2025.1503007", "pmid": "40491919", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12146274"}], "notes": [], "created": "2025-08-11T10:15:53.850Z", "modified": "2025-08-11T10:15:53.853Z"}, {"entity": "publication", "iuid": "78b0c63fefe94913bcd52fec8d95d8db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78b0c63fefe94913bcd52fec8d95d8db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78b0c63fefe94913bcd52fec8d95d8db"}}, "title": "A randomized controlled cross-over trial of differences in acute effects on serum metabolites from isocaloric meals based on red meat, fatty fish, or soy protein.", "authors": [{"family": "Lindqvist", "given": "Helen M", "initials": "HM", "orcid": "0000-0002-2627-0434", "researcher": {"href": "https://publications.scilifelab.se/researcher/d98498df02eb40fb8de3016da37d6f8a.json"}}, {"family": "Hulander", "given": "Erik", "initials": "E", "orcid": "0000-0003-3416-2748", "researcher": {"href": "https://publications.scilifelab.se/researcher/910a2dc80a8a4f449d2a3bf8e4d2f046.json"}}, {"family": "B\u00e4rebring", "given": "Linnea", "initials": "L", "orcid": "0000-0002-1612-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9d45c7e27274cab907ffd3bc92ccfaf.json"}}, {"family": "Gjertsson", "given": "Inger", "initials": "I", "orcid": "0000-0002-9301-4844", "researcher": {"href": "https://publications.scilifelab.se/researcher/56e95592e89f43cba8eb30bd32da1cc8.json"}}, {"family": "Winkvist", "given": "Anna", "initials": "A", "orcid": "0000-0001-9122-7240", "researcher": {"href": "https://publications.scilifelab.se/researcher/e34ca937891145e190390ae9418d2243.json"}}], "type": "journal article", "published": "2025-05-26", "journal": {"title": "Eur J Nutr", "issn": "1436-6207", "volume": "64", "issue": "5", "pages": "187", "issn-l": null}, "abstract": "Reducing red meat intake in the Western diet is beneficial for health and the environment. However, red meat is nutrient-rich, so understanding the impact of substituting it with other protein sources such as fish or plant-based proteins is essential, especially for vulnerable groups like the elderly and those with chronic diseases. The purpose of this study was to study the postprandial response in serum metabolites in women with Rheumatoid Arthritis (RA) after intake of red meat, fatty fish, and soy protein.\n\nWomen with RA (n = 24) consumed isocaloric meals that included burgers made from either red meat, fatty fish, or soy protein in a crossover design. Blood samples were taken in fasting state before the meal (0 h) and at intervals up to 5 h after eating. Nuclear Magnetic Resonance (NMR) analysis quantified serum metabolites, and multivariate models and univariate statistics were applied to compare postprandial metabolite changes across protein sources.\n\nPostprandial metabolite patterns varied significantly by protein type. The fatty fish meal led to a faster and higher increase in metabolites, including creatinine, isoleucine, valine, and trimethylamine N-oxide, compared to red meat. Unidentified lipids also differed. However, metabolite patterns after soy protein were similar to those after red meat.\n\nThis postprandial crossover trial found that intake of fatty fish lead to a quicker and more pronounced increase in key blood concentrations of metabolites compared to red meat. However, metabolite profiles in serum based on NMR-analysis were similar after intake of soy protein compared to red meat.\n\nThe PIRA (Postprandial Inflammation in Rheumatoid Arthritis) trial is Registered at Clinicaltrials.gov (NCT04247009).", "doi": "10.1007/s00394-025-03710-0", "pmid": "40418340", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12106552"}, {"db": "pii", "key": "10.1007/s00394-025-03710-0"}, {"db": "ClinicalTrials.gov", "key": "NCT04247009"}], "notes": [], "created": "2025-11-27T08:05:28.633Z", "modified": "2025-11-27T08:05:28.716Z"}, {"entity": "publication", "iuid": "499254acb4eb4139bf11f17fd8968652", "links": {"self": {"href": "https://publications.scilifelab.se/publication/499254acb4eb4139bf11f17fd8968652.json"}, "display": {"href": "https://publications.scilifelab.se/publication/499254acb4eb4139bf11f17fd8968652"}}, "title": "Modelling POLG mutations in mice unravels a critical role of POL\u03b3\u0392 in regulating phenotypic severity.", "authors": [{"family": "Corr\u00e0", "given": "Samantha", "initials": "S"}, {"family": "Zuppardo", "given": "Alessandro", "initials": "A", "orcid": "0000-0001-9601-3567", "researcher": {"href": "https://publications.scilifelab.se/researcher/308877ae9bac46328666ca4e56b73d26.json"}}, {"family": "Valenzuela", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-5153-8431", "researcher": {"href": "https://publications.scilifelab.se/researcher/16c5cd1a4e8a4d9389514f33049240a5.json"}}, {"family": "Jenninger", "given": "Louise", "initials": "L"}, {"family": "Cerutti", "given": "Raffaele", "initials": "R"}, {"family": "Sillamaa", "given": "Sirelin", "initials": "S", "orcid": "0000-0001-8077-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/29a3fbab3f684386a2e08236bfd8674e.json"}}, {"family": "Hoberg", "given": "Emily", "initials": "E"}, {"family": "Johansson", "given": "Katarina A S", "initials": "KAS", "orcid": "0009-0005-8992-7631", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3bac3ed243c4f0493e0d494f79a7ca2.json"}}, {"family": "Rovsnik", "given": "Urska", "initials": "U"}, {"family": "Volta", "given": "Sara", "initials": "S"}, {"family": "Silva-Pinheiro", "given": "Pedro", "initials": "P", "orcid": "0000-0002-0872-5749", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbc93779b0704e55a91eb4d755255aed.json"}}, {"family": "Davis", "given": "Hannah", "initials": "H"}, {"family": "Trifunovic", "given": "Aleksandra", "initials": "A", "orcid": "0000-0002-5472-3517", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf7d2fa56e714134bc66ca5884b8e86b.json"}}, {"family": "Minczuk", "given": "Michal", "initials": "M", "orcid": "0000-0001-8242-1420", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f03f6f8725149c6938067d043ca4f7f.json"}}, {"family": "Gustafsson", "given": "Claes M", "initials": "CM", "orcid": "0000-0003-3531-8468", "researcher": {"href": "https://publications.scilifelab.se/researcher/2851656430d147dab7a8a32e50fee7b7.json"}}, {"family": "Suomalainen", "given": "Anu", "initials": "A", "orcid": "0000-0003-4833-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/6625705a6d4246c3a5f397008173899f.json"}}, {"family": "Zeviani", "given": "Massimo", "initials": "M"}, {"family": "Macao", "given": "Bertil", "initials": "B", "orcid": "0000-0001-6511-6125", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5445196c3234bdb8686e85f77a66f3f.json"}}, {"family": "Zhu", "given": "Xuefeng", "initials": "X", "orcid": "0000-0002-4759-4446", "researcher": {"href": "https://publications.scilifelab.se/researcher/eebd5f32ac0c48869c90ba2d2ba94fa9.json"}}, {"family": "Falkenberg", "given": "Maria", "initials": "M", "orcid": "0000-0001-8713-173X", "researcher": {"href": "https://publications.scilifelab.se/researcher/562109b99a5c4eb3bd8b92f30014828b.json"}}, {"family": "Viscomi", "given": "Carlo", "initials": "C", "orcid": "0000-0001-6050-0566", "researcher": {"href": "https://publications.scilifelab.se/researcher/e84ba370ae594e6db85d338ab69a02df.json"}}], "type": "journal article", "published": "2025-05-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "4782", "issn-l": "2041-1723"}, "abstract": "DNA polymerase \u03b3 (POL\u03b3), responsible for mitochondrial DNA replication, consists of a catalytic POL\u03b3A subunit and two accessory POL\u03b3B subunits. Mutations in POLG, which encodes POL\u03b3A, lead to various mitochondrial diseases. We investigated the most common POLG mutations (A467T, W748S, G848S, Y955C) by characterizing human and mouse POL\u03b3 variants. Our data reveal that these mutations significantly impair POL\u03b3 activities, with mouse variants exhibiting milder defects. Cryogenic electron microscopy highlighted structural differences between human and mouse POL\u03b3, particularly in the POL\u03b3B subunit, which may explain the higher activity of mouse POL\u03b3 and the reduced severity of mutations in mice. We further generated a panel of mouse models mirroring common human POLG mutations, providing crucial insights into the pathogenesis of POLG-related disorders and establishing robust models for therapeutic development. Our findings emphasize the importance of POL\u03b3B in modulating the severity of POLG mutations.", "doi": "10.1038/s41467-025-60059-y", "pmid": "40404629", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12098916"}, {"db": "pii", "key": "10.1038/s41467-025-60059-y"}], "notes": [], "created": "2025-11-05T13:48:13.014Z", "modified": "2025-11-13T12:47:34.901Z"}, {"entity": "publication", "iuid": "2be38ff9355144368c27f39655529af8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2be38ff9355144368c27f39655529af8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2be38ff9355144368c27f39655529af8"}}, "title": "Development of Langat virus infectious clones as a platform for live-attenuated tick-borne encephalitis vaccine.", "authors": [{"family": "Asghar", "given": "Naveed", "initials": "N"}, {"family": "Jaafar", "given": "Rita", "initials": "R"}, {"family": "Valko", "given": "Anna", "initials": "A"}, {"family": "Merinder", "given": "Olivia", "initials": "O"}, {"family": "Ljungberg", "given": "Karl", "initials": "K"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Johansson", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2025-05-23", "journal": {"title": "Npj Viruses", "issn": "2948-1767", "volume": "3", "issue": "1", "pages": "44", "issn-l": null}, "abstract": "Tick-borne encephalitis (TBE) is one of the most important tick-transmitted diseases in Europe and Asia. With no specific antiviral treatment available, vaccination remains the most effective protective strategy for TBE. Unlike currently available inactivated TBE vaccines that require repeated boosters, live-attenuated vaccines could offer lifelong immunity with a single dose. Langat virus (LGTV) is a naturally attenuated strain of TBE virus (TBEV). In this study, we engineered and rescued four infectious clones (ICs) of LGTV using RNA- and DNA-based reverse genetics methods. The ICs rescued by DNA-based method showed higher genetic stability in cell culture. One of the ICs rescued by DNA-based method was further evaluated in vitro and in vivo, which exhibited growth kinetics and immune profile comparable to the LGTV strain in our laboratory. This reverse genetics platform will be utilized to introduce targeted mutations within the LGTV genome to develop a live-attenuated TBE vaccine.", "doi": "10.1038/s44298-025-00129-6", "pmid": "40410304", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12102213"}, {"db": "pii", "key": "10.1038/s44298-025-00129-6"}], "notes": [], "created": "2025-11-19T15:16:17.785Z", "modified": "2025-11-19T15:16:17.848Z"}, {"entity": "publication", "iuid": "d7319dfddc184dd8b18c231f0797e622", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7319dfddc184dd8b18c231f0797e622.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7319dfddc184dd8b18c231f0797e622"}}, "title": "Three-Dimensional Atomic-Level Structure of an Amorphous Glucagon-Like Peptide-1 Receptor Agonist", "authors": [{"family": "Torodii", "given": "Daria", "initials": "D", "orcid": "0000-0002-5436-9503", "researcher": {"href": "https://publications.scilifelab.se/researcher/39e7638bc1224e9bbeecae7cc64c482f.json"}}, {"family": "Cordova", "given": "Manuel", "initials": "M"}, {"family": "Holmes", "given": "Jacob B", "initials": "JB"}, {"family": "Moutzouri", "given": "Pinelopi", "initials": "P"}, {"family": "Casalini", "given": "Tommaso", "initials": "T", "orcid": "0000-0002-8808-9868", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ea0d278cfa74f3787ab03aae9241cbc.json"}}, {"family": "Nilsson Lill", "given": "Sten O", "initials": "SO"}, {"family": "Pinon", "given": "Arthur C", "initials": "AC"}, {"family": "Knee", "given": "Christopher S", "initials": "CS"}, {"family": "Svensk Ankarberg", "given": "Anna", "initials": "A"}, {"family": "Putra", "given": "Okky Dwichandra", "initials": "OD", "orcid": "0000-0002-6968-1858", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f22d226c3664a9f81990d2a235e0e76.json"}}, {"family": "Schantz", "given": "Staffan", "initials": "S"}, {"family": "Emsley", "given": "Lyndon", "initials": "L", "orcid": "0000-0003-1360-2572", "researcher": {"href": "https://publications.scilifelab.se/researcher/d035a7c9c3c34fbda5feaa334a550910.json"}}], "type": "journal-article", "published": "2025-05-21", "journal": {"title": "J. Am. Chem. Soc.", "issn": "0002-7863", "volume": "147", "issue": "20", "pages": "17077-17087", "issn-l": null}, "abstract": null, "doi": "10.1021/jacs.5c01925", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:01:44.418Z", "modified": "2025-11-27T08:01:44.824Z"}, {"entity": "publication", "iuid": "db4d0488321c44809973ce6d788f31cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db4d0488321c44809973ce6d788f31cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db4d0488321c44809973ce6d788f31cf"}}, "title": "Seasonal dynamics and nutrient controls of biogenic silica in Baltic Sea surface microplankton and picoplankton communities.", "authors": [{"family": "Churakova", "given": "Yelena", "initials": "Y", "orcid": "0000-0002-8017-2122", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e4b7f5ea6e243b6b08008cdfa88c07f.json"}}, {"family": "Aguilera", "given": "Anabella", "initials": "A", "orcid": "0000-0001-6743-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6e88f127e7d49d09f593a57aa4a794e.json"}}, {"family": "Charalampous", "given": "Evangelia", "initials": "E", "orcid": "0000-0002-7724-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5c7828275bf44408584d66ceeefa6b6.json"}}, {"family": "Conley", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0001-9668-9284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d95efcbb3ce8420494cbc2260d2b1aa1.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}], "type": "journal article", "published": "2025-05-21", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "volume": "91", "issue": "5", "pages": "e0067625", "issn-l": "0099-2240"}, "abstract": "In recent years, new contributors to the marine silica cycle have emerged, including pico-sized phytoplankton (<2-3 \u00b5m in size) such as Synechococcus and picoeukaryotes. Their contribution and relevance to silica cycling are still under investigation. Field studies reporting the biogenic silica (bSi) standing stock in the pico-sized fraction are limited to silica-poor oligotrophic environments, and the mechanism of bSi accumulation in picoplankton remains unknown. We investigated the variability of bSi standing stocks in two size fractions (picoplankton, 0.22-3 \u00b5m and microplankton, >3 \u00b5m) in the dissolved silica-replete Baltic Sea via biweekly time series samplings spanning 2 years. Time series data showed that the large changes in bSi standing stock in the Baltic Proper were primarily related to microplankton biomass and community composition. Meanwhile, picoplankton were, at times, surprisingly high contributors to total bSi year-round (up to 21.6%). Simultaneously, we performed microcosm incubation experiments with natural phytoplankton communities in each season to examine how nutrient additions affected bSi concentrations. In these experiments, increases in microplankton bSi were directly correlated to increases in diatom biomass, highlighting their influential role in the Baltic Sea silica cycle. Meanwhile, phosphorus additions triggered an increase in picoplankton bSi accumulation in all experiments. This uncovers a potential control of bSi accumulation in picoplankton, which can help identify the cellular mechanisms behind this process and uncover their role in silica cycling. The results link phytoplankton community composition and silica cycling, which is important for understanding the consequences of organism shifts due to climate change.IMPORTANCEThe marine carbon and silica cycles are tightly intertwined and largely controlled by diatoms. Nevertheless, recent studies, mostly in oligotrophic waters, have proposed new contributors to the marine silica cycle: picoplankton. Here, we report the first study of seasonal dynamics of biogenic silica (bSi) standing stock in microplankton and picoplankton in the silica-replete Baltic Sea. Microplankton bSi dynamics were correlated with changes in composition and biomass. Picoplankton were consistent contributors to bSi, and for the first time in diverse natural communities, we found a direct correlation between phosphorus and bSi accumulation. The results are important for understanding how climate change-predicted phytoplankton composition shifts will affect carbon and silica cycling and provide a direction for future research on nutrient controls of silica accumulation in picoplankton.", "doi": "10.1128/aem.00676-25", "pmid": "40293244", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12094022"}], "notes": [], "created": "2025-11-26T08:38:35.731Z", "modified": "2025-11-26T08:38:36.366Z"}, {"entity": "publication", "iuid": "a16c14ee516a4891a8c7c2d6db78faf4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a16c14ee516a4891a8c7c2d6db78faf4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a16c14ee516a4891a8c7c2d6db78faf4"}}, "title": "Metabolomic-genomic prediction realizes small increases in accuracy of estimated breeding values for daily gain in pigs", "authors": [{"family": "Guo", "given": "Xiangyu", "initials": "X", "orcid": "0000-0001-7354-1519", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb71f9a793c449f1a85d7f9717777017.json"}}, {"family": "Sarup", "given": "Pernille", "initials": "P"}, {"family": "Bay Nord", "given": "Anders", "initials": "A"}, {"family": "Henryon", "given": "Mark", "initials": "M"}, {"family": "Ostersen", "given": "Tage", "initials": "T"}, {"family": "Christensen", "given": "Ole F", "initials": "OF"}], "type": "journal-article", "published": "2025-05-21", "journal": {"title": "Genet. Sel. Evol.", "issn": "1297-9686", "volume": "57", "issue": "1", "issn-l": "0999-193X"}, "abstract": null, "doi": "10.1186/s12711-025-00972-4", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:02:37.683Z", "modified": "2025-11-27T08:02:37.805Z"}, {"entity": "publication", "iuid": "14a490b69be949de8cbbefbdfbe5d0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5"}}, "title": "Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar.", "authors": [{"family": "Miraldo", "given": "A", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Sundh", "given": "J", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "E", "initials": "E"}, {"family": "Buczek", "given": "M", "initials": "M"}, {"family": "Goodsell", "given": "R", "initials": "R"}, {"family": "Johansson", "given": "H", "initials": "H"}, {"family": "Fisher", "given": "B L", "initials": "BL", "orcid": "0000-0002-4653-3270", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4747cc54254e8181f595e6fe21b953.json"}}, {"family": "Raharinjanahary", "given": "D", "initials": "D"}, {"family": "Rajoelison", "given": "E T", "initials": "ET"}, {"family": "Ranaivo", "given": "C", "initials": "C"}, {"family": "Randrianandrasana", "given": "C", "initials": "C"}, {"family": "Rafanomezantsoa", "given": "J-J", "initials": "J"}, {"family": "Manoharan", "given": "L", "initials": "L"}, {"family": "Granqvist", "given": "E", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "van Dijk", "given": "L J A", "initials": "LJA"}, {"family": "Alberg", "given": "L", "initials": "L"}, {"family": "\u00c5hl\u00e9n", "given": "D", "initials": "D"}, {"family": "Aspebo", "given": "M", "initials": "M"}, {"family": "\u00c5str\u00f6m", "given": "S", "initials": "S"}, {"family": "Bellviken", "given": "A", "initials": "A"}, {"family": "Bergman", "given": "P-E", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "S", "initials": "S"}, {"family": "Bj\u00f6rkman", "given": "M P", "initials": "MP", "orcid": "0000-0001-5768-1976", "researcher": {"href": "https://publications.scilifelab.se/researcher/9821ee4a87c74dde82d9a6a4ebc2b1fc.json"}}, {"family": "Deng", "given": "J", "initials": "J"}, {"family": "Desborough", "given": "L", "initials": "L"}, {"family": "Dolff", "given": "E", "initials": "E"}, {"family": "Eliasson", "given": "A", "initials": "A"}, {"family": "Elmquist", "given": "H", "initials": "H"}, {"family": "Emanuelsson", "given": "H", "initials": "H"}, {"family": "Erixon", "given": "R", "initials": "R"}, {"family": "Fahlen", "given": "L", "initials": "L"}, {"family": "Frogner", "given": "C", "initials": "C"}, {"family": "F\u00fcrst", "given": "P", "initials": "P"}, {"family": "Grabs", "given": "A", "initials": "A"}, {"family": "Grudd", "given": "H", "initials": "H", "orcid": "0000-0002-9033-2505", "researcher": {"href": "https://publications.scilifelab.se/researcher/97348870e86e4c75ae6ce0be4cc99699.json"}}, {"family": "Guasconi", "given": "D", "initials": "D"}, {"family": "Gunnarsson", "given": "M", "initials": "M"}, {"family": "H\u00e4ggqvist", "given": "S", "initials": "S"}, {"family": "Hed", "given": "A", "initials": "A"}, {"family": "H\u00f6rnstr\u00f6m", "given": "E", "initials": "E"}, {"family": "J\u00f6nsson", "given": "A", "initials": "A"}, {"family": "Kanerot", "given": "S", "initials": "S"}, {"family": "Karlsson", "given": "A", "initials": "A"}, {"family": "Karlsson", "given": "D", "initials": "D", "orcid": "0000-0003-4639-823X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ecfa3c78df4076bce64c7eeb36ee4f.json"}}, {"family": "Klinth", "given": "M", "initials": "M"}, {"family": "Kraft", "given": "T", "initials": "T", "orcid": "0000-0002-1143-5494", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6da126be9d48658afb96aac9532ead.json"}}, {"family": "Lahti", "given": "R", "initials": "R"}, {"family": "Larsson", "given": "M", "initials": "M"}, {"family": "Lernefalk", "given": "H", "initials": "H"}, {"family": "Lestander", "given": "Y", "initials": "Y"}, {"family": "Lindholm", "given": "L-T", "initials": "L"}, {"family": "Lindholm", "given": "M", "initials": "M"}, {"family": "Ljung", "given": "U", "initials": "U"}, {"family": "Ljung", "given": "K", "initials": "K"}, {"family": "Lundberg", "given": "J", "initials": "J", "orcid": "0000-0003-4316-9183", "researcher": {"href": "https://publications.scilifelab.se/researcher/86b74c200f2b402cad6b82cdf63259c9.json"}}, {"family": "Lundin", "given": "E", "initials": "E", "orcid": "0000-0002-3785-8305", "researcher": {"href": "https://publications.scilifelab.se/researcher/842e65aa96ef4dcaa8af13bf9e3f73f8.json"}}, {"family": "Malmenius", "given": "M", "initials": "M"}, {"family": "Marquina", "given": "D", "initials": "D"}, {"family": "Martinelli", "given": "J", "initials": "J"}, {"family": "Mertz", "given": "L", "initials": "L"}, {"family": "Nilsson", "given": "J", "initials": "J"}, {"family": "Patchett", "given": "A", "initials": "A"}, {"family": "Persson", "given": "N", "initials": "N"}, {"family": "Persson", "given": "J", "initials": "J"}, {"family": "Prus-Frankowska", "given": "M", "initials": "M"}, {"family": "Regazzoni", "given": "E", "initials": "E"}, {"family": "Rosander", "given": "K-G", "initials": "K"}, {"family": "Rydg\u00e5rd", "given": "M", "initials": "M"}, {"family": "Sandblom", "given": "C", "initials": "C"}, {"family": "Skord", "given": "J", "initials": "J"}, {"family": "St\u00e5lhandske", "given": "T", "initials": "T"}, {"family": "Svensson", "given": "F", "initials": "F"}, {"family": "Szpryngiel", "given": "S", "initials": "S", "orcid": "0000-0003-2965-2873", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec77cb9136184887b68a4ae8c4360927.json"}}, {"family": "Tajani", "given": "K", "initials": "K"}, {"family": "Tyboni", "given": "M", "initials": "M"}, {"family": "Ugarph", "given": "C", "initials": "C"}, {"family": "Vestermark", "given": "L", "initials": "L"}, {"family": "Vilhelmsson", "given": "J", "initials": "J"}, {"family": "Wahlgren", "given": "N", "initials": "N"}, {"family": "Wass", "given": "A", "initials": "A"}, {"family": "Wetterstrand", "given": "P", "initials": "P"}, {"family": "\u0141ukasik", "given": "P", "initials": "P", "orcid": "0000-0002-4164-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/71d69a579a304425b70249e7db42ad67.json"}}, {"family": "Tack", "given": "A J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}, {"family": "Andersson", "given": "A F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Roslin", "given": "T", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Ronquist", "given": "F", "initials": "F"}], "type": "journal article", "published": "2025-05-21", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "12", "issue": "1", "pages": "835"}, "abstract": "We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, Malaise trap samples were collected weekly (biweekly or monthly in the winter, when feasible) at 203 locations within 100 sites in Sweden and weekly at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of CO1 (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.", "doi": "10.1038/s41597-025-05151-0", "pmid": "40399316", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12095508"}, {"db": "pii", "key": "10.1038/s41597-025-05151-0"}], "notes": [], "created": "2025-11-19T08:51:31.233Z", "modified": "2025-11-21T12:26:09.639Z"}, {"entity": "publication", "iuid": "2425340e03244da090b07b7a32459592", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2425340e03244da090b07b7a32459592.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2425340e03244da090b07b7a32459592"}}, "title": "The ACBD3 protein coordinates ER-Golgi contacts to enable productive TBEV infection.", "authors": [{"family": "Yau", "given": "Wai-Lok", "initials": "W-L", "orcid": "0009-0007-0386-3919", "researcher": {"href": "https://publications.scilifelab.se/researcher/2044fb19cb8c4ecb94ddb6676da79a7d.json"}}, {"family": "Peters", "given": "Marie B A", "initials": "MBA"}, {"family": "R\u00f6nfeldt", "given": "Sebastian", "initials": "S"}, {"family": "Sorin", "given": "Marie N", "initials": "MN"}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Pulkkinen", "given": "Lauri I A", "initials": "LIA"}, {"family": "Carlson", "given": "Lars-Anders", "initials": "L-A"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}, {"family": "Lundmark", "given": "Richard", "initials": "R", "orcid": "0000-0001-9104-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e1b756caa79468dab0f960e43cd61d3.json"}}], "type": "journal article", "published": "2025-05-20", "journal": {"title": "J. Virol.", "issn": "1098-5514", "volume": "99", "issue": "5", "pages": "e0222424", "issn-l": "0022-538X"}, "abstract": "Flavivirus infection involves extensive remodeling of the endoplasmic reticulum (ER), which is key to both the replication of the viral RNA genome as well as the assembly and release of new virions. However, little is known about how viral proteins and host factors cooperatively facilitate such a vast transformation of the ER, and how this influences the different steps of the viral life cycle. In this study, we screened for host proteins that were enriched in close proximity to the tick-borne encephalitis virus (TBEV) protein NS4B and found that the top candidates were coupled to trafficking between ER exit sites (ERES) and the Golgi. We characterized the role of ACBD3, one of the identified proteins, and showed that it promotes TBEV infection. Depletion of ACBD3 inhibited virus replication and resulted in abnormal transformation of the ER, leading to reduced virion release. ACBD3's proviral mechanism did not involve the recruitment of PI4PK as previously described for enteroviruses. Instead, productive TBEV infection required the full-length ACBD3, which localizes to ER-Golgi contact sites together with NS4B. We propose that NS4B and ACBD3 promote replication by coordinating the transformation of the ER, which is required for RNA replication and particle release. The transformation involves direct coupling to the Golgi which facilitates efficient virion transport.\n\nFlaviviruses like tick-borne encephalitis have significant effects on human health. During flavivirus infection, the viral particles enter the host cells and transform the endoplasmic reticulum (ER), which is a membranous organelle and the main site of cellular protein synthesis. Although this is critical for successful infection, the details of the process are unknown. Here, we found that the viral protein NS4B and the host protein ACBD facilitate this transformation by ensuring that the ER is coupled to the Golgi apparatus, the organelle responsible for transporting material out of the cell. TBEV uses ACBD3 to guarantee that the connection sites between the transformed ER and the Golgi remain functional so that RNA is replicated and the produced viral particles are exported from the cell and can infect further cells. Our work sheds light both on the basic biology of flavivirus infection, and virus-induced remodeling of membranous organelles.", "doi": "10.1128/jvi.02224-24", "pmid": "40207930", "labels": {"Cryo-EM": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service", "Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12090792"}], "notes": [], "created": "2025-10-30T12:10:36.606Z", "modified": "2025-11-20T18:09:57.678Z"}, {"entity": "publication", "iuid": "04c8e47a5ff84a8ab9aaacf566682b62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04c8e47a5ff84a8ab9aaacf566682b62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04c8e47a5ff84a8ab9aaacf566682b62"}}, "title": "Marked mucosal lipid shifts in treatment refractory inflammatory bowel disease: a lipidomic study.", "authors": [{"family": "Moe", "given": "\u00d8ystein K", "initials": "\u00d8K"}, {"family": "Gao", "given": "Qian", "initials": "Q"}, {"family": "Geng", "given": "Dawei", "initials": "D"}, {"family": "Jensen", "given": "Einar", "initials": "E"}, {"family": "Goll", "given": "Rasmus", "initials": "R"}, {"family": "Nestegard", "given": "Oddmund", "initials": "O"}, {"family": "Gundersen", "given": "Mona D", "initials": "MD"}, {"family": "Florholmen", "given": "Jon R", "initials": "JR"}, {"family": "Moritz", "given": "T", "initials": "T"}], "type": "journal article", "published": "2025-05-20", "journal": {"title": "BMC Gastroenterol", "issn": "1471-230X", "volume": "25", "issue": "1", "pages": "389", "issn-l": null}, "abstract": "Mechanisms causing non-response to biological agents in IBD remain to be fully understood. Thus, we aimed to characterize the lipid profile in treatment refractory non-immunogenic patients with adequate trough-levels.\n\nPatients with IBD refractory to treatment with anti-tumour necrosis factor or vedolizumab were included from a Norwegian translation study. Mucosal lipid profiles were compared to reference groups. The reference groups included treatment na\u00efve IBD patients with moderate to severe disease at debut who later achieved remission or response on antiTNFs, IBD patients treated to remission with biological agents, and healthy normal controls. Lipidomics analyses were performed on mucosal biopsies. Statistical analyses of lipid levels were carried out using generalized least squares. Lipidomics data were log2-transformed and auto-scaled before analysis. P-values were adjusted using Benjamini- Hochberg procedure to control the false discovery rate (FDR).\n\nProinflammatory lipids including ceramides and sphingomyelins and protective lipids like glycerophosphocholines and glycerophosphoethanolamines were significantly decreased in treatment refractory UC patients compared to treatment na\u00efve UC patients with moderate to severe disease. Compared to controls, major changes in ceramides (Cer), hexosyl ceramides (HexCer), sphingomyelins (SM), glycerophosphocholines (PC), glycerophosphoethanolamines (PE) and glycerophosphoserines (PS) were observed in treatment refractory UC patients. Refractory CD patients showed minor changes compared to the other CD-groups. There were no significant differences in the mucosal lipid levels of IBD patients in remission compared to normal controls.\n\nThe mucosal lipid profile of treatment refractory UC shows marked shifts compared to treatment na\u00efve UC at debut with moderate to severe inflammation. These are novel findings which possibly indicate dynamic processes of long-standing mucosal inflammation. The mucosal lipid profile of IBD patients in remission seems to be similar to the normal state.", "doi": "10.1186/s12876-025-03944-6", "pmid": "40394475", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12093861"}, {"db": "pii", "key": "10.1186/s12876-025-03944-6"}], "notes": [], "created": "2025-11-18T12:03:41.462Z", "modified": "2025-11-18T12:03:41.478Z"}, {"entity": "publication", "iuid": "e1fc900e192b4bfc94382b7492c4c156", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1fc900e192b4bfc94382b7492c4c156.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1fc900e192b4bfc94382b7492c4c156"}}, "title": "IL1RAP Expression in Human Atherosclerosis: A Target of Novel Antibodies to Reduce Vascular Inflammation and Adhesion.", "authors": [{"family": "Lindkvist", "given": "Madelene", "initials": "M", "orcid": "0000-0002-2732-158X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7049b254bca748e4a6c4edc1eff7f2f6.json"}}, {"family": "G\u00f6thlin Eremo", "given": "Anna", "initials": "A", "orcid": "0000-0002-7498-7157", "researcher": {"href": "https://publications.scilifelab.se/researcher/a00ba00e4d5942888b1b62e4ed0715ae.json"}}, {"family": "Paramel", "given": "Geena Varghese", "initials": "GV", "orcid": "0000-0002-4589-6440", "researcher": {"href": "https://publications.scilifelab.se/researcher/22244d67e37248baa3edd9d12b46c53a.json"}}, {"family": "Anisul Haque", "given": "Sheikh", "initials": "S", "orcid": "0000-0002-0927-4126", "researcher": {"href": "https://publications.scilifelab.se/researcher/74787f0a680f403499a97fb3bc390568.json"}}, {"family": "Rydberg Millrud", "given": "Camilla", "initials": "C"}, {"family": "Rattik", "given": "Sara", "initials": "S"}, {"family": "Gr\u00f6nberg", "given": "Caitr\u00edona", "initials": "C", "orcid": "0009-0000-3776-5566", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab9490c2683d41fa8ebf70558ece4536.json"}}, {"family": "Liberg", "given": "David", "initials": "D", "orcid": "0009-0009-0645-746X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0677a596a8243539a9d19a6c45d936e.json"}}, {"family": "Sirsj\u00f6", "given": "Allan", "initials": "A", "orcid": "0000-0002-0278-4510", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc067d053e94853a8ffffbd3ece4d04.json"}}, {"family": "Frans\u00e9n", "given": "Karin", "initials": "K", "orcid": "0000-0002-9826-0462", "researcher": {"href": "https://publications.scilifelab.se/researcher/070957ad2a8f4815bb9e5c62942bbb03.json"}}], "type": "journal article", "published": "2025-05-20", "journal": {"title": "J Am Heart Assoc", "issn": "2047-9980", "volume": "14", "issue": "10", "pages": "e039557", "issn-l": "2047-9980"}, "abstract": "Blockade of IL1RAP (interleukin 1 receptor associated protein) was recently shown to reduce atherosclerosis in mice, but the effect on human vascular cells is largely unknown. Targeting the IL1RAP coreceptor represents a novel strategy to block the IL1RAP-dependent cytokines IL (interleukin)-1, IL-33, and IL-36. In the present study, we aimed to evaluate the role of novel antibodies targeting IL1RAP to reduce the effects of IL-1\u03b2, IL-33, or IL-36\u03b3 in human vascular cells.\n\nExpression of IL1RAP was observed in human atherosclerotic plaques by immunohistochemistry and microarray and in endothelial cells by flow cytometry. Endothelial cells were cultured with IL-1\u03b2, IL-33, or IL-36\u03b3 cytokines with or without IL1RAP antibodies and analyzed with Olink proteomics, ELISA, Western blot, and real-time quantitative polymerase chain reaction. The functional effect of IL1RAP antibodies on endothelial cells were analyzed with adhesion and permeability assays.\n\nOlink proteomics showed inhibition of the inflammatory proteins LIF (leukemia inhibitory factor), OPG (osteoprotegerin), CCL4 (C-C motif chemokine ligand 4), and MCP-3 (monocyte chemoattractant protein 3) by IL1RAP-blockade in endothelial cells after IL-1\u03b2 stimulation. In addition, the IL1RAP antibodies inhibited IL-1\u03b2, and IL-33 induced IL-6 and IL-8 secretion. Secretion of MCP-1 (monocyte chemoattractant protein 1) was induced by IL-1\u03b2, IL-33, and IL-36\u03b3, and subsequently was inhibited by IL1RAP antibodies. Similar effects were found on mRNA expression level. Endothelial expression of the adhesion markers ICAM1, VCAM1, and SELE were significantly reduced by IL1RAP antibodies, and neutrophil adhesion to endothelial cells induced by IL-1\u03b2 and IL-33 was reduced by IL1RAP blockade. In human atherosclerotic lesions, IL1RAP expression correlated with markers of inflammation like IL6, IL8, and MCP1.\n\nIL1RAP-targeting antibodies can reduce the expression of inflammatory cytokines and markers of adhesion in endothelial cells, which may be of importance for future putative targeted treatments against cardiovascular disease.", "doi": "10.1161/JAHA.124.039557", "pmid": "40371594", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12184588"}], "notes": [], "created": "2025-11-07T13:42:11.218Z", "modified": "2025-11-07T13:42:15.690Z"}, {"entity": "publication", "iuid": "4dba785f8bab418ca9f0391499da9572", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4dba785f8bab418ca9f0391499da9572.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4dba785f8bab418ca9f0391499da9572"}}, "title": "Single-cell RNA-sequencing reveals early mitochondrial dysfunction unique to motor neurons shared across FUS- and TARDBP-ALS.", "authors": [{"family": "Schweingruber", "given": "Christoph", "initials": "C", "orcid": "0000-0003-4505-9068", "researcher": {"href": "https://publications.scilifelab.se/researcher/df74f600399f4fabaa9d186d23172fef.json"}}, {"family": "Nijssen", "given": "Jik", "initials": "J", "orcid": "0000-0003-0013-9750", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e17dd67c1aa45b1b12e8d8a457236b8.json"}}, {"family": "Mechtersheimer", "given": "Jonas", "initials": "J", "orcid": "0000-0001-8818-7671", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d8e9b06cdda42979c1447bd305f5902.json"}}, {"family": "Reber", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4885-3550", "researcher": {"href": "https://publications.scilifelab.se/researcher/c18e3ec9b7b64d3f8a734a76b71e3bbe.json"}}, {"family": "Leb\u0153uf", "given": "M\u00e9lanie", "initials": "M", "orcid": "0000-0003-0033-7159", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a0014951aaa4e0582a0fef1ee11b5b1.json"}}, {"family": "O'Brien", "given": "Niamh L", "initials": "NL", "orcid": "0000-0001-5951-1305", "researcher": {"href": "https://publications.scilifelab.se/researcher/73741194e1794a5ca40148001344ee22.json"}}, {"family": "Mei", "given": "Irene", "initials": "I", "orcid": "0009-0007-8238-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5b33928c6334f4b8c436ace690786c9.json"}}, {"family": "Hedges", "given": "Erin", "initials": "E", "orcid": "0000-0002-2519-9824", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c84bf7c4b754f2094a163b0fede16f4.json"}}, {"family": "Keuper", "given": "Michaela", "initials": "M", "orcid": "0000-0003-0319-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/c290cd22791a4e91aee49265e6739b25.json"}}, {"family": "Benitez", "given": "Julio Aguila", "initials": "JA"}, {"family": "Radoi", "given": "Vlad", "initials": "V", "orcid": "0000-0002-9657-8303", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f50b39d18924acfb4061f5df3acd774.json"}}, {"family": "Jastroch", "given": "Martin", "initials": "M", "orcid": "0000-0003-0358-3865", "researcher": {"href": "https://publications.scilifelab.se/researcher/67ebcd9680e2445497d3a7ac50e7724d.json"}}, {"family": "Ruepp", "given": "Marc-David", "initials": "MD", "orcid": "0000-0003-3264-9800", "researcher": {"href": "https://publications.scilifelab.se/researcher/a720da7447c74bbe8fabedd01b8bea07.json"}}, {"family": "Hedlund", "given": "Eva", "initials": "E", "orcid": "0000-0001-6347-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/d517e76df2e944e09ddbe87b7e0329af.json"}}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "4633", "issn-l": "2041-1723"}, "abstract": "Mutations in FUS and TARDBP cause amyotrophic lateral sclerosis (ALS), but the precise mechanisms of selective motor neuron degeneration remain unresolved. To address if pathomechanisms are shared across mutations and related to either gain- or loss-of-function, we performed single-cell RNA sequencing across isogenic induced pluripotent stem cell-derived neuron types, harbouring FUS P525L, FUS R495X, TARDBP M337V mutations or FUS knockout. Transcriptional changes were far more pronounced in motor neurons than interneurons. About 20% of uniquely dysregulated motor neuron transcripts were shared across FUS mutations, half from gain-of-function. Most indicated mitochondrial impairments, with attenuated pathways shared with mutant TARDBP M337V as well as C9orf72-ALS patient motor neurons. Mitochondrial motility was impaired in ALS motor axons, even with nuclear localized FUS mutants, demonstrating shared toxic gain-of-function mechanisms across FUS- and TARDBP-ALS, uncoupled from protein mislocalization. These early mitochondrial dysfunctions unique to motor neurons may affect survival and represent therapeutic targets in ALS.", "doi": "10.1038/s41467-025-59679-1", "pmid": "40389397", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12089458"}, {"db": "pii", "key": "10.1038/s41467-025-59679-1"}], "notes": [], "created": "2025-10-03T08:47:44.009Z", "modified": "2025-10-03T08:47:45.216Z"}, {"entity": "publication", "iuid": "5b6d8c72800145a294f1fab88be77e43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b6d8c72800145a294f1fab88be77e43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b6d8c72800145a294f1fab88be77e43"}}, "title": "Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication-Related Brain Composition.", "authors": [{"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Moradinour", "given": "Zahra", "initials": "Z"}, {"family": "Katajama", "given": "Rebecca", "initials": "R"}, {"family": "Martin Cerezo", "given": "Maria Luisa", "initials": "ML", "orcid": "0000-0003-3952-2853", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e025902fc04455ad70a33ba146c003.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17788", "issn-l": "0962-1083"}, "abstract": "Domestication involves huge phenotypic shifts via strong directional selection. The resulting changes, often termed the Domestication Syndrome, typically encompass numerous traits; however, the most universal of these are changes in reduced fear of humans (tameness) and brain composition. To assess how early domestication selection may have focused on tameness and its interaction with brain composition, a Red Junglefowl (Gallus gallus) population (the wild progenitor of the domestic chicken) was used to create two lines bidirectionally selected for fear of humans over eight generations of selection. These selection lines were then used to make an intercross population. Using a combination of genome-wide mapping in the intercross and between-line analysis of the selection lines, we show that the genetic loci for tameness co-localise with genetic loci for brain composition and anxiety behaviour. Furthermore, the detected loci for brain composition also co-localise with brain composition loci identified in a separate wild \u00d7 domestic intercross. These results indicate that tameness and brain composition are either pleiotropic or genetically linked, and that tameness selection appears to recapitulate the same loci that have been selected by domestication itself. Therefore, selection for increased tameness could be the initial selection pressure driving the core of the domestication syndrome.", "doi": "10.1111/mec.17788", "pmid": "40386851", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:37:29.894Z", "modified": "2025-11-28T10:51:37.135Z"}, {"entity": "publication", "iuid": "d87a1093323d4610a405b3a7a6fcc248", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d87a1093323d4610a405b3a7a6fcc248.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d87a1093323d4610a405b3a7a6fcc248"}}, "title": "Brain tumors induce immunoregulatory dendritic cells in draining lymph nodes that can be targeted by OX40 agonist treatment.", "authors": [{"family": "Badillo-Godinez", "given": "Oscar", "initials": "O", "orcid": "0000-0002-3840-9448", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a36cfe85dec4e5099c4fb754f8c4b7e.json"}}, {"family": "Niemi", "given": "Jenni", "initials": "J"}, {"family": "Helfridsson", "given": "Liam", "initials": "L"}, {"family": "Karimi", "given": "Shokoufeh", "initials": "S"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M"}, {"family": "Mangukiya", "given": "Hitesh Bhagavanbhai", "initials": "HB", "orcid": "0000-0002-8460-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/d32958c394c749d19d7444dac9fe6c3b.json"}}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "J Immunother Cancer", "issn": "2051-1426", "volume": "13", "issue": "5", "issn-l": null}, "abstract": "Primary and metastatic brain tumors have a poor prognosis, partly owing to the unique characteristics of the central nervous system (CNS) and tumor immune microenvironment (TIME). One distinct feature of the CNS TIME is the limited infiltration and activation of dendritic cells (DCs). The impact of CNS versus non-CNS TIME can be assessed by injecting tumor cells from the same model, either subcutaneously (peripherally) or into the brain. Subcutaneous tumors drain into the tumor-draining lymph nodes in the skin (TdLN-p), whereas brain tumors drain into the deep cervical TdLN (TdLN-c). We previously showed that CNS tumors that are not responsive to immune checkpoint inhibition become responsive when grown peripherally, and that non-responsiveness correlates with a tolerogenic immune response in the local TIME and TdLN-c.\n\nIn this study, we investigated the immunoregulatory potential of cervical DCs (DC-c) compared with that of peripheral DCs (DC-p) using high-resolution flow cytometry, single-cell RNA sequencing, and ex vivo and in vivo functional characterization of TdLNs from mouse models of glioma and lymphoma.\n\nOur analysis revealed that DC-c promoted regulatory T-cell expansion and poorly cytotoxic CD8+ T cells compared with DC-p. Furthermore, we identified OX40 (Tnfrsf4) as a modulator of immunoregulatory DC-c function and found that its antitumor effect depended on lymphocyte trafficking and the DC transcription factor Batf3. CCR7+OX40+ DCs were efficient in antigen processing and presentation, and OX40 agonists further enhanced DC activation. In TIME, the CCR7+OX40+ DCs expressed OX40L, and blocking it promoted Treg formation ex vivo.\n\nOur findings highlight the unique immunoregulatory functions of DC-c in TdLNs and suggest the importance of OX40 signaling through direct effects on CCR7+OX40+ DCs and indirect effects on T cells.", "doi": "10.1136/jitc-2025-011548", "pmid": "40389372", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12090865"}, {"db": "pii", "key": "jitc-2025-011548"}], "notes": [], "created": "2025-09-08T07:10:13.442Z", "modified": "2025-09-08T07:10:13.516Z"}, {"entity": "publication", "iuid": "fec47bc65de942b98146974984fcd1f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fec47bc65de942b98146974984fcd1f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fec47bc65de942b98146974984fcd1f8"}}, "title": "QS molecules change the planktonic/mineral subpopulations distribution of moderately thermophilic leaching bacteria in pyrite and decrease leaching in chalcopyrite.", "authors": [{"family": "Salas", "given": "Beatriz", "initials": "B"}, {"family": "Bellenberg", "given": "S\u00f6ren", "initials": "S"}, {"family": "Nilsson", "given": "Emelie", "initials": "E"}, {"family": "L\u00f3pez-Tomasovic", "given": "Luna", "initials": "L"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Vera", "given": "Mario", "initials": "M"}], "type": "journal article", "published": "2025-05-16", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "16", "pages": "1592588", "issn-l": "1664-302X"}, "abstract": "Biomining is a sustainable alternative to conventional mineral processing that uses acidophilic microorganisms to catalyze the extraction of valuable metals from sulfide minerals. Mixed microbial consortia composed of moderate thermophiles such as Sulfobacillus and some Leptospirillum species improve metal extraction efficiency at higher temperatures compared to pure cultures of mesophiles. However, quorum sensing (QS), which regulates microbial interactions and likely influences bioleaching performance, has not been studied in these species. In this study, treatment of a moderately thermophilic biomining consortium with QS compounds, termed diffusible signal factors (DSF), reduced pyrite and chalcopyrite dissolution via an inhibitory effect on iron oxidation and mineral colonization by the mixed culture. Furthermore, QS molecules changed the distribution of planktonic/mineral subpopulations of the acidophilic species. In addition, DSF compounds induced Acidithiobacillus caldus motility and dispersion from pyrite with a concomitant expansion of Leptospirillum ferriphilum on the mineral surface while in contrast, the acyl-homoserine lactone mediated QS system repressed L. ferriphilum motility. Moreover, the addition of QS molecules induced a second response related to the detrimental effect of high concentrations of fatty acids on cells, with an activation of detoxification mechanisms. Overall, QS regulated key target microbial interactions that opens the possibility to improve chalcopyrite bioleaching in the studied consortia.", "doi": "10.3389/fmicb.2025.1592588", "pmid": "40454366", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12122527"}], "notes": [], "created": "2025-11-24T11:43:25.883Z", "modified": "2025-11-24T11:43:25.894Z"}, {"entity": "publication", "iuid": "5e9b7ea20a944f4c916b3e4d80a02df2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e9b7ea20a944f4c916b3e4d80a02df2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e9b7ea20a944f4c916b3e4d80a02df2"}}, "title": "Preparation for mitosis requires gradual CDK1 activation.", "authors": [{"family": "Akopyan", "given": "Karen", "initials": "K"}, {"family": "Hao", "given": "Zhiyu", "initials": "Z"}, {"family": "Lindqvist", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2025-05-16", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "28", "issue": "5", "pages": "112292", "issn-l": "2589-0042"}, "abstract": "G2 phase is considered as a time in which cells prepare for the large structural changes in the following mitosis. Starting at completion of DNA replication, CDK1 and PLK1 kinase activities gradually increase throughout G2 phase until reaching levels that initiate mitosis. Here, we use a combination of experiments and a data-driven mathematical model to study the connection between DNA replication and mitosis. We find that gradual activation of mitotic kinases ensures CDK1-dependent transcription of factors required for mitosis. In addition, we find that gradual activation of CDK1 coordinates CDK1 and PLK1 activation. Conversely, shortening G2 phase by WEE1 inhibition leads to mitotic delays, which can be partially rescued by expression of constitutively active PLK1. Our results show a function for slow mitotic kinase activation through G2 phase and suggest a mechanism for how the timing of mitotic entry is linked to preparation for mitosis.", "doi": "10.1016/j.isci.2025.112292", "pmid": "40256327", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12008674"}, {"db": "pii", "key": "S2589-0042(25)00553-X"}], "notes": [], "created": "2025-11-28T10:43:44.973Z", "modified": "2025-11-28T10:43:44.977Z"}, {"entity": "publication", "iuid": "59590952121949ceb9a5b5aa71049f5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59590952121949ceb9a5b5aa71049f5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59590952121949ceb9a5b5aa71049f5f"}}, "title": "Modular deregulation of central carbon metabolism for efficient xylose utilization in Saccharomyces cerevisiae.", "authors": [{"family": "Li", "given": "Xiaowei", "initials": "X", "orcid": "0009-0008-2436-7524", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a3dc801f3f84acdbddbe992b4955bd5.json"}}, {"family": "Wang", "given": "Yanyan", "initials": "Y"}, {"family": "Chen", "given": "Xin", "initials": "X", "orcid": "0000-0003-2788-1314", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b77832f3ca408fa8dc1414d8f46552.json"}}, {"family": "Eisentraut", "given": "Leon", "initials": "L"}, {"family": "Zhan", "given": "Chunjun", "initials": "C"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Chen", "given": "Yun", "initials": "Y", "orcid": "0000-0002-2146-6008", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8a0c4c96b7e491496aa0991c7e9a460.json"}}], "type": "journal article", "published": "2025-05-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "4551", "issn-l": "2041-1723"}, "abstract": "The tightly regulated central carbon metabolism in Saccharomyces cerevisiae, intricately linked to carbon sources utilized, poses a significant challenge to engineering efforts aimed at increasing the flux through its different pathways. Here, we present a modular deregulation strategy that enables high conversion rates of xylose through the central carbon metabolism. Specifically, employing a multifaceted approach encompassing five different engineering strategies-promoter engineering, transcription factor manipulation, biosensor construction, introduction of heterologous enzymes, and expression of mutant enzymes we engineer different modules of the central carbon metabolism at both the genetic and enzymatic levels. This leads to an enhanced conversion rate of xylose into acetyl-CoA-derived products, with 3-hydroxypropionic acid (3-HP) serving as a representative case in this study. By implementing a combination of these approaches, the developed yeast strain demonstrates a remarkable enhancement in 3-HP productivity, achieving a 4.7-fold increase when compared to our initially optimized 3-HP producing strain grown on xylose as carbon source. These results illustrate that the rational engineering of yeast central metabolism is a viable approach for boosting the metabolic flux towards acetyl-CoA-derived products on a non-glucose carbon source.", "doi": "10.1038/s41467-025-59966-x", "pmid": "40379631", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12084563"}, {"db": "pii", "key": "10.1038/s41467-025-59966-x"}], "notes": [], "created": "2025-11-27T11:28:28.879Z", "modified": "2025-11-27T11:28:29.069Z"}, {"entity": "publication", "iuid": "7550315fbef140b8a65cc116f93087de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7550315fbef140b8a65cc116f93087de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7550315fbef140b8a65cc116f93087de"}}, "title": "Human proteome distribution atlas for tissue-specific plasma proteome dynamics.", "authors": [{"family": "Malmstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Hauri", "given": "Simon", "initials": "S"}, {"family": "Mohanty", "given": "Tirthankar", "initials": "T"}, {"family": "Scott", "given": "Aaron", "initials": "A"}, {"family": "Karlsson", "given": "Christofer", "initials": "C"}, {"family": "Gueto-Tettay", "given": "Carlos", "initials": "C"}, {"family": "\u00c5hrman", "given": "Emma", "initials": "E"}, {"family": "Nozohoor", "given": "Shahab", "initials": "S"}, {"family": "Tingstedt", "given": "Bobby", "initials": "B"}, {"family": "Regner", "given": "Sara", "initials": "S"}, {"family": "Elfving", "given": "Peter", "initials": "P"}, {"family": "Bjermer", "given": "Leif", "initials": "L"}, {"family": "Forsvall", "given": "Andreas", "initials": "A"}, {"family": "Doyle", "given": "Alexander", "initials": "A"}, {"family": "Magnusson", "given": "Mattias", "initials": "M"}, {"family": "Hedenfalk", "given": "Ingrid", "initials": "I"}, {"family": "Kannisto", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Brandt", "given": "Christian", "initials": "C"}, {"family": "Nilsson", "given": "Emma", "initials": "E"}, {"family": "Dahlin", "given": "Lars B", "initials": "LB"}, {"family": "Malm", "given": "Johan", "initials": "J"}, {"family": "Linder", "given": "Adam", "initials": "A"}, {"family": "Nim\u00e9us", "given": "Emma", "initials": "E"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-05-15", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "188", "issue": "10", "pages": "2810-2822.e16", "issn-l": "0092-8674"}, "abstract": "The plasma proteome is maintained by the influx and efflux of proteins from surrounding organs and cells. To quantify the extent to which different organs and cells impact the plasma proteome in healthy and diseased conditions, we developed a mass-spectrometry-based proteomics strategy to infer the tissue origin of proteins detected in human plasma. We first constructed an extensive human proteome atlas from 18 vascularized organs and the 8 most abundant cell types in blood. The atlas was interfaced with previous RNA and protein atlases to objectively define proteome-wide protein-organ associations to infer the origin and enable the reproducible quantification of organ-specific proteins in plasma. We demonstrate that the resource can determine disease-specific quantitative changes of organ-enriched protein panels in six separate patient cohorts, including sepsis, pancreatitis, and myocardial injury. The strategy can be extended to other diseases to advance our understanding of the processes contributing to plasma proteome dynamics.", "doi": "10.1016/j.cell.2025.03.013", "pmid": "40203824", "labels": {"Clinical Proteomics Lund": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)00286-7"}], "notes": [], "created": "2025-11-28T10:08:51.977Z", "modified": "2025-11-28T10:08:51.981Z"}, {"entity": "publication", "iuid": "a3b56884aa7c4de8a495645ae9c04a3f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3b56884aa7c4de8a495645ae9c04a3f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3b56884aa7c4de8a495645ae9c04a3f"}}, "title": "Cryptic infection of a giant virus in a unicellular green alga.", "authors": [{"family": "Erazo-Garcia", "given": "Maria P", "initials": "MP"}, {"family": "Sheyn", "given": "Uri", "initials": "U", "orcid": "0000-0002-0997-3533", "researcher": {"href": "https://publications.scilifelab.se/researcher/339c239371444eb1b5b92c2ae87287f0.json"}}, {"family": "Barth", "given": "Zachary K", "initials": "ZK", "orcid": "0000-0002-1321-306X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb7321f3a0d448db8f7b874957519c28.json"}}, {"family": "Craig", "given": "Rory J", "initials": "RJ", "orcid": "0000-0002-6262-0008", "researcher": {"href": "https://publications.scilifelab.se/researcher/8205c7b75c064ea19f2a15ca41aa306a.json"}}, {"family": "Wessman", "given": "Petronella", "initials": "P", "orcid": "0009-0005-6425-5090", "researcher": {"href": "https://publications.scilifelab.se/researcher/33a52058c77a445bb89bf43373a85c99.json"}}, {"family": "Jivaji", "given": "Abdeali M", "initials": "AM", "orcid": "0000-0003-2474-9561", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3f3b7a3335e4db0b0cdad826b454d38.json"}}, {"family": "Ray", "given": "W Keith", "initials": "WK", "orcid": "0000-0002-1727-4994", "researcher": {"href": "https://publications.scilifelab.se/researcher/c252eb2f6604423cbf2607d56e0d4876.json"}}, {"family": "Svensson-Coelho", "given": "Maria", "initials": "M", "orcid": "0000-0002-2315-2416", "researcher": {"href": "https://publications.scilifelab.se/researcher/8071837fca404e89bd2d2d2a77e78591.json"}}, {"family": "Cornwallis", "given": "Charlie K", "initials": "CK", "orcid": "0000-0003-1308-3995", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d766d021df4fbeba0d52a624df866d.json"}}, {"family": "Rengefors", "given": "Karin", "initials": "K", "orcid": "0000-0001-6297-9734", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7353dd11fa445f9ff338db5ce8dadd.json"}}, {"family": "Brussaard", "given": "Corina P D", "initials": "CPD", "orcid": "0000-0002-6320-9229", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc835c98bf6344258be39c7f0234cbb8.json"}}, {"family": "Moniruzzaman", "given": "Mohammad", "initials": "M", "orcid": "0000-0001-9337-3874", "researcher": {"href": "https://publications.scilifelab.se/researcher/a73c62107b1b4bfc88368589cf93da3c.json"}}, {"family": "Aylward", "given": "Frank O", "initials": "FO", "orcid": "0000-0002-1279-4050", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3e34cc20250453db387906db0d7038e.json"}}], "type": "journal article", "published": "2025-05-15", "journal": {"title": "Science", "issn": "1095-9203", "volume": "388", "issue": "6748", "pages": "eads6303", "issn-l": "0036-8075"}, "abstract": "Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. In this work, we describe a 617-kilo-base pairs integrated giant viral element in the model green alga Chlamydomonas reinhardtii. We resolved the integrated viral genome using long-read sequencing, identified a putative polintovirus-like integrase, and show that viral particles accumulate primarily during the stationary growth phase. A diverse array of viral-encoded selfish genetic elements is expressed during viral activity, including several Fanzor nuclease-encoding transposable elements. In addition, we show that field isolates of Chlamydomonas spp. harbor signatures of endogenous giant viruses related to the C. reinhardtii virus that exhibit similar infection dynamics, suggesting that giant virus latency is prevalent in natural host communities. Our work describes an unusually large temperate virus of a unicellular eukaryote, substantially expanding the scope of cryptic viral infections in the virosphere.", "doi": "10.1126/science.ads6303", "pmid": "40208960", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2086965"}, {"db": "pmc", "key": "PMC12147526"}], "notes": [], "created": "2025-08-19T13:29:58.027Z", "modified": "2025-08-19T13:29:58.877Z"}, {"entity": "publication", "iuid": "5adffdb972b34ba1ad08ce191ce10297", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5adffdb972b34ba1ad08ce191ce10297.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5adffdb972b34ba1ad08ce191ce10297"}}, "title": "Revised phylogeny of mouflon based on expanded sampling of mitogenomes.", "authors": [{"family": "Mereu", "given": "Paolo", "initials": "P", "orcid": "0000-0001-6615-4828", "researcher": {"href": "https://publications.scilifelab.se/researcher/422d206c68a94124a43bed3c4db41999.json"}}, {"family": "Pirastru", "given": "Monica", "initials": "M"}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P", "orcid": "0000-0001-7678-9691", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a48ddd9e9b491ea55ec2ac0bd4328f.json"}}, {"family": "Ata\u011f", "given": "G\u00f6zde", "initials": "G"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Wilkens", "given": "Barbara", "initials": "B"}, {"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE"}, {"family": "Kaptan", "given": "Damla", "initials": "D", "orcid": "0000-0001-7953-1354", "researcher": {"href": "https://publications.scilifelab.se/researcher/d969faa7d65045298f3ef289d849dfe8.json"}}, {"family": "Zedda", "given": "Marco", "initials": "M", "orcid": "0000-0003-2347-9264", "researcher": {"href": "https://publications.scilifelab.se/researcher/0108c75581c44c61a3f1bcaa0728e77a.json"}}, {"family": "Columbano", "given": "Nicol\u00f2", "initials": "N", "orcid": "0000-0003-2201-8773", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39bcac149fd4b8ca83c833bf86da2f7.json"}}, {"family": "Barbato", "given": "Mario", "initials": "M", "orcid": "0000-0002-7203-1549", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cf7e142b2894c9f8e3249dda9bc6728.json"}}, {"family": "Naitana", "given": "Salvatore", "initials": "S"}, {"family": "Hadjisterkotis", "given": "Eleftherios", "initials": "E"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F", "orcid": "0000-0003-0443-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/676b684e50e04c7686e5ddfd1b9c41a1.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Leoni", "given": "Giovanni Giuseppe", "initials": "GG"}], "type": "journal article", "published": "2025-05-14", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "5", "pages": "e0323354", "issn-l": "1932-6203"}, "abstract": "Mouflons are flagship species of the Mediterranean islands where they persist. Once thought to be the remnants of a European wild sheep population, archaeology suggests they were introduced by humans to the islands of Cyprus in the Early Neolithic (~10,000 years ago) and later to Corsica and Sardinia. Their status as truly wild animals remains a subject of debate. To investigate the phylogenetic relationship between these island populations and other domestic and wild sheep from the Mediterranean region, we sequenced 50 mitogenomes of mouflons from Sardinia and Corsica, and modern and ancient Sardinian domestic sheep. A total of 68 additional publicly available mitogenomes were included in the comparative analysis and used to reconstruct the phylogeny of sheep and its closest wild relative, the mouflon (Ovis gmelini). Our study analyzed the evolutionary relationships within the C-E-X and haplogroup B clusters, showing that: a) Cyprus mouflons are more related to Anatolian and Iranian mouflons belonging to the wild haplogroup X, which seems to be basal to the domestic C and E haplogroups; b) Corsican and Sardinian mouflon arise from basal lineages associated with the early European expansion of domestic sheep. These results highlight the phylogenetic distinctiveness of the mouflon populations from the Mediterranean islands, suggesting a revision of their systematic classification and an update of the nomenclature for Sardinian and Corsican mouflons from the current status of subspecies of domestic sheep (Ovis aries musimon) to subspecies of their wild relatives (Ovis gmelini musimon) which would facilitate conservation efforts.", "doi": "10.1371/journal.pone.0323354", "pmid": "40367058", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Ancient DNA": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12077669"}, {"db": "pii", "key": "PONE-D-25-02476"}], "notes": [], "created": "2025-09-08T07:03:22.964Z", "modified": "2025-11-14T11:09:06.543Z"}, {"entity": "publication", "iuid": "f61af6cf5a7c4a2389ab8f8d63c905f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f61af6cf5a7c4a2389ab8f8d63c905f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f61af6cf5a7c4a2389ab8f8d63c905f2"}}, "title": "Metagenomic biodiversity assessment within an offshore wind farm.", "authors": [{"family": "Serivichyaswat", "given": "Phanu Theodore", "initials": "PT"}, {"family": "Scholte", "given": "Thijs", "initials": "T"}, {"family": "Wilms", "given": "Tim", "initials": "T"}, {"family": "Stranddorf", "given": "Liv", "initials": "L"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}], "type": "journal article", "published": "2025-05-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "16786", "issn-l": "2045-2322"}, "abstract": "Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and around the Horns Rev 1 offshore wind farm in the Danish North Sea. Seawater samples were collected from both within the windfarm and surrounding control sites, sequenced, and analyzed using a combination of DNA k-mer matching and alignment-based classification methods. We identified a wide range of species across the tree of life-highlighting the species richness of this marine ecosystem. Our results revealed a high degree of species diversity congruence between the wind farm and control sites. While this could suggest minimal ecological disruption of the wind farm, we cannot rule out that the influence of ocean currents and water mixing the DNA from different regions dominate the species detection. We detected bioindicator species, such as Thalassiosira, Phaeocystis and Skeletonema, which can provide insights into water quality. Our metagenomic approach also enabled us to obtain population genomics insights for species, such as the European anchovy (Engraulis encrasicolus) and the diatom Rhizosolenia setigera, and genetically confirmed the origin of the invasive Sea walnut (Mnemiopsis leidyi) in the North Sea. This study highlights the potential of genome-wide eDNA metagenomics as a framework for assessing marine biodiversity and detecting population-level genetic signals, contributing to informed and scalable ecosystem monitoring strategies.", "doi": "10.1038/s41598-025-01541-x", "pmid": "40368948", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12078662"}, {"db": "pii", "key": "10.1038/s41598-025-01541-x"}], "notes": [], "created": "2025-11-28T10:46:59.450Z", "modified": "2025-11-28T10:46:59.453Z"}, {"entity": "publication", "iuid": "085e2de78b514987b28baa61cb116ff1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/085e2de78b514987b28baa61cb116ff1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/085e2de78b514987b28baa61cb116ff1"}}, "title": "Combining spatial transcriptomics with tissue morphology.", "authors": [{"family": "Chelebian", "given": "Eduard", "initials": "E", "orcid": "0000-0001-6852-6605", "researcher": {"href": "https://publications.scilifelab.se/researcher/278694af6d7e499f9432c6523da24f25.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "journal article", "published": "2025-05-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "4452", "issn-l": "2041-1723"}, "abstract": "Spatial transcriptomics has transformed our understanding of tissue architecture by preserving the spatial context of gene expression patterns. Simultaneously, advances in imaging AI have enabled extraction of morphological features describing the tissue. This review introduces a framework for categorizing methods that combine spatial transcriptomics with tissue morphology, focusing on either translating or integrating morphological features into spatial transcriptomics. Translation involves using morphology to predict gene expression, creating super-resolution maps or inferring genetic information from H&E-stained samples. Integration enriches spatial transcriptomics by identifying morphological features that complement gene expression. We also explore learning strategies and future directions for this emerging field.", "doi": "10.1038/s41467-025-58989-8", "pmid": "40360467", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12075478"}, {"db": "pii", "key": "10.1038/s41467-025-58989-8"}], "notes": [], "created": "2025-11-25T12:53:04.988Z", "modified": "2025-11-25T12:53:05.109Z"}, {"entity": "publication", "iuid": "4b9d5f5ba9f349129f649f7aa810e2df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b9d5f5ba9f349129f649f7aa810e2df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b9d5f5ba9f349129f649f7aa810e2df"}}, "title": "Combining live fluorescence imaging with in situ cryoelectron tomography sheds light on the septation process in Deinococcus radiodurans.", "authors": [{"family": "Gaifas", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-4875-9422", "researcher": {"href": "https://publications.scilifelab.se/researcher/3731b54cb3d2454d8c6c478a4124f163.json"}}, {"family": "Kleman", "given": "Jean-Philippe", "initials": "JP", "orcid": "0000-0001-5648-5295", "researcher": {"href": "https://publications.scilifelab.se/researcher/a98f9d2950ea42f28404adf9da1c7c4f.json"}}, {"family": "Lacroix", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Schexnaydre", "given": "Erin", "initials": "E"}, {"family": "Trouve", "given": "Jennyfer", "initials": "J"}, {"family": "Morlot", "given": "Cecile", "initials": "C", "orcid": "0000-0002-9295-1035", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e019f1b8fbd4902a1b7b6ba589de8bc.json"}}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Gutsche", "given": "Irina", "initials": "I", "orcid": "0000-0002-1908-3921", "researcher": {"href": "https://publications.scilifelab.se/researcher/102c686796334794a80812a8fe7d7010.json"}}, {"family": "Timmins", "given": "Joanna", "initials": "J", "orcid": "0000-0002-9066-9095", "researcher": {"href": "https://publications.scilifelab.se/researcher/84f0b89fe87b4df190749ca736fd64ff.json"}}], "type": "journal article", "published": "2025-05-13", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "19", "pages": "e2425047122", "issn-l": "0027-8424"}, "abstract": "Cell division is a fundamental biological process that allows a single mother cell to produce two daughter cells. In walled bacteria, different modes of cell division have been reported that are notably associated with distinctive cell shapes. In all cases, division involves a step of septation, corresponding to the growth of a new dividing cell wall, followed by splitting of the two daughter cells. The radiation-resistant Deinococcus radiodurans is a spherical bacterium protected by a thick and unusual cell envelope. It has been reported to divide using a distinctive mode of septation in which two septa originating from opposite sides of the cell progress with a flat leading edge until meeting and fusing at mid-cell. In the present study, we have combined conventional and superresolution fluorescence microscopy of live bacteria with in situ cryogenic electron tomography of bacterial lamellae to investigate the septation process in D. radiodurans. This work provides important insight into i) the complex architecture and multilayered composition of the cell envelope of this bacterium, ii) the unusual \"sliding doors\" septation process and iii) the sequence of events and molecular mechanisms underlying septal closure, including the synthesis of a FtsZ-dependent peptidoglycan layer that rigidifies and straightens the growing septa.", "doi": "10.1073/pnas.2425047122", "pmid": "40327694", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12088418"}], "notes": [], "created": "2025-11-17T10:02:53.569Z", "modified": "2025-11-17T10:02:53.905Z"}, {"entity": "publication", "iuid": "3cc6abe50acb4e6490f16794c487bd1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3cc6abe50acb4e6490f16794c487bd1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3cc6abe50acb4e6490f16794c487bd1b"}}, "title": "Uromodulin velcro sheets and their interaction with uropathogenic E. coli", "authors": [{"family": "Banjara", "given": "Suresh", "initials": "S", "orcid": "0000-0002-2123-8101", "researcher": {"href": "https://publications.scilifelab.se/researcher/b935b5b29c77445aa2e9e4ccd76afd4c.json"}}, {"family": "Wang", "given": "Han", "initials": "H", "orcid": "0000-0002-6445-2095", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a6c888a8fa948a496030381158af8fb.json"}}, {"family": "Schaeffer", "given": "C\u00e9line", "initials": "C", "orcid": "0000-0001-5883-3951", "researcher": {"href": "https://publications.scilifelab.se/researcher/42307cb5448843d6ab2c6f449da28c57.json"}}, {"family": "Stsiapanava", "given": "Alena", "initials": "A", "orcid": "0000-0001-6560-011X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dd9089728fe4d41ab4b6db272e3ed76.json"}}, {"family": "Sandin", "given": "Sara", "initials": "S", "orcid": "0000-0001-6071-2761", "researcher": {"href": "https://publications.scilifelab.se/researcher/a52c9c37f07b465781e64958a0edb780.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Okumura", "given": "Hiroki", "initials": "H", "orcid": "0000-0001-6222-9634", "researcher": {"href": "https://publications.scilifelab.se/researcher/081a2481c86944cfbb399be7b5400620.json"}}, {"family": "Rampoldi", "given": "Luca", "initials": "L", "orcid": "0000-0002-0544-7042", "researcher": {"href": "https://publications.scilifelab.se/researcher/e09ff90439784c1f81cf41b93e9fcede.json"}}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Jovine", "given": "Luca", "initials": "L", "orcid": "0000-0002-2679-6946", "researcher": {"href": "https://publications.scilifelab.se/researcher/8507a7657f6b434ebc572453aa172b1e.json"}}], "type": "posted-content", "published": "2025-05-11", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.05.09.653020", "pmid": null, "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-17T11:19:47.083Z", "modified": "2025-12-18T19:16:01.842Z"}, {"entity": "publication", "iuid": "9f220d0577d84d8fa3e6281e3aa1f84d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f220d0577d84d8fa3e6281e3aa1f84d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f220d0577d84d8fa3e6281e3aa1f84d"}}, "title": "Maternal asthma and newborn DNA methylation.", "authors": [{"family": "Pedersen", "given": "Casper-Emil Tingskov", "initials": "CT"}, {"family": "Hoang", "given": "Thanh T", "initials": "TT"}, {"family": "Jin", "given": "Jianping", "initials": "J"}, {"family": "Starnawska", "given": "Anna", "initials": "A"}, {"family": "Granell", "given": "Raquel", "initials": "R"}, {"family": "Elliott", "given": "Hannah R", "initials": "HR"}, {"family": "Huels", "given": "Anke", "initials": "A"}, {"family": "Zar", "given": "Heather J", "initials": "HJ"}, {"family": "Stein", "given": "Dan J", "initials": "DJ"}, {"family": "Zhang", "given": "Yining", "initials": "Y"}, {"family": "Dekker", "given": "Herman T den", "initials": "HTD"}, {"family": "Duijts", "given": "Liesbeth", "initials": "L"}, {"family": "Felix", "given": "Janine F", "initials": "JF"}, {"family": "Sang\u00fcesa", "given": "J\u00falia", "initials": "J"}, {"family": "Bustamante", "given": "Mariona", "initials": "M"}, {"family": "Casas", "given": "Maribel", "initials": "M"}, {"family": "Vrijheid", "given": "Martine", "initials": "M"}, {"family": "Kadalayil", "given": "Latha", "initials": "L"}, {"family": "Rezwan", "given": "Faisal I", "initials": "FI"}, {"family": "Arshad", "given": "Hasan", "initials": "H"}, {"family": "Holloway", "given": "John W", "initials": "JW"}, {"family": "R\u00f6der", "given": "Stefan", "initials": "S"}, {"family": "Zenclussen", "given": "Ana C", "initials": "AC"}, {"family": "Herberth", "given": "Gunda", "initials": "G"}, {"family": "Staunstrup", "given": "Nicklas Heine", "initials": "NH"}, {"family": "Horsdal", "given": "Henriette Thisted", "initials": "HT"}, {"family": "Mill", "given": "Jonathan", "initials": "J"}, {"family": "Hannon", "given": "Eilis", "initials": "E"}, {"family": "iPSYCH-MINERvA Group", "given": "", "initials": ""}, {"family": "Annesi-Maesano", "given": "Isabella", "initials": "I"}, {"family": "Pesce", "given": "Giancarlo", "initials": "G"}, {"family": "Ba\u00efz", "given": "Nour", "initials": "N"}, {"family": "Heude", "given": "Barbara", "initials": "B"}, {"family": "Hosseinian-Mohazzab", "given": "Sahra", "initials": "S"}, {"family": "Breton", "given": "Carrie V", "initials": "CV"}, {"family": "Harlid", "given": "Sophia", "initials": "S"}, {"family": "Harbs", "given": "Justin", "initials": "J"}, {"family": "Domellof", "given": "Magnus", "initials": "M"}, {"family": "West", "given": "Christina", "initials": "C"}, {"family": "Yeung", "given": "Edwina", "initials": "E"}, {"family": "Zeng", "given": "Xuehuo", "initials": "X"}, {"family": "Nystad", "given": "Wenche", "initials": "W"}, {"family": "H\u00e5berg", "given": "Siri E", "initials": "SE"}, {"family": "Magnus", "given": "Maria C", "initials": "MC"}, {"family": "Schendel", "given": "Diana", "initials": "D"}, {"family": "London", "given": "Stephanie J", "initials": "SJ"}, {"family": "B\u00f8nnelykke", "given": "Klaus", "initials": "K"}], "type": "journal article", "published": "2025-05-10", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "17", "issue": "1", "pages": "79", "issn-l": "1868-7075"}, "abstract": "Prenatal exposure to maternal asthma may influence DNA methylation patterns in offspring, potentially affecting their susceptibility to later diseases including asthma.\n\nTo investigate the relationship between parental asthma and newborn blood DNA methylation.\n\nEpigenome-wide association analyses were conducted in 13 cohorts on 7433 newborns with blood methylation data from the Illumina450K or EPIC array. We used fixed effects meta-analyses to identify differentially methylated CpGs (DMCs) and comb-p to identify differentially methylated regions (DMRs) associated with maternal asthma during pregnancy and maternal asthma ever. Paternal asthma was analyzed for comparison. Models were adjusted for covariates and cell-type composition. We examined whether implicated sites related to gene expression analyses in publicly available data for childhood blood and adult lung.\n\nWe identified 27 CpGs associated with maternal asthma during pregnancy at False Discovery Rate < 0.05 but none for maternal asthma ever. Two distinct CpGs were associated with paternal asthma. We observed 5 DMRs associated with maternal asthma during pregnancy 3 associated with maternal asthma ever and 13 DMRs associated with paternal asthma. Gene expression analysis using data in blood from 832 children and lung from 424 adults showed associations between identified DMCs using maternal asthma and expression of several genes, including HLA genes and HOXA5, previously implicated in asthma or lung function.\n\nParental asthma, especially maternal asthma during pregnancy, may be associated with alterations in newborn DNA methylation. These findings might shed light on underlying mechanisms for asthma susceptibility.", "doi": "10.1186/s13148-025-01858-4", "pmid": "40349045", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12065361"}, {"db": "pii", "key": "10.1186/s13148-025-01858-4"}], "notes": [], "created": "2025-09-08T07:15:22.753Z", "modified": "2025-09-08T07:15:22.764Z"}, {"entity": "publication", "iuid": "9a52b50c972046afbff879afeac9c5ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a52b50c972046afbff879afeac9c5ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a52b50c972046afbff879afeac9c5ee"}}, "title": "Streamlining Multiplexed Tissue Image Analysis with PIP\u03a3X: An Integrated Automated Pipeline for Image Processing and EXploration for Diverse Tissue Types.", "authors": [{"family": "Mardamshina", "given": "Mariya", "initials": "M", "orcid": "0000-0003-0066-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff68d3499c01447b8a48d99b86bd882b.json"}}, {"family": "Navarro", "given": "Frederic Ballllosera", "initials": "FB", "orcid": "0009-0004-0874-9662", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc5ff0811c24659833fe10c7ec2ac8f.json"}}, {"family": "Casals", "given": "Anna Martinez", "initials": "AM", "orcid": "0000-0003-2722-1965", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa27c4c76374453ba3ffe7eafff4b9a.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2025-05-09", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Spatial proteomics via multiplexed tissue imaging is transforming how we study biology, enabling researchers to investigate dozens of markers in a single tissue section and explore how cells behave in their native habitat. While imaging technologies have advanced rapidly, data analyses remain a bottleneck. To address this, we developed PIP\u03a3X (Pipeline for Image Processing and EXploration), a user-friendly, end-to-end open-source software designed to make complex image analysis approachable, even for those with little or no programming skills. PIP\u03a3X combines robust automation with an intuitive graphical user interface, guiding users through each step of the analysis, from image preprocessing and membrane-aware cell segmentation to signal quantification and spatial data exploration. Each feature includes built-in explanations, recommendations, and quality controls to help users make confident choices throughout the process. PIP\u03a3X is compatible with a wide range of multiplexed imaging platforms, and its outputs integrate seamlessly with visualization tools like TissUUmaps and QuPath. Also, it supports downstream applications by enabling direct export of selected cell coordinates for laser microdissection. This functionality facilitates precise isolation of target cell populations for deep proteomic or transcriptomic profiling. With PIP\u03a3X, researchers can extract meaningful biological insights from multiplexed images more easily and robustly, helping to bridge the gap between powerful imaging technologies and real-world scientific discovery.", "doi": "10.1101/2025.05.04.652145", "pmid": "40654620", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12247667"}, {"db": "pii", "key": "2025.05.04.652145"}], "notes": [], "created": "2025-11-25T12:57:48.206Z", "modified": "2025-11-25T12:57:48.395Z"}, {"entity": "publication", "iuid": "313624c3b36d4a3d8322a45a9a99729e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/313624c3b36d4a3d8322a45a9a99729e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/313624c3b36d4a3d8322a45a9a99729e"}}, "title": "Open-flask, ambient temperature direct arylation synthesis of mixed ionic-electronic conductors", "authors": [{"family": "Kimpel", "given": "Joost", "initials": "J", "orcid": "0000-0002-3576-6132", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c64c9e6e6c84e848cde84461fb55d24.json"}}, {"family": "Kim", "given": "Youngseok", "initials": "Y", "orcid": "0000-0002-9584-821X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4046f508d954f36a6c938aa94a454ca.json"}}, {"family": "Schomaker", "given": "Hannes", "initials": "H"}, {"family": "Hinojosa", "given": "Diego R", "initials": "DR", "orcid": "0000-0002-4849-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2bafd0c86f44253856168aedff62ca2.json"}}, {"family": "Asatryan", "given": "Jesika", "initials": "J", "orcid": "0000-0002-8504-1332", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf89c915fd474fe1937f91d6042e0a08.json"}}, {"family": "Mart\u00edn", "given": "Jaime", "initials": "J"}, {"family": "Kroon", "given": "Renee", "initials": "R", "orcid": "0000-0001-8053-4288", "researcher": {"href": "https://publications.scilifelab.se/researcher/26f7dc50e9284f87ad913e893f14e69e.json"}}, {"family": "Sommer", "given": "Michael", "initials": "M", "orcid": "0000-0002-2377-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c0656ed9bca4ea28c9810b08ee61d64.json"}}, {"family": "M\u00fcller", "given": "Christian", "initials": "C", "orcid": "0000-0001-7859-7909", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fc06198eb0c4a3eb17d052d8ef124ae.json"}}], "type": "journal-article", "published": "2025-05-09", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "19", "issn-l": "2375-2548"}, "abstract": null, "doi": "10.1126/sciadv.adv8168", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:06:19.926Z", "modified": "2025-11-27T08:06:20.867Z"}, {"entity": "publication", "iuid": "61c0fa23525e49e1bab7b0fa7910bbfa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61c0fa23525e49e1bab7b0fa7910bbfa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61c0fa23525e49e1bab7b0fa7910bbfa"}}, "title": "Multiplex quantification of endocrine proteins in volumetric dried blood spots.", "authors": [{"family": "Stauch", "given": "William", "initials": "W"}, {"family": "Olausson", "given": "Johan", "initials": "J"}, {"family": "Bendes", "given": "Annika", "initials": "A"}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM"}], "type": "journal article", "published": "2025-05-09", "journal": {"title": "Clin Proteomics", "issn": "1542-6416", "volume": "22", "issue": "1", "pages": "18", "issn-l": null}, "abstract": "Circulating proteins are routinely quantified from liquid biopsies to deduce health and disease. Among these are endocrine protein hormones, which regulate human growth, development, metabolism, and reproduction. Most commonly, these proteins are analyzed in plasma or serum prepared from venous blood draws. Recently, devices for quantitative capillary sampling from a finger prick have emerged, but their utility for clinical testing remains to be explored.\n\nTo study the analytical capabilities of quantitative dried blood spots (qDBS), we quantified the luteinizing hormone subunit beta (LHB), follicle-stimulating hormone subunit beta (FSHB), thyroid-stimulating hormone subunit beta (TSHB), prolactin (PRL), and growth hormone 1 (GH1) by multiplexed immunoassays. We determined the performance of the endocrine hormone assays in paired qDBS and EDTA plasma samples from 100 donors (90% females) aged 4 to 78. Lastly, we compared the protein levels with those from an accredited clinical chemistry laboratory.\n\nThe multiplexed analysis showed precise protein quantifications in qDBS (mean CV = 8.3%), high concordance with plasma levels (r = 0.88 to 0.99), and accuracy being matrix- and protein-dependent (recovery: 80-225%). Using the current protocol and sample dilutions, reported protein concentrations were 1.2 to 7.5 times higher in plasma than in qDBS eluates. Concentrations from multiplexed plasma assays agreed with the clinical data (r = 0.87 to 0.99) and decreased slightly when comparing clinical plasma data with multiplexed qDBS assays (r = 0.76 to 0.98). Significant increases in age-related FSHB and LHB levels were observed in females in all specimens and assays (p < 0.01).\n\nThis study shows the suitability of modern qDBS devices for quantifying clinically informative proteins in multiplexed assays and highlights the need for future work on specimen-specific optimization and standards. Volumetric DBS sampling offers new routines for accurate protein quantification for precision medicine.", "doi": "10.1186/s12014-025-09539-3", "pmid": "40346485", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12063380"}, {"db": "pii", "key": "10.1186/s12014-025-09539-3"}], "notes": [], "created": "2025-11-07T14:11:28.396Z", "modified": "2025-11-07T14:11:28.402Z"}, {"entity": "publication", "iuid": "188369759b0648d5ae25d06f97ae8ef1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/188369759b0648d5ae25d06f97ae8ef1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/188369759b0648d5ae25d06f97ae8ef1"}}, "title": "CpG island methylator phenotype classification improves risk assessment in pediatric T-cell acute lymphoblastic leukemia.", "authors": [{"family": "Sch\u00e4fer Hackenhaar", "given": "Fernanda", "initials": "F", "orcid": "0000-0002-9395-2216", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ac3981903a34a4d855647822d5339d1.json"}}, {"family": "Refhagen", "given": "Nina", "initials": "N"}, {"family": "Hagleitner", "given": "Melanie", "initials": "M"}, {"family": "van Leeuwen", "given": "Frank", "initials": "F", "orcid": "0000-0003-1107-6513", "researcher": {"href": "https://publications.scilifelab.se/researcher/97425d5c32d14c86b3b8414b24f6a387.json"}}, {"family": "Marquart", "given": "Hanne Vibeke", "initials": "HV", "orcid": "0000-0001-9740-6522", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9476b7116154ea9990d7c61c675c794.json"}}, {"family": "Madsen", "given": "Hans Ole", "initials": "HO"}, {"family": "Landfors", "given": "Mattias", "initials": "M", "orcid": "0000-0003-3974-4245", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e2393ca69324818ac8bcb976da908be.json"}}, {"family": "Osterman", "given": "Pia", "initials": "P"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Flaegstad", "given": "Trond", "initials": "T"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur", "initials": "\u00d3"}, {"family": "Kanerva", "given": "Jukka", "initials": "J"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Heyman", "given": "Mats", "initials": "M", "orcid": "0000-0001-7637-1949", "researcher": {"href": "https://publications.scilifelab.se/researcher/d810139e533a4c2493e62b3e03bb9623.json"}}, {"family": "Nor\u00e9n Nystr\u00f6m", "given": "Ulrika", "initials": "U", "orcid": "0000-0001-5606-5442", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f7a89bc35d4e72b4b2c0d4252b69f0.json"}}, {"family": "Hultdin", "given": "Magnus", "initials": "M"}, {"family": "Degerman", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2783-0712", "researcher": {"href": "https://publications.scilifelab.se/researcher/8611162e883645f59195c4221199967f.json"}}], "type": "journal article", "published": "2025-05-08", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "145", "issue": "19", "pages": "2161-2178", "issn-l": "0006-4971"}, "abstract": "Current intensive treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has substantial side effects, highlighting a need for novel biomarkers to improve risk stratification. Canonical biomarkers, such as genetics and immunophenotype, are largely not used in pediatric T-ALL stratification. This study aimed to validate the prognostic relevance of DNA methylation CpG island methylator phenotype (CIMP) risk stratification in 2 pediatric T-ALL patient cohorts: the Nordic Society of Paediatric Haematology (NOPHO) ALL2008 T-ALL study cohort (n = 192) and the Dutch Childhood Oncology Group (DCOG) ALL-10/ALL-11 validation cohorts (n = 156). Both cohorts revealed that combining CIMP classification at diagnosis with measurable residual disease (MRD) at treatment day 29 (D29) or 33 (D33) significantly improved outcome prediction. The poor prognosis subgroup, characterized by CIMP low/D29 or D33 MRD \u2265 0.1%, had a cumulative incidence of relapse (pCIR5yr) of 29% and 23% and overall survival (pOS5yr) of 59.7% and 65.4%, in NOPHO and DCOG, respectively. Conversely, a good prognosis subgroup was also identified representing CIMP high/D29 or D33 MRD < 0.1% with pCIR5yr of 0% and 3.4% and pOS5yr of 98.2% and 94.8%, in NOPHO and DCOG, respectively. For NOPHO, MRD was also evaluated on D15, and the relapse prediction accuracy of CIMP/D29 MRD (0.79) and CIMP/D15 MRD (0.75) classification was comparable, indicating potential for earlier stratification. The evaluation of the biology behind the CIMP subgroups revealed associations with transcriptome profiles, genomic aberrations, and mitotic history, suggesting distinct routes for leukemia development. In conclusion, integrating MRD assessment with the novel CIMP biomarker has the potential to improve risk stratification in pediatric T-ALL and guide future therapeutic decisions.", "doi": "10.1182/blood.2024026027", "pmid": "39841000", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "535228"}], "notes": [], "created": "2025-05-12T06:17:29.072Z", "modified": "2025-05-12T06:17:30.354Z"}, {"entity": "publication", "iuid": "00a31f576c644716af0aa708f1dee11c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00a31f576c644716af0aa708f1dee11c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00a31f576c644716af0aa708f1dee11c"}}, "title": "Challenging the \"Undruggable\"\u2500Targeting STAT3 but Identifying Potent TrkA-Targeted Inhibitors.", "authors": [{"family": "Iliev", "given": "Petar", "initials": "P"}, {"family": "McCutcheon", "given": "Conall", "initials": "C"}, {"family": "Admas", "given": "Tizita H", "initials": "TH"}, {"family": "Reithmeier", "given": "Anja", "initials": "A"}, {"family": "Lopez McDonald", "given": "Melanie", "initials": "M"}, {"family": "van Outryve", "given": "Alexandre", "initials": "A"}, {"family": "Hanke", "given": "Danielle", "initials": "D"}, {"family": "Brown", "given": "Jennifer I", "initials": "JI"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "Toillon", "given": "Robert-Alain", "initials": "R"}, {"family": "Frank", "given": "David A", "initials": "DA", "orcid": "0000-0002-7698-8364", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7a0375f5f3b4b35ae27da2ac34cbaf5.json"}}, {"family": "Page", "given": "Brent D G", "initials": "BDG", "orcid": "0000-0002-2101-1329", "researcher": {"href": "https://publications.scilifelab.se/researcher/87dde8251a714d26b3b7cc045b47061f.json"}}], "type": "journal article", "published": "2025-05-08", "journal": {"title": "J. Med. Chem.", "issn": "1520-4804", "issn-l": "0022-2623", "volume": "68", "issue": "9", "pages": "9501-9524"}, "abstract": "Signal transducer and activator of transcription 3 (STAT3) is a promising yet challenging anticancer drug target due to its complex signaling and limited \"druggability\". To this end, we herein highlight a target engagement-focused screening and optimization pipeline pursuing the discovery of novel STAT3 inhibitors. From a STAT3 differential scanning fluorimetry high-throughput screen, we identified compounds that appeared to stabilize STAT3 toward thermal aggregation and moderately inhibited cellular STAT3 activity. Subsequent evaluation using complementary and orthogonal assays revealed their high affinity for tropomyosin receptor kinase A (TrkA). Applying a similar target engagement-inspired approach, we refined inhibitor binding and selectivity toward TrkA, showing efficacy in cellular TrkA cancer models. Top compound, PI-15, demonstrated successful target engagement in a cellular thermal shift assay and potently inhibited TrkA activity in cancer cells. These approaches highlight the importance of prioritizing rigorous target engagement validation early in the drug discovery pipeline, resulting in promising new inhibitors.", "doi": "10.1021/acs.jmedchem.5c00214", "pmid": "40245441", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-04-22T08:44:53.004Z", "modified": "2025-11-25T11:33:45.515Z"}, {"entity": "publication", "iuid": "8c6967586d3c4def943eaead301e16a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c6967586d3c4def943eaead301e16a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c6967586d3c4def943eaead301e16a6"}}, "title": "Anti-integrin \u03b1v\u03b26 IgG antibody as a diagnostic and prognostic marker in ulcerative colitis: A cross-sectional and longitudinal study defining a specific disease phenotype.", "authors": [{"family": "Pertsinidou", "given": "Eleftheria", "initials": "E", "orcid": "0000-0002-8492-4045", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2d82952fdfe4adfbf152907224cac6a.json"}}, {"family": "Salomon", "given": "Benita", "initials": "B", "orcid": "0009-0002-8951-9839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0b9a6d679bd49e9bc9aa042d46d09c2.json"}}, {"family": "Bergemalm", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1906-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50a7ccd948a492f900b8d44d5fc7f3b.json"}}, {"family": "Salihovic", "given": "Samira", "initials": "S", "orcid": "0000-0001-5752-4196", "researcher": {"href": "https://publications.scilifelab.se/researcher/df1fba46be0541838544241a1e5aeeed.json"}}, {"family": "Hedin", "given": "Charlotte R H", "initials": "CRH", "orcid": "0000-0002-4921-8516", "researcher": {"href": "https://publications.scilifelab.se/researcher/d451be670f7f456ebca935690af79076.json"}}, {"family": "Ling Lundstr\u00f6m", "given": "Maria", "initials": "M", "orcid": "0000-0001-5518-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9c830b64f10403896bf3fd32c8e0afc.json"}}, {"family": "Keita", "given": "\u00c5sa V", "initials": "\u00c5V", "orcid": "0000-0002-6820-0215", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f0a7516d7104295be67073e6d5c04af.json"}}, {"family": "Magnusson", "given": "Maria K", "initials": "MK", "orcid": "0000-0002-8888-4968", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa4ee61498234362819679d3c13745a3.json"}}, {"family": "Eriksson", "given": "Carl", "initials": "C", "orcid": "0000-0002-1046-383X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf81d9aaa93645ae91dc40ebe9151b0d.json"}}, {"family": "Bengtson", "given": "May-Bente", "initials": "MB", "orcid": "0000-0002-5615-7141", "researcher": {"href": "https://publications.scilifelab.se/researcher/bae2f822ebea4830a0222ea80e16abd4.json"}}, {"family": "Gr\u00e4nn\u00f6", "given": "Olle", "initials": "O", "orcid": "0000-0002-4329-1659", "researcher": {"href": "https://publications.scilifelab.se/researcher/927332e01b4f44bbb588b3e52ddbd9af.json"}}, {"family": "Aabrekk", "given": "Tone B", "initials": "TB"}, {"family": "Mov\u00e9rare", "given": "Robert", "initials": "R", "orcid": "0000-0001-6611-5036", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef0011b9d8494f2694be45235a3dcc5f.json"}}, {"family": "Rydell", "given": "Niclas", "initials": "N", "orcid": "0000-0001-5661-1343", "researcher": {"href": "https://publications.scilifelab.se/researcher/23740102f75e4bde928938135eee6a08.json"}}, {"family": "Ekoff", "given": "Helena", "initials": "H", "orcid": "0000-0002-9746-114X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd1fd7f42ee44dcc86abe80f4877d89c.json"}}, {"family": "R\u00f6nnelid", "given": "Johan", "initials": "J", "orcid": "0000-0003-1186-3226", "researcher": {"href": "https://publications.scilifelab.se/researcher/25d1ba81c51a4bca974e84c9ea117cbe.json"}}, {"family": "BIO-IBD consortium\n", "given": "", "initials": ""}, {"family": "D'Amato", "given": "Mauro", "initials": "M", "orcid": "0000-0003-2743-5197", "researcher": {"href": "https://publications.scilifelab.se/researcher/538f828b3e61418fad903e0184c545cd.json"}}, {"family": "Detlie", "given": "Trond E", "initials": "TE", "orcid": "0000-0002-1576-5298", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd4da2d237d418cbf2b33851424fac6.json"}}, {"family": "Huppertz-Hauss", "given": "Gert", "initials": "G", "orcid": "0000-0002-5693-8773", "researcher": {"href": "https://publications.scilifelab.se/researcher/98caba3288924613b0a082f77783b174.json"}}, {"family": "Opheim", "given": "Randi", "initials": "R", "orcid": "0000-0002-0513-1435", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba159aa19a24409b8581a3f07af9943.json"}}, {"family": "Ricanek", "given": "Petr", "initials": "P", "orcid": "0000-0003-2454-7388", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d60d0651fa645189b12695cff6686cd.json"}}, {"family": "Kristensen", "given": "Vendel A", "initials": "VA", "orcid": "0000-0002-0876-8634", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ae40659dd99447f9b445b650d6890e5.json"}}, {"family": "\u00d6hman", "given": "Lena", "initials": "L", "orcid": "0000-0001-8142-2106", "researcher": {"href": "https://publications.scilifelab.se/researcher/79239c8719b24eba951c4e1702952d5e.json"}}, {"family": "S\u00f6derholm", "given": "Johan D", "initials": "JD", "orcid": "0000-0002-3250-5367", "researcher": {"href": "https://publications.scilifelab.se/researcher/24c3e1f92a7449caa5db6e47e9d7bca7.json"}}, {"family": "Kruse", "given": "Robert", "initials": "R", "orcid": "0000-0003-1785-8540", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad3ea1c83bcf4ee0b7f1af08206f8c9a.json"}}, {"family": "Lindqvist", "given": "Carl M", "initials": "CM", "orcid": "0000-0003-3887-9519", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc425582c7134cfaa889ad4fd117a573.json"}}, {"family": "Carlson", "given": "Marie", "initials": "M", "orcid": "0000-0002-3762-8489", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e51ed20d984b688456dd957e1eda32.json"}}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "H\u00f8ivik", "given": "Marte L", "initials": "ML", "orcid": "0000-0002-0104-465X", "researcher": {"href": "https://publications.scilifelab.se/researcher/874d02c909b44d88bafd0f3ee8b8d945.json"}}, {"family": "Halfvarson", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0122-7234", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c18b8a6cc54dfa8ad14b0c97261bfa.json"}}], "type": "journal article", "published": "2025-05-08", "journal": {"title": "J Crohns Colitis", "issn": "1876-4479", "volume": "19", "issue": "5", "issn-l": null}, "abstract": "The diagnostic and prognostic properties of anti-integrin \u03b1v\u03b26 immunoglobulin G (IgG) autoantibodies in ulcerative colitis (UC) are poorly understood. We aimed to assess the diagnostic performance of anti-integrin \u03b1v\u03b26 autoantibodies and examine their association with disease outcomes.\n\nSerum samples from a Swedish inception cohort of patients with suspected inflammatory bowel disease (IBD, n = 473) were analyzed using an in-house fluorescence enzyme immunoassay based on EliA technology. Findings were validated in a Norwegian population-based inception cohort (n = 570). Diagnostic performance was assessed by calculating the area under the curve (AUC) with 95% confidence intervals and determining sensitivity and specificity. Reclassification was evaluated using the net reclassification index.\n\nIn the discovery cohort, patients with UC, IBD-unclassified, or colonic Crohn's disease exhibited higher median autoantibody levels compared to symptomatic and healthy controls. In the validation cohort, the autoantibody demonstrated 79% sensitivity and 94% specificity for UC vs symptomatic controls at a cut-off of 400 UA/l. Its diagnostic performance (AUC = 0.92, 95% CI, 0.89-0.95) was superior to hs-CRP (AUC = 0.65, 95% CI, 0.60-0.70, P < .001) and faecal calprotectin (fcalpro) (AUC = 0.88, 95% CI, 0.84-0.92, P = .09). Combining the autoantibody with fcalpro further improved diagnostic accuracy (AUC = 0.97, 95% CI, 0.95-0.98) and patient reclassification (P < .001). Autoantibody positivity was associated with a severe phenotype of UC, characterised by increased inflammatory activity and higher IL-17A and granzyme B levels. Higher autoantibody levels were linked to an aggressive disease course, remaining stable in aggressive UC but decreasing in indolent disease (P = .003).\n\nAnti-integrin \u03b1v\u03b26 is a reliable diagnostic and prognostic marker for UC, with potential clinical implementation.", "doi": "10.1093/ecco-jcc/jjaf062", "pmid": "40251889", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12086997"}, {"db": "pii", "key": "8116397"}], "notes": [], "created": "2025-11-25T19:22:40.889Z", "modified": "2025-11-25T19:22:42.026Z"}, {"entity": "publication", "iuid": "592bb323bd1c4346b9df99f55f08eb97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/592bb323bd1c4346b9df99f55f08eb97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/592bb323bd1c4346b9df99f55f08eb97"}}, "title": "Elucidation of short linear motif-based interactions of the MIT and rhodanese domains of the ubiquitin-specific protease 8.", "authors": [{"family": "Konstantinou", "given": "Aimiliani", "initials": "A"}, {"family": "Varga", "given": "Julia K", "initials": "JK"}, {"family": "C\u00f3rdova-P\u00e9rez", "given": "Alicia", "initials": "A"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Gomez-Lucas", "given": "Lidia", "initials": "L"}, {"family": "Schueler-Furman", "given": "Ora", "initials": "O"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "Kulathu", "given": "Yogesh", "initials": "Y"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}], "type": "journal article", "published": "2025-05-06", "journal": {"title": "Biol. Direct", "issn": "1745-6150", "volume": "20", "issue": "1", "pages": "59", "issn-l": "1745-6150"}, "abstract": "Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme with essential functions in protein trafficking and stability. It is a multidomain protein, with an N-terminal MIT (microtubule interacting and trafficking) domain, followed by a non-catalytic rhodanese (Rhod) domain, a long intrinsically disordered region, and a C-terminal catalytic domain. The N-terminal MIT domain of USP8 is known to mediate protein-protein interactions through binding to short linear motifs. The non-catalytic Rhod domain is also involved in protein-protein interactions, however detailed insights into these interactions remain limited. In this study we explore the short linear motif-based interactions of the MIT and Rhod domains of USP8 using a combination of proteomic peptide-phage display, peptide arrays and deep mutational scanning. We show that the MIT domain can bind ligands with a general [DE][LIF]x{2,3}R[FYIL]xxL[LV] consensus motif. We uncover that the rhodanese domain of USP8 is a peptide-binding domain, and define two distinct binding motifs (Rx[LI]xGxxxPxxL and G[LV][DE][IM]WExKxxxLxE) for this domain by deep mutational scanning of two different peptide ligands. Using the motif information, we predict binding sites within known USP8 interactors and substrates and validate interactions through peptide array analysis. Our findings demonstrate that both the USP8 MIT and rhodanese domains are peptide-binding domains that can be bound by degenerate and distinct binding motifs. The detailed information on the peptide binding preference of the two N-terminal domains of USP8 provide novel insights into the molecular recognition events that underlie the function of this essential deubiquitinating enzyme.", "doi": "10.1186/s13062-025-00638-7", "pmid": "40329301", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12057046"}, {"db": "pii", "key": "10.1186/s13062-025-00638-7"}], "notes": [], "created": "2025-09-08T11:30:02.875Z", "modified": "2025-09-08T11:30:02.896Z"}, {"entity": "publication", "iuid": "b4b525d6233c4b08b95c7e458b774907", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4b525d6233c4b08b95c7e458b774907.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4b525d6233c4b08b95c7e458b774907"}}, "title": "Sleeping for two: a cross-sectional study on associations between objectively measured sleep during early to mid-pregnancy and maternal and fetal outcomes and inflammatory biomarker profiles.", "authors": [{"family": "Macdonald", "given": "Caitlin", "initials": "C"}, {"family": "Pitsillos", "given": "Tryfonas", "initials": "T"}, {"family": "Wikstr\u00f6m", "given": "Anna-Karin", "initials": "AK"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}, {"family": "Meerlo", "given": "Peter", "initials": "P"}, {"family": "Olivier", "given": "Jocelien", "initials": "J"}, {"family": "Prins", "given": "Jelmer", "initials": "J"}, {"family": "Poromaa", "given": "Inger Sundstr\u00f6m", "initials": "IS"}, {"family": "Kallak", "given": "Theodora Kunovac", "initials": "TK"}], "type": "journal article", "published": "2025-05-05", "journal": {"title": "BMC Pregnancy Childbirth", "issn": "1471-2393", "volume": "25", "issue": "1", "pages": "533", "issn-l": null}, "abstract": "Pregnant women often experience subjective sleep disturbances shown to be associated with maternal and fetal outcomes. However, subjectively experienced sleep often deviates from objective measurements. Therefore, the aim of this study was to explore the relationship between objectively measured sleep in early to mid-pregnancy and maternal and fetal outcomes and inflammatory biomarkers.\n\nA total of 1,610 pregnant women aged 18 or older from the Safe Physical Activity in Pregnancy (SPAP) study were recruited during early (week 10-14) to mid-pregnancy (week 16-19). Blood samples were taken and sleep was monitored using an Actiwatch, tracking total sleep time, sleep efficiency, wake after sleep onset, and sleep onset latency for 7 days in early to mid-pregnancy. A combined sleep categorisation was created using total sleep time and sleep efficiency to categorise participants into three sleep quality groups: Good, Intermediate, and Poor. Maternal and fetal outcomes were collected via questionnaires, medical records, and plasma samples were analysed using the Olink cardiovascular paneI Il (n = 407).\n\nA total of 1,444 participants were included. The women were categorized as good sleepers (50.4%), intermediate (32.6%), or poor sleepers (17.0%) based on the distribution of the participant's sleep parameters. Poor sleep was more common in women born outside Europe, those with higher pre-gestational BMI, and those with pre-pregnancy diabetes. Sleep groups did not differ in metabolic factors. Poor sleep was associated with an increased likelihood of requiring an emergency caesarean section (AOR = 1.86, 95% CI 1.13-3.05). No significant associations were found for other outcomes such as pre-eclampsia, premature birth, small for gestational age etc. Nine inflammatory biomarkers were significantly lower in poor sleepers, while one marker was higher.\n\nPoor sleep in early to mid-pregnancy was more common in pregnant women with pre-pregnancy diabetes, obesity, and those born outside of Europe. Poor sleep was associated with a higher likelihood of emergency caesarean section, but no other maternal or fetal outcomes. An overall trend was observed towards lower levels of inflammatory markers in women that slept poorly; however, additional studies are needed to better understand the immune system's role in the relationship between sleep, maternal health, and maternal and fetal outcomes. Possible mechanisms underlying these associations warrant further research.", "doi": "10.1186/s12884-025-07634-9", "pmid": "40325393", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12054240"}, {"db": "pii", "key": "10.1186/s12884-025-07634-9"}], "notes": [], "created": "2025-11-25T19:22:36.417Z", "modified": "2025-11-25T19:22:36.460Z"}, {"entity": "publication", "iuid": "dfca2e28bc7947fdad65ae9bd1ac974e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfca2e28bc7947fdad65ae9bd1ac974e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfca2e28bc7947fdad65ae9bd1ac974e"}}, "title": "Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease.", "authors": [{"family": "Barba-Reyes", "given": "Juan M", "initials": "JM"}, {"family": "Harder", "given": "Lisbeth", "initials": "L"}, {"family": "Marco Salas", "given": "Sergio", "initials": "S"}, {"family": "Jaisa-Aad", "given": "Methasit", "initials": "M"}, {"family": "Mu\u00f1oz-Castro", "given": "Clara", "initials": "C"}, {"family": "Garma", "given": "Leonardo D", "initials": "LD"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Hyman", "given": "Bradley T", "initials": "BT"}, {"family": "Serrano-Pozo", "given": "Alberto", "initials": "A"}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana B", "initials": "AB"}], "type": "journal article", "published": "2025-05-05", "journal": {"title": "Acta Neuropathol.", "issn": "1432-0533", "volume": "149", "issue": "1", "pages": "46", "issn-l": "0001-6322"}, "abstract": "Oligodendroglia are the responsible cells for myelination in the central nervous system and their involvement in Parkinson's disease (PD) is poorly understood. We performed sn-RNA-seq and image-based spatial transcriptomics of human caudate nucleus and putamen (dorsal striatum) from PD and control brain donors to elucidate the diversity of oligodendroglia and how they are affected by the disease. We profiled a total of ~ 200.000 oligodendroglial nuclei, defining 15 subclasses, from precursor to mature cells, 4 of which are disease-associated. These PD-specific populations are characterized by the overexpression of heat shock proteins, as well as distinct expression signatures related to immune responses, myelination alterations, and disrupted cell signaling pathways. We have also identified impairments in cell communication and oligodendrocyte development, evidenced by changes in neurotransmitter receptors expression and cell adhesion molecules. In addition, we observed significant disruptions in oligodendrocyte development, with aberrant differentiation trajectories and shifts in cell proportions, particularly in the transition from mature oligodendrocytes to disease-associated states. Quantitative immunohistochemical analysis revealed decreased myelin levels in the PD striatum, which correlated with transcriptomic alterations. Furthermore, spatial transcriptomics mapping revealed the distinct localization of disease-associated populations within the striatum, with evidence of impaired myelin integrity. Thus, we uncover oligodendroglia as a critical cell type in PD and a potential new therapeutic target for myelin-based interventions.", "doi": "10.1007/s00401-025-02884-5", "pmid": "40323467", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12053221"}, {"db": "pii", "key": "10.1007/s00401-025-02884-5"}], "notes": [], "created": "2025-11-19T08:34:23.054Z", "modified": "2025-11-28T06:50:44.043Z"}, {"entity": "publication", "iuid": "91178b96e4634225bca3796acbab2508", "links": {"self": {"href": "https://publications.scilifelab.se/publication/91178b96e4634225bca3796acbab2508.json"}, "display": {"href": "https://publications.scilifelab.se/publication/91178b96e4634225bca3796acbab2508"}}, "title": "Maintaining the Integral Membrane Proteome: Revisiting the Functional Repertoire of Integral Membrane Proteases", "authors": [{"family": "Freml\u00e9n", "given": "Hannah", "initials": "H"}, {"family": "Burmann", "given": "Bj\u00f6rn M", "initials": "BM", "orcid": "0000-0002-3135-7964", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a6d61fc1a64677874973c3247b1eb4.json"}}], "type": "journal-article", "published": "2025-05-05", "journal": {"title": "ChemBioChem", "issn": "1439-4227", "volume": "26", "issue": "9", "issn-l": null}, "abstract": null, "doi": "10.1002/cbic.202500048", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:02:41.576Z", "modified": "2025-11-27T08:02:41.649Z"}, {"entity": "publication", "iuid": "0269c77319e74b068198bff24d911079", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0269c77319e74b068198bff24d911079.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0269c77319e74b068198bff24d911079"}}, "title": "Integrative analyses of circulating microRNA expression profile in hexavalent chromium exposed workers - A cross-sectional study within the SafeChrom project.", "authors": [{"family": "Jiang", "given": "Zheshun", "initials": "Z"}, {"family": "Pan", "given": "Mengyu", "initials": "M"}, {"family": "Liu", "given": "Yishan", "initials": "Y"}, {"family": "Lundh", "given": "Thomas", "initials": "T"}, {"family": "Pineda", "given": "Daniela", "initials": "D"}, {"family": "Schenk", "given": "Linda", "initials": "L"}, {"family": "Saber", "given": "Anne T", "initials": "AT"}, {"family": "Vogel", "given": "Ulla", "initials": "U"}, {"family": "Ljunggren", "given": "Stefan", "initials": "S"}, {"family": "Ricklund", "given": "Niklas", "initials": "N"}, {"family": "Engfeldt", "given": "Malin", "initials": "M"}, {"family": "Krais", "given": "Annette M", "initials": "AM"}, {"family": "Broberg", "given": "Karin", "initials": "K"}, {"family": "SafeChrom Project Team", "given": "", "initials": ""}], "type": "journal article", "published": "2025-05-05", "journal": {"title": "J Hazard Mater", "issn": "1873-3336", "volume": "488", "pages": "137367", "issn-l": null}, "abstract": "Exposure to hexavalent chromium (Cr(VI)) can occur during occupational activities and leading lung cancer. MicroRNA (miRNA) plays an important part in carcinogenesis. Whether Cr(VI) exposure causes cancer-related miRNA changes is yet uncharacterized.\n\nThis study included 89 Cr(VI) exposed workers and 47 controls. MiRNAs were extracted from plasma followed by library preparations, miRNA sequencing, and differentially expressed miRNAs (DEMs) analysis. To understand the underlying biological functions, we used bioinformatics approaches, and qPCR was performed to validate the expression of potential target genes.\n\nA total of 2100 miRNAs were detected. In the exposed workers, 59 DEMs were identified: 21 up-regulated and 38 down-regulated. Target genes for both up- and down-regulated DEMs were significantly enriched in: miRNAs in cancer, small cell lung cancer and non-small cell lung cancer. Protein-protein interactions showed a high number of interactions, in which CCNE2, CDK4 and E2F1 were predicted as hub genes, and the messenger RNA expression of those genes was significantly higher in the exposed workers compared with controls.\n\nOur study suggests that low-to-moderate Cr(VI) exposure results in differential expression of lung-cancer-related miRNAs and associated target genes. Further studies are needed to validate our findings and clarify whether these changes predict cancer risk.", "doi": "10.1016/j.jhazmat.2025.137367", "pmid": "40098212", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S0304-3894(25)00279-1"}], "notes": [], "created": "2025-09-29T11:23:20.679Z", "modified": "2025-09-29T11:23:20.682Z"}, {"entity": "publication", "iuid": "550244a1fd7b43d2b226e88bda919913", "links": {"self": {"href": "https://publications.scilifelab.se/publication/550244a1fd7b43d2b226e88bda919913.json"}, "display": {"href": "https://publications.scilifelab.se/publication/550244a1fd7b43d2b226e88bda919913"}}, "title": "External validation of plasma CSF1 as a preoperative prognostic marker in patients with resectable intrahepatic cholangiocarcinoma.", "authors": [{"family": "Akiki", "given": "Antonio", "initials": "A"}, {"family": "Jacobsson", "given": "Hanna", "initials": "H"}, {"family": "Nouairia", "given": "Ghada", "initials": "G"}, {"family": "Cornillet", "given": "Martin", "initials": "M"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK"}, {"family": "Sparrelid", "given": "Ernesto", "initials": "E"}, {"family": "Taflin", "given": "Helena", "initials": "H"}, {"family": "Jansson", "given": "Hannes", "initials": "H"}], "type": "journal article", "published": "2025-05-04", "journal": {"title": "Eur J Surg Oncol", "issn": "1532-2157", "volume": "51", "issue": "8", "pages": "110123", "issn-l": "0748-7983"}, "abstract": "Long-term prognosis after resection for intrahepatic cholangiocarcinoma (iCCA) remains poor and the preoperative oncological risk assessment is difficult. Two immune system-related plasma proteins, colony stimulating factor 1 (CSF1) and TNF-related apoptosis-inducing ligand (TRAIL), were previously indicated as prognostic factors in iCCA. This study aimed to externally validate CSF1 and TRAIL as preoperative prognostic markers for patients with resectable iCCA.\n\nPreoperative plasma CSF1 and TRAIL concentrations (pg/mL) were determined from prospectively collected biobank samples by multiplex immunoanalysis, for patients with resectable iCCA operated at two tertiary referral centers. Primary outcome was overall survival (OS), analyzed by Kaplan-Meier method and Cox regression. Secondary outcome was disease-free survival (DFS). Discrimination was evaluated with concordance indices (C-index) and prognostic performance assessed with calibration curves.\n\nSixty-one patients with resection for iCCA were included. CSF1 was associated with both OS (hazard ratio [HR] 1.03, 95 % confidence interval [CI] 1.01-1.05) and DFS (HR 1.02, 95 % CI 1.00-1.04). Median OS was eight months for patients with CSF1 levels in the upper quartile (\u2265158 pg/mL), compared to the overall median OS of 47 months. While TRAIL was not significantly associated with OS (P = 0.216), levels in the lower quartile (\u2264256 pg/mL) were associated with short DFS (P = 0.004). The C-index of CSF1 for OS was 0.70, with excellent calibration for three- and five-year OS.\n\nPreoperative plasma CSF1 was validated as a novel, well-calibrated predictor of poor survival in resectable iCCA, which could assist the preoperative risk assessment. Low plasma TRAIL was associated with early recurrence.", "doi": "10.1016/j.ejso.2025.110123", "pmid": "40347719", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "S0748-7983(25)00551-7"}], "notes": [], "created": "2025-05-21T09:41:10.600Z", "modified": "2025-05-21T09:41:10.603Z"}, {"entity": "publication", "iuid": "c8a545c9d69c4c4b810807806cf7c10a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8a545c9d69c4c4b810807806cf7c10a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8a545c9d69c4c4b810807806cf7c10a"}}, "title": "Vikby \u2013 g\u00e5rd, gravar och g\u00e5rdsritualer i T\u00e4by", "authors": [{"family": "Hamilton", "given": "John", "initials": "J"}, {"family": "Lindberg", "given": "Magnus", "initials": "M"}, {"family": "Andersson", "given": "Lars", "initials": "L"}, {"family": "Arcini Ahlstr\u00f6m", "given": "Caroline", "initials": "C"}, {"family": "Bergman", "given": "Jonas", "initials": "J"}, {"family": "Beronius J\u00f6rpeland", "given": "Lena", "initials": "L"}, {"family": "B\u00e4ck", "given": "Mathias", "initials": "M"}, {"family": "Englund", "given": "Mia", "initials": "M"}, {"family": "Grandin", "given": "Lena", "initials": "L"}, {"family": "Heimdahl", "given": "Jens", "initials": "J"}, {"family": "Magnell", "given": "Ola", "initials": "O"}, {"family": "Plikk", "given": "Anna", "initials": "A"}], "type": null, "published": "2025-05-02", "journal": {"title": "Uppdragsarkeologiska rapporter, diarenummer 431-2360-2020", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": null, "pmid": null, "labels": {"Ancient DNA": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T09:29:04.301Z", "modified": "2025-11-27T09:29:04.301Z"}, {"entity": "publication", "iuid": "63a842231cd742ccb297c01941f01486", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63a842231cd742ccb297c01941f01486.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63a842231cd742ccb297c01941f01486"}}, "title": "Unexpectedly low recombination rates and presence of hotspots in termite genomes.", "authors": [{"family": "Everitt", "given": "Turid", "initials": "T", "orcid": "0000-0002-6273-4507", "researcher": {"href": "https://publications.scilifelab.se/researcher/403d4411d0a748eaad9d5810f68e1875.json"}}, {"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T", "orcid": "0000-0003-2929-0585", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ecda02e06b04ead95eefe4e4ee9eed8.json"}}, {"family": "Elsner", "given": "Daniel", "initials": "D"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Liu", "given": "Yuanzhen", "initials": "Y"}, {"family": "Larva", "given": "Tuuli", "initials": "T"}, {"family": "Korb", "given": "Judith", "initials": "J", "orcid": "0000-0001-9577-9376", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95a4169232b4fba987bf584d68d41a6.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2025-05-02", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "35", "issue": "5", "pages": "1124-1137", "issn-l": "1088-9051"}, "abstract": "Meiotic recombination is a fundamental evolutionary process that facilitates adaptation and the removal of deleterious genetic variation. Social Hymenoptera exhibit some of the highest recombination rates among metazoans, whereas high recombination rates have not been found among nonsocial species from this insect order. It is unknown whether elevated recombination rates are a ubiquitous feature of all social insects. In many metazoan taxa, recombination is mainly restricted to hotspots a few kilobases in length. However, little is known about the prevalence of recombination hotspots in insect genomes. Here we infer recombination rate and its fine-scale variation across the genomes of two social species from the insect order Blattodea: the termites Macrotermes bellicosus and Cryptotermes secundus We used linkage disequilibrium-based methods to infer recombination rate. We infer that recombination rates are close to 1 cM/Mb in both species, similar to the average metazoan rate. We also observe a highly punctate distribution of recombination in both termite genomes, indicative of the presence of recombination hotspots. We infer the presence of full-length PRDM9 genes in the genomes of both species, which suggests recombination hotspots in termites might be determined by PRDM9, as they are in mammals. We also find that recombination rates in genes are correlated with inferred levels of germline DNA methylation. The finding of low recombination rates in termites indicates that eusociality is not universally connected to elevated recombination rate. We speculate that the elevated recombination rates in social Hymenoptera are instead promoted by intense selection among haploid males.", "doi": "10.1101/gr.279180.124", "pmid": "40113265", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12047536"}, {"db": "pii", "key": "gr.279180.124"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2025-11-21T15:54:31.653Z", "modified": "2025-11-21T15:54:32.018Z"}, {"entity": "publication", "iuid": "063e2f807e9e47229d68693273e02694", "links": {"self": {"href": "https://publications.scilifelab.se/publication/063e2f807e9e47229d68693273e02694.json"}, "display": {"href": "https://publications.scilifelab.se/publication/063e2f807e9e47229d68693273e02694"}}, "title": "Museum Ecologies", "authors": [{"family": "Fredengren", "given": "Christina", "initials": "C"}, {"family": "Ewing", "given": "Annica", "initials": "A"}, {"family": "Owman", "given": "Caroline", "initials": "C"}, {"family": "Holmstedt", "given": "Janna", "initials": "J"}], "type": "journal-article", "published": "2025-05-01", "journal": {"title": "Mus. Soc.", "issn": "1479-8360", "issn-l": null, "volume": "23", "issue": "1", "pages": null}, "abstract": null, "doi": "10.29311/mas.v23i1.4698", "pmid": null, "labels": {"Ancient DNA": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2025-05-26T06:37:00.260Z", "modified": "2025-05-27T08:16:55.595Z"}, {"entity": "publication", "iuid": "604652c10c274e4ba56020ffc3d7cc80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/604652c10c274e4ba56020ffc3d7cc80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/604652c10c274e4ba56020ffc3d7cc80"}}, "title": "The value of age of onset and family history as predictors of molecular diagnosis in a Swedish cohort of inherited retinal disease.", "authors": [{"family": "De Geer", "given": "Karl", "initials": "K", "orcid": "0000-0001-7849-2082", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ad65632cb414637bdfaa7bd65f9d1b8.json"}}, {"family": "L\u00f6fgren", "given": "Stefan", "initials": "S"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Bj\u00f6rck", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Acta Ophthalmol", "issn": "1755-3768", "volume": "103", "issue": "3", "pages": "327-338", "issn-l": null}, "abstract": "This study aimed to characterize clinical and genetic findings in a Swedish cohort with inherited retinal disease (IRD), identify predictors for achieving a molecular diagnosis and evaluate the effects of increased genetic testing over time.\n\nClinical and genetic data from 324 nonrelated IRD index individuals referred for genetic testing in the Stockholm region between 2016 and 2023 were collected retrospectively and analysed by clinical subtype, age of onset and testing period (2016-2020 vs. 2021-2023). Logistic regression was used to calculate odds ratios for age of onset and family history on the likelihood of achieving a molecular diagnosis.\n\nThe diagnostic yield was 55% and involved 56 genes. In 10% of solved individuals, the molecular diagnosis refined the clinical diagnosis. For each 1-year increase in age of onset, the odds of achieving a molecular diagnosis decreased by 3% (odds ratio 0.97, 95% confidence interval 0.96-0.98). A positive family history doubled the odds (odds ratio 2.1, 95% confidence interval 1.3-3.4). The use of genetic testing increased 2.1-fold and the number of molecular diagnoses increased 1.6-fold relative to the population of the Stockholm region between the two testing periods.\n\nThis study adds to the knowledge of the clinical and genetic landscape of IRDs in Sweden and establishes age of onset and family history as significant predictors for achieving a molecular diagnosis. Increased genetic testing on a population level substantially increased the number of individuals receiving a molecular diagnosis with a high diagnostic yield compared to other rare diseases.", "doi": "10.1111/aos.16804", "pmid": "39643591", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11986402"}], "notes": [], "created": "2025-11-18T20:43:16.158Z", "modified": "2025-11-18T20:44:57.046Z"}, {"entity": "publication", "iuid": "83610878dd0841ce951291a366a5ca6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83610878dd0841ce951291a366a5ca6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83610878dd0841ce951291a366a5ca6e"}}, "title": "TOR1AIP2 as a candidate gene for dystonia-hemichorea/hemiballism.", "authors": [{"family": "Kafantari", "given": "Efthymia", "initials": "E"}, {"family": "Hernandez", "given": "Victoria J", "initials": "VJ"}, {"family": "Necp\u00e1l", "given": "J\u00e1n", "initials": "J"}, {"family": "Leonidou", "given": "Marina", "initials": "M"}, {"family": "Baureder", "given": "Regina", "initials": "R"}, {"family": "Hedberg-Oldfors", "given": "Carola", "initials": "C"}, {"family": "Jech", "given": "Robert", "initials": "R"}, {"family": "Zech", "given": "Michael", "initials": "M"}, {"family": "Schwartz", "given": "Thomas U", "initials": "TU"}, {"family": "Puschmann", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Parkinsonism Relat Disord", "issn": "1873-5126", "volume": "134", "pages": "107781", "issn-l": null}, "abstract": "Dystonia is a movement disorder characterized by genetic and clinical heterogeneity. A recurring p.(Glu303del)-deletion in TOR1A is a well-established cause for DYT-TOR1A (DYT1), an autosomal dominant early-onset isolated dystonia. TOR1A encodes TorsinA, an AAA + ATPase located in the nuclear envelope. By whole exome analyses of a family with a novel dystonia-hemichorea-/hemiballism phenotype, we identified a TOR1AIP2 NM_001199260.2 c.1234A > G p.(Arg412Gly) variant. The variant is very rare in databases and was absent from whole exome data from >1000 dystonia patients. TOR1AIP2 encodes LULL1, a transmembrane protein that activates TorsinA, and correct interaction between TorsinA and LULL1 is essential for proper nuclear envelope architecture. The p.(Arg412Gly) variant disrupts the binding interface between TorsinA and LULL1 around p.Arg412; this same interface is also impaired in DYT1. Functional analyses via a co-purification assay revealed that interaction between TorsinA-LULL1Arg412Gly is weaker than the wild-type interaction, and that it resembles the situation in DYT1 (TorsinA\u0394E303-LULL1). A second family with milder dystonia, hemichorea, and stereotypic leg flexion during gait and a TOR1AIP2 p.(Gln338His) variant was identified. The clinical phenotype of both families shared proximal arm movements, and flutter in facial musculature. Expressivity of the movement disorder symptoms was variable. Several proteins in the nuclear envelope have been implicated in various forms of neurodevelopmental disorders with dystonia. Taken together, our findings suggest TOR1AIP2 as a new candidate gene implicated in a complex hereditary movement disorder with dystonia and hemichorea/hemiballism.", "doi": "10.1016/j.parkreldis.2025.107781", "pmid": "40088780", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pii", "key": "S1353-8020(25)00522-X"}], "notes": [], "created": "2025-11-13T07:37:15.267Z", "modified": "2025-11-13T07:37:15.307Z"}, {"entity": "publication", "iuid": "199651cd602343e0a5e4219bf69d29f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/199651cd602343e0a5e4219bf69d29f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/199651cd602343e0a5e4219bf69d29f4"}}, "title": "Structural Battery Electrolytes Based on a Cross\u2010Linked Methacrylate Polymer and a Protic Ionic Liquid: Is There an Optimal Composition?", "authors": [{"family": "Abdou", "given": "Nicole", "initials": "N", "orcid": "0009-0003-0907-7725", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f1406e1686740939cad716c9ab894d9.json"}}, {"family": "Pipertzis", "given": "Achilleas", "initials": "A", "orcid": "0009-0001-8569-6670", "researcher": {"href": "https://publications.scilifelab.se/researcher/736fa3a4a56e47de983e9c5d7cc8267c.json"}}, {"family": "Chaudhary", "given": "Richa", "initials": "R", "orcid": "0000-0002-9960-5266", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fe64181638445d19813568ad0112d9c.json"}}, {"family": "Even\u00e4s", "given": "Lars", "initials": "L", "orcid": "0000-0002-6580-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d5546ed87b0480aae72d8574db96911.json"}}, {"family": "Xu", "given": "Johanna", "initials": "J", "orcid": "0000-0003-3186-9561", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccc837268c2a4c7794f29fa1838d64bb.json"}}, {"family": "Asp", "given": "Leif E", "initials": "LE", "orcid": "0000-0003-0630-2037", "researcher": {"href": "https://publications.scilifelab.se/researcher/fddb1f9141c44becbd2f2515f98a1b0d.json"}}, {"family": "Swenson", "given": "Jan", "initials": "J", "orcid": "0000-0001-5640-4766", "researcher": {"href": "https://publications.scilifelab.se/researcher/20791829da1540ed9327857790d65940.json"}}, {"family": "Martinelli", "given": "Anna", "initials": "A", "orcid": "0000-0001-9885-5901", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4adbd00ead04caaaa107e57fbe67c7b.json"}}], "type": "journal-article", "published": "2025-05-00", "journal": {"title": "Adv Energy and Sustain Res", "issn": "2699-9412", "volume": "6", "issue": "5", "issn-l": null}, "abstract": null, "doi": "10.1002/aesr.202500013", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:06:38.147Z", "modified": "2025-11-27T08:06:38.438Z"}, {"entity": "publication", "iuid": "54e65a8ce2c94cf5ac271086444360f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54e65a8ce2c94cf5ac271086444360f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54e65a8ce2c94cf5ac271086444360f9"}}, "title": "Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq.", "authors": [{"family": "Pappas", "given": "Fotis", "initials": "F", "orcid": "0000-0003-3696-5069", "researcher": {"href": "https://publications.scilifelab.se/researcher/238d355f0f5f4dd798fdc7f58d4c5a41.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Debes", "given": "Paul V", "initials": "PV", "orcid": "0000-0003-4491-9564", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1887c01f5b343e19e398b3fcd96ba14.json"}}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "134", "issue": "5", "pages": "293-305", "issn-l": "0018-067X"}, "abstract": "Differential DNA methylation due to epigenetic phenomena is crucial in regulating gene expression. Understanding the consequences of such differential expression on sperm quality parameters may provide insights into the underlying mechanisms of male reproductive success. Nonetheless, male fertility in fish remains understudied despite its critical importance to overall reproductive success in nature and captivity. This study investigated the DNA methylation landscape in spermatozoa of domesticated Arctic charr (Salvelinus alpinus) and its associations with sperm quality parameters. Computer assisted-semen analysis (CASA) was performed in 47 sperm samples of farmed Arctic charr, followed by enzymatic methylation sequencing (EM-seq). Our results showed that the DNA of Arctic charr sperm is highly methylated (mean value of ~86%), though variations were observed in genomic features involved in gene regulation. Methylation at variable CpG sites exhibited regional correlation decaying by physical distance, while methylation similarities among individuals were strongly coupled with genetic variation and mirrored pedigree structure. Comethylation network analyses for promoters, CpG islands and first introns revealed genomic modules significantly correlated with sperm quality traits (p < 0.05; Bonferroni adjusted), with distinct patterns suggesting a resource trade-off between sperm concentration and kinematics. Furthermore, annotation and gene-set enrichment analysis highlighted biological mechanisms related to spermatogenesis, cytoskeletal regulation, and mitochondrial function, all vital to sperm physiology. These findings suggest that DNA methylation is a critical and fundamental factor influencing male fertility in Arctic charr, providing insights into the underlying mechanisms of male reproductive success.", "doi": "10.1038/s41437-025-00756-y", "pmid": "40097595", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12056074"}, {"db": "pii", "key": "10.1038/s41437-025-00756-y"}], "notes": [], "created": "2025-09-08T06:59:19.759Z", "modified": "2025-11-14T11:06:34.293Z"}, {"entity": "publication", "iuid": "ef4de967f197431087541882ba0bdb59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef4de967f197431087541882ba0bdb59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef4de967f197431087541882ba0bdb59"}}, "title": "Sex pheromone biosynthesis in the Oriental fruit moth Grapholita molesta involves \u03948 desaturation.", "authors": [{"family": "Dam", "given": "Marie Inger", "initials": "MI"}, {"family": "Ding", "given": "Bao-Jian", "initials": "BJ"}, {"family": "Brauburger", "given": "Kristina", "initials": "K"}, {"family": "Wang", "given": "Hong-Lei", "initials": "HL"}, {"family": "Powell", "given": "Daniel", "initials": "D"}, {"family": "Groot", "given": "Astrid T", "initials": "AT"}, {"family": "Heckel", "given": "David G", "initials": "DG"}, {"family": "L\u00f6fstedt", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Insect Biochem. Mol. Biol.", "issn": "1879-0240", "pages": "104307", "volume": "180", "issn-l": "0965-1748"}, "abstract": "The Oriental fruit moth Grapholita molesta is distributed throughout temperate regions and considered to be a pest in peach production and other high-value fruit crops in the rose family. Insecticide treatment has led to resistance development, but the use of sex pheromones in pest management has shown great promise. We investigated the pheromone biosynthesis pathway in G. molesta with the aim of elucidating pheromone evolution in the Olethreutinae subfamily of moths and harnessing pathway genes in biotechnological production of sex pheromone for use in pest management. In vivo labelling experiments suggested that an uncommon \u03948 fatty acyl desaturase is involved in sex pheromone biosynthesis. CRISPR/Cas9 knock-out of the highly expressed candidate desaturase gene Gmol_CPRQ almost completely blocked the production of \u03948 pheromone components in vivo. Heterologous expression of Gmol_CPRQ protein in yeast- or Sf9 insect cells, however, failed to demonstrate the expected \u03948 desaturase activity. Instead, \u03949 desaturase activity was observed. Co-expression in the yeast system of the electron donor, cytochrome b5, from G. molesta still produced only \u03949 desaturase activity. We suggest that Gmol_CPRQ is intimately involved in pheromone production in vivo, via an unknown reaction mechanism that may possibly involve another co-factor that is absent in the yeast and Sf9 expression systems, or depend on its subcellular site of activity. Solving this puzzle will shed further light on pheromone biosynthesis in the family Tortricidae and will be required for successful biotechnological production of fatty acids and pheromones requiring \u03948 desaturation.", "doi": "10.1016/j.ibmb.2025.104307", "pmid": "40169039", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0965-1748(25)00051-7"}], "notes": [], "created": "2025-04-07T09:58:55.450Z", "modified": "2025-11-28T10:43:19.399Z"}, {"entity": "publication", "iuid": "346db8ab17674ec68f1e0b0051075be5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/346db8ab17674ec68f1e0b0051075be5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/346db8ab17674ec68f1e0b0051075be5"}}, "title": "Proteins associated with preserved ratio impaired spirometry.", "authors": [{"family": "Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-8552-4510", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca522368e5c04156b2cf775b42d1e4b2.json"}}, {"family": "Zhou", "given": "Xingwu", "initials": "X"}, {"family": "Behndig", "given": "Annelie F", "initials": "AF"}, {"family": "Caidahl", "given": "Kenneth", "initials": "K"}, {"family": "Egesten", "given": "Arne", "initials": "A"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-8618-9152", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40c03613a3a46368ed855fc95b79e31.json"}}, {"family": "Engvall", "given": "Jan E", "initials": "JE", "orcid": "0000-0002-5716-5098", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dc825fc91ea40afa83516f8fd649b97.json"}}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Hamrefors", "given": "Viktor", "initials": "V", "orcid": "0000-0002-8475-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ceb9dab3bf841da9cc06a51d53a296f.json"}}, {"family": "Janson", "given": "Christer", "initials": "C", "orcid": "0000-0001-5093-6980", "researcher": {"href": "https://publications.scilifelab.se/researcher/bae457d633714159a73704f9ebe7bfa6.json"}}, {"family": "Johnsson", "given": "\u00c5se", "initials": "\u00c5"}, {"family": "Lindberg", "given": "Anne", "initials": "A", "orcid": "0000-0002-3292-7471", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ae273fae3f74964b42c6cc110951d64.json"}}, {"family": "Mannila", "given": "Maria", "initials": "M"}, {"family": "Nystr\u00f6m", "given": "Fredrik H", "initials": "FH"}, {"family": "Olin", "given": "Anna-Carin", "initials": "AC", "orcid": "0000-0001-6674-9020", "researcher": {"href": "https://publications.scilifelab.se/researcher/1142993cab2b44a09a1f1e7e2bf8783a.json"}}, {"family": "Sk\u00f6ld", "given": "C Magnus", "initials": "CM"}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S", "orcid": "0000-0001-9225-1306", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13944767ad9446e885ce32ca88afebd.json"}}, {"family": "Tanash", "given": "Hanan", "initials": "H"}, {"family": "Tor\u00e9n", "given": "Kjell", "initials": "K"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ"}, {"family": "Malinovschi", "given": "Andrei", "initials": "A", "orcid": "0000-0002-4098-7765", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c246a24a09a4e67836f7ca6f1282610.json"}}, {"family": "Blomberg", "given": "Anders", "initials": "A", "orcid": "0000-0002-2452-7347", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c5b4f5240384d718af7db5d501c637d.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "ERJ Open Res", "issn": "2312-0541", "volume": "11", "issue": "3", "issn-l": "2312-0541"}, "abstract": "Preserved ratio impaired spirometry (PRISm) is a spirometry pattern of interest regarding incident airflow obstruction and higher mortality risk. We applied a proteomic approach to gain more insight into the biological mechanisms associated with PRISm.\n\nFrom the population-based Swedish Cardiopulmonary Bioimage Study (SCAPIS), participants in the Main (n=4835) and Pilot (n=1054) studies, were included as discovery and replication cohorts. The lower limit of normal (LLN) of post-bronchodilator forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC was defined as the fifth percentile in healthy, never-smoking SCAPIS participants. Participants were subdivided into five groups: reference: FEV1/FVC\u2265LLN and FEV1\u2265LLN and FVC\u2265LLN (n=4084)); mild chronic airflow limitation (CAL): FEV1/FVC<LLN and FEV1\u2265LLN (n=278); moderate-severe CAL: FEV1/FVC<LLN and FEV1<LLN (n=170); restrictive spirometric pattern (RSP): FEV1/FVC \u2265LLN and FVC<LLN (n=238); and PRISm: FEV1/FVC\u2265LLN and FEV1<LLN (n=238). Proximity extension assays were used to measure 168 proteins. The associations of each standardised protein were assessed with each study group by multiple linear regression models, adjusting for age, sex, body mass index (BMI), smoking, physical activity and study centres, and corrected for multiple testing to control for a false discovery rate of 5%.\n\nEight proteins were associated with PRISm and replicated: tumour necrosis factor receptor superfamily member 10A, interleukin-6, paraoxonase 3 (negative association), renin, urokinase plasminogen activator surface receptor (U-PAR), E-selectin, matrix metalloproteinase 7 and chitinase-3-like protein 1. Interleukin-6 and U-PAR were also associated with moderate-severe CAL and E-selectin with RSP. In addition, five other proteins were associated with moderate-severe CAL and three with RSP.\n\nProtein profile in PRISm differs from other spirometric patterns suggesting specific disease mechanisms.", "doi": "10.1183/23120541.01045-2024", "pmid": "40589910", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12208607"}, {"db": "pii", "key": "01045-2024"}], "notes": [], "created": "2025-11-25T19:23:20.139Z", "modified": "2025-11-25T19:23:20.300Z"}, {"entity": "publication", "iuid": "058afb33780a418b91456de19503c18b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/058afb33780a418b91456de19503c18b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/058afb33780a418b91456de19503c18b"}}, "title": "Protein profiling in intensive care unit-treated COVID-19 patients identifies biomarkers of residual lung abnormalities.", "authors": [{"family": "Kalafatis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0003-2917-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ce0556e21db41a9a8d5d617bfed2c06.json"}}, {"family": "Bj\u00f6rnson", "given": "Mikael", "initials": "M"}, {"family": "Svobodov\u00e1", "given": "Barbora", "initials": "B", "orcid": "0000-0001-5615-893X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d82ffff652149d088e1733ddfec7d8f.json"}}, {"family": "Kistner", "given": "Anna", "initials": "A", "orcid": "0000-0002-7942-3211", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddd1c55300a54c45abd696a1e67f58e3.json"}}, {"family": "Nygren-Bonnier", "given": "Malin", "initials": "M"}, {"family": "Runold", "given": "Michael", "initials": "M"}, {"family": "Bruchfeld", "given": "Judith", "initials": "J"}, {"family": "Wheelock", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Dellgren", "given": "G\u00f6ran", "initials": "G"}, {"family": "Elowsson", "given": "Linda", "initials": "L", "orcid": "0000-0002-0457-0188", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbbb463f47424eacb4387f0d6015bdb9.json"}}, {"family": "Westergren-Thorsson", "given": "Gunilla", "initials": "G"}, {"family": "Sk\u00f6ld", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "ERJ Open Res", "issn": "2312-0541", "volume": "11", "issue": "3", "issn-l": "2312-0541"}, "abstract": "In this study, we combine proteomics with functional parameters and imaging to examine potential biomarkers that may identify patients at risk of developing persistent lung sequelae following coronavirus disease 2019 (COVID-19).\n\nWe performed multiplex profiling of serum and collected clinical data from intensive care unit (ICU)-treated patients with COVID-19 (n=43) at 4 and 10 months post hospitalisation.\n\nFour months post discharge, patients with COVID-19 demonstrated lower % predicted forced vital capacity (72.2% versus 113% (p<0.0001)) and % predicted forced expiratory volume in 1 s (74.5% versus 103% (p<0.0001)) compared with healthy controls. A persistent upregulation (versus healthy controls) of inflammatory and remodelling factors, including among others, Galectin-1 (Gal-1), C-X-C motif chemokine 13 (CXCL13), monocyte chemoattractant protein 3 (MCP-3) and matrix metalloproteinase 7 (MMP7), were observed. Patients with moderate to severe parenchymal involvement (>5% of lung tissue) on high-resolution computed tomography (HRCT) had higher levels of the proteins lysosomal associated membrane protein-3 (LAMP3) and MMP7 compared with patients with minor (<5%) or no findings on HRCT. Both proteins demonstrated consecutive associations to lung function and parenchymal involvement. Histological evaluation of LAMP3 in lung tissue confirmed LAMP3 localisation to alveolar type 2 cells in more preserved areas of the parenchyma. However, areas of remodelling were devoid of LAMP3 concurrent with the appearance of KRT5+ and KRT17+ basal cells.\n\nDespite functional and radiological improvements following COVID-19, persistent upregulation of inflammation and remodelling factors were observed. Similarities in the expression of LAMP3 in COVID-19 and idiopathic pulmonary fibrosis may suggest it as a potential biomarker for chronic lung damage.", "doi": "10.1183/23120541.00981-2024", "pmid": "40551787", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12183704"}, {"db": "pii", "key": "00981-2024"}], "notes": [], "created": "2025-11-25T19:23:02.144Z", "modified": "2025-11-25T19:23:02.316Z"}, {"entity": "publication", "iuid": "7a9207954e064e188159483708b530ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a9207954e064e188159483708b530ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a9207954e064e188159483708b530ef"}}, "title": "Neural ensembles that encode nocifensive mechanical and heat pain in mouse spinal cord.", "authors": [{"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J"}, {"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Magnusson", "given": "Kajsa A", "initials": "KA", "orcid": "0000-0001-9159-2985", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf40497aadb44dabafaba5e8126d68a.json"}}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Calvo-Enrique", "given": "Laura", "initials": "L", "orcid": "0000-0002-9428-3974", "researcher": {"href": "https://publications.scilifelab.se/researcher/42206cbfcbb04c0188bea08535937cec.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Albisetti", "given": "Gioele W", "initials": "GW"}, {"family": "Ceder", "given": "Mikaela M", "initials": "MM"}, {"family": "Henriksson", "given": "Katharina", "initials": "K"}, {"family": "Leavitt", "given": "Andrew D", "initials": "AD"}, {"family": "Zeilhofer", "given": "Hanns Ulrich", "initials": "HU", "orcid": "0000-0001-6954-4629", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8c122280e0449e6bcdc144cfdf2ebd8.json"}}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T", "orcid": "0000-0002-3587-0116", "researcher": {"href": "https://publications.scilifelab.se/researcher/e228cd63f3a84d999ca3781c53a18f27.json"}}, {"family": "Lagerstr\u00f6m", "given": "Malin C", "initials": "MC"}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "28", "issue": "5", "pages": "1012-1023", "issn-l": "1097-6256"}, "abstract": "Acute pain is an unpleasant experience caused by noxious stimuli. How the spinal neural circuits attribute differences in quality of noxious information remains unknown. By means of genetic capturing, activity manipulation and single-cell RNA sequencing, we identified distinct neural ensembles in the adult mouse spinal cord encoding mechanical and heat pain. Reactivation or silencing of these ensembles potentiated or stopped, respectively, paw shaking, lifting and licking within but not across the stimuli modalities. Within ensembles, polymodal Gal+ inhibitory neurons with monosynaptic contacts to A-fiber sensory neurons gated pain transmission independent of modality. Peripheral nerve injury led to inferred microglia-driven inflammation and an ensemble transition with decreased recruitment of Gal+ inhibitory neurons and increased excitatory drive. Forced activation of Gal+ neurons reversed hypersensitivity associated with neuropathy. Our results reveal the existence of a spinal representation that forms the neural basis of the discriminative and defensive qualities of acute pain, and these neurons are under the control of a shared feed-forward inhibition.", "doi": "10.1038/s41593-025-01921-6", "pmid": "40128392", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12081300"}, {"db": "pii", "key": "10.1038/s41593-025-01921-6"}], "notes": [], "created": "2025-04-07T09:57:28.435Z", "modified": "2025-11-28T10:46:43.366Z"}, {"entity": "publication", "iuid": "2db32f8194a7438484ff5bbd2844c22e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2db32f8194a7438484ff5bbd2844c22e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2db32f8194a7438484ff5bbd2844c22e"}}, "title": "Mutational signatures and kataegis in pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Gunnarsson", "given": "Rebeqa", "initials": "R", "orcid": "0000-0002-2283-786X", "researcher": {"href": "https://publications.scilifelab.se/researcher/12601745d2c74562bf83d22879f212eb.json"}}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Biloglav", "given": "Andrea", "initials": "A"}, {"family": "Lundin-Str\u00f6m", "given": "Kristina B", "initials": "KB"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Olsson-Arvidsson", "given": "Linda", "initials": "L"}, {"family": "Paulsson", "given": "Kajsa", "initials": "K"}, {"family": "Johansson", "given": "Bertil", "initials": "B"}], "type": "letter", "published": "2025-05-00", "journal": {"title": "Hemasphere", "issn": "2572-9241", "volume": "9", "issue": "5", "pages": "e70136", "issn-l": null}, "abstract": null, "doi": "10.1002/hem3.70136", "pmid": "40395431", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12088958"}, {"db": "pii", "key": "HEM370136"}, {"db": "figshare", "key": "10.6084/m9.figshare.28053263"}], "notes": [], "created": "2025-09-08T07:07:08.984Z", "modified": "2025-09-08T07:07:09.087Z"}, {"entity": "publication", "iuid": "c7627b55efd14033b6996b8c5aab3b0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7627b55efd14033b6996b8c5aab3b0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7627b55efd14033b6996b8c5aab3b0d"}}, "title": "Large Inversions Shape Diversification and Genome Evolution in Common Quails.", "authors": [{"family": "Ravagni", "given": "Sara", "initials": "S", "orcid": "0000-0003-0320-3447", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb16a7faa1a4952b3247d440d2cdf5f.json"}}, {"family": "Montero-Mendieta", "given": "Santiago", "initials": "S", "orcid": "0000-0002-8350-4655", "researcher": {"href": "https://publications.scilifelab.se/researcher/c23cf6e0a3d84637b564cd4ece502dfa.json"}}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0003-0291-7819", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7aebc9371db4bbcb03eaef58473fc3e.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Rodr\u00edguez-Teijeiro", "given": "Jos\u00e9 Domingo", "initials": "JD"}, {"family": "Sanchez-Donoso", "given": "Ines", "initials": "I"}, {"family": "Vil\u00e0", "given": "Carles", "initials": "C"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "9", "pages": "e17740"}, "abstract": "Chromosomal inversions, by suppressing recombination, can profoundly shape genome evolution and drive adaptation. In the common quail (Coturnix coturnix), a highly mobile bird with a vast Palearctic breeding range, we previously identified a massive inversion on chromosome 1 associated with distinct phenotypes and restricted geographic distribution. Here, using a new de novo genome assembly, we characterise this inversion and uncover additional, ancient structural variation on chromosome 2 that segregates across the species' range: either two putatively linked inversions or a single, large inversion that appears as two due to scaffolding limitations. Together, the inversions encompass a remarkable 15.6% of the quail genome (153.6 Mbp), creating highly divergent haplotypes that diverged over a million years ago. While the chromosome 1 inversion is linked to phenotypic differences, including morphology and migratory behaviour, the chromosome 2 inversion(s) show no such association. Notably, all inversion regions exhibit reduced effective population size and a relaxation of purifying selection, evidenced by elevated nonsynonymous-to-synonymous substitution ratios (N/S). This suggests that inversions, particularly the geographically restricted one on chromosome 1, may act as engines of diversification, accelerating the accumulation of functional variation and potentially contributing to local adaptation, especially within isolated island populations. Our findings demonstrate how large-scale chromosomal rearrangements can compartmentalise a genome, fostering distinct evolutionary trajectories within a single, highly mobile species.", "doi": "10.1111/mec.17740", "pmid": "40183764", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null, "NGI Other": null}, "xrefs": [], "notes": [], "created": "2025-08-19T13:25:18.999Z", "modified": "2025-11-19T08:38:35.719Z"}, {"entity": "publication", "iuid": "403ee779ad0242188b01c12a86d2372d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/403ee779ad0242188b01c12a86d2372d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/403ee779ad0242188b01c12a86d2372d"}}, "title": "Intermediate Monocytes and High Levels of Chemokine CCL3 Are Associated With Increased Risk of Atrial Fibrillation in the General Population.", "authors": [{"family": "Sveen", "given": "Kari Anne", "initials": "KA", "orcid": "0000-0002-1034-9965", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bdf179c8dd74091bd071a659de73816.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG", "orcid": "0000-0001-6285-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e50df6bb7f4194a52546dbd5652e84.json"}}, {"family": "Goncalves", "given": "Isabel", "initials": "I", "orcid": "0000-0002-2935-0181", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cb42ac6ae8458ea9aaaa1dec1717d9.json"}}, {"family": "Edsfeldt", "given": "Andreas", "initials": "A", "orcid": "0000-0002-2691-9192", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4d8310d9d834bd791b791424774b989.json"}}, {"family": "Engelbertsen", "given": "Daniel", "initials": "D", "orcid": "0000-0002-0289-5210", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc4f0e42f9444337adb276360c27c5cc.json"}}, {"family": "Johnson", "given": "Linda S", "initials": "LS", "orcid": "0000-0002-2249-8220", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa7398daec4e4ffaaa4b2b05ef8906a9.json"}}, {"family": "Melander", "given": "Olle", "initials": "O", "orcid": "0000-0002-2581-484X", "researcher": {"href": "https://publications.scilifelab.se/researcher/868a7e41aa054097a85575aa1d9658cc.json"}}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-8618-9152", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40c03613a3a46368ed855fc95b79e31.json"}}, {"family": "Nilsson", "given": "Jan", "initials": "J", "orcid": "0000-0002-9752-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8777140448bc47f0a7984db3c15c0e23.json"}}, {"family": "Bj\u00f6rkbacka", "given": "Harry", "initials": "H", "orcid": "0000-0003-3918-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f4c07bc840f491d843f67a9932d5f3a.json"}}, {"family": "Bengtsson", "given": "Eva", "initials": "E", "orcid": "0000-0001-7075-1772", "researcher": {"href": "https://publications.scilifelab.se/researcher/fde391a1fac24b6ea0e58db2fe1ff6d3.json"}}], "type": "letter", "published": "2025-05-00", "journal": {"title": "Circ Arrhythm Electrophysiol", "issn": "1941-3084", "volume": "18", "issue": "5", "pages": "e013621", "issn-l": null}, "abstract": null, "doi": "10.1161/CIRCEP.124.013621", "pmid": "40242861", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12094257"}], "notes": [], "created": "2025-11-25T19:23:13.321Z", "modified": "2025-11-25T19:23:13.511Z"}, {"entity": "publication", "iuid": "11bfd5f14ab244ff92ef3f20ae9e9e15", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11bfd5f14ab244ff92ef3f20ae9e9e15.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11bfd5f14ab244ff92ef3f20ae9e9e15"}}, "title": "Identification of biallelic POLA2 variants in two families with an autosomal recessive telomere biology disorder.", "authors": [{"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Chun-On", "given": "Pattra", "initials": "P"}, {"family": "Rafati", "given": "Maryam", "initials": "M", "orcid": "0000-0001-7118-3412", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c0841d69cd04a5ea7292b73726b408a.json"}}, {"family": "McReynolds", "given": "Lisa J", "initials": "LJ", "orcid": "0000-0002-1018-1453", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf05c99cb8d34fa2ab0f09739da95295.json"}}, {"family": "Norberg", "given": "Anna", "initials": "A"}, {"family": "Moura", "given": "Pedro Luis", "initials": "PL", "orcid": "0000-0002-0493-5394", "researcher": {"href": "https://publications.scilifelab.se/researcher/12216bfd20fa4056b844842908efc829.json"}}, {"family": "Pesonen", "given": "Ida", "initials": "I"}, {"family": "Chaireti", "given": "Roza", "initials": "R"}, {"family": "Gr\u00f6nros S\u00f6derholm", "given": "Boa", "initials": "B"}, {"family": "Burlin", "given": "Julia", "initials": "J"}, {"family": "Ryd\u00e9n", "given": "Jenny", "initials": "J"}, {"family": "Lindberg", "given": "Eva Hellstr\u00f6m", "initials": "EH"}, {"family": "Giri", "given": "Neelam", "initials": "N"}, {"family": "Savage", "given": "Sharon A", "initials": "SA", "orcid": "0000-0001-6006-0740", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ebbcf2fee6945d2b1173ff0e4109674.json"}}, {"family": "Agarwal", "given": "Suneet", "initials": "S"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Tesi", "given": "Bianca", "initials": "B", "orcid": "0000-0002-8253-2507", "researcher": {"href": "https://publications.scilifelab.se/researcher/96a994cd257c4833a4efe79e26b900ff.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "volume": "33", "issue": "5", "pages": "580-587", "issn-l": "1018-4813"}, "abstract": "POLA2 encodes the accessory subunit of DNA polymerase \u03b1 (pol\u03b1)/primase, which is crucial for telomere C-strand fill-in. Incomplete fill-in of the C-rich telomeric strand after DNA replication has been proposed as a mechanism for Coats plus syndrome, a phenotype within the broader spectrum of telomere biology disorders (TBD). Coats plus syndrome has so far been associated with pathogenic variants in POT1, CTC1, and STN1. Here we report the findings of biallelic deleterious rare variants in POLA2 gene detected by whole genome sequencing and segregation analysis in five young adults from two unrelated families. All five individuals displayed abnormally short telomeres and a clinical phenotype suggesting a TBD disorder with Coats plus features including retinal and gastrointestinal telangiectasias. Our results suggest POLA2 as a novel autosomal recessive gene for a TBD with Coats plus features.", "doi": "10.1038/s41431-024-01722-8", "pmid": "39616267", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12048608"}, {"db": "pii", "key": "10.1038/s41431-024-01722-8"}], "notes": [], "created": "2025-11-18T20:43:12.167Z", "modified": "2025-11-18T20:44:44.102Z"}, {"entity": "publication", "iuid": "62778e40786e4985a36189beca08011f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62778e40786e4985a36189beca08011f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62778e40786e4985a36189beca08011f"}}, "title": "High-throughput biodiversity surveying sheds new light on the brightest of insect taxa.", "authors": [{"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Goodsell", "given": "Robert M", "initials": "RM"}, {"family": "Bengsson", "given": "Bengt-\u00c5ke", "initials": "B\u00c5"}, {"family": "Mutanen", "given": "Marko", "initials": "M"}, {"family": "Klinth", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0003-4755-6682", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c16d303d21743df8d9b9eebb4d2376b.json"}}, {"family": "van Dijk", "given": "Laura J A", "initials": "LJA", "orcid": "0000-0003-1015-8496", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c9432c19234fd5bc5dfc0a037dae0f.json"}}, {"family": "\u0141ukasik", "given": "Piotr", "initials": "P", "orcid": "0000-0002-4164-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/71d69a579a304425b70249e7db42ad67.json"}}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}, {"family": "Andersson", "given": "Anders", "initials": "A"}, {"family": "Tack", "given": "Ayco Jerome Michel", "initials": "AJM"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "292", "issue": "2046", "pages": "20242974", "issn-l": "0962-8452"}, "abstract": "DNA metabarcoding of species-rich taxa is becoming a popular high-throughput method for biodiversity inventories. Unfortunately, its accuracy and efficiency remain unclear, as results mostly pertain to poorly known taxa in underexplored regions. This study evaluates what an extensive sampling effort combined with metabarcoding can tell us about the lepidopteran fauna of Sweden-one of the best-understood insect taxa in one of the most-surveyed countries of the world. We deployed 197 Malaise traps across Sweden for a year, generating 4749 bulk samples for metabarcoding, and compared the results to existing data sources. We detected more than half (1535) of the 2990 known Swedish lepidopteran species and 323 species not reported during the sampling period by other data providers. Full-length barcoding confirmed three new species for the country, substantial range extensions for two species and eight genetically distinct barcode variants potentially representing new species, one of which has since been described. Most new records represented small, inconspicuous species from poorly surveyed regions, highlighting components of the fauna overlooked by traditional surveying. These findings demonstrate that DNA metabarcoding is a highly efficient and accurate biodiversity sampling method, capable of yielding significant new discoveries even for the most well known of insect faunas.", "doi": "10.1098/rspb.2024.2974", "pmid": "40359979", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12074807"}], "notes": [], "created": "2025-11-21T14:25:36.120Z", "modified": "2025-11-21T14:25:36.343Z"}, {"entity": "publication", "iuid": "9acd6d2506e0447f8aa0f0cacf60d06c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9acd6d2506e0447f8aa0f0cacf60d06c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9acd6d2506e0447f8aa0f0cacf60d06c"}}, "title": "Hemagglutinin Protease HapA Associated With Vibrio cholerae Outer Membrane Vesicles (OMVs) Disrupts Tight and Adherens Junctions.", "authors": [{"family": "Baryalai", "given": "Palwasha", "initials": "P"}, {"family": "Irenaeus", "given": "David", "initials": "D"}, {"family": "Toh", "given": "Eric", "initials": "E"}, {"family": "Ramstedt", "given": "Madeleine", "initials": "M"}, {"family": "Uhlin", "given": "Bernt Eric", "initials": "BE"}, {"family": "Nadeem", "given": "Aftab", "initials": "A"}, {"family": "Wai", "given": "Sun Nyunt", "initials": "SN", "orcid": "0000-0003-4793-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/261986c5cf8f48878b74c4f60cc7af69.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "J Extracell Vesicles", "issn": "2001-3078", "volume": "14", "issue": "5", "pages": "e70092", "issn-l": "2001-3078"}, "abstract": "This study explores the virulence mechanisms of Vibrio cholerae, with a particular emphasis on HapA, a zinc metalloprotease delivered via outer membrane vesicles (OMVs). The findings reveal that OMV-associated HapA disrupts the integrity of tight and adherens junctions in intestinal epithelial cell models more effectively than its purified counterpart, suggesting that association with OMVs substantially potentiates the pathogenic effects of HapA. The study further details the uptake of V. cholerae OMVs by epithelial cells, as well as their targeted degradation of key junctional proteins, including claudin, ZO-1, and \u03b2-catenin. These results highlight the critical role of OMV-associated HapA in compromising epithelial barrier function. Additionally, the use of spheroids and intestinal organoids in our experiments provides deeper insight into bacterial pathogenesis, offering valuable information for the development of targeted therapeutic strategies.", "doi": "10.1002/jev2.70092", "pmid": "40415227", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12104216"}], "notes": [], "created": "2025-10-30T12:00:24.910Z", "modified": "2025-10-30T12:00:25.087Z"}, {"entity": "publication", "iuid": "102255837dfd43148aaedb132eaadffa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/102255837dfd43148aaedb132eaadffa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/102255837dfd43148aaedb132eaadffa"}}, "title": "Genome-wide association study of direct oral anticoagulants and their relation to bleeding.", "authors": [{"family": "Attelind", "given": "Sofia", "initials": "S", "orcid": "0000-0002-7631-7376", "researcher": {"href": "https://publications.scilifelab.se/researcher/1544b43ea7d14369a4fb6de3174a1d00.json"}}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0003-3465-3280", "researcher": {"href": "https://publications.scilifelab.se/researcher/968cb3fe072d4ed09739e8be6668d168.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Eur J Clin Pharmacol", "issn": "1432-1041", "volume": "81", "issue": "5", "pages": "771-783", "issn-l": null}, "abstract": "Direct oral anticoagulants (DOACs) are used to prevent and treat thromboembolic events in adults. We aimed to investigate whether pharmacogenomic variation contributes to the risk of bleeding during DOAC treatment.\n\nCases were recruited from reports of bleeding sent to the Swedish Medical Products Agency (n = 129, 60% men, 93% Swedish, 89% on factor Xa inhibitors) and compared with population controls (n = 4891) and a subset matched for exposure to DOACs (n = 353). We performed a genome-wide association study, with analyses of candidate single nucleotide polymorphisms (SNPs) and candidate gene set analyses.\n\nForty-four cases had major, 37 minor, and 48 clinically relevant non-major (CRNM) bleeding. When cases were compared with matched controls, BAIAP2L2 rs142001534 was significantly associated with any bleeding and major/CRNM bleeding (P = 4.66 \u00d7 10-8 and P = 3.28 \u00d7 10-8, respectively). The candidate SNP CYP3A5 rs776746 was significantly associated with major and major/CRNM bleeding (P = 0.00020 and P = 0.00025, respectively), and ABCG2 rs2231142 was nominally associated with any bleeding (P = 0.01499). Rare coding variants in the candidate gene VWF were significantly associated with any bleeding (P = 0.00296).\n\nBAIAP2L2, CYP3A5, ABCG2, and VWF may be associated with bleeding in DOAC-treated patients. The risk estimates of the candidate variants in CYP3A5 and ABCG2 were in the same direction as in previous studies. The Von Willebrand Factor gene (VWF) is linked to hereditary bleeding disorders, while there is no previous evidence of bleeding associated with BAIAP2L2.", "doi": "10.1007/s00228-025-03821-x", "pmid": "40116934", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12003525"}, {"db": "pii", "key": "10.1007/s00228-025-03821-x"}], "notes": [], "created": "2025-09-08T11:34:07.950Z", "modified": "2025-09-08T11:34:08.131Z"}, {"entity": "publication", "iuid": "e22c083918a9414f9a025d7a080c9352", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e22c083918a9414f9a025d7a080c9352.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e22c083918a9414f9a025d7a080c9352"}}, "title": "Fertilizer\u2010induced soil carbon rapidly disappears after clearcutting in boreal production forests", "authors": [{"family": "Boeraeve", "given": "Margaux", "initials": "M", "orcid": "0000-0003-2835-9798", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2288143def9454793855ef5dc790f6c.json"}}, {"family": "Granath", "given": "Gustaf", "initials": "G", "orcid": "0000-0002-3632-9102", "researcher": {"href": "https://publications.scilifelab.se/researcher/232d1b8a07454b5f802624dd91d68597.json"}}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD", "orcid": "0000-0002-3384-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a40688d33545a19c3c666940bda255.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Strengbom", "given": "Joachim", "initials": "J", "orcid": "0000-0002-1720-5016", "researcher": {"href": "https://publications.scilifelab.se/researcher/3311ed539845455b9bad3e84907133de.json"}}], "type": "journal-article", "published": "2025-05-00", "journal": {"title": "Journal of Applied Ecology", "issn": "0021-8901", "volume": "62", "issue": "5", "pages": "1202-1215", "issn-l": null}, "abstract": null, "doi": "10.1111/1365-2664.70034", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-08-19T13:19:20.312Z", "modified": "2025-08-19T13:19:20.414Z"}, {"entity": "publication", "iuid": "cc91895d782a4623b95f8d39c736a4cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc91895d782a4623b95f8d39c736a4cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc91895d782a4623b95f8d39c736a4cf"}}, "title": "Error Reduction in Leukemia Machine Learning Classification With Conformal Prediction.", "authors": [{"family": "Lysenkova Wiklander", "given": "Mariya", "initials": "M", "orcid": "0000-0002-0012-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/48850e5606b9470caa6b130286055388.json"}}, {"family": "Zachariah", "given": "Dave", "initials": "D", "orcid": "0000-0002-6698-0166", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdf118819f654f32ad53f994e83c227d.json"}}, {"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "JCO Clin Cancer Inform", "issn": "2473-4276", "volume": "9", "pages": "e2400324", "issn-l": null}, "abstract": "Recent advances in machine learning have led to the development of classifiers that predict molecular subtypes of acute lymphoblastic leukemia (ALL) using RNA-sequencing (RNA-seq) data. Although these models have shown promising results, they often lack robust performance guarantees. The aim of this study was three-fold: to quantify the uncertainty of these classifiers, to provide prediction sets that control the false-negative rate (FNR), and to perform implicit error reduction by transforming incorrect predictions into uncertain predictions.\n\nConformal prediction (CP) is a distribution-agnostic framework for generating statistically calibrated prediction sets whose size reflects model uncertainty. In this study, we applied an extension called conformal risk control to three RNA-seq ALL subtype classifiers. Leveraging RNA-seq data from 1,227 patient samples taken at diagnosis, we developed a multiclass conformal predictor ALLCoP, which generates statistically guaranteed FNR-controlled prediction sets.\n\nALLCoP was able to create prediction sets with specified FNR tolerances ranging from 7.5% to 30%. In a validation cohort, ALLCoP successfully reduced the FNR of the ALLIUM RNA-seq ALL subtype classifier from 8.95% to 3.5%. For patients whose subtype was not previously known, the use of ALLCoP was able to reduce the occurrence of empty predictions from 37% to 17%. Notably, up to 34% of the multiple-class prediction sets included the PAX5alt subtype, suggesting that increased prediction set size may reflect secondary aberrations and biological complexity, contributing to classifier uncertainty. Finally, ALLCoP was validated on two additional RNA-seq ALL subtype classifiers, ALLSorts and ALLCatchR.\n\nOur results highlight the potential of CP in enhancing the use of oncologic RNA-seq subtyping classifiers and also in uncovering additional molecular aberrations of potential clinical importance.", "doi": "10.1200/CCI-24-00324", "pmid": "40435436", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12133051"}], "notes": [], "created": "2025-11-07T07:27:00.813Z", "modified": "2025-11-14T11:08:56.250Z"}, {"entity": "publication", "iuid": "101c596d383544ef828f7cb89f4f13db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/101c596d383544ef828f7cb89f4f13db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/101c596d383544ef828f7cb89f4f13db"}}, "title": "Effects of lipid-based nutrient supplements on gut markers in stunted children: Secondary analysis of a randomised trial.", "authors": [{"family": "Pesu", "given": "Hannah", "initials": "H"}, {"family": "Mbabazi", "given": "Joseph", "initials": "J"}, {"family": "Mutumba", "given": "Rolland", "initials": "R"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Johnsen", "given": "Peter R", "initials": "PR"}, {"family": "Fr\u00f8ki\u00e6r", "given": "Hanne", "initials": "H"}, {"family": "Olsen", "given": "Mette F", "initials": "MF"}, {"family": "M\u00f8lgaard", "given": "Christian", "initials": "C"}, {"family": "Michaelsen", "given": "Kim F", "initials": "KF"}, {"family": "Ritz", "given": "Christian", "initials": "C"}, {"family": "Filteau", "given": "Suzanne", "initials": "S"}, {"family": "Briend", "given": "Andr\u00e9", "initials": "A"}, {"family": "Mupere", "given": "Ezekiel", "initials": "E"}, {"family": "Friis", "given": "Henrik", "initials": "H"}, {"family": "Grenov", "given": "Benedikte", "initials": "B", "orcid": "0000-0003-0259-7851", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7abbb4b2a744838839fc2daeac5dd5a.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "J Pediatr Gastroenterol Nutr", "issn": "1536-4801", "volume": "80", "issue": "5", "pages": "889-898", "issn-l": null}, "abstract": "To examine the effects of lipid-based nutrient supplements (LNS) containing milk protein (MP) and/or whey permeate (WP) on markers of intestinal inflammation and enterocyte mass among stunted children. Furthermore, to explore whether gut status modifies effects of LNS on growth and micronutrient status.\n\nIn a 2 \u00d7 2 factorial trial 12-59 months-old Ugandan children with stunting were randomized to four LNS formulations (100 g/day for 12 weeks) containing MP or soy protein and WP or maltodextrin, or to no supplementation. Linear mixed-effects models were used to explore faecal myeloperoxidase (f-MPO) and plasma citrulline (p-cit) as outcomes and modifiers of the intervention effects (ISRCTN13093195).\n\nOf 750 children, mean \u00b1 SD age was 32.0 \u00b1 11.7 months and height-for-age Z-score was -3.02 \u00b1 0.74. Neither MP nor WP had effects on p-cit or f-MPO. f-MPO decreased over time among controls (ratio of change 0.54, 95% confidence interval [CI]: 0.35, 0.84), but not among those given LNS (0.99, 95% CI: 0.79, 1.23) (p = 0.016). In contrast, LNS had no effect on p-cit (p = 0.27). The effect of LNS on cobalamin (B12) status was reduced in children with p-cit <20 \u00b5mol/L; whereby there was 20% (95% CI: 2, 35) lower increase in plasma cobalamin and 59% (95% CI: 13, 125) smaller decrease in plasma methylmalonic acid. p-cit or f-MPO did not modify the effects of LNS on growth or other micronutrient markers.\n\nLNS had no effect on enterocyte mass and possibly increased intestinal inflammation. The effect of LNS on cobalamin status was reduced in those with low enterocyte mass.", "doi": "10.1002/jpn3.70023", "pmid": "40033718", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12066887"}], "notes": [], "created": "2025-11-27T11:23:57.649Z", "modified": "2025-11-27T11:23:57.767Z"}, {"entity": "publication", "iuid": "da040e812a93400d8e2d085b287e2d33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da040e812a93400d8e2d085b287e2d33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da040e812a93400d8e2d085b287e2d33"}}, "title": "Characterization of Extracellular Vesicles Derived From Human Precision-Cut Liver Slices in Metabolic Dysfunction-Associated Steatotic Liver Disease.", "authors": [{"family": "Geng", "given": "Yana", "initials": "Y", "orcid": "0000-0003-1529-0875", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd1524719c71429bba79b708066b5874.json"}}, {"family": "Luo", "given": "Ke", "initials": "K"}, {"family": "Stam", "given": "Janine", "initials": "J"}, {"family": "Oosterhuis", "given": "Dorenda", "initials": "D"}, {"family": "Gorter", "given": "Alan R", "initials": "AR"}, {"family": "van den Heuvel", "given": "Marius", "initials": "M"}, {"family": "Crescitelli", "given": "Rossella", "initials": "R", "orcid": "0000-0002-1714-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d4b955f26ca4a679deb090e30d0ccf1.json"}}, {"family": "de Meijer", "given": "Vincent E", "initials": "VE"}, {"family": "Wolters", "given": "Justina C", "initials": "JC"}, {"family": "Olinga", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "J Extracell Biol", "issn": "2768-2811", "volume": "4", "issue": "5", "pages": "e70043", "issn-l": null}, "abstract": "Extracellular vesicles (EVs) are cell-produced, membrane-surrounded vesicles that harbour the biological features of donor cells. In the current study, we are the first to isolate and characterize EVs isolated from human precision-cut liver slices (PCLS), obtained from both healthy and metabolic dysfunction-associated steatohepatitis (MASH) cirrhotic livers. PCLS derived from patients can faithfully represent disease conditions in humans. EVs were isolated from human PCLS after incubating in normal medium or modified medium that mimics the pathophysiological environment of metabolic dysfunction associated liver disease (MASLD). MASH PCLS produced higher amounts of EVs compared to healthy PCLS (p < 0.001). Mass spectrometry revealed that around 300 proteins were significantly different in EVs derived from MASH PCLS versus healthy PCLS (FDR < 0.05), irrespective of the type of medium. Significantly changed EV proteins were largely involved in signalling receptor binding function and showed potential in promoting fibrosis. In the liver, these ligand-associated receptors are highly expressed in hepatic stellate cells, and the MASH EVs functionally promoted the activation of hepatic stellate cells. Furthermore, the amounts of EpCAM and ITGA3 in EVs were positively associated with the progression of MASLD, which suggests the use of liver-derived EVs as potential biomarkers for MASLD. Characterization of EVs derived from human PCLS may assist future studies in investigating the pathogenesis and identifying liver-specific EVs as biomarkers of MASLD.", "doi": "10.1002/jex2.70043", "pmid": "40313415", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12042696"}, {"db": "pii", "key": "JEX270043"}], "notes": [], "created": "2025-11-05T13:50:42.948Z", "modified": "2025-11-05T13:50:43.051Z"}, {"entity": "publication", "iuid": "29c97bfb137b4ac8b38bc0c1a89c70a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29c97bfb137b4ac8b38bc0c1a89c70a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29c97bfb137b4ac8b38bc0c1a89c70a9"}}, "title": "Blood biomarkers of Alzheimer's disease and 12-year muscle strength trajectories in community-dwelling older adults: a cohort study.", "authors": [{"family": "Ornago", "given": "Alice M", "initials": "AM"}, {"family": "Pinardi", "given": "Elena", "initials": "E"}, {"family": "Grande", "given": "Giulia", "initials": "G"}, {"family": "Valletta", "given": "Martina", "initials": "M"}, {"family": "Calder\u00f3n-Larra\u00f1aga", "given": "Amaia", "initials": "A"}, {"family": "Andersson", "given": "Sarah", "initials": "S"}, {"family": "Calvani", "given": "Riccardo", "initials": "R"}, {"family": "Picca", "given": "Anna", "initials": "A"}, {"family": "Marzetti", "given": "Emanuele", "initials": "E"}, {"family": "Winblad", "given": "Bengt", "initials": "B"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Bellelli", "given": "Giuseppe", "initials": "G"}, {"family": "Vetrano", "given": "Davide L", "initials": "DL"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Lancet Healthy Longev", "issn": "2666-7568", "volume": "6", "issue": "5", "pages": "100715", "issn-l": null}, "abstract": "Age-related muscle function decline is a major impediment to healthy ageing. We aimed to investigate the association between a panel of Alzheimer's disease-related biomarkers and longitudinal trajectories of muscle strength, while exploring the influence of cognitive function.\n\nIn this cohort study, we gathered data from the Swedish National study on Aging and Care in Kungsholmen (SNAC-K), an ongoing prospective study that includes adults aged 60 years and older, from central Stockholm, Sweden. We included data from baseline to the fourth follow-up (March 21, 2001, to Dec 31, 2016). Seven Alzheimer's disease-related blood biomarkers were measured in dementia-free, community dwelling participants: total tau, phosphorylated tau181 (p-tau181), phosphorylated tau217 (p-tau217), amyloid \u03b2 40 and 42, neurofilament light chain, and glial fibrillary acidic protein (GFAP). Muscle strength was measured through the handgrip strength and chair-stand tests. Linear mixed models were used to explore the association between baseline Alzheimer's disease-related biomarkers and muscle strength trajectories.\n\nThe baseline SNAC-K cohort included 3363 individuals, of whom 1953 participants were included in our analyses (mean age 70\u00b72 [SD 9\u00b71] years; 780 [39\u00b79%] male and 1173 [60\u00b71%] female participants). In adjusted models, higher concentrations of p-tau181 (\u03b2 per year 0\u00b793 [95% CI 0\u00b771 to 1\u00b716]; p<0\u00b70001), p-tau217 (\u03b2 per year 1\u00b731 [1\u00b703 to 1\u00b758]; p<0\u00b70001), neurofilament light chain (\u03b2 per year 0\u00b776 [0\u00b756 to 0\u00b796]; p<0\u00b70001), and GFAP (\u03b2 per year 0\u00b737 [0\u00b721 to 0\u00b753]; p<0\u00b70001) were associated with an accelerated decline of chair-stand performance over time. The adjustment for Mini-Mental State Examination (MMSE) score led to the attenuation of these associations. Higher concentrations of p-tau181 (\u03b2 per year -0\u00b712 [95% CI -0\u00b717 to -0\u00b707]; p<0\u00b70001), p-tau217 (\u03b2 per year -0\u00b713 [-0\u00b720 to -0\u00b707]; p<0\u00b70001), and neurofilament light chain (\u03b2 per year -0\u00b705 [-0\u00b709 to -0\u00b7001]; p=0\u00b7047) were also associated with faster handgrip strength decline, with no attenuation after adjusting for MMSE score. Sex-specific differences were observed, with female participants showing a stronger association between biomarker concentrations and muscle strength decline than male participants, particularly in the chair-stand test.\n\nOur findings suggest that blood Alzheimer's disease-related biomarkers might help estimate progressive muscle strength decline among older adults, elucidating the influence of brain pathology and cognitive ageing on this association. These Alzheimer's disease-related biomarkers could aid in identifying individuals for early intervention to prevent sarcopenia.\n\nThe Swedish Research Council, the Swedish Ministry of Health and Social Affairs, and the County Councils and Municipalities.", "doi": "10.1016/j.lanhl.2025.100715", "pmid": "40414227", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2666-7568(25)00034-0"}], "notes": [], "created": "2025-09-21T09:52:33.303Z", "modified": "2025-09-21T09:52:33.361Z"}, {"entity": "publication", "iuid": "ef42f05457244d9398ea8f053490771c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef42f05457244d9398ea8f053490771c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef42f05457244d9398ea8f053490771c"}}, "title": "Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes.", "authors": [{"family": "Pinder", "given": "Matthew I M", "initials": "MIM", "orcid": "0000-0003-4407-0214", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6d9f52178249f3995c3d276fbc2728.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Blossom", "given": "Hannah", "initials": "H"}, {"family": "Svensson", "given": "Marie", "initials": "M"}, {"family": "Rengefors", "given": "Karin", "initials": "K", "orcid": "0000-0001-6297-9734", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7353dd11fa445f9ff338db5ce8dadd.json"}}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "25", "issue": "4", "pages": "e14067", "issn-l": "1755-098X"}, "abstract": "Evolutionary changes in populations of microbes, such as microalgae, cannot be traced using conventional metabarcoding loci as they lack intraspecific resolution. Consequently, selection and competition processes among strains of the same species cannot be resolved without elaborate isolation, culturing, and genotyping efforts. Bamboozle, a new bioinformatic tool introduced here, scans the entire genome of a species and identifies allele-rich barcodes that enable direct identification of different genetic strains from a population using amplicon sequencing of a single DNA sample. We demonstrate its usefulness by identifying hypervariable barcoding loci (< 500 bp) from genomic data in two microalgal species, the diploid diatom Skeletonema marinoi and the haploid chlorophyte Chlamydomonas reinhardtii. Across the two genomes, four and twenty-two loci, respectively, were identified that could in silico resolve all analysed genotypes. All of the identified loci are within protein-coding genes with various metabolic functions. Single nucleotide polymorphisms (SNPs) provided the most reliable genetic markers, and among 54 strains of S. marinoi, three 500 bp loci contained, on average, 46 SNPs, 103 strain-specific alleles, and displayed 100% heterozygosity. This high level of heterozygosity was identified as a novel opportunity to improve strain quantification and detect false positive artefacts during denoising of amplicon sequences. Finally, we illustrate how metabarcoding of a single genetic locus can be used to track abundances of S. marinoi strains in an artificial selection experiment. As future genomic datasets become available and DNA sequencing technologies develop, Bamboozle has flexible user settings enabling optimal barcodes to be designed for other species and applications.", "doi": "10.1111/1755-0998.14067", "pmid": "39903046", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11969633"}], "notes": [], "created": "2025-11-21T11:38:37.352Z", "modified": "2025-11-21T11:38:37.527Z"}, {"entity": "publication", "iuid": "c1c3b39dad864eed8d1aa7429c86a4dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1c3b39dad864eed8d1aa7429c86a4dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1c3b39dad864eed8d1aa7429c86a4dc"}}, "title": "A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening.", "authors": [{"family": "Gilardet", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-4851-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f507b07ed934c73988dfd0537254485.json"}}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Garc\u00eda", "given": "Gonzalo Oteo", "initials": "GO"}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G"}, {"family": "Douka", "given": "Katerina", "initials": "K"}, {"family": "Wooller", "given": "Matthew J", "initials": "MJ"}, {"family": "Rowe", "given": "Timothy", "initials": "T"}, {"family": "Martin", "given": "Michael D", "initials": "MD"}, {"family": "Le Moullec", "given": "Mathilde", "initials": "M"}, {"family": "Anisimov", "given": "Michail", "initials": "M"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "25", "issue": "4", "pages": "e14077", "issn-l": "1755-098X"}, "abstract": "Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancient DNA laboratories and have even been automated on robotic platforms. Robots offer a solution for high-throughput screening but the costs, as well as necessity for trained technicians and engineers, can be prohibitive for some laboratories. Here, we present a high-throughput alternative to robot-based ancient DNA extraction using a 96-column plate. When compared to routine single MinElute columns, we retrieved highly similar endogenous DNA contents, an important metric in ancient DNA screening. Mitogenomes with a coverage depth greater than 0.1\u00d7 could be generated and allowed for taxonomic assignment. However, average fragment lengths, DNA damage and library complexities significantly differed between methods but these differences became nonsignificant after modification of our library purification protocol. Our high-throughput extraction method allows generation of 96 extracts within approximately 4 hours of laboratory work while bringing the cost down by ~39% compared to using single columns. Additionally, we formally demonstrate that the addition of Tween-20 during the elution step results in higher complexity libraries, thereby enabling higher genome coverage for the same sequencing effort.", "doi": "10.1111/1755-0998.14077", "pmid": "39912442", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11969639"}, {"db": "RefSeq", "key": "GCA_018282365.1"}, {"db": "RefSeq", "key": "KX269145.1"}, {"db": "RefSeq", "key": "GCA_951394145.1"}, {"db": "RefSeq", "key": "NC_007703.1"}, {"db": "RefSeq", "key": "GCA_024166365.1"}, {"db": "RefSeq", "key": "DQ188829.2"}, {"db": "RefSeq", "key": "NC_007596.2"}], "notes": [], "created": "2026-02-26T11:50:43.248Z", "modified": "2026-02-26T11:50:43.282Z"}, {"entity": "publication", "iuid": "08b6731fb6f641a6a182b86cc3382112", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08b6731fb6f641a6a182b86cc3382112.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08b6731fb6f641a6a182b86cc3382112"}}, "title": "Maternal Adiponectin Decreases Placenta Nutrient Transport in Mice.", "authors": [{"family": "Samad", "given": "Manisha", "initials": "M", "orcid": "0009-0004-4926-9104", "researcher": {"href": "https://publications.scilifelab.se/researcher/bebdb554cab54dfeae35d7884add29d2.json"}}, {"family": "Ulfenborg", "given": "Benjamin", "initials": "B"}, {"family": "Soleimani Sani", "given": "Sahar", "initials": "S"}, {"family": "Bauz\u00e1 Thorbr\u00fcgge", "given": "Marco", "initials": "M"}, {"family": "Mohan Shrestha", "given": "Man", "initials": "M"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Maliqueo", "given": "Manuel", "initials": "M"}, {"family": "Stener-Victorin", "given": "Elisabet", "initials": "E", "orcid": "0000-0002-3424-1502", "researcher": {"href": "https://publications.scilifelab.se/researcher/b56343efabb34afa9baecef059417a3a.json"}}, {"family": "Wernstedt Asterholm", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0755-5784", "researcher": {"href": "https://publications.scilifelab.se/researcher/45e1e47469f942fe8392109ca802f78c.json"}}, {"family": "Benrick", "given": "Anna", "initials": "A", "orcid": "0000-0003-4616-6789", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b2939d573c04f0abc063ac18e97bd40.json"}}], "type": "journal article", "published": "2025-04-30", "journal": {"title": "FASEB J.", "issn": "1530-6860", "volume": "39", "issue": "8", "pages": "e70556", "issn-l": "0892-6638"}, "abstract": "Women with obesity who develop gestational diabetes have lower serum adiponectin throughout pregnancy, suggesting that low levels impair the ability to handle metabolic challenges during pregnancy. The placenta expresses adiponectin receptors, and adiponectin could therefore indirectly affect the developing fetus. Here, we aimed to investigate how elevated maternal and fetal adiponectin affect placental function, fetal growth, and metabolism during pregnancy in normal-weight and obese mice. Wild-type (wt) and adiponectin-overexpressing (APNtg) mice were fed normal chow or a high fat/high sucrose (HF/HS) diet 8 weeks before and during pregnancy to induce obesity. Mice were euthanized and dissected on gestational day 18.5. Lipid, glucose, and amino acid tracers were administered to the obese pregnant dams to study nutrient uptake. The effects of elevated adiponectin on fetal liver and placental function were further investigated using global proteomics. A 40%-50% increase in serum adiponectin reduced fetal growth in dams fed a HF/HS diet, but not a normal chow diet. The uptake of glucose, lipid, and amino acid tracer was lower, along with decreased expression of several amino acid transporters in the placenta of APNtg dams on HF/HS diet. This suggests that adiponectin decreases placental transfer of nutrients. Livers of fetuses from APNtg dams showed downregulated lipid and amino acid metabolic pathways possibly reflecting an energy deficit. In conclusion, elevated serum adiponectin in obese dams reduced the placental transfer of nutrients, resulting in fetal growth restriction and altered fetal liver function. Maternal adiponectin levels were the main driver of placenta function. While this could be beneficial for pregnancy-related complications like babies born large for their gestation age, our study indicates that adiponectin should be in an optimal concentration range, neither too low nor too high, to prevent these complications.", "doi": "10.1096/fj.202403251RR", "pmid": "40249643", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12007623"}], "notes": [], "created": "2025-10-23T13:07:33.398Z", "modified": "2025-10-23T13:07:33.650Z"}, {"entity": "publication", "iuid": "e8147f938ad64b01a966c699c60dd5ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8147f938ad64b01a966c699c60dd5ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8147f938ad64b01a966c699c60dd5ee"}}, "title": "High Content Imaging in Drug Discovery", "authors": [], "type": "edited-book", "published": "2025-04-30", "journal": {"title": "ISBN: 978-1-83767-186-1", "issn": "ISBN: 978-1-83767-186-1", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1039/9781837676941", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2025-05-05T09:05:33.732Z", "modified": "2025-12-18T19:18:11.230Z"}, {"entity": "publication", "iuid": "f76f0d3a713a4e599c005a45f6173c07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f76f0d3a713a4e599c005a45f6173c07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f76f0d3a713a4e599c005a45f6173c07"}}, "title": "BTB/POZ-MATH proteins regulate Arabidopsis seedling development by promoting auxin-independent degradation of the Aux/IAA protein IAA10.", "authors": [{"family": "Ban", "given": "Zhaonan", "initials": "Z", "orcid": "0009-0004-5447-2027", "researcher": {"href": "https://publications.scilifelab.se/researcher/46c1dcf5b9444095b77449e6faaf984c.json"}}, {"family": "Hou", "given": "Yueh-Ju", "initials": "YJ", "orcid": "0000-0002-2750-4167", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c659cd3e4674b409d4d140adcd6a7dc.json"}}, {"family": "Ku", "given": "Ellyse", "initials": "E", "orcid": "0009-0000-4363-8678", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8c883c7bae74c38b793fc5d49536926.json"}}, {"family": "Zhu", "given": "YingLin", "initials": "Y"}, {"family": "Hu", "given": "Yun", "initials": "Y", "orcid": "0000-0002-6932-958X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9eff5ce3dc84a64891ef0ae8576ea61.json"}}, {"family": "Karadanaian", "given": "Natalie", "initials": "N", "orcid": "0009-0008-2033-4733", "researcher": {"href": "https://publications.scilifelab.se/researcher/261278a78ea84a35a88c9107e1448548.json"}}, {"family": "Zhao", "given": "Yunde", "initials": "Y", "orcid": "0000-0002-7224-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc3ca1242324997b85fd4ccd5178520.json"}}, {"family": "Estelle", "given": "Mark", "initials": "M", "orcid": "0000-0002-2613-8652", "researcher": {"href": "https://publications.scilifelab.se/researcher/96ecde5a1c5740629a4891794207d073.json"}}], "type": "journal article", "published": "2025-04-30", "journal": {"title": "Plant Physiol.", "issn": "1532-2548", "volume": "198", "issue": "1", "issn-l": "0032-0889"}, "abstract": "After germination, seedlings undergo etiolated development (skotomorphogenesis), enabling them to grow toward the soil surface. In Arabidopsis (Arabidopsis thaliana), etiolated seedlings exhibit rapid hypocotyl elongation, apical hook formation, and closed cotyledons to protect the meristem. In this study, we found that high-order mutants in the BPM (BTB/POZ-MATH) gene family displayed defects in seedling development, characterized by a shorter hypocotyl, early apical hook opening, and opened cotyledons in the dark. BPM1, BPM2, BPM4, and BPM5 exhibited distinct expression patterns and subcellular localization in etiolated seedlings. In a hypocotyl segment assay, the bpm mutants showed defects in auxin response, indicating impaired auxin signaling in the hypocotyl. Expression of the auxin reporter DR5:GFP was also altered in the bpm1,4,5 mutant in various tissues compared with the wild type. Furthermore, yeast 2-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assay analyses showed that BPM1 interacts with IAA10. Experiments in protoplasts indicated that BPM1 promotes IAA10 ubiquitylation and degradation, which was supported by greater IAA10 protein accumulation in the bpm1,4,5 mutant background. In addition, IAA10 overexpression resulted in phenotypes similar to those of the bpm mutants, indicating that the BPMs may target the Aux/IAA proteins for ubiquitylation and degradation. Overall, our findings shed light on the key roles of the BPMs in auxin signaling during seedling development.", "doi": "10.1093/plphys/kiaf155", "pmid": "40257842", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12043071"}, {"db": "pii", "key": "8126202"}], "notes": [], "created": "2025-11-18T12:06:39.582Z", "modified": "2025-11-18T12:06:39.933Z"}, {"entity": "publication", "iuid": "b0c1d831145149dea42f664622f9d614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0c1d831145149dea42f664622f9d614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0c1d831145149dea42f664622f9d614"}}, "title": "The overlooked trio: sleep duration, sampling time and physical exercise alter levels of olink-assessed blood biomarkers of cardiovascular risk.", "authors": [{"family": "Brand\u00e3o", "given": "Luiz Eduardo Mateus", "initials": "LEM"}, {"family": "Zhang", "given": "Lei", "initials": "L"}, {"family": "Grip", "given": "Anastasia", "initials": "A"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "K\u00e5ks", "given": "Emil", "initials": "E"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Sigurdardottir", "given": "Fjola", "initials": "F"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Espes", "given": "Daniel", "initials": "D"}, {"family": "Omland", "given": "Torbj\u00f8rn", "initials": "T"}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "Benedict", "given": "Christian", "initials": "C"}, {"family": "Cedernaes", "given": "Jonathan", "initials": "J"}], "type": "letter", "published": "2025-04-29", "journal": {"title": "Biomark Res", "issn": "2050-7771", "volume": "13", "issue": "1", "pages": "67", "issn-l": null}, "abstract": "Biomarker profiling from biofluids such as blood are widely measured in clinical research, using for example Olink proteomics panels. One such research focus area is cardiovascular disease (CVD), for which chronic sleep restriction (SR) is a risk factor. However, it remains unclear whether blood levels of commonly measured CVD biomarkers are sensitive to acute dynamic factors such as SR, physical exercise (PEx), and time of day. In this crossover design, 16 normal-weight, healthy men underwent three highly standardized in-lab nights of SR (4.25 h/night) and normal sleep (NS, 8.5 h/night) in randomized order, with 88 CVD blood protein biomarkers quantified using the Olink technology (and selected validation using ELISA) in the morning, evening, and immediately before and repeatedly after 30 min of high-intensity exercise. We found significant time-of-day-dependent changes in several CVD biomarkers. Whereas several proteins were exercise-induced across sleep conditions (such as the canonical exerkines IL- 6 and BDNF), exercise-induced proteomic dynamics differed in response to recurrent SR, compared with following NS. Moreover, SR compared with NS resulted in a biomarker profile previously associated with increased prospective risk of several CVDs across large-scale cohorts (such as higher circulating levels of IL-27 and LGALS9). Our findings highlight how dynamic physiology can modulate CVD biomarker levels. These results also underscore the need to consider sleep duration as a key determinant of cardiovascular health-an emphasis reflected in recent American Heart Association guidelines. Further studies in women, older individuals, and patients with prior CVD, and across different chronotypes and dietary schedules are warranted.", "doi": "10.1186/s40364-025-00776-0", "pmid": "40301994", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12038921"}, {"db": "pii", "key": "10.1186/s40364-025-00776-0"}], "notes": [], "created": "2025-10-06T11:43:23.271Z", "modified": "2025-11-25T19:21:06.056Z"}, {"entity": "publication", "iuid": "bebf3754bd684c6193cb41b10e65ba73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bebf3754bd684c6193cb41b10e65ba73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bebf3754bd684c6193cb41b10e65ba73"}}, "title": "Structure and Inhibition of the Human Na+/H+ Exchanger SLC9B2.", "authors": [{"family": "Jung", "given": "Sukkyeong", "initials": "S"}, {"family": "Kokane", "given": "Surabhi", "initials": "S"}, {"family": "Li", "given": "Hang", "initials": "H"}, {"family": "Iwata", "given": "So", "initials": "S"}, {"family": "Nomura", "given": "Norimichi", "initials": "N", "orcid": "0000-0002-6330-2239", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b604af54f4a49f8a7884fbd70d99101.json"}}, {"family": "Drew", "given": "David", "initials": "D", "orcid": "0000-0001-8866-6349", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc19844f8147480fb0af2e437744131b.json"}}], "type": "journal article", "published": "2025-04-29", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "9", "issn-l": null}, "abstract": "The sodium/proton exchanger NHA2, also known as SLC9B2, is important for insulin secretion, renal blood pressure regulation, and electrolyte retention. Recent structures of bison NHA2 has revealed its unique 14-transmembrane helix architecture, which is different from SLC9A/NHE members made up from 13-TM helices. Sodium/proton exchangers are functional homodimers, and the additional N-terminal helix in NHA2 was found to alter homodimer assembly. Here, we present the cryo-electron microscopy structures of apo human NHA2 in complex with a Fab fragment and also with the inhibitor phloretin bound at 2.8 and 2.9 \u00c5 resolution, respectively. We show how phosphatidic acid (PA) lipids bind to the homodimer interface of NHA2 on the extracellular side, which we propose has a regulatory role linked to cell volume regulation. The ion binding site of human NHA2 has a salt bridge interaction between the ion binding aspartate D278 and R432, an interaction previously broken in the bison NHA2 structure, and these differences suggest a possible ion coupling mechanism. Lastly, the human NHA2 structure in complex with phloretin offers a template for structure-guided drug design, potentially leading to the development of more selective and potent NHA2 inhibitors.", "doi": "10.3390/ijms26094221", "pmid": "40362458", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12072577"}, {"db": "pii", "key": "ijms26094221"}], "notes": [], "created": "2025-11-23T22:22:48.254Z", "modified": "2025-11-23T22:22:48.286Z"}, {"entity": "publication", "iuid": "6072fdc2c2a64ec5ad2b7aa1a93ddf0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6072fdc2c2a64ec5ad2b7aa1a93ddf0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6072fdc2c2a64ec5ad2b7aa1a93ddf0b"}}, "title": "Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI.", "authors": [{"family": "Bj\u00e4rterot", "given": "Patrik", "initials": "P"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Shariatgorji", "given": "Reza", "initials": "R"}, {"family": "Vallianatou", "given": "Theodosia", "initials": "T", "orcid": "0000-0002-1477-7756", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae610b7669754328a119654fdfcd6af4.json"}}, {"family": "Kaya", "given": "Ibrahim", "initials": "I"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}], "type": "journal article", "published": "2025-04-29", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "97", "issue": "16", "pages": "9033-9041", "issn-l": "0003-2700"}, "abstract": "Here, we introduce Met-ID, a graphical user interface software designed to efficiently identify metabolites from MALDI-MSI data sets. Met-ID enables annotation of m/z features from any type of MALDI-MSI experiment, involving either derivatizing or conventional matrices. It utilizes structural information for derivatizing matrices to generate a subset of targets that contain only functional groups specific to the derivatization agent. The software is able to identify multiple derivatization sites on the same molecule, facilitating identification of the derivatized compound. This ability is exemplified by FMP-10, a reactive matrix that assists the covalent charge-tagging of molecules containing phenolic hydroxyl and/or primary or secondary amine groups. Met-ID also permits users to recalibrate data with known m/z ratios, boosting confidence in mass match results. Furthermore, Met-ID includes a database featuring MS2 spectra of numerous chemical standards, consisting of neurotransmitters and metabolites derivatized with FMP-10, alongside peaks for FMP-10 itself, all accessible directly through the software. The MS2 spectral database supports user-uploaded spectra and enables comparison of these spectra with user-provided tissue MS2 spectra for similarity assessment. Although initially installed with basic data, Met-ID is designed to be customizable, encouraging users to tailor the software to their specific needs. While several MSI-oriented software solutions exist, Met-ID combines both MS1 and MS2 functionalities. Developed in alignment with the FAIR Guiding Principles for scientific software, Met-ID is freely available as an open-source tool on GitHub, ensuring wide accessibility and collaboration.", "doi": "10.1021/acs.analchem.5c00633", "pmid": "40253716", "labels": {"Spatial Mass Spectrometry": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12044586"}], "notes": [], "created": "2025-11-21T09:59:55.456Z", "modified": "2025-11-21T09:59:55.515Z"}, {"entity": "publication", "iuid": "c894a8b4aad0439fba39b3372706eac5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c894a8b4aad0439fba39b3372706eac5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c894a8b4aad0439fba39b3372706eac5"}}, "title": "Identification of TRIM21 and TRIM14 as Antiviral Factors Against Langat and Zika Viruses.", "authors": [{"family": "Tran", "given": "Pham-Tue-Hung", "initials": "PT", "orcid": "0000-0002-8366-9310", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f2bf1bdd4049408825fe9a91815e3a.json"}}, {"family": "Kabir", "given": "Mir Himayet", "initials": "MH"}, {"family": "Asghar", "given": "Naveed", "initials": "N", "orcid": "0000-0003-4442-8503", "researcher": {"href": "https://publications.scilifelab.se/researcher/d162f92509c44b509e72b95bfcb89456.json"}}, {"family": "Hathaway", "given": "Matthew R", "initials": "MR"}, {"family": "Hayderi", "given": "Assim", "initials": "A"}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}, {"family": "Karlsson", "given": "Anders", "initials": "A", "orcid": "0000-0002-2927-481X", "researcher": {"href": "https://publications.scilifelab.se/researcher/47af21fe1dd34c45909bc7268b6da563.json"}}, {"family": "Taylor", "given": "Travis", "initials": "T", "orcid": "0000-0002-3819-8548", "researcher": {"href": "https://publications.scilifelab.se/researcher/75eb75025424490cb6dd702ec569e966.json"}}, {"family": "Melik", "given": "Wessam", "initials": "W", "orcid": "0000-0001-9876-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/791933a0971046d0b5dbfb7c66e8853b.json"}}, {"family": "Johansson", "given": "Magnus", "initials": "M", "orcid": "0000-0003-3962-2141", "researcher": {"href": "https://publications.scilifelab.se/researcher/e62f28d803604d9b959eee6f29855b60.json"}}], "type": "journal article", "published": "2025-04-29", "journal": {"title": "Viruses", "issn": "1999-4915", "volume": "17", "issue": "5", "issn-l": "1999-4915"}, "abstract": "Flaviviruses are usually transmitted to humans via mosquito or tick bites, whose infections may lead to severe diseases and fatality. During intracellular infection, they remodel the endoplasmic reticulum (ER) membrane to generate compartments scaffolding the replication complex (RC) where replication of the viral genome takes place. In this study, we purified the ER membrane fraction of virus infected cells to identify the proteins that were enriched during flavivirus infection. We found that tripartite motif-containing proteins (TRIMs) including TRIM38, TRIM21, and TRIM14 were significantly enriched during infection with mosquito-borne (West Nile virus strain Kunjin and Zika virus (ZIKV)) and tick-borne (Langat virus (LGTV)) flaviviruses. Further characterizations showed that TRIM21 and TRIM14 act as restriction factors against ZIKV and LGTV, while TRIM38 hinders ZIKV infection. These TRIMs worked as interferon-stimulated genes to mediate IFN-I response against LGTV and ZIKV infections. Restriction of ZIKV by TRIM14 and TRIM38 coincides with their colocalization with ZIKV NS3. TRIM14-mediated LGTV restriction coincides with its colocalization with LGTV NS3 and NS5 proteins. However, TRIM21 did not colocalize with ZIKV and LGTV NS3 or NS5 protein suggesting its antiviral activity is not dependent on direct targeting the viral enzyme. Finally, we demonstrated that overexpression of TRIM21 and TRIM14 restricted LGTV replication.", "doi": "10.3390/v17050644", "pmid": "40431659", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12116035"}, {"db": "pii", "key": "v17050644"}], "notes": [], "created": "2025-10-23T16:15:17.125Z", "modified": "2025-10-23T16:15:17.777Z"}, {"entity": "publication", "iuid": "1f4e4d96c44643488989943e6820d31a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f4e4d96c44643488989943e6820d31a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f4e4d96c44643488989943e6820d31a"}}, "title": "Antibody reactivity in cerebrospinal fluid and serum against the insulin-insulin-like growth factor 2 (INS-IGF2) protein is associated with psychotic symptomatology in patients with schizophrenia or related psychosis.", "authors": [{"family": "Melkersson", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2025-04-28", "journal": {"title": "Neuro Endocrinol. Lett.", "issn": "2354-4716", "volume": "46", "issue": "1", "pages": "1-14", "issn-l": "0172-780X"}, "abstract": "Evidence has accumulated that an autoimmune-mediated process may underlie development of schizophrenia, and in two recent studies, we found increased antibody reactivity against the insulin receptor-A (INSR-A) and insulin-like growth factor 1 receptor (IGF1R) and their ligands (insulin and insulin-like growth factor 1) in cerebrospinal fluid (CSF) and/ or serum from patients with schizophrenia or related psychosis. The aim of this study was to analyze antibody reactivity in schizophrenia against the insulin-insulin-like growth factor 2 (INS-IGF2) protein, which hypothetically also may be a ligand to INSR-A and IGF1R and involved in the pathogenesis of schizophrenia.\n\nPatients with schizophrenia or related psychosis and controls were analyzed regarding antibody reactivity against INS-IGF2 in CSF (n = 12/ n = 11) and serum (n = 17/ n = 11), using bead-based antigen arrays of one protein fragment and 24 peptides of this protein. Additionally, the patients were assessed for clinical symptoms with the Positive and Negative Syndrome Scale (PANSS) for schizophrenia.\n\nSignificantly higher antibody reactivity against the peptides 11 and 12 was found in patients in partial than full symptom remission. Patients' antibody reactivity against the peptides 5, 11 and 12 correlated positively to their PANSS scores of positive symptoms. Furthermore, significantly higher antibody reactivity against the peptides 2, 3, 10 and 22 was found in patients with, than without, heredity for diabetes mellitus type 1 or 2.\n\nThe findings in this study pointed that the INS-IGF2 protein may be present in the CNS and involved in the autoimmune-mediated process underlying the development of schizophrenia.", "doi": null, "pmid": "40319454", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "46012502"}], "notes": [], "created": "2025-09-10T08:13:51.362Z", "modified": "2025-09-10T08:13:51.369Z"}, {"entity": "publication", "iuid": "b5cc99856bf64c30bfe02525fafc7f83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5cc99856bf64c30bfe02525fafc7f83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5cc99856bf64c30bfe02525fafc7f83"}}, "title": "Significant Associations Between Blood Cell Counts and Plasma Cytokines, Chemokines, and Growth Factors.", "authors": [{"family": "Eriksson", "given": "Lars B", "initials": "LB", "orcid": "0009-0002-1818-7347", "researcher": {"href": "https://publications.scilifelab.se/researcher/44d17c21be93409fb4d5bc5de121b497.json"}}, {"family": "Eriksson", "given": "Mats B", "initials": "MB", "orcid": "0000-0002-3178-4210", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfcf6caaeeea422997c259d802e7e6f8.json"}}, {"family": "Gordh", "given": "Torsten", "initials": "T", "orcid": "0000-0003-1454-3148", "researcher": {"href": "https://publications.scilifelab.se/researcher/de40b19a854f4dda88986d2e00e8f091.json"}}, {"family": "Larsson", "given": "Anders O", "initials": "AO", "orcid": "0000-0003-3161-0402", "researcher": {"href": "https://publications.scilifelab.se/researcher/2276de26382b402aa384ac231f30f156.json"}}], "type": "journal article", "published": "2025-04-25", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "9", "pages": "4065", "issn-l": null}, "abstract": "The cytokine network plays a crucial role in regulating immune responses and facilitating intercellular communication. Cytokines are essential in numerous physiological and pathological processes. This study aimed to investigate associations between blood cell counts and a broad range of cytokines, chemokines, and growth factors. We included one hundred and sixty-five essentially healthy individuals in this study, which was approved by the Swedish Ethical Review Authority (Dnr 2015/378) and registered in EudraCT (2014-004235-39). Blood samples were collected for blood cell counts and analysis of cytokines, chemokines, and growth factors using the Proseek Multiplex Inflammation kit, Olink Bioscience, Uppsala, Sweden. Correlations between the different markers were calculated using Spearman rank correlations, adjusted for multiplicity and for multiple testing, with a significance threshold of p < 0.05. There were significant associations between platelet count and 23 cytokines, between white blood cell count and 8 cytokines, and between erythrocyte volume fractions and 19 cytokines. IL-6 had a central role within the cytokine network associated with platelets and was also associated with white blood cells and neutrophil cells. These findings emphasize the integrated nature of immune and hematological responses, where blood cell parameters are associated with systemic cytokine activity. The observed intercytokine associations, including cross-family interactions, may help to highlight regulatory pathways, providing potential targets for biomarker development and therapeutic intervention in immune-mediated conditions.", "doi": "10.3390/ijms26094065", "pmid": "40362303", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12072032"}, {"db": "pii", "key": "ijms26094065"}], "notes": [], "created": "2025-11-25T19:22:44.406Z", "modified": "2026-02-11T12:57:44.138Z"}, {"entity": "publication", "iuid": "303527db99344e4783365b6316dcc907", "links": {"self": {"href": "https://publications.scilifelab.se/publication/303527db99344e4783365b6316dcc907.json"}, "display": {"href": "https://publications.scilifelab.se/publication/303527db99344e4783365b6316dcc907"}}, "title": "Longitudinal changes in blood-borne geroscience biomarkers: results from a population-based study.", "authors": [{"family": "Picca", "given": "Anna", "initials": "A"}, {"family": "Nguyen", "given": "Ngoc Viet", "initials": "NV"}, {"family": "Calvani", "given": "Riccardo", "initials": "R"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Marzetti", "given": "Emanuele", "initials": "E"}, {"family": "Calder\u00f3n-Larra\u00f1aga", "given": "Amaia", "initials": "A"}, {"family": "Vetrano", "given": "Davide Liborio", "initials": "DL", "orcid": "0000-0002-3099-4830", "researcher": {"href": "https://publications.scilifelab.se/researcher/06867644d5f14eef958737353517f53d.json"}}], "type": "journal article", "published": "2025-04-24", "journal": {"title": "Geroscience", "issn": "2509-2723", "issn-l": null}, "abstract": "Multi-marker approaches are well suited for untangling the intrinsic complexity of aging and related conditions. Herein, we quantified (1) baseline concentrations of a panel of geroscience biomarkers pertaining to four biological domains (i.e., metabolism, inflammation, vascular/organ dysfunction and cellular senescence, and neurodegeneration) in individuals aged \u226560 years; (2) investigated linear and non-linear changes in biomarker levels over a 6-year period according to age and sex; and (3) described the relationships among geroscience biomarkers at baseline and follow-up. We found that repeated measures of age-dependent changes of 47 blood-borne biomarkers over 6 years had differential associations depending on the biological domains. The most relevant biomolecules in the associations between age and repeated assessments were (1) adiponectin, C-peptide, renin (metabolism), (2) CXCL10, IL-1\u03b1, IL-1\u03b2, IL-6, IL-10, IL-12p70, MPO (inflammation), (3) cystatin C, MMP7, MMP12, VCAM-1 (vascular/organ dysfunction and cellular senescence), and (4) S100B and Tau protein (neurodegeneration). Among these molecules, a negative association with increasing age was found for IL-1\u03b1, IL-1\u03b2, IL-12p70, S100B, and Tau protein. Non-linear relationships were also identified with age for IGFBP-1, leptin, \u03b22M, TNFRSF1B, fibrinogen, GDF-15, N-cadherin, and BDNF. Our results indicate that inflammatory and metabolic biomolecules are strongly associated with aging over 6 years of follow-up. Whether the biological pathways reflected by these biomarkers contribute to the aging process or are associated with negative health-related events needs to be explored through comprehensive multi-omics longitudinal analysis in larger cohorts.", "doi": "10.1007/s11357-025-01666-x", "pmid": "40272732", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s11357-025-01666-x"}], "notes": [], "created": "2025-09-21T09:52:30.611Z", "modified": "2025-09-21T09:52:30.798Z"}, {"entity": "publication", "iuid": "e2d13bad5737495b893d34596e3fee25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2d13bad5737495b893d34596e3fee25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2d13bad5737495b893d34596e3fee25"}}, "title": "Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis.", "authors": [{"family": "Sreenivasan", "given": "Akshai Parakkal", "initials": "AP"}, {"family": "Vaivade", "given": "Aina", "initials": "A"}, {"family": "Noui", "given": "Yassine", "initials": "Y", "orcid": "0000-0002-0513-7546", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e4b7066daf4084b24fdbbac41e3c9e.json"}}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE", "orcid": "0000-0002-4137-5517", "researcher": {"href": "https://publications.scilifelab.se/researcher/23c186a5ec4f46479fe0db63caa77ed2.json"}}, {"family": "Burman", "given": "Joachim", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K"}], "type": "journal article", "published": "2025-04-24", "journal": {"title": "NPJ Digit Med", "issn": "2398-6352", "volume": "8", "issue": "1", "pages": "224", "issn-l": null}, "abstract": "Accurate assessment of progression and disease course in multiple sclerosis (MS) is vital for timely and appropriate clinical intervention. The gradual transition from relapsing-remitting MS (RRMS) to secondary progressive MS (SPMS) is often diagnosed retrospectively with a typical delay of three years. To address this diagnostic delay, we developed a predictive model that uses electronic health records to distinguish between RRMS and SPMS at each individual visit. To enable reliable predictions, conformal prediction was implemented at the individual patient level with a confidence of 93%. Our model accurately predicted the change in diagnosis from RRMS to SPMS for patients who transitioned during the study period. Additionally, we identified new patients who, with high probability, are in the transition phase but have not yet received a clinical diagnosis. Our methodology aids in monitoring MS progression and proactively identifying transitioning patients. An anonymized model is available at https://msp-tracker.serve.scilifelab.se/ .", "doi": "10.1038/s41746-025-01616-z", "pmid": "40275055", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41746-025-01616-z"}], "notes": [], "created": "2025-04-25T09:40:03.092Z", "modified": "2025-04-25T09:40:06.333Z"}, {"entity": "publication", "iuid": "408127f4edb9428db0ff41f5175bbd16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/408127f4edb9428db0ff41f5175bbd16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/408127f4edb9428db0ff41f5175bbd16"}}, "title": "A CRISPR homing screen finds a chloroquine resistance transporter-like protein of the Plasmodium oocyst essential for mosquito transmission of malaria.", "authors": [{"family": "Balakrishnan", "given": "Arjun", "initials": "A", "orcid": "0000-0002-8845-5741", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bd36ee6f81049b09972a9ad3f56dae4.json"}}, {"family": "Hunziker", "given": "Mirjam", "initials": "M"}, {"family": "Tiwary", "given": "Puja", "initials": "P"}, {"family": "Pandey", "given": "Vikash", "initials": "V"}, {"family": "Drew", "given": "David", "initials": "D", "orcid": "0000-0001-8866-6349", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc19844f8147480fb0af2e437744131b.json"}}, {"family": "Billker", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1716-168X", "researcher": {"href": "https://publications.scilifelab.se/researcher/baa3de453a8047688800db0d5a14e291.json"}}], "type": "journal article", "published": "2025-04-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "3895", "issn-l": "2041-1723"}, "abstract": "Genetic screens with barcoded PlasmoGEM vectors have identified thousands of Plasmodium berghei gene functions in haploid blood stages, gametocytes and liver stages. However, the formation of diploid cells by fertilisation has hindered similar research on the parasites' mosquito stages. In this study, we develop a scalable genetic system that uses barcoded gene targeting vectors equipped with a CRISPR-mediated homing mechanism to generate homozygous loss-of-function mutants after one parent introduces a modified allele into the zygote. To achieve this, we use vectors additionally expressing a target gene specific gRNA. When integrated into one of the parental alleles it directs Cas9 to the intact allele after fertilisation, leading to its disruption. This homing strategy is 90% effective at generating homozygous gene editing of a fluorescence-tagged reporter locus in the oocyst. A pilot screen identifies PBANKA_0916000 as a chloroquine resistance transporter-like protein (CRTL) essential for oocyst growth and sporogony, pointing to an unexpected importance for malaria transmission of the poorly understood digestive vacuole of the oocyst that contains hemozoin granules. Homing screens provide a method for the systematic discovery of malaria transmission genes whose first essential functions are after fertilisation in the bloodmeal, enabling their potential as targets for transmission-blocking interventions to be assessed.", "doi": "10.1038/s41467-025-59099-1", "pmid": "40274854", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Cryo-EM": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12022033"}, {"db": "pii", "key": "10.1038/s41467-025-59099-1"}], "notes": [], "created": "2025-09-29T11:07:05.501Z", "modified": "2025-11-18T13:13:42.205Z"}, {"entity": "publication", "iuid": "bf30bef38e144822aa0db8832eae0142", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf30bef38e144822aa0db8832eae0142.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf30bef38e144822aa0db8832eae0142"}}, "title": "The evaluation of biogenic silica in brackish and freshwater strains reveals links between phylogeny and silica accumulation in picocyanobacteria.", "authors": [{"family": "Aguilera", "given": "Anabella", "initials": "A", "orcid": "0000-0001-6743-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6e88f127e7d49d09f593a57aa4a794e.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Charalampous", "given": "Evangelia", "initials": "E"}, {"family": "Churakova", "given": "Yelena", "initials": "Y"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "\u015aliwi\u0144ska-Wilczewska", "given": "Sylwia", "initials": "S"}, {"family": "Conley", "given": "Daniel J", "initials": "DJ"}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}], "type": "journal article", "published": "2025-04-23", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "issn-l": "0099-2240", "volume": "91", "issue": "4", "pages": "e0252724"}, "abstract": "Through biosilicification, organisms incorporate dissolved silica (dSi) and deposit it as biogenic silica (bSi), driving the silicon (Si) cycle in aquatic systems. While Si accumulation in marine picocyanobacteria has been recently observed, its mechanisms and ecological implications remain unclear. This study investigates biosilicification in marine and brackish picocyanobacteria of the Synechococcus clade and two model freshwater coccoid cyanobacteria. Brackish strains showed significantly higher Si quotas when supplemented with external dSi (100 \u00b5M) compared to controls (up to 60.0 \u00b1 7.3 amol Si.cell-1 versus 9.2 to 16.3 \u00b1 2.9 amol Si.cell-1). Conversely, freshwater strains displayed no significant differences in Si quotas between dSi-enriched treatments and controls, emphasizing that not all phytoplanktons without an obligate Si requirement accumulate this element. The Si-accumulating marine and brackish picocyanobacteria clustered within the Synechococcus clade, whereas their freshwater counterparts formed a distinct sister group, suggesting a link between phylogeny and silicification. Rapid culture growth caused increased pH and led to dSi precipitation, influencing apparent dSi uptake; this was mitigated by pH control through bubbling. This phenomenon has significant implications for natural systems affected by phytoplankton blooms. In such environments, pH-induced silicon precipitation may reduce dSi availability impacting Si-dependent populations like diatoms. Our findings suggest brackish picocyanobacteria could significantly influence the Si cycle through at least two mechanisms: cellular Si accumulation and biologically induced changes in dSi concentrations.IMPORTANCEThis work provides the first evidence of biogenic silica accumulation in brackish picocyanobacteria and uncovers a link between phylogeny and biosilicification patterns. Our findings demonstrate that picocyanobacterial growth induces pH-dependent silica precipitation, which could lead to overestimations of cellular Si quotas by up to 85%. This process may drive substantial silica precipitation in highly productive freshwater and coastal marine systems, with potential effects on silica cycling and the population dynamics of Si-dependent phytoplankton. The extent of biosilicification in modern picocyanobacteria offers insights into the rock record, shedding light on the evolutionary and ecological dynamics that influence sedimentary processes and the preservation of biosilicification signatures in geological formations. Overall, this research adds to the significant impact that microorganisms lacking an obligate silica requirement may have on silica dynamics.", "doi": "10.1128/aem.02527-24", "pmid": "40145754", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12016540"}], "notes": [], "created": "2025-08-19T13:32:14.905Z", "modified": "2025-11-28T10:52:04.161Z"}, {"entity": "publication", "iuid": "79747f23f5454fac8fc495846688fdc5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79747f23f5454fac8fc495846688fdc5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79747f23f5454fac8fc495846688fdc5"}}, "title": "Pregnancy is associated with a simultaneous but independent increase in circulating CD177pos and immature low-density granulocytes.", "authors": [{"family": "Dahlstrand Rudin", "given": "Agnes", "initials": "A", "orcid": "0000-0002-4362-8645", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d06d9a382b47d1ab027f9c5ccf1a6c.json"}}, {"family": "Torell", "given": "Agnes", "initials": "A", "orcid": "0000-0002-5063-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b18cdec677534f81ace4f1019c1e259f.json"}}, {"family": "Popovic", "given": "Jordan", "initials": "J"}, {"family": "Stockfelt", "given": "Marit", "initials": "M", "orcid": "0000-0002-4438-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/acd0cab678fd43c9b3d7033f0d736dde.json"}}, {"family": "Jacobsson", "given": "Bo", "initials": "B", "orcid": "0000-0001-5079-2374", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6968816ded4a50b1029ee3f4afbeed.json"}}, {"family": "Rudin", "given": "Anna", "initials": "A", "orcid": "0000-0002-4137-1276", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa2b87964bc0472b88fa4267ee23c483.json"}}, {"family": "Christenson", "given": "Karin", "initials": "K", "orcid": "0000-0003-2489-2253", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fdedf6000064ace8915482db6725fa6.json"}}, {"family": "Lundell", "given": "Anna-Carin", "initials": "AC", "orcid": "0000-0002-4303-8266", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dcec31a10cc444fb6da5a0ca8e94a45.json"}}, {"family": "Bylund", "given": "Johan", "initials": "J", "orcid": "0000-0002-9094-6478", "researcher": {"href": "https://publications.scilifelab.se/researcher/782377f783314bcdb2d2c6d9be4532de.json"}}], "type": "journal article", "published": "2025-04-23", "journal": {"title": "J Leukoc Biol", "issn": "0741-5400", "volume": "117", "issue": "4", "issn-l": null}, "abstract": "The neutrophil marker CD177 (NB1, HNA-2a) is expressed by 0-100% of circulating neutrophils in any given donor, dividing neutrophils into 2 distinct subpopulations (CD177pos and CD177neg). High proportions of CD177pos blood neutrophils have been linked to both systemic infections and a range of inflammatory pathologies, but whether this is a cause or a consequence of disease is not known. Many conditions displaying elevated CD177pos neutrophil proportions are also accompanied by the presence of circulating low-density granulocytes. Accordingly, it is tempting to speculate that these 2 events are connected (i.e. that proportions of CD177pos neutrophils increase as a result of an enlarged pool of circulating low-density granulocytes). A temporary increase in CD177pos neutrophils, in combination with the presence of low-density granulocytes, has been reported during pregnancy. The present study aimed to investigate whether elevated proportions of CD177pos neutrophils in peripheral blood from pregnant women can be attributed to the presence of low-density granulocytes. We found that low-density granulocytes were indeed present in pregnancy and included both immature and activated mature neutrophils. The proportion of CD177pos low-density granulocytes increased over time during pregnancy and correlated with a simultaneous increase in immature cells. However, most immature neutrophils were CD177neg, meaning that increased release of immature cells cannot explain the increased proportions of the CD177pos subtype. Therefore, although low-density granulocytes and CD177pos neutrophils are expanded simultaneously during pregnancy, these events occur independently from each other.", "doi": "10.1093/jleuko/qiae255", "pmid": "39698836", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "7928531"}], "notes": [], "created": "2025-11-20T18:09:55.773Z", "modified": "2025-11-20T18:09:56.315Z"}, {"entity": "publication", "iuid": "fd4bf8d0823746af8250499b9667f9cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd4bf8d0823746af8250499b9667f9cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd4bf8d0823746af8250499b9667f9cf"}}, "title": "Sex differences in DNMT3A-mutant clonal hematopoiesis and the effects of estrogen.", "authors": [{"family": "Stomper", "given": "Julia", "initials": "J"}, {"family": "Niroula", "given": "Abhishek", "initials": "A"}, {"family": "Belizaire", "given": "Roger", "initials": "R"}, {"family": "McConkey", "given": "Marie", "initials": "M"}, {"family": "Bandaru", "given": "Tagore Sanketh", "initials": "TS"}, {"family": "Ebert", "given": "Benjamin L", "initials": "BL"}], "type": "journal article", "published": "2025-04-22", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "44", "issue": "4", "pages": "115494", "issn-l": null}, "abstract": "Blood cancers are generally more common in males, and the prevalence of most mutations that drive clonal hematopoiesis and myeloid malignancies is higher in males. In contrast, hematopoietic DNMT3A mutations are more common in females. Among \u223c450,000 participants in the UK Biobank, the prevalence of DNMT3A mutations and copy-number abnormalities is higher in females than males. In a murine model, Dnmt3a-mutant hematopoietic stem cells (HSCs) from unperturbed female mice had increased stemness gene expression compared to male and wild-type (WT) mice. Estrogen regulates HSCs, and we found that Dnmt3a mutations maintain stemness in the setting of estrogen-induced proliferative stress. Dnmt3a-mutant myeloid cells outcompeted WT cells under chronic estrogen treatment, an effect that was dependent on cell-intrinsic estrogen receptor alpha activity. Our studies indicate that estrogen might contribute to the female predominance of DNMT3A-mutant clonal hematopoiesis.", "doi": "10.1016/j.celrep.2025.115494", "pmid": "40178977", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(25)00265-7"}], "notes": [], "created": "2025-11-28T10:42:21.144Z", "modified": "2025-11-28T10:42:21.151Z"}, {"entity": "publication", "iuid": "dd9e13e9976344fe908694d445f72f2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd9e13e9976344fe908694d445f72f2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd9e13e9976344fe908694d445f72f2b"}}, "title": "Omics Approach for Personalised Prevention of Type 2 Diabetes Mellitus for African and European Populations (OPTIMA): a protocol paper.", "authors": [{"family": "Goedecke", "given": "Julia H", "initials": "JH", "orcid": "0000-0001-6795-4771", "researcher": {"href": "https://publications.scilifelab.se/researcher/81baadfd5cf74300afbf96759a2f1da2.json"}}, {"family": "Danquah", "given": "Ina", "initials": "I"}, {"family": "Abidha", "given": "Carol Akinyi", "initials": "CA"}, {"family": "Agyemang", "given": "Charles", "initials": "C"}, {"family": "Albers", "given": "Hannah Maike", "initials": "HM"}, {"family": "Amoah", "given": "Stephen", "initials": "S"}, {"family": "Brunius", "given": "Carl", "initials": "C"}, {"family": "Chorell", "given": "Elin", "initials": "E"}, {"family": "Hoosen", "given": "Fatima", "initials": "F"}, {"family": "Fortuin-de Smidt", "given": "Melony", "initials": "M"}, {"family": "H\u00f6rnsten", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Karlsson", "given": "Therese", "initials": "T"}, {"family": "Lindholm", "given": "Lars", "initials": "L"}, {"family": "Mendham", "given": "Amy E", "initials": "AE", "orcid": "0000-0002-1959-6698", "researcher": {"href": "https://publications.scilifelab.se/researcher/f24326b5bf344d9798eda2c36ad04c6f.json"}}, {"family": "Micklesfield", "given": "Lisa K", "initials": "LK", "orcid": "0000-0002-4994-0779", "researcher": {"href": "https://publications.scilifelab.se/researcher/5612ae5336394e20972f8d7f79b78ab9.json"}}, {"family": "Meili", "given": "Kaspar Walter", "initials": "KW"}, {"family": "Noerman", "given": "Stefania", "initials": "S"}, {"family": "Otten", "given": "Julia", "initials": "J", "orcid": "0000-0001-9016-1139", "researcher": {"href": "https://publications.scilifelab.se/researcher/0038b9a380164700b77cda3879133a29.json"}}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S", "orcid": "0000-0001-9225-1306", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13944767ad9446e885ce32ca88afebd.json"}}, {"family": "van der Linden", "given": "Eva L", "initials": "EL", "orcid": "0000-0002-4037-1717", "researcher": {"href": "https://publications.scilifelab.se/researcher/eccf3f02edc142709e76ec1ec655597a.json"}}, {"family": "Wittenbecher", "given": "Clemens", "initials": "C"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Olsson", "given": "Tommy", "initials": "T"}], "type": "journal article", "published": "2025-04-22", "journal": {"title": "BMJ Open", "issn": "2044-6055", "volume": "15", "issue": "4", "pages": "e099108", "issn-l": null}, "abstract": "The prevalence of type 2 diabetes (T2D) within sub-Saharan Africa (SSA) is increasing. Despite the pathophysiology of T2D differing by ethnicity and sex, risk stratification and guidelines for the prevention of T2D are generic, relying on evidence from studies including predominantly Europeans. Accordingly, this study aims to develop ethnic-specific and sex-specific risk prediction models for the early detection of dysglycaemia (impaired glucose tolerance and T2D) to inform clinically feasible, culturally acceptable and cost-effective risk management and prevention strategies using dietary modification in SSA and European populations.\n\nThis multinational collaboration will include the prospective cohort data from two African cohorts, the Middle-Aged Soweto Cohort from South Africa and the Research on Obesity and Diabetes among African Migrants Prospective cohort from Ghana and migrants living in Europe, and a Swedish cohort, the Pre-Swedish CArdioPulmonary bioImage Study. Targeted proteomics, as well as targeted and untargeted metabolomics, will be performed at baseline to discover known and novel ethnic-specific and sex-specific biomarkers that predict incident dysglycaemia in the different longitudinal cohorts. Dietary patterns that explain maximum variation in the biomarker profiles and that associate with dysglycaemia will be identified in the SSA and European cohorts and used to build the prototypes for dietary interventions to prevent T2D. A comparative cost-effectiveness analysis of the dietary interventions will be estimated in the different populations. Finally, the perceptions of at-risk participants and healthcare providers regarding ethnic-specific and sex-specific dietary recommendations for the prevention of T2D will be assessed using focus group discussions and in-depth interviews in South Africa, Ghana, Germany (Ghanaian migrants) and Sweden.\n\nEthical clearance has been obtained from all participating sites. The study results will be disseminated at scientific conferences and in journal publications, and through community engagement events and diabetes organisations in the respective countries.", "doi": "10.1136/bmjopen-2025-099108", "pmid": "40262963", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12015709"}, {"db": "pii", "key": "bmjopen-2025-099108"}], "notes": [], "created": "2025-11-27T11:28:11.932Z", "modified": "2025-11-27T11:28:12.140Z"}, {"entity": "publication", "iuid": "078638bca66c4645a3fe9d948edc54ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/078638bca66c4645a3fe9d948edc54ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/078638bca66c4645a3fe9d948edc54ba"}}, "title": "Mapping effective microRNA pairing beyond the seed using abasic modifications.", "authors": [{"family": "Kosek", "given": "David M", "initials": "DM", "orcid": "0000-0002-0192-4761", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c830a2538b64080ba47428cdd6c92b3.json"}}, {"family": "Petzold", "given": "Katja", "initials": "K", "orcid": "0000-0001-9470-0347", "researcher": {"href": "https://publications.scilifelab.se/researcher/946f0162cdb0411493968f363c943ad5.json"}}, {"family": "Andersson", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8608-625X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7313cdcd5f41d4a567a6c315aac3a1.json"}}], "type": "journal article", "published": "2025-04-22", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "8", "issn-l": "0305-1048"}, "abstract": "MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression by base-pairing to complementary sites in messenger RNAs (mRNAs). The primary element for site recognition is the seed region (nucleotides 2-8 in the miRNA), but for a minority of sites pairing outside the seed increases efficiency, with the supplementary region (nucleotides 13-16) typically having the greatest impact. However, the structural determinants of effective pairing outside the seed are not fully understood. Here, we use abasic modified nucleotides to disrupt pairing to residues 13 and 14 of miR-34a and measure the effect of this modification compared to wild-type miR-34a on the cellular transcriptome and proteome using RNA-seq and mass spectrometry. We find that a subset of sites with predicted supplementary pairing are affected by miRNA transfection, with up to two-fold decreases in site repression at the mRNA level. We show that miR-34a 3'-pairing is sensitive to GU wobble pairs in a position-specific manner and favors bulges in the miRNA over the target. These results were validated with luciferase reporter assays. Overall, this study demonstrates a novel methodological approach for elucidating the role of specific miRNA residues in target site selection, advancing our understanding of miRNA-mediated gene regulation.", "doi": "10.1093/nar/gkaf364", "pmid": "40298108", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12038393"}, {"db": "pii", "key": "8121647"}], "notes": [], "created": "2025-11-27T13:03:14.944Z", "modified": "2025-11-27T13:03:15.405Z"}, {"entity": "publication", "iuid": "eba679997f32456a948f17cc10289938", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eba679997f32456a948f17cc10289938.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eba679997f32456a948f17cc10289938"}}, "title": "Prognostic Value of the Circulating Tumor DNA Fraction in Metastatic Castration-resistant Prostate Cancer: Results from the ProBio Platform Trial.", "authors": [{"family": "Crippa", "given": "Alessio", "initials": "A"}, {"family": "Laere", "given": "Bram De", "initials": "B"}, {"family": "Discacciati", "given": "Andrea", "initials": "A"}, {"family": "Larsson", "given": "Berit", "initials": "B"}, {"family": "Persson", "given": "Maria", "initials": "M"}, {"family": "Johansson", "given": "Susanne", "initials": "S"}, {"family": "D'hondt", "given": "Sanne", "initials": "S"}, {"family": "Hj\u00e4lm-Eriksson", "given": "Marie", "initials": "M"}, {"family": "Pettersson", "given": "Linn", "initials": "L"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Ull\u00e9n", "given": "Anders", "initials": "A"}, {"family": "Lumen", "given": "Nicolaas", "initials": "N"}, {"family": "Karlsson", "given": "Camilla Thellenberg", "initials": "CT"}, {"family": "Sandz\u00e9n", "given": "Johan", "initials": "J"}, {"family": "J\u00e4nes", "given": "Elin", "initials": "E"}, {"family": "Ghysel", "given": "Christophe", "initials": "C"}, {"family": "Olsson", "given": "Martha", "initials": "M"}, {"family": "Sautois", "given": "Brieuc", "initials": "B"}, {"family": "Schatteman", "given": "Peter", "initials": "P"}, {"family": "Roock", "given": "Wendy De", "initials": "W"}, {"family": "Bruwaene", "given": "Siska Van", "initials": "SV"}, {"family": "Verbiene", "given": "Ingrida", "initials": "I"}, {"family": "Darras", "given": "Jochen", "initials": "J"}, {"family": "Everaert", "given": "Els", "initials": "E"}, {"family": "Maeseneer", "given": "Daan De", "initials": "D"}, {"family": "Anden", "given": "Mats", "initials": "M"}, {"family": "Strijbos", "given": "Michiel", "initials": "M"}, {"family": "Luyten", "given": "Daisy", "initials": "D"}, {"family": "Mortezavi", "given": "Ashkan", "initials": "A"}, {"family": "Oldenburg", "given": "Jan", "initials": "J"}, {"family": "Ost", "given": "Piet", "initials": "P"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "ProBio Investigators", "given": "", "initials": ""}], "type": "journal article", "published": "2025-04-21", "journal": {"title": "Eur Urol Oncol", "issn": "2588-9311", "issn-l": null}, "abstract": "The aim of this study was to evaluate the prognostic value of undetectable circulating tumor DNA (ctDNA) and the dose-response relationship between ctDNA levels and survival outcomes in metastatic castration-resistant prostate cancer (mCRPC).\n\nWe analyzed data for patients enrolled in the ProBio trial up to November 2022 who received an androgen receptor pathway inhibitor or taxane. We compared survival outcomes between patients with undetectable ctDNA and those with detectable ctDNA randomized to physician's choice or investigational arms. Time to no longer clinically benefiting (NLCB) and overall survival (OS) were assessed using Bayesian survival models, with results reported as survival time ratios (STRs). Dose-response relationships were estimated using spike-at-zero models.\n\nA total of 220 patients were included, of whom 139 had detectable ctDNA (56 in the physician's choice arm, 83 in investigational arms) and 81 had undetectable ctDNA. In comparison to the undetectable ctDNA group, the physician's choice arm had 60% shorter time to NLCB (STR 0.40, 90% credible interval [CrI] 0.31-0.51) and 51% shorter OS (STR 0.49, 90% CrI 0.38-0.61). Similar results were observed in comparison to the investigational arms. Dose-response analysis revealed that the undetectable ctDNA group had twofold longer time to NLCB (STR 2.05, 90% CrI 1.66-2.57) and 1.6-fold longer OS (STR 1.63, 90% CrI 1.33-2.05) in comparison to the subgroup with a ctDNA fraction of 2.5%. Every 10-point increment in the ctDNA fraction corresponded to a 10% reduction in NLCB and OS times.\n\nUndetectable ctDNA at baseline predicts superior prognosis in mCRPC, suggesting potential for treatment de-escalation and less intensive monitoring for this subgroup of patients. This trial is registered on ClinicalTrials.gov as NCT03903835.", "doi": "10.1016/j.euo.2025.02.002", "pmid": "40263079", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S2588-9311(25)00037-9"}, {"db": "ClinicalTrials.gov", "key": "NCT03903835"}], "notes": [], "created": "2025-11-18T17:28:38.658Z", "modified": "2025-11-18T20:45:43.260Z"}, {"entity": "publication", "iuid": "fd8026fc626a4b06a20c3d7bb29a29e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd8026fc626a4b06a20c3d7bb29a29e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd8026fc626a4b06a20c3d7bb29a29e6"}}, "title": "Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Jansson", "given": "Ingela", "initials": "I", "orcid": "0000-0002-2255-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/44e799cd5f7f4343955b0a261ff6df96.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Packer", "given": "Craig", "initials": "C", "orcid": "0000-0002-3939-8162", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cacbf9051428186cf6fe23d4f8a02.json"}}, {"family": "Norman", "given": "Anita", "initials": "A"}, {"family": "Kissui", "given": "Bernard M", "initials": "BM"}, {"family": "E Mjingo", "given": "Ernest", "initials": "E"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1246-5046", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccdce43407204828b73bce24fc4e6453.json"}}], "type": "journal article", "published": "2025-04-21", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "640", "issn-l": "2399-3642"}, "abstract": "Small, isolated populations are at greater risk of genome erosion than larger populations. Successful conservation efforts may lead to demographic recovery and mitigate the negative genetic effects of bottlenecks. However, constrained gene flow can hamper genomic recovery. Here, we use population genomic analyses and forward simulations to assess the genomic impacts of near extinction in the isolated Ngorongoro Crater lion (Panthera leo) sub-population. We show that 200 years of quasi-isolation and the recent epizootic in 1962 resulted in a two-fold increase in inbreeding and an excess in the frequency of highly deleterious mutations relative to other populations of the Greater Serengeti. There was little evidence for purging of genetic load. Furthermore, forward simulations indicate that higher gene flow from outside of the Crater is needed to prevent future genomic erosion in the population, with a minimum of one to five effective male migrants per decade required to reduce the risk of long-term inbreeding depression and reduction in genetic diversity. Our results suggest that in spite of a rapid post-epizootic demographic recovery since the 1970s, continued isolation of the population driven by habitat fragmentation and potentially male territoriality, exacerbate the effects of genome erosion.", "doi": "10.1038/s42003-025-07986-0", "pmid": "40258987", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12012037"}, {"db": "pii", "key": "10.1038/s42003-025-07986-0"}], "notes": [], "created": "2025-05-26T07:51:41.058Z", "modified": "2025-11-14T11:07:11.711Z"}, {"entity": "publication", "iuid": "fd157c0bb88e4108b85ea4bbd4680ee9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd157c0bb88e4108b85ea4bbd4680ee9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd157c0bb88e4108b85ea4bbd4680ee9"}}, "title": "Abstract 6469: Defining architectural tissue features and cell composition of IDH-mutant gliomas", "authors": [{"family": "Tom\u00e0s", "given": "Elisabet Rodr\u00edguez", "initials": "ER"}, {"family": "Leiss", "given": "Lina", "initials": "L"}, {"family": "Tabiev", "given": "Rasul", "initials": "R"}, {"family": "Nysj\u00f6", "given": "Fredrik", "initials": "F"}, {"family": "Klemm", "given": "Anna", "initials": "A"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C"}, {"family": "Bontell", "given": "Thomas Olsson", "initials": "TO"}, {"family": "D\u00e9nes", "given": "Anna", "initials": "A"}, {"family": "Jakola", "given": "Asgeir S", "initials": "AS"}, {"family": "Smits", "given": "Anja", "initials": "A"}, {"family": "\u00d6stman", "given": "Arne", "initials": "A"}], "type": "journal-article", "published": "2025-04-21", "journal": {"issn": "0008-5472", "volume": "85", "issue": "8_Supplement_1", "pages": "6469-6469", "title": "Cancer Res", "issn-l": "0008-5472"}, "abstract": null, "doi": "10.1158/1538-7445.am2025-6469", "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-12-10T08:14:50.820Z", "modified": "2025-12-10T08:14:50.851Z"}, {"entity": "publication", "iuid": "f9e0fcd794fd47fe9f5bb17cd10c2f79", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9e0fcd794fd47fe9f5bb17cd10c2f79.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9e0fcd794fd47fe9f5bb17cd10c2f79"}}, "title": "Targeted inhibition of WIP1 and histone H3K27 demethylase activity synergistically suppresses neuroblastoma growth.", "authors": [{"family": "Treis", "given": "Diana", "initials": "D", "orcid": "0000-0002-7887-9436", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4ba612265714e60adca9d33db4bed9f.json"}}, {"family": "Lundberg", "given": "Kristina Ihrmark", "initials": "KI"}, {"family": "Bell", "given": "Nicola", "initials": "N"}, {"family": "Polychronopoulos", "given": "Panagiotis Alkinoos", "initials": "PA"}, {"family": "T\u00fcmmler", "given": "Conny", "initials": "C", "orcid": "0000-0002-5530-4752", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a938c192b2d42a89ac210024bfab7a5.json"}}, {"family": "\u00c5kerlund", "given": "Emma", "initials": "E"}, {"family": "Aliverti", "given": "Stefania", "initials": "S"}, {"family": "Lilienthal", "given": "Ingrid", "initials": "I"}, {"family": "Pepich", "given": "Adena", "initials": "A"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4645bc97a8024c548111802101b83571.json"}}, {"family": "Sakaguchi", "given": "Kazuyasu", "initials": "K", "orcid": "0000-0002-8434-4171", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ce1a573aec14041873a5a5700c224c9.json"}}, {"family": "Kogner", "given": "Per", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications.scilifelab.se/researcher/e963274b921a4a2c8263f509334d4e22.json"}}, {"family": "Johnsen", "given": "John Inge", "initials": "JI", "orcid": "0000-0003-1277-812X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5b7b4c780349afacf3063e311c334e.json"}}, {"family": "Wickstr\u00f6m", "given": "Malin", "initials": "M", "orcid": "0000-0001-5214-9956", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd8b895bc0a4dca89c4170f85d3ebb4.json"}}], "type": "journal article", "published": "2025-04-19", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "16", "issue": "1", "pages": "318", "issn-l": "2041-4889"}, "abstract": "High-risk neuroblastoma frequently exhibits segmental gain of chromosome 17q, including the locus of PPM1D, which encodes the phosphatase WIP1, a regulator of p53 activity, DNA repair, and apoptosis. High expression of PPM1D is correlated to poor prognosis, and genetic or pharmacologic inhibition of WIP1 suppresses neuroblastoma growth. Here, we show that combining drugs that target WIP1 and H3K27 demethylation induces synergistic cytotoxicity in neuroblastoma. We screened 527 different compounds together with inhibitors of WIP1 and identified a strong cytotoxic synergism between the WIP1 inhibitor SL-176 and GSK-J4, a specific inhibitor of the H3K27 demethylase JMJD3. Viability assays in neuroblastoma cell lines and treatment of tumor spheroids confirmed the synergistic effect of combining SL-176 with GSK-J4. Immunoblot experiments demonstrated a marked effect on WIP1 downstream targets and apoptosis markers, while qPCR showed a synergistic upregulation of p53 downstream targets PUMA and p21. RNA sequencing revealed a vast number of differentially expressed genes, suggesting a pervasive effect of this drug combination on transcription, with enrichment of pathways involved in DNA damage response. Finally, this drug combination was confirmed to reduce tumor growth in zebrafish xenograft experiments. In conclusion, the combination of the WIP1 inhibitor SL-176 and the epigenetic modifier GSK-J4 induces synergistic cytotoxicity in neuroblastoma cells by potentiating p53 downstream effects.", "doi": "10.1038/s41419-025-07658-1", "pmid": "40253363", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12009370"}, {"db": "pii", "key": "10.1038/s41419-025-07658-1"}], "notes": [], "created": "2025-11-28T10:45:07.721Z", "modified": "2025-11-28T10:45:08.055Z"}, {"entity": "publication", "iuid": "60516cb3deb24e3e8dc96a6a70f370d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60516cb3deb24e3e8dc96a6a70f370d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60516cb3deb24e3e8dc96a6a70f370d9"}}, "title": "Karyotype evolution and speciation in Orthoptera.", "authors": [{"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Castillo", "given": "Elio R D", "initials": "ERD", "orcid": "0000-0003-0154-8337", "researcher": {"href": "https://publications.scilifelab.se/researcher/87fc69a8a2554d24aa7f7170d5a01aee.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}], "type": "journal article", "published": "2025-04-19", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "volume": "38", "issue": "4", "pages": "516-529", "issn-l": "1010-061X"}, "abstract": "Karyotype evolution might fuel speciation and can thereby contribute to species diversity. To test the hypothesis that speciation and karyotype change are linked, we estimated anagenetic and cladogenetic rates of karyotype evolution as well as speciation rates in Orthoptera. We compiled the male diploid chromosome number and the number of visible chromosome arms (the fundamental number) from published sources for 1,541 species. Chromosome-associated speciation rates were estimated by jointly modelling cladogenetic and anagenetic character evolution and the phylogenetic birth-death process in a Bayesian statistical framework using a subset of 516 species from 14 families. Our findings unveiled heterogeneity among orthopteran families in the pace of karyotype evolution and whether it was linked to speciation. In 6/14 clades, we found evidence supporting speciation-associated (cladogenetic) karyotype changes, while in 6/14 clades karyotype evolution was primarily anagenetic. The remaining clades (2/14) showed uncertainty in favour of either model. We further analyzed whether flightless phenotype, and thus less mobile species, showed higher rates of karyotype evolution. We showed that the flightless phenotype is associated with the rate of chromosome loss. The finding indicates contrasting patterns of karyotype evolution within specific orthopteran lineages, thus emphasizing substantial diversity in the pace of this evolutionary process. It also implies that substantial changes in chromosome number, arising from instances of chromosomal gains and losses, are recurring events in orthopterans that are associated with reproductive isolation and speciation, at least in some groups.", "doi": "10.1093/jeb/voaf018", "pmid": "39987462", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "8030560"}], "notes": [], "created": "2025-11-28T10:49:47.860Z", "modified": "2025-11-28T10:49:47.984Z"}, {"entity": "publication", "iuid": "c98d5ccd590e4c039a3d963c2cbb2bd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c98d5ccd590e4c039a3d963c2cbb2bd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c98d5ccd590e4c039a3d963c2cbb2bd1"}}, "title": "Disruption-induced changes in syntrophic propionate and acetate oxidation: flocculation, cell proximity, and microbial activity.", "authors": [{"family": "Weng", "given": "Nils", "initials": "N"}, {"family": "Najafabadi", "given": "Hossein Nadali", "initials": "HN"}, {"family": "Westerholm", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2025-04-19", "journal": {"title": "Biotechnol Biofuels Bioprod", "issn": "2731-3654", "issn-l": null, "volume": "18", "issue": "1", "pages": "45"}, "abstract": "Syntrophic propionate- and acetate-oxidising bacteria (SPOB and SAOB) play a crucial role in biogas production, particularly under high ammonia conditions that are common in anaerobic degradation of protein-rich waste streams. These bacteria rely on close interactions with hydrogenotrophic methanogens to facilitate interspecies electron transfer and maintain thermodynamic feasibility. However, the impact of mixing-induced disruption of these essential syntrophic interactions in biogas systems remains largely unexplored. This study investigates how magnetic stirring and orbital shaking influence degradation dynamics, microbial community composition, and gene expression in syntrophic enrichment communities under high-ammonia conditions.\r\n\r\nStirring significantly delayed the initiation of propionate degradation in one culture and completely inhibited it in the other two parallel cultures, whereas acetate degradation was less affected. Computational fluid dynamics modelling revealed that stirring generated higher shear rates (~ 20 s-1) and uniform cell distribution, while shaking led to lower shear rates and cell accumulation at the bottom of the culture bottle. Visual observations confirmed that stirring inhibited floc formation, while shaking promoted larger flocs compared to the static control condition, which formed smaller flocs and a sheet-like biofilm. Microbial community analysis identified substrate type and degradation progress as primary drivers of community structure, with motion displaying minimal influence. However, metatranscriptomic analysis revealed that motion-induced gene downregulation was associated with motility, surface sensing, and biofilm formation in SAOB and another bacterial species expressing genes for the glycine synthase reductase pathway. Stirring also suppressed oxalate-formate antiporter expression in SPOB, suggesting its dependence on spatial proximity for this energy-conserving mechanism. The strongest gene expression changes of stirring were observed in methanogens, indicating a coupling of the first and last steps of hydrogenotrophic methanogenesis, likely an adaptive strategy for efficient energy conservation. Other downregulated genes included ferrous iron transporters and electron transfer-associated enzymes.\r\n\r\nThis study highlights that stirring critically disrupts the initial syntrophic connection between SPOB and methanogens, whereas SAOB communities exhibit greater tolerance to shear stress and disruptive conditions that inhibits aggregate formation. These findings emphasize the importance of carefully managing mixing regimes, especially when attempting to reactivate ammonia-tolerant syntrophic propionate degraders in biogas systems experiencing rapid propionate accumulation under high-ammonia conditions.", "doi": "10.1186/s13068-025-02644-3", "pmid": "40253350", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC12008871"}, {"db": "pii", "key": "10.1186/s13068-025-02644-3"}], "notes": [], "created": "2025-09-08T11:37:37.001Z", "modified": "2025-10-08T15:40:18.553Z"}, {"entity": "publication", "iuid": "d8643fc1bb1a43d3b9fd1f76d1c85fec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d8643fc1bb1a43d3b9fd1f76d1c85fec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d8643fc1bb1a43d3b9fd1f76d1c85fec"}}, "title": "Structural mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis.", "authors": [{"family": "Gonz\u00e1lez-L\u00f3pez", "given": "Adri\u00e1n", "initials": "A", "orcid": "0000-0002-4302-6855", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cdef9bebbf940a5812ce94fa81519e9.json"}}, {"family": "Ge", "given": "Xueliang", "initials": "X", "orcid": "0000-0001-7954-3195", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d0da6ede33c4780ba09400c10b80565.json"}}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e2b9321c1064208b9c0a1b11dde571d.json"}}, {"family": "Sihlbom Wallem", "given": "Carina", "initials": "C"}, {"family": "Sanyal", "given": "Suparna", "initials": "S", "orcid": "0000-0002-7124-792X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c5ffabce284f28885f6594da1460d6.json"}}, {"family": "Selmer", "given": "Maria", "initials": "M", "orcid": "0000-0001-9079-2774", "researcher": {"href": "https://publications.scilifelab.se/researcher/860221451df4451b8c035ff4cf25c812.json"}}], "type": "journal article", "published": "2025-04-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "3693", "issn-l": "2041-1723"}, "abstract": "The antibiotic resistance protein FusB rescues protein synthesis from inhibition by fusidic acid (FA), which locks elongation factor G (EF-G) to the ribosome after GTP hydrolysis. Here, we present time-resolved single-particle cryo-EM structures explaining the mechanism of FusB-mediated rescue. FusB binds to the FA-trapped EF-G on the ribosome, causing large-scale conformational changes of EF-G that break interactions with the ribosome, tRNA, and mRNA. This leads to dissociation of EF-G from the ribosome, followed by FA release. We also observe two independent binding sites of FusB on the classical-state ribosome, overlapping with the binding site of EF-G to each of the ribosomal subunits, yet not inhibiting tRNA delivery. The affinity of FusB to the ribosome and the concentration of FusB in S. aureus during FusB-mediated resistance support that direct binding of FusB to ribosomes could occur in the cell. Our results reveal an intricate resistance mechanism involving specific interactions of FusB with both EF-G and the ribosome, and a non-canonical release pathway of EF-G.", "doi": "10.1038/s41467-025-58902-3", "pmid": "40251147", "labels": {"Cryo-EM": "Service", "Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12008383"}, {"db": "pii", "key": "10.1038/s41467-025-58902-3"}], "notes": [], "created": "2025-04-24T09:33:19.909Z", "modified": "2025-10-29T14:59:52.946Z"}, {"entity": "publication", "iuid": "ff9cb80f60b040cfa8d506bea536c913", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff9cb80f60b040cfa8d506bea536c913.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff9cb80f60b040cfa8d506bea536c913"}}, "title": "A zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing.", "authors": [{"family": "Morales Castro", "given": "Rodrigo A", "initials": "RA"}, {"family": "Kern", "given": "Bianca C", "initials": "BC"}, {"family": "D\u00edaz-Basabe", "given": "Ang\u00e9lica", "initials": "A"}, {"family": "Meinen", "given": "Eveline R", "initials": "ER"}, {"family": "Zhao", "given": "Danxia", "initials": "D"}, {"family": "Zhou", "given": "Yuqing", "initials": "Y"}, {"family": "Castillo", "given": "Francisca", "initials": "F"}, {"family": "Monasterio", "given": "Gustavo", "initials": "G"}, {"family": "Farcas", "given": "Vlad", "initials": "V"}, {"family": "Ch\u00e1vez", "given": "Myra N", "initials": "MN"}, {"family": "Fransson", "given": "Jennifer", "initials": "J"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ"}], "type": "journal article", "published": "2025-04-17", "journal": {"title": "Mucosal Immunol", "issn": "1935-3456", "issn-l": "1933-0219"}, "abstract": "Promoting intestinal regeneration and enhancing mucosal healing have emerged as promising therapeutic alternatives for treating intestinal disorders that compromise epithelial barrier integrity and function. However, the cellular and molecular mechanisms underlying these processes remain poorly understood. This knowledge gap is partly due to the lack of reliable and cost-effective in vivo models for studying the mechanisms governing intestinal damage and regeneration. Here, we developed a controlled, inducible, and targeted intestinal epithelial cell (IEC) ablation transgenic zebrafish model that recapitulates features of intestinal damage and regeneration observed in humans. Single-cell RNAseq and live imaging revealed accumulation of macrophages in the recovering intestine, contributing to its regeneration. Furthermore, we observed overexpression of insulin-like growth factor binding protein 1a (igfbp1a) during intestinal damage. Morpholino-mediated knockdown of igfbp1a exacerbated intestinal damage and impaired subsequent regeneration. In summary, we introduced a novel zebrafish model of intestinal damage that enables in vivo high-throughput screening for identifying and validating novel modulators of mucosal healing and intestinal regeneration.", "doi": "10.1016/j.mucimm.2025.04.004", "pmid": "40252728", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "S1933-0219(25)00042-X"}], "notes": [], "created": "2025-08-01T08:44:14.561Z", "modified": "2025-08-01T08:44:14.567Z"}, {"entity": "publication", "iuid": "fe11d7e323b2447091d2e5073a72931f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe11d7e323b2447091d2e5073a72931f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe11d7e323b2447091d2e5073a72931f"}}, "title": "Breast cancer patient-derived scaffolds enhance the understanding of PD-L1 regulation and T cell cytotoxicity.", "authors": [{"family": "Garre", "given": "Elena", "initials": "E", "orcid": "0000-0002-3827-4977", "researcher": {"href": "https://publications.scilifelab.se/researcher/90df2c41baee4b0c98035fbc5f77a438.json"}}, {"family": "Rhost", "given": "Sara", "initials": "S"}, {"family": "Gustafsson", "given": "Anna", "initials": "A"}, {"family": "Szeponik", "given": "Louis", "initials": "L", "orcid": "0000-0002-8627-6969", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca113a84f7d14ae89fc0165885e21972.json"}}, {"family": "Araujo", "given": "Thais Fenz", "initials": "TF"}, {"family": "Quiding-J\u00e4rbrink", "given": "Marianne", "initials": "M"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}, {"family": "Landberg", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9004-9403", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa3b79caacba4566897f136a1200476f.json"}}], "type": "journal article", "published": "2025-04-16", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "621", "issn-l": "2399-3642"}, "abstract": "Recent advances as well as obstacles for immune-based cancer treatment strategies, highlight the notable impact of patient cancer microenvironments on the immune cells and immune targets. Here, we use patient-derived scaffolds (PDS) generated from 110 primary breast cancers to monitor the impact of the cancer microenvironment on immune regulators. Pronounced variation in PD-L1 expression is observed in cancer cells adapted to different patient scaffolds. This variation is further linked to clinical observations and correlated with specific proteins detected in the cell-free PDSs using mass spectrometry. When adding T cells to the PDS-based cancer cultures, the killing efficiency of activated T cells vary between the cultures, whereas non-activated T cells modulate the cancer cell PD-L1 expression to treatment-predictive values, matching killing capacities of activated T cells. Surviving cancer cells show enrichment in cancer stem cell and epithelial-to-mesenchymal transition (EMT) features, suggesting that T cells may not efficiently target cells with metastatic potential. We conclude that clinically relevant insights in how to optimally target and guide immune-based cancer therapies can be obtained by including patient-derived scaffolds and cues from the cancer microenvironment in cancer patient handling and drug development.", "doi": "10.1038/s42003-025-08054-3", "pmid": "40240529", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12003762"}, {"db": "pii", "key": "10.1038/s42003-025-08054-3"}], "notes": [], "created": "2025-10-23T16:17:59.440Z", "modified": "2025-10-23T16:17:59.771Z"}, {"entity": "publication", "iuid": "84bb39aa7a504a65be8100a8fd9d1a79", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84bb39aa7a504a65be8100a8fd9d1a79.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84bb39aa7a504a65be8100a8fd9d1a79"}}, "title": "Amino acid restriction sensitizes lung cancer cells to ferroptosis via GCN2-dependent activation of the integrated stress response", "authors": [{"family": "Garellick", "given": "Viktor J", "initials": "VJ"}, {"family": "Gul", "given": "Nadia", "initials": "N"}, {"family": "Horrieh", "given": "Parvin", "initials": "P"}, {"family": "Mustafa", "given": "Dyar", "initials": "D"}, {"family": "Patel", "given": "Angana A H", "initials": "AAH"}, {"family": "Dankis", "given": "Martin", "initials": "M"}, {"family": "Alvarez", "given": "Samantha", "initials": "S"}, {"family": "Berndtson", "given": "Johanna", "initials": "J"}, {"family": "Schwartz", "given": "Maria", "initials": "M"}, {"family": "Persson", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8427-0232", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2a654d9571c4faeac9cd4294e67958d.json"}}, {"family": "Zahirovic", "given": "Fikret", "initials": "F"}, {"family": "Wiel", "given": "Clotilde", "initials": "C"}, {"family": "Sayin", "given": "Volkan I", "initials": "VI"}, {"family": "Lindahl", "given": "Per", "initials": "P"}], "type": "posted-content", "published": "2025-04-16", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.04.10.648120", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-05T13:50:40.411Z", "modified": "2025-12-18T19:16:46.266Z"}, {"entity": "publication", "iuid": "db834613fba7481d870d2cb2fd958282", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db834613fba7481d870d2cb2fd958282.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db834613fba7481d870d2cb2fd958282"}}, "title": "In vivo composition of the mitochondrial nucleoid in mice.", "authors": [{"family": "Garc\u00eda-Villegas", "given": "Rodolfo", "initials": "R"}, {"family": "Odenthal", "given": "Franka", "initials": "F"}, {"family": "Giannoula", "given": "Yvonne", "initials": "Y"}, {"family": "Bonekamp", "given": "Nina A", "initials": "NA"}, {"family": "K\u00fchl", "given": "Inge", "initials": "I"}, {"family": "Park", "given": "Chan Bae", "initials": "CB"}, {"family": "Sp\u00e5hr", "given": "Henrik", "initials": "H"}, {"family": "Motori", "given": "Elisa", "initials": "E"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Larsson", "given": "Nils-G\u00f6ran", "initials": "NG"}], "type": "journal article", "published": "2025-04-15", "journal": {"title": "Biochimica et Biophysica Acta (BBA) - Molecular Cell Research", "issn": "1879-2596", "pages": "119955", "issn-l": "0167-4889"}, "abstract": "Mitochondrial DNA (mtDNA) is compacted into dynamic structures called mitochondrial nucleoids (mt-nucleoids), with the mitochondrial transcription factor A (TFAM) as the core packaging protein. We generated bacterial artificial chromosome (BAC) transgenic mice expressing FLAG-tagged TFAM protein (Tfam-FLAGBAC mice) to investigate the mt-nucleoid composition in vivo. Importantly, we show that the TFAM-FLAG protein is functional and complements the absence of the wild-type TFAM protein in homozygous Tfam knockout mice. We performed immunoprecipitation experiments from different mouse tissues and identified 12 proteins as core mt-nucleoid components by proteomics analysis. Among these, eight proteins correspond to mtDNA replication and transcription factors, while the other four are involved in the mitoribosome assembly. In addition, we used the Tfam-FLAGBAC mice to identify ten proteins that may stabilize TFAM-FLAG upon depletion of the mitochondrial RNA polymerase despite the absence of mtDNA and induction of the LONP1 protease. Finally, we evaluated the changes in mt-nucleoids caused by very high levels of TFAM unraveling nine interactors that could counteract the high TFAM levels to maintain active mtDNA transcription. Altogether, we demonstrate that the Tfam-FLAGBAC mice are a valuable tool for investigating the mt-nucleoid composition in vivo.", "doi": "10.1016/j.bbamcr.2025.119955", "pmid": "40246179", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0167-4889(25)00060-6"}], "notes": [], "created": "2025-04-25T09:31:35.087Z", "modified": "2025-04-25T09:31:35.092Z"}, {"entity": "publication", "iuid": "ef163e2ed5814790a0934534c9cd7801", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef163e2ed5814790a0934534c9cd7801.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef163e2ed5814790a0934534c9cd7801"}}, "title": "Hyperplex PCR enables highly multiplexed analysis of point mutations in wastewater: Long-term SARS-CoV-2 variant surveillance in Sweden as a case study.", "authors": [{"family": "Soares", "given": "Ruben R G", "initials": "RRG"}, {"family": "Varg", "given": "Javier Edo", "initials": "JE"}, {"family": "Szab\u00f3", "given": "Attila", "initials": "A"}, {"family": "Kluge", "given": "Mariana", "initials": "M"}, {"family": "Petrini", "given": "Filip", "initials": "F"}, {"family": "Psallida", "given": "Margarita", "initials": "M"}, {"family": "Olszewski", "given": "Pawe\u0142", "initials": "P"}, {"family": "Nikou", "given": "Danai V", "initials": "DV"}, {"family": "Owusu-Agyeman", "given": "Isaac", "initials": "I"}, {"family": "Perez-Zabaleta", "given": "Mariel", "initials": "M"}, {"family": "Cetecioglu", "given": "Zeynep", "initials": "Z"}, {"family": "Naseem", "given": "Umear", "initials": "U"}, {"family": "Malmberg", "given": "Maja", "initials": "M"}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ"}], "type": "journal article", "published": "2025-04-15", "journal": {"title": "Water Res.", "issn": "1879-2448", "volume": "274", "pages": "123154", "issn-l": "0043-1354"}, "abstract": "Wastewater-based surveillance (WBS) allows the analysis of pathogens, chemicals or other biomarkers in wastewater to derive unbiased epidemiological information at population scale. After re-gaining attention during the SARS-CoV-2 pandemic, the field holds promise as a surveillance and early warning system by tracking emerging pathogens with pandemic potential. Expanding the current toolbox of analytical techniques for wastewater analysis, we explored the use of Hyperplex PCR (hpPCR) to analyse SARS-CoV-2 mutations in wastewater samples collected weekly in up to 22 sites across Sweden between October 2022 and December 2023. The samples were tested using a probe panel ranging from 10- to 18-plex, continuously adapted within 1-2 weeks to quantify relevant mutations of concern over time. For cross-validation, the samples were simultaneously analysed with commonly used methods including quantitative PCR (qPCR) and next-generation sequencing (NGS). hpPCR is demonstrated herein to provide (1) systematic single nucleotide specificity with a straightforward probe design, (2) high multiplexity with minimal panel re-optimization requirements and (3) 4-5-week earlier mutation detection relative to NGS with comparable performance of mutation frequency quantification (Pearson r = 0.88, n = 50). Hence, hpPCR is shown to be a powerful complementary tool to the current workflow involving NGS and qPCR by facilitating the assembly of dynamic high-plex panels compatible with high-frequency monitoring of multiple key pathogens and/or variants in WBS.", "doi": "10.1016/j.watres.2025.123154", "pmid": "39847906", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S0043-1354(25)00068-5"}], "notes": [], "created": "2025-11-24T10:14:36.366Z", "modified": "2025-11-24T10:14:36.393Z"}, {"entity": "publication", "iuid": "2d39103c65ba42bc8ab59ced2d09c8e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d39103c65ba42bc8ab59ced2d09c8e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d39103c65ba42bc8ab59ced2d09c8e3"}}, "title": "Deciphering immune predictors of immunotherapy response: A multiomics approach at the pan-cancer level.", "authors": [{"family": "Li", "given": "Xuexin", "initials": "X"}, {"family": "Pan", "given": "Lu", "initials": "L"}, {"family": "Li", "given": "Weiyuan", "initials": "W"}, {"family": "Liu", "given": "Bingyang", "initials": "B"}, {"family": "Xiao", "given": "Chunjie", "initials": "C"}, {"family": "Chew", "given": "Valerie", "initials": "V"}, {"family": "Zhang", "given": "Xuan", "initials": "X"}, {"family": "Long", "given": "Wang", "initials": "W"}, {"family": "Ginhoux", "given": "Florent", "initials": "F"}, {"family": "Loscalzo", "given": "Joseph", "initials": "J"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Zhang", "given": "Xiaolu", "initials": "X"}, {"family": "Sheng", "given": "Ren", "initials": "R"}, {"family": "Wang", "given": "Zhenning", "initials": "Z"}], "type": "journal article", "published": "2025-04-15", "journal": {"title": "Cell Reports Medicine", "issn": "2666-3791", "volume": "6", "issue": "4", "pages": "101992", "issn-l": "2666-3791"}, "abstract": "Immune checkpoint blockade (ICB) therapy has transformed cancer treatment, yet many patients fail to respond. Employing single-cell multiomics, we unveil T cell dynamics influencing ICB response across 480 pan-cancer and 27 normal tissue samples. We identify four immunotherapy response-associated T cells (IRATs) linked to responsiveness or resistance and analyze their pseudotemporal patterns, regulatory mechanisms, and T cell receptor clonal expansion profiles specific to each response. Notably, transforming growth factor \u03b21 (TGF-\u03b21)+ CD4+ and Temra CD8+ T cells negatively correlate with therapy response, in stark contrast to the positive response associated with CXCL13+ CD4+ and CD8+ T cells. Validation with a cohort of 23 colorectal cancer (CRC) samples confirms the significant impact of TGF-\u03b21+ CD4+ and CXCL13+ CD4+ and CD8+ T cells on ICB efficacy. Our study highlights the effectiveness of single-cell multiomics in pinpointing immune markers predictive of immunotherapy outcomes, providing an important resource for crafting targeted immunotherapies for successful ICB treatment across cancers.", "doi": "10.1016/j.xcrm.2025.101992", "pmid": "40054456", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12047473"}, {"db": "pii", "key": "S2666-3791(25)00065-5"}], "notes": [], "created": "2025-11-28T10:44:41.630Z", "modified": "2025-11-28T10:44:41.638Z"}, {"entity": "publication", "iuid": "81e743c1db534da7b81add01457132f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81e743c1db534da7b81add01457132f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81e743c1db534da7b81add01457132f5"}}, "title": "Choline levels in the pregenual anterior cingulate cortex associated with unpleasant pain experience and anxiety.", "authors": [{"family": "Hudhud", "given": "Lina", "initials": "L"}, {"family": "Hauksson", "given": "J\u00f3n", "initials": "J"}, {"family": "Haney", "given": "Michael", "initials": "M"}, {"family": "Sparrman", "given": "Tobias", "initials": "T"}, {"family": "Eriksson", "given": "Johan", "initials": "J"}, {"family": "Lindgren", "given": "Lenita", "initials": "L"}], "type": "journal article", "published": "2025-04-15", "journal": {"title": "Neuroimage", "issn": "1095-9572", "volume": "310", "pages": "121153", "issn-l": "1053-8119"}, "abstract": "In vivo proton magnetic resonance spectroscopy is a non-invasive technique used to measure biochemical molecules such as choline, glutamate, glutamine, and \u03b3-Aminobutyric acid (GABA), many of which are relevant to anxiety and pain. However, the relationship between these neurotransmitters/metabolites and their implications for anxiety and subjective experience of pain is not yet fully understood. The objective of this cross-sectional study was to investigate the association between anxiety and pain ratings with levels of total choline, glutamate and GABA in brain regions known to be involved in anxiety and emotional experience of pain, specifically pregenual anterior cingulate cortex (pgACC) and dorsal anterior cingulate cortex (dACC). The levels of the neurotransmitters/metabolites were measured using GABA-edited Mescher-Garwood PRESS for GABA measurements, with the OFF-sequence measurements for total choline (tCho) and Glx (combined glutamate + glutamine). The total choline (tCho) signal in our analysis included glycerophosphocholine (GPC) and phosphocholine (PC), which is consistent with standard practices in MRS studies. This approach ensures a robust estimation of tCho concentrations across participants. The study collected data from 38 participants (17 males and 21 females). The analysis revealed a significant correlation between anxiety ratings before a standardized pain provocation and the rated pain unpleasantness during the pain provocation. tCho correlated negatively with these parameters in pgACC. A linear regression analysis indicated that tCho levels in pgACC have a significant negative association with anxiety and perceived pain when controlling for age, depressive symptoms, and alcohol and tobacco intake. We also found that sex significantly moderates the relationship between pgACC choline levels and pain unpleasantness. The study suggests that levels of choline, an essential precursor of acetylcholine, are associated with anxiety and perceived pain. These levels may influence how Glx and GABA contribute to affective pain experiences by modulating the balance between excitatory and inhibitory signals. However, future research is needed to identify the mechanisms involved. Furthermore, the study indicates that sex is a significant factor in this relationship, with lower choline levels being associated with higher pain ratings in females but not in males. This highlights the significance of addressing sex as a biological factor in pain research to better understand the different responses to treatments and to facilitate the development of more effective interventions in the future.", "doi": "10.1016/j.neuroimage.2025.121153", "pmid": "40101868", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1053-8119(25)00155-7"}], "notes": [], "created": "2025-06-11T13:33:14.831Z", "modified": "2025-10-17T13:03:52.281Z"}, {"entity": "publication", "iuid": "d0db3a7ac77747bcb2f5ea10c50753c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d0db3a7ac77747bcb2f5ea10c50753c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d0db3a7ac77747bcb2f5ea10c50753c3"}}, "title": "High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.", "authors": [{"family": "Kop", "given": "Linnea F M", "initials": "LFM"}, {"family": "Koch", "given": "Hanna", "initials": "H", "orcid": "0000-0002-8550-9871", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c6dc824bdf348b28c5f363410e8f902.json"}}, {"family": "Dalcin Martins", "given": "Paula", "initials": "P"}, {"family": "Suarez", "given": "Carolina", "initials": "C"}, {"family": "Kara\u010di\u0107", "given": "Sabina", "initials": "S"}, {"family": "Persson", "given": "Frank", "initials": "F"}, {"family": "Wil\u00e9n", "given": "Britt-Marie", "initials": "BM", "orcid": "0000-0001-6155-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/17fcd853ec9d43bda259e8d440a92eb7.json"}}, {"family": "Hagelia", "given": "Per", "initials": "P"}, {"family": "Jetten", "given": "Mike S M", "initials": "MSM", "orcid": "0000-0002-4691-7039", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b43ecab3b254c8eb61a10099e3fda63.json"}}, {"family": "L\u00fccker", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-2935-4454", "researcher": {"href": "https://publications.scilifelab.se/researcher/b294f448452543be8ee8b6e4e2c38d89.json"}}], "type": "journal article", "published": "2025-04-14", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "101", "issue": "5", "issn-l": "0168-6496"}, "abstract": "Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7 \u00b1 15% but a wide range between 1.2% and 61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.", "doi": "10.1093/femsec/fiaf032", "pmid": "40156577", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11995701"}, {"db": "pii", "key": "8099923"}], "notes": [], "created": "2025-11-28T10:48:50.076Z", "modified": "2025-11-28T10:48:50.216Z"}, {"entity": "publication", "iuid": "650438cf2d6f4f049208fceb9d81c9cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/650438cf2d6f4f049208fceb9d81c9cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/650438cf2d6f4f049208fceb9d81c9cc"}}, "title": "Deep targeted sequencing of circulating tumor DNA to inform treatment in patients with metastatic castration-resistant prostate cancer.", "authors": [{"family": "N\u00f8rgaard", "given": "Maibritt", "initials": "M"}, {"family": "Rusan", "given": "Maria", "initials": "M"}, {"family": "Kondrup", "given": "Karoline", "initials": "K"}, {"family": "S\u00f8rensen", "given": "Ea Marie Givskov", "initials": "EMG"}, {"family": "Weiss", "given": "Simone", "initials": "S"}, {"family": "Bjerre", "given": "Marianne Trier", "initials": "MT"}, {"family": "Freds\u00f8e", "given": "Jacob", "initials": "J"}, {"family": "Vang", "given": "S\u00f8ren", "initials": "S"}, {"family": "Jensen", "given": "J\u00f8rgen Bjerggaard", "initials": "JB"}, {"family": "De Laere", "given": "Bram", "initials": "B"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Borre", "given": "Michael", "initials": "M"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "S\u00f8rensen", "given": "Karina Dalsgaard", "initials": "KD"}], "type": "journal article", "published": "2025-04-14", "journal": {"title": "J. Exp. Clin. Cancer Res.", "issn": "1756-9966", "volume": "44", "issue": "1", "pages": "120", "issn-l": "1756-9966"}, "abstract": "Intrinsic and acquired resistance to second-generation anti-androgens pose a significant clinical challenge in the treatment of metastatic castration-resistant prostate cancer (mCRPC). Novel biomarkers to predict treatment response and inform alternative treatment options are urgently needed.\n\nDeep targeted sequencing, with a prostate cancer-specific gene panel, was performed on circulating tumor DNA (ctDNA) and germline DNA from blood of mCRPC patients recruited in Denmark (n = 53), prior to starting first-line treatment with enzalutamide or abiraterone acetate, and for a subset of patients also at progression (n = 18). Likely clonal hematopoietic variants were filtered out. Genomic findings were correlated to clinical outcomes (PSA progression-free survival (PFS), overall survival (OS)). Intrinsic resistance candidate biomarkers were considered by enrichment analysis of nonresponders vs. responders. Genomic alterations at progression were considered as possible drivers of acquired resistance. Clinical actionability was assessed based on OncoKB and ESCAT.\n\nSomatic alterations in PTEN, cell cycle regulators (CCND1, CDKN1B, CDKN2A, and RB1) and chromatin modulators (CHD1, ARID1A) were associated with significantly shorter PFS and OS, also after adjusting for ctDNA% in multivariate Cox regression analysis. The associations with poorer outcomes for alterations in PTEN and chromatin modulators were validated in an external dataset. Patients with primary resistance to enzalutamide/abiraterone had enrichment for BRAF amplification and CHD1 loss, while responders had enrichment for TMPRSS2 fusions. AR resistance mutations emerged in 22% of patients at progression. These were mutually exclusive with other alterations that may confer resistance (i.e., activating CTNNB1 mutations, combined TP53/RB1 loss). Clinically actionable alterations, primarily in homologous recombination repair genes, were found in 54.7% and 49.0% of patients (OncoKB and ESCAT, respectively), with few additional alterations detected at progression. Level I alterations were identified in 41.5% of patients employing OncoKB, however only in 13.2% based on ESCAT.\n\nOur study identifies known and novel prognostic and predictive biomarker candidates in patients with mCRPC undergoing first-line treatment with enzalutamide or abiraterone acetate. It further provides real-world evidence of the significant potential of genomic profiling of ctDNA to inform treatment in this setting. Clinical trials are warranted to advance the implementation of ctDNA-based biomarkers into clinical practice.", "doi": "10.1186/s13046-025-03356-0", "pmid": "40229848", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11998381"}, {"db": "pii", "key": "10.1186/s13046-025-03356-0"}], "notes": [], "created": "2025-11-18T20:45:35.762Z", "modified": "2025-11-18T20:45:35.776Z"}, {"entity": "publication", "iuid": "ea02a9d91f01487699dfd46f4cfa7598", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea02a9d91f01487699dfd46f4cfa7598.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea02a9d91f01487699dfd46f4cfa7598"}}, "title": "Contamination on inner walls of syringes used for compounding and administration of hazardous drugs.", "authors": [{"family": "Sessink", "given": "Paul", "initials": "P", "orcid": "0000-0002-8580-0044", "researcher": {"href": "https://publications.scilifelab.se/researcher/364227f01c6845919e0a0c5b01eb4e58.json"}}, {"family": "Tans", "given": "Birgit", "initials": "B"}, {"family": "Devolder", "given": "David", "initials": "D"}], "type": "journal article", "published": "2025-04-13", "journal": {"title": "J Oncol Pharm Pract", "issn": "1477-092X", "pages": "10781552251332884", "issn-l": null}, "abstract": "PurposeThe aim of the study was to measure contamination on inner walls of syringes used for compounding hazardous drugs. As the syringes have an open connection to the environment, evaporation of the drugs could result in environmental contamination and potential exposure of healthcare workers.MethodsForty-three 50 mL BD Plastipak luer lock syringes were collected after single use in compounding hazardous drugs. The inner wall of the barrel was wiped for each syringe. Potential remaining contamination was also measured by liquid extraction to verify the effectiveness of the wiping procedure. Six hazardous drugs were tested. Liquid chromatography tandem mass spectrometry was used for the analysis of cyclophosphamide, doxorubicin, 5-fluorouracil, ifosfamide, and methotrexate. Platinum analysis of cisplatin was performed with voltammetry.ResultsContamination was found for all cyclophosphamide, doxorubicin, ifosfamide, and methotrexate syringes, for eight out of ten 5-fluorouracil syringes, and for none of the cisplatin syringes. Contamination as part of the dose transferred differs between the drugs showing the highest contamination for doxorubicin (median 21.90 ppm) followed by cyclophosphamide (median 1.24 ppm), and ifosfamide (median 0.60 ppm). The lowest contamination was measured for 5-fluorouracil (median 0.02 ppm) and methotrexate (median 0.006 ppm).ConclusionContamination was found on almost all syringes and differs between the drugs indicating some drugs stick more to the inner walls and plunger shafts than others. Contamination implies a potential exposure risk as hazardous drugs could evaporate from the open syringes, contaminate the working environment, and expose healthcare workers.", "doi": "10.1177/10781552251332884", "pmid": "40223332", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2025-07-08T13:56:25.955Z", "modified": "2025-11-04T11:38:05.351Z"}, {"entity": "publication", "iuid": "784df73e8dc84ac78534a0c33e5aec03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/784df73e8dc84ac78534a0c33e5aec03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/784df73e8dc84ac78534a0c33e5aec03"}}, "title": "Cytoskeletal alterations in neuronal cells implicate Toxoplasma gondii secretory machinery and host microRNA-containing extracellular vesicles.", "authors": [{"family": "Mazza", "given": "Thomas", "initials": "T"}, {"family": "Aslanzadeh", "given": "Morteza", "initials": "M"}, {"family": "Berentsen", "given": "L\u00efse", "initials": "L"}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Barragan", "given": "Antonio", "initials": "A", "orcid": "0000-0001-7746-9964", "researcher": {"href": "https://publications.scilifelab.se/researcher/4eefb95f00db42e3891769f384269c6c.json"}}], "type": "journal article", "published": "2025-04-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "12606", "issn-l": "2045-2322"}, "abstract": "The widespread protozoan Toxoplasma gondii chronically infects neural tissue in vertebrates and is linked to various neurological and neuropsychiatric disorders in humans. However, its effects on sparsely infected neurons and on broader neural circuits remain elusive. Our study reveals that T. gondii infection disrupts cytoskeletal dynamics in SH-SY5Y neuronal cells and primary cortical neurons. Infected neuronal cells undergo significant cytomorphological changes, including retraction of dendritic extensions and alterations in microtubule and F-actin networks, across both parasite genotypes I and II. These cytoskeletal alterations were notably diminished in cells exposed to T. gondii mutants with impaired secretion via the MYR translocon, and were independent of intraneuronal parasite replication. Moreover, a bystander effect was observed, with supernatants from T. gondii-challenged cells inducing similar cytoskeletal changes in uninfected cells. Analyses of extracellular vesicles (EVs) in supernatants revealed differential expression of host microRNAs in response to infection, most notably the upregulation of miR-221-3p, a microRNA not previously associated with T. gondii. The data indicate that unidentified parasite-derived effector(s) secreted via the MYR translocon, in conjunction with MYR-independently induced EV-associated host microRNAs, mediate cytoskeletal alterations in both infected and bystander neuronal cells. The findings provide new insights into molecular mechanisms by which T. gondii infection may disrupt neural networks, shedding light on its potential role in neuronal dysregulation.", "doi": "10.1038/s41598-025-96298-8", "pmid": "40221584", "labels": {"NGI Short read": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Other": "Collaborative", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11993698"}, {"db": "pii", "key": "10.1038/s41598-025-96298-8"}], "notes": [], "created": "2025-06-03T09:17:07.614Z", "modified": "2025-06-03T09:17:07.717Z"}, {"entity": "publication", "iuid": "6160f0e6036b43428cd4b86676a636f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6160f0e6036b43428cd4b86676a636f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6160f0e6036b43428cd4b86676a636f2"}}, "title": "AutoLEI: An XDS-based Graphical User Interface for Automated Real-time and Offline Batch 3D ED/MicroED Data Processing", "authors": [{"family": "Wang", "given": "Lei", "initials": "L", "orcid": "0000-0002-7398-1124", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd71b3e4c1b541d8b7f894e7670635f7.json"}}, {"family": "Chen", "given": "Yinlin", "initials": "Y", "orcid": "0000-0001-7878-2063", "researcher": {"href": "https://publications.scilifelab.se/researcher/7382f35d7b454945a408671eab73efbf.json"}}, {"family": "Hutchinson", "given": "Emma Scaletti", "initials": "ES", "orcid": "0000-0002-8741-8981", "researcher": {"href": "https://publications.scilifelab.se/researcher/34a21e353ecb49eba831f7b0d68e024a.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Hofer", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-9248-6989", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcf436f51b14189b0c6668e6903afd8.json"}}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}], "type": "posted-content", "published": "2025-04-12", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.04.12.648515", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-26T08:59:34.724Z", "modified": "2025-12-18T19:17:06.658Z"}, {"entity": "publication", "iuid": "b41a066fba2b43eebb34302ff802267c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b41a066fba2b43eebb34302ff802267c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b41a066fba2b43eebb34302ff802267c"}}, "title": "Inflammatory and lipemic response to red meat intake in women with and without Rheumatoid Arthritis: a single meal study within a randomized controlled trial", "authors": [{"family": "S\u00e4llstr\u00f6m", "given": "Torsten", "initials": "T", "orcid": "0009-0001-4818-2531", "researcher": {"href": "https://publications.scilifelab.se/researcher/29042005e6f9498f81cef90894434bcf.json"}}, {"family": "B\u00e4rebring", "given": "Linnea", "initials": "L", "orcid": "0000-0002-1612-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9d45c7e27274cab907ffd3bc92ccfaf.json"}}, {"family": "Hulander", "given": "Erik", "initials": "E", "orcid": "0000-0003-3416-2748", "researcher": {"href": "https://publications.scilifelab.se/researcher/910a2dc80a8a4f449d2a3bf8e4d2f046.json"}}, {"family": "Gjertsson", "given": "Inger", "initials": "I", "orcid": "0000-0002-9301-4844", "researcher": {"href": "https://publications.scilifelab.se/researcher/56e95592e89f43cba8eb30bd32da1cc8.json"}}, {"family": "Winkvist", "given": "Anna", "initials": "A", "orcid": "0000-0001-9122-7240", "researcher": {"href": "https://publications.scilifelab.se/researcher/e34ca937891145e190390ae9418d2243.json"}}, {"family": "Lindqvist", "given": "Helen M", "initials": "HM", "orcid": "0000-0002-2627-0434", "researcher": {"href": "https://publications.scilifelab.se/researcher/d98498df02eb40fb8de3016da37d6f8a.json"}}], "type": "journal-article", "published": "2025-04-11", "journal": {"title": "BMC Nutr", "issn": "2055-0928", "volume": "11", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1186/s40795-025-01055-9", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:05:15.808Z", "modified": "2025-11-27T08:05:15.982Z"}, {"entity": "publication", "iuid": "d8da721b5a754880850c219d6fcb8c87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d8da721b5a754880850c219d6fcb8c87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d8da721b5a754880850c219d6fcb8c87"}}, "title": "Antibacterial compounds against non-growing and intracellular bacteria", "authors": [{"family": "Kaldalu", "given": "Niilo", "initials": "N"}, {"family": "B\u0113rzi\u0146\u0161", "given": "Normunds", "initials": "N"}, {"family": "Berglund Fick", "given": "Stina", "initials": "S"}, {"family": "Sharma", "given": "Atin", "initials": "A"}, {"family": "Andersson", "given": "Naomi Charlotta", "initials": "NC"}, {"family": "Aedla", "given": "J\u00fcri", "initials": "J"}, {"family": "Hinnu", "given": "Mariliis", "initials": "M"}, {"family": "Puhar", "given": "Andrea", "initials": "A"}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V"}, {"family": "Tenson", "given": "Tanel", "initials": "T"}], "type": "journal-article", "published": "2025-04-11", "journal": {"title": "npj Antimicrob Resist", "issn": "2731-8745", "volume": "3", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1038/s44259-025-00097-0", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-04-23T09:29:46.436Z", "modified": "2025-10-17T13:04:26.690Z"}, {"entity": "publication", "iuid": "9e856a21e11244789a7890b2151f1617", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e856a21e11244789a7890b2151f1617.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e856a21e11244789a7890b2151f1617"}}, "title": "A red fluorescent lifeact marker to study actin morphology in podocytes.", "authors": [{"family": "Wiesner", "given": "Eva", "initials": "E"}, {"family": "Binz-Lotter", "given": "Julia", "initials": "J"}, {"family": "Tr\u00f6der", "given": "Simon E", "initials": "SE"}, {"family": "Unnersj\u00f6-Jess", "given": "David", "initials": "D"}, {"family": "Rutkowski", "given": "Nelli", "initials": "N"}, {"family": "Zevnik", "given": "Branko", "initials": "B"}, {"family": "Schermer", "given": "Bernhard", "initials": "B"}, {"family": "Benzing", "given": "Thomas", "initials": "T"}, {"family": "Wedlich-S\u00f6ldner", "given": "Roland", "initials": "R"}, {"family": "Hackl", "given": "Matthias J", "initials": "MJ"}], "type": "journal article", "published": "2025-04-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "12386", "issn-l": "2045-2322"}, "abstract": "F-actin is a major component of the cellular cytoskeleton, responsible for maintaining cell shape, enabling movement and facilitating intracellular transport. In the kidney, glomerular podocytes are highly dependent on their actin cytoskeleton shaping their unique foot processes. Hereditary mutations in actin-binding proteins cause focal segmental glomerulosclerosis, while other organs remain largely unaffected. So far, actin visualization in podocytes has been limited to electron microscopy or indirect immunofluorescent labeling of actin-binding proteins. However, the short F-actin-binding peptide Lifeact enables researchers to study actin dynamics in vitro and in vivo with minimal interference with actin metabolism. Here we introduce a new mouse model with conditional expression of a Lifeact.mScarlet-I fusion protein providing red labeling of actin. Cre recombinase-mediated activity allows cell-specific and mosaic expression in podocytes, enabling selective labeling of individual cells to contrast with non-expressing neighboring cells. Transgenic mice are born healthy and young animals display no kidney-related phenotype. By intravital imaging and super-resolution microscopy, we show subcellular localization of actin to the foot processes in a resolution previously only obtainable by electron microscopy. Our novel mouse line provides the opportunity to study the actin cytoskeleton in podocytes and other cell types by intravital imaging and other conventional light microscopy techniques.", "doi": "10.1038/s41598-025-96822-w", "pmid": "40216917", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11992033"}, {"db": "pii", "key": "10.1038/s41598-025-96822-w"}], "notes": [], "created": "2025-04-18T09:49:47.683Z", "modified": "2025-04-18T09:49:47.688Z"}, {"entity": "publication", "iuid": "5693c08391ae49c7a5b87864c53e6f34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5693c08391ae49c7a5b87864c53e6f34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5693c08391ae49c7a5b87864c53e6f34"}}, "title": "Nuclear AGO2 supports influenza A virus replication through type-I interferon regulation.", "authors": [{"family": "Huang", "given": "Hsiang-Chi", "initials": "HC"}, {"family": "Fong", "given": "Michelle", "initials": "M"}, {"family": "Nowak", "given": "Iwona", "initials": "I"}, {"family": "Shcherbinina", "given": "Evgeniia", "initials": "E"}, {"family": "Lobo", "given": "Vivian", "initials": "V"}, {"family": "Besavilla", "given": "Danica F", "initials": "DF"}, {"family": "Huynh", "given": "Hang T", "initials": "HT"}, {"family": "Sch\u00f6n", "given": "Karin", "initials": "K"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "Fernandez", "given": "Carola", "initials": "C"}, {"family": "Patel", "given": "Angana A H", "initials": "AAH"}, {"family": "Wiel", "given": "Clotilde", "initials": "C"}, {"family": "Sayin", "given": "Volkan I", "initials": "VI"}, {"family": "Anastasakis", "given": "Dimitrios G", "initials": "DG"}, {"family": "Angeletti", "given": "Davide", "initials": "D", "orcid": "0000-0002-5256-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae59c12bf82b4ad9a8d9ad8603d03d9c.json"}}, {"family": "Sarshad", "given": "Aishe A", "initials": "AA", "orcid": "0000-0001-7153-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c62bd8dbe34b5da39de17d6a2a06ab.json"}}], "type": "journal article", "published": "2025-04-10", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "53", "issue": "7", "pages": null}, "abstract": "The role of Argonaute (AGO) proteins and the RNA interference (RNAi) machinery in mammalian antiviral response has been debated. Therefore, we set out to investigate how mammalian RNAi impacts influenza A virus (IAV) infection. We reveal that IAV infection triggers nuclear accumulation of AGO2, which is directly facilitated by p53 activation. Mechanistically, we show that IAV induces nuclear AGO2 targeting of TRIM71and type-I interferon-pathway genes for silencing. Accordingly, Tp53-/- mice do not accumulate nuclear AGO2 and demonstrate decreased susceptibility to IAV infection. Hence, the RNAi machinery is highjacked by the virus to evade the immune system and support viral replication. Furthermore, the FDA-approved drug, arsenic trioxide, prevents p53 nuclear translocation, increases interferon response and decreases viral replication in vitro and in a mouse model in vivo. Our data indicate that targeting the AGO2:p53-mediated silencing of innate immunity may offer a promising strategy to mitigate viral infections.", "doi": "10.1093/nar/gkaf268", "pmid": "40219968", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11992678"}, {"db": "pii", "key": "8112696"}], "notes": [], "created": "2025-04-16T07:03:31.301Z", "modified": "2025-09-08T11:29:59.901Z"}, {"entity": "publication", "iuid": "59b7b1a3171445408a05b3c342c2dc3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59b7b1a3171445408a05b3c342c2dc3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59b7b1a3171445408a05b3c342c2dc3b"}}, "title": "Genome-wide comparison reveals large structural variants in cassava landraces.", "authors": [{"family": "Landi", "given": "Michael", "initials": "M"}, {"family": "Carluccio", "given": "Anna Vittoria", "initials": "AV"}, {"family": "Shah", "given": "Trushar", "initials": "T"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Stavolone", "given": "Livia", "initials": "L"}, {"family": "Falquet", "given": "Laurent", "initials": "L"}, {"family": "Gisel", "given": "Andreas", "initials": "A"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2025-04-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "362", "issn-l": "1471-2164"}, "abstract": "Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava (Manihot esculenta Crantz). We aim to explore its presence and variability across multiple cassava landraces, providing insights into its genomic significance and potential implications.\n\nWe validated the presence of the 9.7 Mbp segment in the TMEB117 genome, distinguishing it from other published cassava genome assemblies. By mapping short-read sequencing data from 16 cassava landraces to TMEB117 chromosome 12, we observed variability in read mapping, suggesting that while all genotypes contain the insertion region, some exhibit missing segments or sequence differences. Further analysis revealed two unique genes associated with deacetylase activity, HDA14 and SRT2, within the insertion. Additionally, the MUDR-Mutator transposable element was significantly overrepresented in this region.\n\nThis study uncovers a large structural variant in the TMEB117 cassava genome, highlighting its variability among different genotypes. The enrichment of HDA14 and SRT2 genes and the MUDR-Mutator elements within the insertion suggests potential functional significance, though further research is needed to explore this. These findings provide important insights into the role of structural variations in shaping cassava genomic diversity.", "doi": "10.1186/s12864-025-11523-y", "pmid": "40211122", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11987339"}, {"db": "pii", "key": "10.1186/s12864-025-11523-y"}], "notes": [], "created": "2025-09-08T06:59:22.722Z", "modified": "2025-09-08T06:59:22.728Z"}, {"entity": "publication", "iuid": "8d39cfcb44534542bd0c90298b595b82", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d39cfcb44534542bd0c90298b595b82.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d39cfcb44534542bd0c90298b595b82"}}, "title": "Dual GSK-3\u03b2/HDAC Inhibitors Enhance the Efficacy of Macrophages to Control Mycobacterium tuberculosis Infection.", "authors": [{"family": "Kalsum", "given": "Sadaf", "initials": "S"}, {"family": "Xu", "given": "Ruilan", "initials": "R"}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Huang", "given": "Shengjie", "initials": "S"}, {"family": "Lerm", "given": "Maria", "initials": "M", "orcid": "0000-0002-5092-9892", "researcher": {"href": "https://publications.scilifelab.se/researcher/6645c25a513f4bb8a24d11fd80c1b23d.json"}}, {"family": "Chen", "given": "Yuqing", "initials": "Y"}, {"family": "Lourda", "given": "Magda", "initials": "M", "orcid": "0000-0003-3155-1123", "researcher": {"href": "https://publications.scilifelab.se/researcher/64d9a0bc6b5d4039af5bc308a97eaad6.json"}}, {"family": "Zhou", "given": "Yang", "initials": "Y"}, {"family": "Brighenti", "given": "Susanna", "initials": "S", "orcid": "0000-0001-8540-153X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2503448ccfc34f3585f260f1ecd41a63.json"}}], "type": "journal article", "published": "2025-04-09", "journal": {"title": "Biomolecules", "issn": "2218-273X", "volume": "15", "issue": "4", "pages": "550", "issn-l": null}, "abstract": "Multitarget drug discovery, including host-directed therapy, is particularly promising for tuberculosis (TB) due to the resilience of Mycobacterium tuberculosis (Mtb) as well as the complexity of the host's immune response. In this proof-of-concept study, we used high-content imaging to test a novel panel of dual glycogen synthase kinase 3 beta (GSK-3\u03b2) and histone deacetylase (HDAC) 1 and 6 inhibitor candidates for their efficacy in reducing the growth of green fluorescent protein (GFP)-expressing mycobacteria in human primary macrophages. We demonstrate that all ten test compounds, also including the GSK-3\u03b2 inhibitor SB415286, exhibit an antimycobacterial effect of 20-60% at low micromolar doses and are non-toxic to host cells. Mtb growth showed a positive correlation with the respective 50% inhibitory concentration (IC50) values of GSK-3\u03b2, HDAC1, and HDAC6 in each compound, indicating that compounds with a potent IC50 value for HDAC1, in particular, corresponded to higher antimycobacterial activity. Furthermore, the results from multiparametric flow cytometry and a customized multiplex RNA array demonstrated that SB415286 and selected compounds, C02 and C06, could modulate immune polarization and inflammation in Mtb-infected macrophages involving an enhanced expression of CCL2, IL-10 and S100A9, but a decrease in inflammatory mediators including COX-2, TNF-\u03b1, and NF\u03baB. These data suggest that GSK-3\u03b2 inhibition alone can decrease the intracellular growth of mycobacteria and regulate macrophage inflammation, while dual GSK-3\u03b2/HDAC inhibitors enhance this efficacy. Accordingly, the tailored design of dual GSK-3\u03b2/HDAC inhibitors could represent an innovative approach to host-directed therapy in TB.", "doi": "10.3390/biom15040550", "pmid": "40305296", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12024928"}, {"db": "pii", "key": "biom15040550"}], "notes": [], "created": "2025-04-23T10:13:20.668Z", "modified": "2025-10-17T13:04:26.720Z"}, {"entity": "publication", "iuid": "e84df26075a4401cac144c75bbbf1de9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e84df26075a4401cac144c75bbbf1de9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e84df26075a4401cac144c75bbbf1de9"}}, "title": "Design, Synthesis, and Biophysical Characterization of Pyridine Bis\u2010Quinazoline Derivatives as Selective G\u2010Quadruplex DNA Stabilizers", "authors": [{"family": "Nath Das", "given": "Rabindra", "initials": "R", "orcid": "0000-0001-6347-2169", "researcher": {"href": "https://publications.scilifelab.se/researcher/fec8d8bcbe8648258cfbab86693c77c6.json"}}, {"family": "Chorell", "given": "Erik", "initials": "E", "orcid": "0000-0003-2523-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/ada783ae0a824621a3b8e1024aae13a4.json"}}], "type": "journal-article", "published": "2025-04-09", "journal": {"title": "Chem. Eur. J.", "issn": "0947-6539", "volume": "31", "issue": "21", "issn-l": "0947-6539"}, "abstract": null, "doi": "10.1002/chem.202404689", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2025-04-23T09:42:14.931Z", "modified": "2025-10-17T13:04:26.742Z"}, {"entity": "publication", "iuid": "65d238883e88460db7508d91180825eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65d238883e88460db7508d91180825eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65d238883e88460db7508d91180825eb"}}, "title": "AMPK activator ATX-304 reduces oxidative stress and improves MASLD via metabolic switching.", "authors": [{"family": "Holm", "given": "Emanuel", "initials": "E"}, {"family": "Vermeulen", "given": "Isabeau", "initials": "I"}, {"family": "Parween", "given": "Saba", "initials": "S"}, {"family": "L\u00f3pez-P\u00e9rez", "given": "Ana", "initials": "A"}, {"family": "Cillero-Pastor", "given": "Berta", "initials": "B"}, {"family": "Vandenbosch", "given": "Michiel", "initials": "M"}, {"family": "Remeseiro", "given": "Silvia", "initials": "S"}, {"family": "H\u00f6rnblad", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2025-04-08", "journal": {"title": "JCI Insight", "issn": "2379-3708", "volume": "10", "issue": "7", "issn-l": "2379-3708"}, "abstract": "Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver disease worldwide for which there is only one approved treatment. Adenosine monophosphate-activated protein kinase (AMPK) is an interesting therapeutic target since it acts as a central regulator of cellular metabolism. Despite efforts to target AMPK, no direct activators have yet been approved for treatment of this disease. This study investigated the effect of the AMPK activator ATX-304 in a preclinical mouse model of progressive fatty liver disease. The data demonstrated that ATX-304 diminishes body fat mass, lowers blood cholesterol levels, and mitigates general liver steatosis and the development of liver fibrosis, but with pronounced local heterogeneities. The beneficial effects of ATX-304 treatment were accompanied by a shift in the liver metabolic program, including increased fatty acid oxidation, reduced lipid synthesis, as well as remodeling of cholesterol and lipid transport. We also observed variations in lipid distribution among liver lobes in response to ATX-304, and a shift in the zonal distribution of lipid droplets upon treatment. Taken together, our data suggested that ATX-304 holds promise as a potential treatment for MASLD.", "doi": "10.1172/jci.insight.179990", "pmid": "40197369", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11981618"}, {"db": "pii", "key": "179990"}], "notes": [], "created": "2025-11-28T10:52:19.502Z", "modified": "2025-11-28T10:52:19.542Z"}, {"entity": "publication", "iuid": "9131502607dc43228aa1e381cff87f1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9131502607dc43228aa1e381cff87f1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9131502607dc43228aa1e381cff87f1b"}}, "title": "Metabolic readouts of tumor instructed normal tissues (TINT) identify aggressive prostate cancer subgroups for tailored therapy.", "authors": [{"family": "Dudka", "given": "Ilona", "initials": "I"}, {"family": "Figueira", "given": "Jo\u00e3o", "initials": "J"}, {"family": "Wikstr\u00f6m", "given": "Pernilla", "initials": "P"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "Gr\u00f6bner", "given": "Gerhard", "initials": "G"}], "type": "journal article", "published": "2025-04-07", "journal": {"title": "Front Mol Biosci", "issn": "2296-889X", "volume": "12", "pages": "1426949", "issn-l": "2296-889X"}, "abstract": "Prostate cancer (PC) diagnosis relies on histopathological examination of prostate biopsies, which is restricted by insufficient sampling of all tumors present. Including samples from non-PC but tumor instructed normal tissues (TINT) may increase the diagnostic power by displaying the adaptive responses in benign tissues near tumors.\n\nHere, we applied high-resolution magic angle spinning nuclear magnetic resonance (HR MAS NMR) to identify metabolomic biomarkers of possible diagnostic value in benign prostate tissues near low/high-grade tumors.\n\nBenign samples near high-grade tumors (B ISUP 3 + 4) exhibited altered metabolic profiles compared to those close to low-grade tumors (B ISUP 1 + 2). The levels of six metabolites differentiated between the two groups; myo-inositol, lysine, serine and combined signal of lysine/leucine/arginine were increased in benign samples near high-grade tumors (B ISUP 3 + 4) compared to near low-grade tumors (B ISUP 1 + 2), while levels of ethanolamine and lactate were decreased. Additionally, we revealed metabolic differences in non-cancer tissues as a function of their distance to the nearest tumor. Eight metabolites (glutathione, glutamate, combined signal of glutamate/glutamine - glx, glycerol, inosine, ethanolamine, serine and arginine) differentiated between benign tissue located close to the tumor (d \u2264 5 mm) compared to those far away (d \u2265 1 cm).\n\nOur HR MAS NMR-based approach identified metabolic signatures in prostate biopsies that reflect the response of benign tissues to the presence of nearby located tumors in the same prostate and confirmed the power of the TINT concept for improved PC diagnostics and understanding of tumor-tissue interactions.", "doi": "10.3389/fmolb.2025.1426949", "pmid": "40260402", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12009692"}, {"db": "pii", "key": "1426949"}], "notes": [], "created": "2025-06-11T13:33:18.247Z", "modified": "2025-10-17T13:03:52.323Z"}, {"entity": "publication", "iuid": "8eacebd3e6af468a86f743da46649c11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8eacebd3e6af468a86f743da46649c11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8eacebd3e6af468a86f743da46649c11"}}, "title": "How and why to monitor social networks in dairy cows", "authors": [{"family": "Marina", "given": "Hector", "initials": "H"}, {"family": "Hansson", "given": "Ida", "initials": "I"}, {"family": "Ren", "given": "Keni", "initials": "K"}, {"family": "Fikse", "given": "Freddy", "initials": "F"}, {"family": "Gussmann", "given": "Maya Katrin", "initials": "MK"}, {"family": "Nielsen", "given": "Per Peetz", "initials": "PP"}, {"family": "Skarin", "given": "Anna", "initials": "A"}, {"family": "Woudstra", "given": "Svenja", "initials": "S"}, {"family": "R\u00f6nneg\u00e5rd", "given": "Lars", "initials": "L"}], "type": "journal-article", "published": "2025-04-07", "journal": {"title": "Front. Anim. Sci.", "issn": "2673-6225", "volume": "6", "issn-l": null}, "abstract": null, "doi": "10.3389/fanim.2025.1556812", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:54:18.823Z", "modified": "2025-11-28T10:54:18.860Z"}, {"entity": "publication", "iuid": "51ce839b84434f3e9204c2e6d80fcb2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51ce839b84434f3e9204c2e6d80fcb2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51ce839b84434f3e9204c2e6d80fcb2e"}}, "title": "Environmental drivers of the resistome across the Baltic Sea.", "authors": [{"family": "Serrana", "given": "Joeselle M", "initials": "JM", "orcid": "0000-0002-6967-5407", "researcher": {"href": "https://publications.scilifelab.se/researcher/d042aa918de14e1bb1403a00779c0160.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}, {"family": "Dessirier", "given": "Beno\u00eet", "initials": "B", "orcid": "0000-0002-2261-4279", "researcher": {"href": "https://publications.scilifelab.se/researcher/76223b9a5bd34863a822d5e8f8242540.json"}}, {"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Posselt", "given": "Malte", "initials": "M", "orcid": "0000-0001-8979-8044", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1b4854ced5246e8a3b79d6ab03cdde1.json"}}], "type": "journal article", "published": "2025-04-07", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "13", "issue": "1", "pages": "92", "issn-l": "2049-2618"}, "abstract": "Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.\n\nWe analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150 km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition.\n\nWe presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems. Video Abstract.", "doi": "10.1186/s40168-025-02086-x", "pmid": "40189545", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11974054"}, {"db": "pii", "key": "10.1186/s40168-025-02086-x"}], "notes": [], "created": "2025-11-28T10:53:22.401Z", "modified": "2025-11-28T10:53:22.543Z"}, {"entity": "publication", "iuid": "0a472783b44b468ea76f2796c228b8f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a472783b44b468ea76f2796c228b8f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a472783b44b468ea76f2796c228b8f4"}}, "title": "Comparison of the proteomic landscape in experimental ischemia reperfusion with versus without ischemic preconditioning.", "authors": [{"family": "Kakaei", "given": "Yalda", "initials": "Y"}, {"family": "Hussain", "given": "Shafaat", "initials": "S"}, {"family": "Elmahdy", "given": "Ahmed", "initials": "A"}, {"family": "Berger", "given": "Evelin", "initials": "E"}, {"family": "Shekka Espinosa", "given": "Aaron", "initials": "A"}, {"family": "Sevastianova", "given": "Valentyna", "initials": "V"}, {"family": "Sheybani", "given": "Zahra", "initials": "Z"}, {"family": "Al-Awar", "given": "Amin", "initials": "A"}, {"family": "Kalani", "given": "Mana", "initials": "M"}, {"family": "Jha", "given": "Sandeep", "initials": "S"}, {"family": "Zulfaj", "given": "Ermir", "initials": "E"}, {"family": "Nejat", "given": "Amirali", "initials": "A"}, {"family": "Jha", "given": "Abhishek", "initials": "A"}, {"family": "Pylova", "given": "Tetiana", "initials": "T"}, {"family": "Krasnikova", "given": "Maryna", "initials": "M"}, {"family": "Andersson", "given": "Erik Axel", "initials": "EA"}, {"family": "Silva", "given": "Vagner Ramon Rodrigues", "initials": "VRR"}, {"family": "Omerovic", "given": "Elmir", "initials": "E"}, {"family": "Redfors", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2025-04-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "11836", "issn-l": "2045-2322"}, "abstract": "Myocardial ischemic preconditioning (IPC) enhances myocardial resilience to ischemic injury. Myocardial stunning is a transient, reversible dysfunction, while necrosis involves irreversible cell death. The relationship between IPC, stunning, and necrosis is not well understood, requiring further molecular investigation. This study aimed to investigate the proteomic changes associated with IPC, focusing on its relationship with myocardial stunning and necrosis. A novel 13.5-minute ischemia-reperfusion (I/R) rat model was specifically chosen to induce myocardial stunning, providing a unique approach to assess IPC effects in this context. Rats underwent either IPC with two 5-minute ischemia/reperfusion cycles followed by a 13.5-minute ischemic period or the procedure without IPC (no ischemic preconditioning, NIPC). Myocardial samples were collected at early (T1) and 4-hour post-reperfusion (T2) time points for proteomic analysis. Protein levels were quantified by differential labeling using TMTpro reagents, and subsequent liquid chromatography-mass spectrometry. IPC induced upregulation of proteins involved in endocytosis and Fc gamma R-mediated phagocytosis pathways at T1, while downregulating proteins related to tissue remodeling, immune response, and coagulation at T2. Conversely, NIPC exhibited upregulation of proteins associated with tissue damage and inflammation. IPC rats demonstrated enhanced leukocyte migration, complement activation, and immune response between T1 and T2. Consistent proteomic changes were observed between T1 and T2 in IPC vs. NIPC groups, and common alterations between IPC T2 vs. T1 and NIPC T2 vs. T1 comparisons underline shared pathways in cardiac complement and coagulation cascades. Our study reveals distinct proteomic changes induced by IPC in the context of myocardial stunning and necrosis. IPC activates early protective pathways, attenuates tissue damage and inflammation, and preserves myocardial function. These findings underscore IPC's reparative potential and identify myocardial stunning as an important, transient adaptation, which may have implications for supportive clinical management in I/R.", "doi": "10.1038/s41598-025-90735-4", "pmid": "40195349", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11976975"}, {"db": "pii", "key": "10.1038/s41598-025-90735-4"}], "notes": [], "created": "2025-10-23T11:18:47.789Z", "modified": "2025-10-23T11:18:47.794Z"}, {"entity": "publication", "iuid": "3396351b6e2e4b1383f9a8c4e3fc8cc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3396351b6e2e4b1383f9a8c4e3fc8cc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3396351b6e2e4b1383f9a8c4e3fc8cc1"}}, "title": "Genetic aetiologies in relation to response to the ketogenic diet in 226 children with epilepsy.", "authors": [{"family": "Dahlin", "given": "Maria", "initials": "M"}, {"family": "St\u00f6dberg", "given": "Tommy", "initials": "T"}, {"family": "Ekman", "given": "Elin", "initials": "E"}, {"family": "T\u00f6h\u00f6nen", "given": "Virpi", "initials": "V"}, {"family": "Wedell", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-04-05", "journal": {"title": "Brain Commun", "issn": "2632-1297", "volume": "7", "issue": "2", "pages": "fcaf134", "issn-l": null}, "abstract": "A ketogenic diet is used in children with drug-resistant epilepsy but predictors for efficacy are largely lacking. Our aim was to evaluate if causative genetic variants could predict seizure response to the ketogenic diet. A cohort study of 226 children with refractory epilepsy and classic ketogenic diet treatment for at least 3 months (76.9% of the 294 who started) was performed. The median age at diet start was 5.1 years (range 0.1-17.8), 118 were girls and 108 boys. They had previous trials of a median of 6.0 anti-seizure medications (range 0-12) and intellectual disability was found in 87%. Seizure response (\u226550% reduction) was found in 138/226 patients (61.1%) at 3 months, 121 (53.5%) at 6 months, 107 (47.3%) at 1 year and in 80 (37.0%) at 2 years follow-up of ketogenic diet. Age of epilepsy onset was lower and combined epilepsy type less common in responders compared to non-responders but no differences were found for specific seizure types, ketogenic ratio or beta-hydroxybutyric acid blood levels. A causative pathogenic/likely pathogenic variant was detected in 107/153 = 69.9% in 48 different genes. Next generation sequencing was used in 91/226 (40%) cases with a diagnostic yield of 58.2% (53/91). In comparison with cases without a revealed genetic aetiology, patients with a causative genetic variant had less atonic seizures and epileptic spasms and a better seizure response with 17.3% seizure free and 25% with >90% seizure reduction at 2-year follow-up. Causative variants in SLC2A1, SCN1A, STXBP1 and PAFAH1B1 showed significant diet response (P < 0.05) and good efficacy was also associated with DEPDC5, GLDC, KCNT1, PDHA1, SLC25A12 and TSC1. Causative variants in COL4A1 and DYNC1H1 were among genes linked to a lack of response. To our knowledge not described previously, we report a good ketogenic diet response related to causative variants in CSNK2A1, FARS2, GABRB3, GRIN1, KCNA2, KCTD3, STX1B and SLC16A2 but a lack of response for causative variants in CLN5, GLI3, MACF1, MAGEL2, NANS, NEMO/IKBKG, RORB, SLC17A5 and UFSP2. After grouping of genes into functional groups, causative variants in transporter genes had the best response (P = 0.009) and variants in other membrane-related proteins (ion channels and neurotransmitter receptors) also showed good efficacy. However, the gene group related to cell structural integrity and/or homeostasis had the worst diet response (P = 0.00006). In conclusion, our results support that causative genetic variants may be used as prognostic markers of ketogenic diet response, constituting an example in the expanding area of precision medicine.", "doi": "10.1093/braincomms/fcaf134", "pmid": "40290421", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12022961"}, {"db": "pii", "key": "fcaf134"}], "notes": [], "created": "2025-11-21T09:08:03.972Z", "modified": "2025-11-21T09:08:03.984Z"}, {"entity": "publication", "iuid": "84d24b25b89b4baeae292e3f47cb2cff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84d24b25b89b4baeae292e3f47cb2cff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84d24b25b89b4baeae292e3f47cb2cff"}}, "title": "Genetic, clinical, lifestyle and sociodemographic risk factors for head and neck cancer: A UK Biobank study.", "authors": [{"family": "Tuomi", "given": "Lisa", "initials": "L"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ", "orcid": "0000-0003-0834-5540", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d528a2bce6c40829c1a6fed69c9f9ef.json"}}, {"family": "Rawshani", "given": "Araz", "initials": "A"}, {"family": "Andersson", "given": "Erik", "initials": "E", "orcid": "0009-0001-0567-2020", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e5d9cebf84645728ad5a54a7c986068.json"}}, {"family": "Orozco", "given": "Alina", "initials": "A"}, {"family": "Finizia", "given": "Caterina", "initials": "C"}], "type": "journal article", "published": "2025-04-04", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "20", "issue": "4", "pages": "e0318889"}, "abstract": "Despite a steady decline in tobacco smoking, head and neck cancer (HNC) incidence rates are on the rise. Therefore, novel risk factors for HNC are needed to identify at-risk patients at an early stage. Here, we used genetic, clinical, lifestyle, and sociodemographic data from UK Biobank (UKB) to evaluate the relative importance of known risk factors for HNC and identify novel predictors of HNC risk.\r\n\r\nAll participants in the UKB between 2006 and 2021 were stratified into HNC cases and controls at baseline (cases: n = 534; controls: n = 501833) or during follow-up (cases: n = 1587; controls: n = 500246). A cross-sectional description of risk factors (clinical characteristics, lifestyle and sociodemographic) for HNC at baseline was performed, followed by multivariate Cox regression analysis (adjusted for age and sex) and gradient boosting machine learning to determine the relative importance of predictors (phenotypic predictors and SNPs) of HNC development after baseline.\r\n\r\nIn addition to known risk factors for HNC (age, male sex, smoking and alcohol consumption habits, occupation), we show that smoking cessation at \u2264 40 years of age is the strongest predictor of HNC risk. Although SNPs may play a role in HNC development, a predictive model containing phenotypic variables and SNPs (C-index 0.75) did not significantly outperform a model containing the phenotypic predictors alone (C-index 0.73).\r\n\r\nTaken together, this study demonstrates that phenotypic variables such as past tobacco smoking habits, occupation, facial pain, education, pulmonary function, and anthropometric measures can be used to predict HNC risk.", "doi": "10.1371/journal.pone.0318889", "pmid": "40184367", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11970685"}, {"db": "pii", "key": "PONE-D-24-47676"}], "notes": [], "created": "2025-07-08T13:57:43.239Z", "modified": "2025-11-04T11:53:17.498Z"}, {"entity": "publication", "iuid": "a624b6ccad7b449fa079200d5b4a545f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a624b6ccad7b449fa079200d5b4a545f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a624b6ccad7b449fa079200d5b4a545f"}}, "title": "Genetic influence of a STAU2 frameshift mutation and RELN regulatory elements on performance in Icelandic horses.", "authors": [{"family": "Sigur\u00f0ard\u00f3ttir", "given": "Hei\u00f0r\u00fan", "initials": "H"}, {"family": "Eriksson", "given": "Susanne", "initials": "S"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Rhodin", "given": "Marie", "initials": "M"}, {"family": "Albertsd\u00f3ttir", "given": "Elsa", "initials": "E"}, {"family": "Kristjansson", "given": "Thorvaldur", "initials": "T"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}], "type": "journal article", "published": "2025-04-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "11641", "issn-l": "2045-2322"}, "abstract": "Selection for performance in horse breeding benefits from precise genetic insights at a molecular level, but knowledge remains limited. This study used whole-genome sequences of 39 elite and non-elite Icelandic horses to identify candidate causal variants linked to previously identified haplotypes in the STAU2 and RELN genes affecting pace and other gaits. A frameshift variant in linkage disequilibrium with the previously identified haplotypes in the STAU2 gene (r2 = 0.85) was identified within a predicted STAU2 transcript. This variant alters the amino acid sequence and introduces a premature stop codon but does not appear harmful or disease-causing and is potentially unique to equine biology. A large portion of the RELN haplotype overlapped with an H3K27me3 modification mark, suggesting a regulatory role of this region. Despite the small sample size, the RELN haplotype's effects were validated for t\u00f6lt, trot, and canter/gallop. Additionally, the RELN haplotype significantly influenced the age at which horses were presented for breeding field tests, indicating a potential role of the region in precocity and trainability. Functional experiments are needed to further investigate the regions' influences on biological processes and their potential impact on horse performance.", "doi": "10.1038/s41598-025-95593-8", "pmid": "40185812", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11971302"}, {"db": "pii", "key": "10.1038/s41598-025-95593-8"}], "notes": [], "created": "2025-11-07T07:27:05.828Z", "modified": "2025-11-14T11:07:06.654Z"}, {"entity": "publication", "iuid": "5a3168f3bf534a2380eced3612fd46f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a3168f3bf534a2380eced3612fd46f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a3168f3bf534a2380eced3612fd46f3"}}, "title": "Ectoderm barcoding reveals neural and cochlear compartmentalization.", "authors": [{"family": "de Haan", "given": "Sandra", "initials": "S", "orcid": "0000-0001-9335-1149", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec4f3aeba7b449a9b0973f235b26eb9d.json"}}, {"family": "He", "given": "Jingyan", "initials": "J", "orcid": "0000-0002-7405-5800", "researcher": {"href": "https://publications.scilifelab.se/researcher/01a69849650d4fd0897fb4e983824d05.json"}}, {"family": "Corbat", "given": "Agustin A", "initials": "AA", "orcid": "0000-0001-8068-3486", "researcher": {"href": "https://publications.scilifelab.se/researcher/b05e4776694041d6bd47b35b69a23304.json"}}, {"family": "Belicova", "given": "Lenka", "initials": "L", "orcid": "0000-0002-6687-630X", "researcher": {"href": "https://publications.scilifelab.se/researcher/149297e7f15e4a3281be3895d45725e3.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M"}, {"family": "Vinsland", "given": "Elin", "initials": "E", "orcid": "0000-0001-9695-9192", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c7bf61b0d3348d9b966a7a018c8859d.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Kelley", "given": "Matthew W", "initials": "MW", "orcid": "0000-0001-7367-8697", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bcfe32fbc984d0a8aee2e897db13489.json"}}, {"family": "Andersson", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8608-625X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7313cdcd5f41d4a567a6c315aac3a1.json"}}], "type": "journal article", "published": "2025-04-04", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "388", "issue": "6742", "pages": "60-68"}, "abstract": "Placodes and the neural crest are defining features of vertebrates. In this study, we investigate their lineages in mice using in utero approaches. We demonstrated that nanoinjection at embryonic day 7.5 targeted the ectoderm, including the future nervous system, placodes, and neural crest, allowing highly efficient manipulation of the future nervous system and inner ear. By using heritable DNA barcodes and high-throughput next-generation single-cell lineage tracing, we elucidated convergent differentiation pathways and identified distinct nervous system-, neural crest-, and otic placode-derived lineages. Clonal analyses identified early neural and cochlear compartmentalization, linking differentiated cell types to their progenitors or cellular siblings. This provides foundational insights for neuroscience and developmental biology.", "doi": "10.1126/science.adq9248", "pmid": "40179197", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-04-15T07:21:08.071Z", "modified": "2025-11-28T10:51:53.564Z"}, {"entity": "publication", "iuid": "859055d5fe394252bb2808f0d2a3394e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/859055d5fe394252bb2808f0d2a3394e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/859055d5fe394252bb2808f0d2a3394e"}}, "title": "ATP1A3 dysfunction causes motor hyperexcitability and afterhyperpolarization loss in a dystonia model.", "authors": [{"family": "Akkuratov", "given": "Evgeny E", "initials": "EE"}, {"family": "Sorrell", "given": "Francesca", "initials": "F"}, {"family": "Picton", "given": "Laurence D", "initials": "LD"}, {"family": "Sousa", "given": "Vasco C", "initials": "VC"}, {"family": "Paucar", "given": "Martin", "initials": "M", "orcid": "0000-0003-3735-1480", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbc592904eb5402ea48a624471d4b939.json"}}, {"family": "Jans", "given": "Daniel", "initials": "D", "orcid": "0000-0002-6356-9742", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe197a6a51a946a7a6c01f4c9c6cce08.json"}}, {"family": "Svensson", "given": "Lill-Britt", "initials": "LB"}, {"family": "Lindskog", "given": "Maria", "initials": "M", "orcid": "0000-0001-9484-1983", "researcher": {"href": "https://publications.scilifelab.se/researcher/1592b4e2f1354bdd8b35f384dcac78c2.json"}}, {"family": "Fritz", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9722-7425", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec61383c813443f29dea569ea935b284.json"}}, {"family": "Liebmann", "given": "Thomas", "initials": "T"}, {"family": "Sillar", "given": "Keith T", "initials": "KT"}, {"family": "Rosewich", "given": "Hendrik", "initials": "H", "orcid": "0000-0003-4692-5511", "researcher": {"href": "https://publications.scilifelab.se/researcher/fffad5ec5d2d48a78573e71d7ba3c2dd.json"}}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Miles", "given": "Gareth B", "initials": "GB"}, {"family": "Aperia", "given": "Anita", "initials": "A"}], "type": "journal article", "published": "2025-04-03", "journal": {"title": "Brain", "issn": "1460-2156", "volume": "148", "issue": "4", "pages": "1099-1105", "issn-l": "0006-8950"}, "abstract": "Mutations in the gene encoding the alpha3 Na+/K+-ATPase isoform (ATP1A3) lead to movement disorders that manifest with dystonia, a common neurological symptom with many different origins, but for which the underlying molecular mechanisms remain poorly understood. We have generated an ATP1A3 mutant mouse that displays motor impairments and a hyperexcitable motor phenotype compatible with dystonia. We show that neurons harbouring this mutation are compromised in their ability to extrude raised levels of intracellular sodium, highlighting a profound deficit in neuronal sodium homeostasis. We show that the spinal motor network in ATP1A3 mutant mice has a reduced responsiveness to activity-dependent rises in intracellular sodium and that this is accompanied by loss of the Na+/K+-ATPase-mediated afterhyperpolarization in motor neurons. Taken together, our data support that the alpha3 Na+/K+-ATPase is important for cellular and spinal motor network homeostasis. These insights suggest that it may be useful to consider ways to compensate for this loss of a critical afterhyperpolarization-dependent control of neuronal excitability when developing future therapies for dystonia.", "doi": "10.1093/brain/awae373", "pmid": "39533828", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11967811"}, {"db": "pii", "key": "7896743"}], "notes": [], "created": "2024-11-18T09:02:43.236Z", "modified": "2025-11-12T11:33:48.972Z"}, {"entity": "publication", "iuid": "8a7bae2f936e4bcc9925c359d0c16bee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a7bae2f936e4bcc9925c359d0c16bee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a7bae2f936e4bcc9925c359d0c16bee"}}, "title": "The protein kinases KIPK and KIPK-LIKE1 suppress overbending during negative hypocotyl gravitropic growth in Arabidopsis.", "authors": [{"family": "Xiao", "given": "Yao", "initials": "Y", "orcid": "0000-0002-3078-7225", "researcher": {"href": "https://publications.scilifelab.se/researcher/715a0cc6b0aa48a19c6ec8d490483099.json"}}, {"family": "Zourelidou", "given": "Melina", "initials": "M", "orcid": "0000-0001-5218-4583", "researcher": {"href": "https://publications.scilifelab.se/researcher/91bc2aafe5d1413ba423b4817e4d56a5.json"}}, {"family": "Bassukas", "given": "Alkistis E Lanassa", "initials": "AEL", "orcid": "0000-0002-3506-8537", "researcher": {"href": "https://publications.scilifelab.se/researcher/67a6c1e57c3240b4887135181fded7a1.json"}}, {"family": "Weller", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-0231-595X", "researcher": {"href": "https://publications.scilifelab.se/researcher/74a4512ba6cb4b30b67b45be0e8dcfe8.json"}}, {"family": "Janacek", "given": "Dorina P", "initials": "DP"}, {"family": "\u0160imura", "given": "Jan", "initials": "J"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Hammes", "given": "Ulrich Z", "initials": "UZ", "orcid": "0000-0002-3663-4908", "researcher": {"href": "https://publications.scilifelab.se/researcher/a309d5de361a4f0cb48b3aa91d547e91.json"}}, {"family": "Li", "given": "Jia", "initials": "J"}, {"family": "Schwechheimer", "given": "Claus", "initials": "C", "orcid": "0000-0003-0269-2330", "researcher": {"href": "https://publications.scilifelab.se/researcher/21804ba0de6944e3b69f04a446ea75df.json"}}], "type": "journal article", "published": "2025-04-02", "journal": {"title": "Plant Cell", "issn": "1532-298X", "volume": "37", "issue": "4", "issn-l": "1040-4651"}, "abstract": "Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).", "doi": "10.1093/plcell/koaf056", "pmid": "40261964", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12013712"}, {"db": "pii", "key": "8117847"}], "notes": [], "created": "2025-11-18T12:16:35.413Z", "modified": "2025-11-18T12:16:35.856Z"}, {"entity": "publication", "iuid": "872ce4cf695e4085883f7519f1ec7712", "links": {"self": {"href": "https://publications.scilifelab.se/publication/872ce4cf695e4085883f7519f1ec7712.json"}, "display": {"href": "https://publications.scilifelab.se/publication/872ce4cf695e4085883f7519f1ec7712"}}, "title": "The identity of Canthydrus testaceus (Boheman, 1858) and a new faunistic record of Sternocanthus indicus (Wehncke, 1876) (Coleoptera: Noteridae).", "authors": [{"family": "Toledo", "given": "Mario E", "initials": "ME"}, {"family": "Negri", "given": "Ilaria", "initials": "I"}, {"family": "Bergsten", "given": "Johannes", "initials": "J"}], "type": "journal article", "published": "2025-04-02", "journal": {"title": "Zootaxa", "issn": "1175-5334", "volume": "5618", "issue": "2", "pages": "284-286", "issn-l": null}, "abstract": null, "doi": "10.11646/zootaxa.5618.2.7", "pmid": "40173460", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-21T13:15:43.074Z", "modified": "2025-11-21T13:15:43.092Z"}, {"entity": "publication", "iuid": "e75a307f49d94747b12d89e0fb944131", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e75a307f49d94747b12d89e0fb944131.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e75a307f49d94747b12d89e0fb944131"}}, "title": "On the origin of an insular hybrid butterfly lineage.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Nolen", "given": "Zachary J", "initials": "ZJ"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2025-04-02", "journal": {"title": "Evolution", "issn": "1558-5646", "volume": "79", "issue": "4", "pages": "510-524", "issn-l": "0014-3820"}, "abstract": "A new species can form through hybridization between species. Hybrid speciation in animals has been intensely debated, partly because hard evidence for the process has been difficult to obtain. Here, we report the discovery of a European hybrid butterfly lineage, a finding that can be considered surprising given the intense and long-term study of European butterflies. The lineage we describe is mainly inhabiting an island in the Baltic Sea and was previously designated as a subspecies (horkei) of one of the parental species (Aricia artaxerxes). By analyzing whole-genome resequencing data and developing a novel cluster analysis based on historical recombination events (Fisher junctions), we determine that horkei originated by hybridization between the nonsister species A. artaxerxes and A. agestis. This hybridization event occurred approximately 54,000 years ago, predating the last glaciation of the current distribution range. Horkei must therefore have persisted long enough to be able to colonize its current range, despite that this area lies between the current distributions of the parental species. The hybrid origin, the maintenance of genomic integrity across times of dramatic climate change, and the expression of a combination of parental traits suggest that horkei could be in the process of hybrid speciation.", "doi": "10.1093/evolut/qpaf017", "pmid": "39869437", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7984342"}], "notes": [], "created": "2025-11-21T13:35:47.293Z", "modified": "2025-11-28T10:48:44.944Z"}, {"entity": "publication", "iuid": "bb84c8f0da2546d197d9be264a758437", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb84c8f0da2546d197d9be264a758437.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb84c8f0da2546d197d9be264a758437"}}, "title": "Design and application of a fluorescent probe for imaging of endogenous Bruton's tyrosine kinase with preserved enzymatic activity.", "authors": [{"family": "Valaka", "given": "Anna P", "initials": "AP", "orcid": "0009-0008-7007-6971", "researcher": {"href": "https://publications.scilifelab.se/researcher/90c945c6f7b84acc8fc0097ec194332e.json"}}, {"family": "Nystr\u00f6m", "given": "Hampus", "initials": "H", "orcid": "0009-0006-8139-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/a763c1525ea446bd913291a2599ea9f7.json"}}, {"family": "H\u00e5versen", "given": "Liliana", "initials": "L"}, {"family": "Benitez-Martin", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1821-9388", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1fcdd6e053b462998fe7f463be60d96.json"}}, {"family": "Sch\u00e4fer", "given": "Clara", "initials": "C", "orcid": "0000-0001-7634-3980", "researcher": {"href": "https://publications.scilifelab.se/researcher/58fcf0b78e574d5f9a52fcab14632117.json"}}, {"family": "Jang", "given": "Woo Suk", "initials": "WS"}, {"family": "Camponeschi", "given": "Alessandro", "initials": "A", "orcid": "0000-0002-6472-2438", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccbaffafd6a24f4abed1e402219fa472.json"}}, {"family": "Andr\u00e9asson", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4695-7943", "researcher": {"href": "https://publications.scilifelab.se/researcher/28eb5affb5664c54be9171dfce6bea15.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Gr\u00f8tli", "given": "Morten", "initials": "M", "orcid": "0000-0003-3621-4222", "researcher": {"href": "https://publications.scilifelab.se/researcher/764706606bcb4afba1150af332c0f124.json"}}], "type": "journal article", "published": "2025-04-02", "journal": {"title": "RSC Chem Biol", "issn": "2633-0679", "issn-l": null, "volume": "6", "issue": "4", "pages": "618-629"}, "abstract": "Fluorophore integration into proteins within living cells is essential for exploring proteins in their natural environment. Bruton's tyrosine kinase (BTK), is a validated oncology target and is crucial for B cell proliferation and activation. Developing BTK-labelling probes is key to understand BTK's dynamic signalling pathway. In this work, we aimed to develop a novel fluorescent labelling probe for endogenous BTK imaging while preserving its enzymatic activity. Evobrutinib, a second-generation BTK inhibitor with high selectivity, was chosen as the scaffold. We designed two probes, Evo-1 and Evo-2, with a BODIPY fluorescent group, guided by molecular modelling. The synthesis was achieved using optimised Suzuki-Miyaura cross-coupling and amide coupling reactions. Biochemical assays confirmed covalent binding to Cys481 of BTK while preserving its enzymatic activity. Labelling of endogenous BTK with Evo-2 with reduced off-target effects in Ramos cells was validated in cellular assays. The dynamic signalling pathway of BTK in its native environment was investigated by confocal microscopy with Evo-2. This methodology is a valuable asset in the chemical biology toolbox for studying protein dynamics and interactions in real time without interfering with the protein activity.", "doi": "10.1039/d4cb00313f", "pmid": "40026844", "labels": {"Glycoproteomics and MS Proteomics": "Service", "Integrated Microscopy Technologies Gothenburg": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11867108"}, {"db": "pii", "key": "d4cb00313f"}], "notes": [], "created": "2025-10-23T16:03:12.593Z", "modified": "2025-11-27T13:34:09.343Z"}, {"entity": "publication", "iuid": "a609fcce04e94ce4a51830b45ac8941d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a609fcce04e94ce4a51830b45ac8941d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a609fcce04e94ce4a51830b45ac8941d"}}, "title": "A Million Years of Mammoth Mitogenome Evolution.", "authors": [{"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Thomas Thorpe", "given": "Jessica A", "initials": "JA", "orcid": "0000-0003-2302-2387", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7ce837837546e48d5debf6d6aa9b41.json"}}, {"family": "Li", "given": "Wenxi", "initials": "W", "orcid": "0009-0001-5130-9521", "researcher": {"href": "https://publications.scilifelab.se/researcher/f001ea19092e433b9abc9431fe45b63e.json"}}, {"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "Pe\u010dnerov\u00e1", "given": "Patricia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "Barlow", "given": "Axel", "initials": "A", "orcid": "0000-0002-5532-9458", "researcher": {"href": "https://publications.scilifelab.se/researcher/293d4982ed124c75896e1838bab18b8f.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Henneberger", "given": "Kirstin", "initials": "K"}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Moreland", "given": "Kelsey N", "initials": "KN", "orcid": "0000-0002-3571-0876", "researcher": {"href": "https://publications.scilifelab.se/researcher/b44fb07639f84500b325ea44d7faf08d.json"}}, {"family": "Paijmans", "given": "Johanna L A", "initials": "JLA", "orcid": "0000-0002-1938-7052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bac46fda6c98402aa8743eeacef7a962.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Wijnands", "given": "Flore", "initials": "F", "orcid": "0009-0009-6254-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/06418b4f9e90443d94452c87fb0b0588.json"}}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/daed8b59096b411dac9ad2bbe6ac84b4.json"}}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Hall", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-6998-0156", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcfa42cd57c645ba868b8ab621a1be14.json"}}, {"family": "Hewitson", "given": "Susan", "initials": "S", "orcid": "0000-0003-0091-012X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0a989b12c524e859eb20fdc38d2c111.json"}}, {"family": "Mol", "given": "Dick", "initials": "D", "orcid": "0009-0005-4772-4625", "researcher": {"href": "https://publications.scilifelab.se/researcher/9baa2917aafa4ab59b27c7be2a2f246a.json"}}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P", "orcid": "0000-0001-6547-9890", "researcher": {"href": "https://publications.scilifelab.se/researcher/14e81a9e6a164940a46a57249be26006.json"}}, {"family": "Sablin", "given": "Mikhail", "initials": "M", "orcid": "0000-0002-2773-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/3355f7b5b291492b8ff2119fd74adbaf.json"}}, {"family": "Vartanyan", "given": "Sergey", "initials": "S", "orcid": "0000-0001-7806-4053", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c472e06d8fa43a0b8a5575d5aec48e8.json"}}, {"family": "Zazula", "given": "Grant D", "initials": "GD", "orcid": "0000-0001-8436-1783", "researcher": {"href": "https://publications.scilifelab.se/researcher/077650a2501a49eaa9aba0a8b8fc4a56.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/156889b432944198909e4842f841a296.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M", "orcid": "0000-0003-0441-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/f18713dbd0044cb2bd6dfc3bad1cf349.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2025-04-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "42", "issue": "4", "pages": null}, "abstract": "The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.", "doi": "10.1093/molbev/msaf065", "pmid": "40202893", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11980863"}, {"db": "pii", "key": "8107989"}], "notes": [], "created": "2025-05-05T12:32:34.796Z", "modified": "2025-11-28T10:49:58.497Z"}, {"entity": "publication", "iuid": "55cf470fcf0949d2ac3046c067d4655f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55cf470fcf0949d2ac3046c067d4655f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55cf470fcf0949d2ac3046c067d4655f"}}, "title": "WOMEN WITH KNEE OSTEOARTHRITIS: POST-MENOPAUSAL PROGESTERONE IS LINKED TO PAIN INTENSITY, RADIOGRAPHIC SCORE, AND SYNOVIAL ALTERATION", "authors": [{"family": "Corciulo", "given": "Carmen", "initials": "C"}, {"family": "Askar", "given": "Fadi", "initials": "F"}, {"family": "Chatziagorou", "given": "Georgios", "initials": "G"}, {"family": "Wustenhagen", "given": "Sofia", "initials": "S"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Berger", "given": "Evelin", "initials": "E"}, {"family": "Ekman", "given": "Anna", "initials": "A"}, {"family": "Rudin", "given": "Anna", "initials": "A"}], "type": "journal-article", "published": "2025-04-00", "journal": {"title": "Osteoarthr. Cartil.", "issn": "1063-4584", "volume": "33", "pages": "S428", "issn-l": null}, "abstract": null, "doi": "10.1016/j.joca.2025.02.624", "pmid": null, "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-07-08T13:52:35.926Z", "modified": "2025-11-04T11:33:38.540Z"}, {"entity": "publication", "iuid": "5ac793dd249344008f500a4190f4df49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ac793dd249344008f500a4190f4df49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ac793dd249344008f500a4190f4df49"}}, "title": "Three cases with chronic obsessive compulsive disorder report gains in wellbeing and function following rituximab treatment.", "authors": [{"family": "Gallwitz", "given": "Maike", "initials": "M", "orcid": "0000-0001-9030-5470", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b150eb79b914a6a8e44b28f74f411fd.json"}}, {"family": "Lindqvist", "given": "Isa", "initials": "I", "orcid": "0000-0002-5384-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/69d00ee1a68845a0bef066173e7c565d.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Rasmusson", "given": "Annica J", "initials": "AJ", "orcid": "0000-0002-7228-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef833f6dd204c189586fba5c33d1d58.json"}}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Hus\u00e9n", "given": "Evelina", "initials": "E"}, {"family": "Borin", "given": "Jesper", "initials": "J"}, {"family": "van der Spek", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-2203-0652", "researcher": {"href": "https://publications.scilifelab.se/researcher/16f1b64d48d44a95ba9e7bc082076032.json"}}, {"family": "Sabbagh", "given": "Nour", "initials": "N"}, {"family": "Widgren", "given": "Anna", "initials": "A"}, {"family": "Bergquist", "given": "Jonas", "initials": "J", "orcid": "0000-0002-4597-041X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d745034529f3423abbea230b4e586d20.json"}}, {"family": "Cervenka", "given": "Simon", "initials": "S"}, {"family": "Burman", "given": "Joachim", "initials": "J"}, {"family": "Cunningham", "given": "Janet L", "initials": "JL", "orcid": "0000-0001-7876-7779", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab30dd6c6874bc7a227a8699c4a7085.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Mol. Psychiatry", "issn": "1476-5578", "volume": "30", "issue": "4", "pages": "1396-1406", "issn-l": "1359-4184"}, "abstract": "Immunological aetiology is supported for a subgroup with obsessive compulsive disorder (OCD) and conceptualized as autoimmune OCD. The longitudinal clinical course is detailed for three severely ill cases with OCD and indications of immunological involvement with off-label rituximab treatment every six months. All cases showed clear and sustained gains regarding symptom burden and function for over 2.5 years. Brief Psychiatric Rating Scale and Yale-Brown Obsessive-Compulsive Inventory Scale scores decreased 67-100% and 44-92%, respectively. These complex cases, prior to rituximab, had very low functioning and disease duration has been eight, nine and 16 years respectively. All three patients had been unsuccessfully treated with at least two antidepressants or anxiolytics, one neuroleptic and cognitive behavioural therapy. Clinical phenotypes and findings were suggestive of possible autoimmune OCD. Indirect immunohistochemistry detected cerebral spinal fluid (CSF) antibodies in all three cases including a novel anti-neuronal staining pattern against mouse thalamic cells. Exploratory analyses of CSF markers and proteomics identified elevated levels of sCD27 and markers indicative of complement pathway activation when compared to CSF from healthy controls. Multidisciplinary collaboration, advanced clinical investigations and rituximab treatment are feasible in a psychiatric setting. The case histories provide a proof of principle for the newly proposed criteria for autoimmune OCD. The findings suggest that clinical red flags and biological measures may predict rituximab response in chronic treatment-resistant OCD. The report provides orientation that may inform the hypotheses and design of future treatment trials.", "doi": "10.1038/s41380-024-02750-y", "pmid": "39304742", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11919689"}, {"db": "pii", "key": "10.1038/s41380-024-02750-y"}], "notes": [], "created": "2025-11-25T19:23:17.778Z", "modified": "2025-11-25T19:23:18.055Z"}, {"entity": "publication", "iuid": "9e83db438c76477d933a978f004ad331", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e83db438c76477d933a978f004ad331.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e83db438c76477d933a978f004ad331"}}, "title": "The prognostic value of changes in Ki67 following neoadjuvant chemotherapy in residual triple-negative breast cancer: a Swedish nationwide registry-based study.", "authors": [{"family": "Nyqvist-Streng", "given": "Jenny", "initials": "J", "orcid": "0000-0002-9934-8407", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d469c2479504629b74b0e87733e97e8.json"}}, {"family": "Helou", "given": "Mikael", "initials": "M"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Chamalidou", "given": "Chaido", "initials": "C"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Breast Cancer Res. Treat.", "issn": "1573-7217", "volume": "210", "issue": "3", "pages": "719-736", "issn-l": "0167-6806"}, "abstract": "To evaluate the prognostic significance of changes in pre- and post-neoadjuvant chemotherapy (NACT) Ki67 in patients with primary invasive triple-negative breast cancer (TNBC).\n\nPopulation-based registry data were retrieved for patients diagnosed with TNBC between 2007 and 2021 (n = 9262). Multivariable Cox regression analysis was performed for disease-specific survival (DSS) and overall survival (OS) adjusted for age and residual disease in the breast and nodes (RDBN).\n\nOf the 1777 TNBC patients receiving NACT, 54 achieved pathologic complete response (pCR) and 755 had residual disease. Most patients were overweight with stage II disease (78%), grade 3 tumors (53%), and RDBN score 3 (42%). Compared to baseline, tumor size (30 vs. 15 mm; P < 0.0001) and Ki67 levels (63% vs. 48%; P < 2.2e - 16) generally decreased after NACT. Although only 5% of samples increased in size, Ki67 levels often remained unchanged (75%) or increased (0.9%) after treatment, respectively. However, 34% of patients discontinued treatment. Patients showing no changes in Ki67% had more unfavorable OS (P < 0.0001) and DSS (P = 0.00032), with significantly lower 5-year survival probabilities (OS: 66%; DSS: 78%) than those with decreased Ki67% (OS: 87%; DSS: 89%). All patients reaching pCR were alive 5 years after diagnosis. However, only the RDBN score was an independent predictor of survival in the multivariable analyses.\n\nKi67 often remained unchanged in TNBC patients treated with neoadjuvant chemotherapy, resulting in adverse clinical outcomes. These findings highlight the need for individualized treatment regimens and dynamic monitoring of TNBC patients with high Ki67 post-NACT.", "doi": "10.1007/s10549-025-07610-z", "pmid": "39799529", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11953087"}, {"db": "pii", "key": "10.1007/s10549-025-07610-z"}], "notes": [], "created": "2025-07-08T13:56:01.508Z", "modified": "2025-11-04T11:37:20.468Z"}, {"entity": "publication", "iuid": "aebab6081ba14fa69b3ca92ae5a3e10d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aebab6081ba14fa69b3ca92ae5a3e10d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aebab6081ba14fa69b3ca92ae5a3e10d"}}, "title": "The guinea pig serves as an alternative model to study human preimplantation development.", "authors": [{"family": "Canizo", "given": "Jesica Romina", "initials": "JR"}, {"family": "Zhao", "given": "Cheng", "initials": "C", "orcid": "0000-0003-0518-5924", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cd6a95b29e44b3fa8fed63033d26393.json"}}, {"family": "Petropoulos", "given": "Sophie", "initials": "S", "orcid": "0000-0003-2293-8238", "researcher": {"href": "https://publications.scilifelab.se/researcher/0766fd90df1f4199a000eb84b06e2d31.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat Cell Biol", "issn": "1476-4679", "volume": "27", "issue": "4", "pages": "696-710", "issn-l": null}, "abstract": "Preimplantation development is an important window of human embryogenesis. However, ethical constraints and the limitations involved in studying human embryos often necessitate the use of alternative model systems. Here we identify the guinea pig as a promising small animal model to study human preimplantation development. Using single-cell RNA-sequencing, we generated an atlas of guinea pig preimplantation development, revealing its close resemblance to early human embryogenesis in terms of the timing of compaction, early-, mid- and late-blastocyst formation, and implantation, and the spatio-temporal expression of key lineage markers. We also show conserved roles of Hippo, MEK-ERK and JAK-STAT signalling. Furthermore, multi-species analysis highlights the spatio-temporal expression of conserved and divergent genes during preimplantation development and pluripotency. The guinea pig serves as a valuable animal model for advancing preimplantation development and stem cell research, and can be leveraged to better understand the longer-term impact of early exposures on offspring outcomes.", "doi": "10.1038/s41556-025-01642-9", "pmid": "40185949", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11991919"}, {"db": "pii", "key": "10.1038/s41556-025-01642-9"}], "notes": [], "created": "2025-11-28T10:46:11.150Z", "modified": "2025-11-28T10:46:11.192Z"}, {"entity": "publication", "iuid": "e5ec896ec4b746b18014404aab2efc68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5ec896ec4b746b18014404aab2efc68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5ec896ec4b746b18014404aab2efc68"}}, "title": "The Development of Selective Chemical Probes for Serine Arginine Protein Kinase 3.", "authors": [{"family": "Hanke", "given": "Danielle", "initials": "D"}, {"family": "McCutcheon", "given": "Conall", "initials": "C"}, {"family": "Page", "given": "Brent D G", "initials": "BDG"}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Chem Biol Drug Des", "issn": "1747-0285", "volume": "105", "issue": "4", "pages": "e70101", "issn-l": "1747-0277"}, "abstract": "The serine arginine protein kinases (SRPKs) are a family of kinases whose irregular function is implicated in cancer and viral infections. While the roles of SRPK1 and SRPK2 in disease are well established, much less is known about SRPK3. There are several studies implicating SRPK3 in breast cancer, but the mechanism is still unknown. This work describes the first-reported SRPK3 chemical probes that show excellent selectivity over the other SRPKs. 1-(4-cyanophenyl)-3-phenylurea was identified as an initial hit for SRPK3 through a kinase screen. Subsequent rounds of in silico docking, medicinal chemistry optimization, and biochemical assays were performed to increase its potency and selectivity for SRPK3. Six top compounds were identified that displayed single digit micromolar IC50 values in SRPK3 activity assays and negligible inhibition of SRPK1 or SRPK2. These six compounds demonstrated impairment of breast cancer cell viability that correlated with their biochemical IC50 values, suggesting that they can be used as tools to study the biological functions of SRPK3 in breast cancer. With an enhanced understanding of SRPK3's biological function, it may emerge as a meaningful drug target, wherein our top inhibitors could be further optimized to produce novel cancer therapeutics.", "doi": "10.1111/cbdd.70101", "pmid": "40176684", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11966184"}], "notes": [], "created": "2025-04-23T09:37:29.387Z", "modified": "2025-11-25T11:32:34.391Z"}, {"entity": "publication", "iuid": "1c9a0fdf573d4502b5e15290bb4ff7c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c9a0fdf573d4502b5e15290bb4ff7c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c9a0fdf573d4502b5e15290bb4ff7c4"}}, "title": "Simulation-based evaluation of the impact of dose fractionation study design on antibiotic PKPD analyses.", "authors": [{"family": "Saporta", "given": "Rapha\u00ebl", "initials": "R", "orcid": "0009-0005-3459-6839", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd6182f1a444461297717e0afc0a4b5f.json"}}, {"family": "Madan", "given": "Muskan", "initials": "M"}, {"family": "Friberg", "given": "Lena E", "initials": "LE", "orcid": "0000-0002-2979-679X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23b6e6225d15433f8eccc444c450adfc.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "JAC Antimicrob Resist", "issn": "2632-1823", "volume": "7", "issue": "2", "pages": "dlaf057", "issn-l": null}, "abstract": "To evaluate the impact of antibiotic dose fractionation study design on pharmacokinetic/pharmacodynamic (PK/PD) indices and PKPD model estimation.\n\nPKPD models for meropenem and polymyxin B (PMB) were applied to (i) simulate various dose fractionation studies in mice to derive PK/PD indices and efficacy targets and (ii) perform stochastic simulations and estimations evaluating which efficacy assessment times, in addition to 24 h, would improve the estimation of drug effect parameters.\n\nThe R 2 values of PK/PD indices were primarily influenced by reductions of the dosing intervals for meropenem and by decreases of the lowest total daily dose for PMB. For certain study designs (e.g. frequent administration of higher meropenem doses), R 2 values for fT > MIC and fAUC/MIC were similar. Efficacy target magnitudes were also sensitive to the selected doses. Additional efficacy assessment times improved parameter accuracy (e.g. 40% reduction in relative root mean squared error of PMB effect slope). The model parameter accuracy was more affected by the selection of time points for meropenem, which included resistance, than for PMB. Efficacy measurements in the first hours after treatment start (e.g. 2 and 6 h), in addition to 24 h, were essential for resistance characterization.\n\nThe choice of doses and fractionations impacted PK/PD index selection and efficacy target magnitude. Depending on the antibiotic, the dose or fractionation selection appeared to be the most critical. Early treatment efficacy measurements were beneficial to PKPD model-based analyses, particularly to describe resistance processes.", "doi": "10.1093/jacamr/dlaf057", "pmid": "40224358", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11986329"}, {"db": "pii", "key": "dlaf057"}], "notes": [], "created": "2025-11-28T10:49:42.617Z", "modified": "2025-11-28T10:49:42.769Z"}, {"entity": "publication", "iuid": "33f7c1d27c724a188e43c1e941c7eaac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33f7c1d27c724a188e43c1e941c7eaac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33f7c1d27c724a188e43c1e941c7eaac"}}, "title": "Rapid traversal of vast chemical space using machine learning-guided docking screens.", "authors": [{"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d46047fab4247caaeecf31be6da987f.json"}}, {"family": "Cabeza de Vaca", "given": "Israel", "initials": "I"}, {"family": "Sparring", "given": "Leonard", "initials": "L"}, {"family": "Brea", "given": "Jos\u00e9", "initials": "J"}, {"family": "Mart\u00ednez", "given": "Ant\u00f3n Leandro", "initials": "AL", "orcid": "0000-0002-1595-3459", "researcher": {"href": "https://publications.scilifelab.se/researcher/46b781fca7af46b49699abf9f063c390.json"}}, {"family": "Kahlous", "given": "Nour Aldin", "initials": "NA", "orcid": "0000-0002-7744-1491", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7e3d259da7a4b6d97973a0de8b3d497.json"}}, {"family": "Radchenko", "given": "Dmytro S", "initials": "DS", "orcid": "0000-0001-5444-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/df4077c366bc4f4a8b422762c0be9cfe.json"}}, {"family": "Moroz", "given": "Yurii S", "initials": "YS", "orcid": "0000-0001-6073-002X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8586d3b69b4782bed34192411a02e5.json"}}, {"family": "Loza", "given": "Mar\u00eda Isabel", "initials": "MI", "orcid": "0000-0003-4730-0863", "researcher": {"href": "https://publications.scilifelab.se/researcher/16ba410826ea43aaa8e14e8bb14e6fac.json"}}, {"family": "Norinder", "given": "Ulf", "initials": "U", "orcid": "0000-0003-3107-331X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecd436012ccc4e29bd07b730fbda51c3.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7d91087358e46e38bb1b7110dc0b214.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat Comput Sci", "issn": "2662-8457", "volume": "5", "issue": "4", "pages": "301-312", "issn-l": null}, "abstract": "The accelerating growth of make-on-demand chemical libraries provides unprecedented opportunities to identify starting points for drug discovery with virtual screening. However, these multi-billion-scale libraries are challenging to screen, even for the fastest structure-based docking methods. Here we explore a strategy that combines machine learning and molecular docking to enable rapid virtual screening of databases containing billions of compounds. In our workflow, a classification algorithm is trained to identify top-scoring compounds based on molecular docking of 1 million compounds to the target protein. The conformal prediction framework is then used to make selections from the multi-billion-scale library, reducing the number of compounds to be scored by docking. The CatBoost classifier showed an optimal balance between speed and accuracy and was used to adapt the workflow for screens of ultralarge libraries. Application to a library of 3.5 billion compounds demonstrated that our protocol can reduce the computational cost of structure-based virtual screening by more than 1,000-fold. Experimental testing of predictions identified ligands of G protein-coupled receptors and demonstrated that our approach enables discovery of compounds with multi-target activity tailored for therapeutic effect.", "doi": "10.1038/s43588-025-00777-x", "pmid": "40082701", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12021657"}, {"db": "pii", "key": "10.1038/s43588-025-00777-x"}], "notes": [], "created": "2025-11-28T10:47:46.133Z", "modified": "2025-11-28T10:47:46.396Z"}, {"entity": "publication", "iuid": "d1498245bf174acb9c4f482f29f424f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1498245bf174acb9c4f482f29f424f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1498245bf174acb9c4f482f29f424f2"}}, "title": "Preclinical Protein Signatures of Crohn's Disease and Ulcerative Colitis: A Nested Case-Control Study Within Large Population-Based Cohorts.", "authors": [{"family": "Gr\u00e4nn\u00f6", "given": "Olle", "initials": "O"}, {"family": "Bergemalm", "given": "Daniel", "initials": "D"}, {"family": "Salomon", "given": "Benita", "initials": "B"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Hedin", "given": "Charlotte R H", "initials": "CRH"}, {"family": "Carlson", "given": "Marie", "initials": "M"}, {"family": "Dannenberg", "given": "Katharina", "initials": "K"}, {"family": "Andersson", "given": "Erik", "initials": "E"}, {"family": "Keita", "given": "\u00c5sa V", "initials": "\u00c5V"}, {"family": "Magnusson", "given": "Maria K", "initials": "MK"}, {"family": "Eriksson", "given": "Carl", "initials": "C"}, {"family": "Lanka", "given": "Vivekananda", "initials": "V"}, {"family": "BIOIBD consortium", "given": "", "initials": ""}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "\u00d6hman", "given": "Lena", "initials": "L"}, {"family": "S\u00f6derholm", "given": "Johan D", "initials": "JD"}, {"family": "Hultdin", "given": "Johan", "initials": "J"}, {"family": "Kruse", "given": "Robert", "initials": "R"}, {"family": "Cao", "given": "Yang", "initials": "Y"}, {"family": "Repsilber", "given": "Dirk", "initials": "D"}, {"family": "Grip", "given": "Olof", "initials": "O"}, {"family": "Karling", "given": "Pontus", "initials": "P"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Gastroenterology", "issn": "1528-0012", "volume": "168", "issue": "4", "pages": "741-753", "issn-l": "0016-5085"}, "abstract": "Biomarkers are needed to identify individuals at elevated risk of inflammatory bowel disease. This study aimed to identify protein signatures predictive of inflammatory bowel disease.\n\nUsing large population-based cohorts (n \u2265180,000), blood samples were obtained from individuals who later in life were diagnosed with inflammatory bowel disease and compared with age and sex-matched controls, free from inflammatory bowel disease during follow-up. A total of 178 proteins were measured on Olink platforms. We used machine-learning methods to identify protein signatures of preclinical disease in the discovery cohort (n = 312). Their performance was validated in an external preclinical cohort (n = 222) and assessed in an inception cohort (n = 144) and a preclinical twin cohort (n = 102).\n\nIn the discovery cohort, a signature of 29 proteins differentiated preclinical Crohn's disease (CD) cases from controls, with an area under the curve (AUC) of 0.85. Its performance was confirmed in the preclinical validation (AUC = 0.87) and the inception cohort (AUC = 1.0). In preclinical samples, downregulated (but not upregulated) proteins related to gut barrier integrity and macrophage functionality correlated with time to diagnosis of CD. The preclinical ulcerative colitis signature had a significant, albeit lower, predictive ability in the discovery (AUC = 0.77), validation (AUC = 0.67), and inception cohorts (AUC = 0.95). The preclinical signature for CD demonstrated an AUC of 0.89 when comparing twins with preclinical CD with matched external healthy twins, but its predictive ability was lower (AUC = 0.58; P = .04) when comparing them with their healthy twin siblings, that is, when accounting for genetic and shared environmental factors.\n\nWe identified protein signatures for predicting a future diagnosis of CD and ulcerative colitis, validated across independent cohorts. In the context of CD, the signature offers potential for early prediction.", "doi": "10.1053/j.gastro.2024.11.006", "pmid": "39608683", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "S0016-5085(24)05741-X"}], "notes": [], "created": "2025-11-25T19:20:21.670Z", "modified": "2025-11-25T19:20:21.686Z"}, {"entity": "publication", "iuid": "732c1709c77041de8566ee89d1282007", "links": {"self": {"href": "https://publications.scilifelab.se/publication/732c1709c77041de8566ee89d1282007.json"}, "display": {"href": "https://publications.scilifelab.se/publication/732c1709c77041de8566ee89d1282007"}}, "title": "Plasma H3Cit-DNA Discriminates Between Cancer and Inflammation in a Cohort of Patients with Unspecific Cancer Symptoms.", "authors": [{"family": "Wannberg", "given": "Fredrika", "initials": "F"}, {"family": "Hjalmar", "given": "Viktoria", "initials": "V"}, {"family": "Ng", "given": "Henry", "initials": "H"}, {"family": "Johansson", "given": "Caroline", "initials": "C"}, {"family": "Probert", "given": "Fay", "initials": "F"}, {"family": "Phillipson", "given": "Mia", "initials": "M"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Gordon", "given": "Max", "initials": "M"}, {"family": "Mackman", "given": "Nigel", "initials": "N"}, {"family": "Rosell", "given": "Axel", "initials": "A"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Inflammation", "issn": "1573-2576", "volume": "48", "issue": "2", "pages": "760-769", "issn-l": null}, "abstract": "Cancer detection is challenging, especially in patients with unspecific cancer symptoms. Biomarkers could identify patients at high risk of cancer. Prior studies indicate that neutrophil extracellular traps (NETs) are associated with cancer, but also with autoimmune and infectious diseases. The objective of this prospective study was to investigate markers associated with NET formation (nucleosomal citrullinated histone 3 [H3Cit-DNA], cell free DNA [cfDNA] and neutrophil elastase [NE]), and c-reactive protein (CRP) in patients with unspecific cancer symptoms, such as fatigue, weight loss or radiological sign of malignancy without an apparent primary tumor, referred to the Diagnostic Center at Danderyd Hospital in Sweden. Blood samples were drawn on admission, before cancer diagnosis. Out of 475 patients, 160 (34%) were diagnosed with cancer, 56 (12%) with autoimmune disease, 32 (7%) with infectious disease, 71 (15%) with other diseases and 156 (33%) received no diagnosis. H3Cit-DNA, cfDNA, NE and CRP were significantly higher in patients with cancer compared to patients without cancer (p < 0.0001, p < 0.0001, p = 0.004, and p = 0.0002 respectively). H3Cit-DNA, but not cfDNA, NE or CRP, was significantly elevated in patients with cancer compared to patients with autoimmune disease (p = 0.0001). H3Cit-DNA, cfDNA, NE or CRP did not differ between cancer and infectious disease. In conclusion, H3Cit-DNA is elevated in patients diagnosed with cancer compared to non-cancer patients with the same symptomatology. Further studies should evaluate if H3Cit-DNA could aid in selecting patients that would benefit the most from a rapid cancer diagnostic work-up.", "doi": "10.1007/s10753-024-02085-4", "pmid": "38941006", "labels": {"Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12053196"}, {"db": "pii", "key": "10.1007/s10753-024-02085-4"}], "notes": [], "created": "2025-11-25T19:16:32.092Z", "modified": "2025-11-25T19:19:39.203Z"}, {"entity": "publication", "iuid": "87266d8a6f284e2198986f59a2abeff9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87266d8a6f284e2198986f59a2abeff9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87266d8a6f284e2198986f59a2abeff9"}}, "title": "Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.", "authors": [{"family": "Marco Salas", "given": "Sergio", "initials": "S", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Kuemmerle", "given": "Louis B", "initials": "LB", "orcid": "0000-0002-9193-1243", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d339771ed9a4559ad56a63e9e4e9e80.json"}}, {"family": "Mattsson-Langseth", "given": "Christoffer", "initials": "C"}, {"family": "Tismeyer", "given": "Sebastian", "initials": "S"}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Hu", "given": "Taobo", "initials": "T", "orcid": "0000-0001-5124-7167", "researcher": {"href": "https://publications.scilifelab.se/researcher/b693c14571864cfcb6f3b36cce183f12.json"}}, {"family": "Rehman", "given": "Habib", "initials": "H", "orcid": "0000-0002-8671-982X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dff0d9994c0f4237a5afbcd66d706dbf.json"}}, {"family": "Grillo", "given": "Marco", "initials": "M", "orcid": "0000-0003-2155-0645", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd8bec6567444558acbcbd1b3d28f7a.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Helgadottir", "given": "Saga", "initials": "S"}, {"family": "Tiklova", "given": "Katarina", "initials": "K"}, {"family": "Andersson", "given": "Axel", "initials": "A", "orcid": "0000-0002-4714-3127", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027f6b47684ff4be205e2d547c5f8a.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Chatzinikolaou", "given": "Maria", "initials": "M"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f.json"}}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b82068719d43448992741da54e00bd.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Ishaque", "given": "Naveed", "initials": "N", "orcid": "0000-0002-8426-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38be333e07614a13bf8c559e7935381a.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "4", "pages": "813-823", "issn-l": "1548-7091"}, "abstract": "The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as an independent analysis of the performance of Xenium, and provides best practices and recommendations for analysis of such datasets.", "doi": "10.1038/s41592-025-02617-2", "pmid": "40082609", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "BioImage Informatics": "Collaborative", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11978515"}, {"db": "pii", "key": "10.1038/s41592-025-02617-2"}], "notes": [], "created": "2025-11-21T12:56:02.504Z", "modified": "2025-11-28T06:50:06.581Z"}, {"entity": "publication", "iuid": "47168257d65a46dcb0727839411bb59e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47168257d65a46dcb0727839411bb59e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47168257d65a46dcb0727839411bb59e"}}, "title": "One Year of Oral Immunotherapy Impacts the Gut Microbiota and Plasma Metabolome of Peanut-Allergic Young Children.", "authors": [{"family": "Badolati", "given": "Isabella", "initials": "I", "orcid": "0000-0001-6619-6884", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83945ce36374fea9c78b960e4eef2da.json"}}, {"family": "de Jong", "given": "Ymke", "initials": "Y", "orcid": "0009-0002-4795-1279", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ff40c059d544d582c96f79e8a171c5.json"}}, {"family": "Uhl", "given": "Carina", "initials": "C", "orcid": "0000-0002-5454-4105", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e8cef98bcd84907948e9289701821bb.json"}}, {"family": "Ullberg", "given": "Josefin", "initials": "J", "orcid": "0000-0003-0996-4773", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab9a65e518b44b0db4cf9143f8880964.json"}}, {"family": "Joustra", "given": "Marleen", "initials": "M"}, {"family": "Fagerberg", "given": "Ulrika Lorentzon", "initials": "UL", "orcid": "0000-0003-2727-7280", "researcher": {"href": "https://publications.scilifelab.se/researcher/707a5d995b09487bbfc325c3c74a7b4a.json"}}, {"family": "Nilsson", "given": "Caroline", "initials": "C", "orcid": "0000-0003-2040-8428", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1bb0016587e47aa847718e4f9836fd3.json"}}, {"family": "Asarnoj", "given": "Anna", "initials": "A", "orcid": "0000-0002-0797-2369", "researcher": {"href": "https://publications.scilifelab.se/researcher/14fb103c7b5a4863b6f454fb80c4e733.json"}}, {"family": "Sverremark-Ekstr\u00f6m", "given": "Eva", "initials": "E", "orcid": "0000-0001-6271-8681", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7519ea4bf1f43dcab124c3d62b489db.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Clin Exp Allergy", "issn": "1365-2222", "volume": "55", "issue": "4", "pages": "340-343", "issn-l": "0954-7894"}, "abstract": null, "doi": "10.1111/cea.14607", "pmid": "39602883", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11994247"}], "notes": [], "created": "2025-11-18T12:06:36.463Z", "modified": "2025-11-18T12:06:37.070Z"}, {"entity": "publication", "iuid": "a00e2c7e27384bc3be5381131267492f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a00e2c7e27384bc3be5381131267492f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a00e2c7e27384bc3be5381131267492f"}}, "title": "Non\u2010Native Earthworms Alter Carbon Sequestration in Arctic Tundra Ecosystems", "authors": [{"family": "Jonsson", "given": "H", "initials": "H", "orcid": "0000-0003-4552-1945", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc27fd775f0c4b0cab69e1b98e3a2522.json"}}, {"family": "Blume\u2010Werry", "given": "G", "initials": "G"}, {"family": "Wackett", "given": "A A", "initials": "AA", "orcid": "0000-0003-1850-0997", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ec1591d9b404f0580c80238e0382393.json"}}, {"family": "Olofsson", "given": "J", "initials": "J"}, {"family": "Arvidsson", "given": "E", "initials": "E"}, {"family": "Sparrman", "given": "T", "initials": "T"}, {"family": "Klaminder", "given": "J", "initials": "J"}], "type": "journal-article", "published": "2025-04-00", "journal": {"title": "JGR Biogeosciences", "issn": "2169-8953", "volume": "130", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.1029/2024jg008598", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-06-11T13:33:12.259Z", "modified": "2025-10-17T13:03:52.361Z"}, {"entity": "publication", "iuid": "ceaf1969c97a4727bf39dfdf61d788be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ceaf1969c97a4727bf39dfdf61d788be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ceaf1969c97a4727bf39dfdf61d788be"}}, "title": "MIA40 suppresses cell death induced by apoptosis-inducing factor 1.", "authors": [{"family": "Mussulini", "given": "Ben Hur Marins", "initials": "BHM", "orcid": "0000-0003-4321-5709", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5d73d54bba342edbc4af1606bf7af79.json"}}, {"family": "Maruszczak", "given": "Klaudia K", "initials": "KK", "orcid": "0000-0003-4080-9368", "researcher": {"href": "https://publications.scilifelab.se/researcher/456fceca130940b8a46137d5d2756043.json"}}, {"family": "Draczkowski", "given": "Piotr", "initials": "P", "orcid": "0000-0002-9408-2670", "researcher": {"href": "https://publications.scilifelab.se/researcher/efa7492df2464ccdb31320e4f5bb51e9.json"}}, {"family": "Borrero-Landazabal", "given": "Mayra A", "initials": "MA", "orcid": "0000-0003-3464-4042", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a6bac5b1045422abddc2b136642cf4a.json"}}, {"family": "Ayyamperumal", "given": "Selvaraj", "initials": "S", "orcid": "0000-0003-2634-391X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe24ea5ef2494e60b633aea581c0bc89.json"}}, {"family": "Wnorowski", "given": "Artur", "initials": "A"}, {"family": "Wasilewski", "given": "Michal", "initials": "M", "orcid": "0000-0002-4890-5103", "researcher": {"href": "https://publications.scilifelab.se/researcher/772c69846aff4fd081a53a7f704eaff2.json"}}, {"family": "Chacinska", "given": "Agnieszka", "initials": "A", "orcid": "0000-0002-2832-2568", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f6574d6e83b4e65a2721be9527de5ff.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "EMBO Rep.", "issn": "1469-3178", "volume": "26", "issue": "7", "pages": "1835-1862", "issn-l": "1469-221X"}, "abstract": "Mitochondria harbor respiratory complexes that perform oxidative phosphorylation. Complex I is the first enzyme of the respiratory chain that oxidizes NADH. A dysfunction in complex I can result in higher cellular levels of NADH, which in turn strengthens the interaction between apoptosis-inducing factor 1 (AIFM1) and Mitochondrial intermembrane space import and assembly protein 40 (MIA40) in the mitochondrial intermembrane space. We investigated whether MIA40 modulates the activity of AIFM1 upon increased NADH/NAD+ balance. We found that in model cells characterized by an increase in NADH the AIFM1-MIA40 interaction is strengthened and these cells demonstrate resistance to AIFM1-induced cell death. Either silencing of MIA40, rescue of complex I, or depletion of NADH through the expression of yeast NADH-ubiquinone oxidoreductase-2 sensitized NDUFA13-KO cells to AIFM1-induced cell death. These findings indicate that the complex of MIA40 and AIFM1 suppresses AIFM1-induced cell death in a NADH-dependent manner. This study identifies an effector complex involved in regulating the programmed cell death that accommodates the metabolic changes in the cell and provides a molecular explanation for AIFM1-mediated chemoresistance of cancer cells.", "doi": "10.1038/s44319-025-00406-8", "pmid": "40055465", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11976965"}, {"db": "pii", "key": "10.1038/s44319-025-00406-8"}], "notes": [], "created": "2025-11-25T08:59:24.731Z", "modified": "2025-11-25T08:59:25.528Z"}, {"entity": "publication", "iuid": "dd3b9e495f154236a9c26473858d9e33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd3b9e495f154236a9c26473858d9e33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd3b9e495f154236a9c26473858d9e33"}}, "title": "IER3: exploring its dual function as an oncogene and tumor suppressor.", "authors": [{"family": "Kanduri", "given": "Meena", "initials": "M", "orcid": "0000-0003-2781-4779", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0c8993f8119475d98d8f4ca1e77abff.json"}}, {"family": "Subhash", "given": "Santhilal", "initials": "S", "orcid": "0000-0002-0077-4597", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ca22115b7c9444ab2056126a1c9d36d.json"}}, {"family": "Putino", "given": "Rossana", "initials": "R"}, {"family": "Mahale", "given": "Sagar", "initials": "S"}, {"family": "Kanduri", "given": "Chandrasekhar", "initials": "C", "orcid": "0000-0001-6271-9078", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8da9c5c5d0c48f9ae08549027375512.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Cancer Gene Ther", "issn": "1476-5500", "volume": "32", "issue": "4", "pages": "450-463", "issn-l": null}, "abstract": "The IER3 gene has a complex role in cancer biology, acting either as a tumor suppressor or an oncogene, depending on the cancer type. This duality underscores the complexity and importance of molecular pathways in modulating cancer behavior. Despite its significance in cancer development, there is a dearth of studies elucidating the exact mechanisms underlying IER3's involvement in modulating cancer behavior. Here, utilizing cervical carcinoma and neuroblastoma (NB) cell lines as model systems we characterized the pathways that mediate the functional switch between the oncogenic and tumor suppressor roles of IER3. In HeLa cells, IER3 expression promotes an oncogenic program that includes immediate early response pathway genes such as EGR2, FOS, and JUN. However, in NB cells, IER3 suppresses the EGR2-dependent oncogenic program. This differential regulation of EGR2 by IER3 involves epigenetic modulation of the EGR2 promoter. IER3 dependent tumor suppressor pathway in NB cells relies on ADAM19 gene. Thus, our findings uncover the molecular pathways that dictate the context-dependent roles of IER3 in cancer, providing insights into its dual functionality in different cancer types.", "doi": "10.1038/s41417-025-00891-y", "pmid": "40090972", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11976266"}, {"db": "pii", "key": "10.1038/s41417-025-00891-y"}], "notes": [], "created": "2025-11-28T10:44:57.184Z", "modified": "2025-11-28T10:44:57.463Z"}, {"entity": "publication", "iuid": "2e02af05ec4f41039901b42de46ac5b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e02af05ec4f41039901b42de46ac5b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e02af05ec4f41039901b42de46ac5b8"}}, "title": "Host Plasma Microenvironment in Immunometabolically Impaired HIV Infection Leads to Dysregulated Monocyte Function and Synaptic Transmission Ex Vivo.", "authors": [{"family": "Mikaeloff", "given": "Flora", "initials": "F"}, {"family": "Gelpi", "given": "Marco", "initials": "M"}, {"family": "Esc\u00f3s", "given": "Alejandra", "initials": "A"}, {"family": "Wang", "given": "Tianqi", "initials": "T"}, {"family": "Gupta", "given": "Soham", "initials": "S"}, {"family": "Olofsson", "given": "Anna", "initials": "A"}, {"family": "Akusj\u00e4rvi", "given": "Sara Svensson", "initials": "SS"}, {"family": "Schuster", "given": "Sabrina", "initials": "S"}, {"family": "Naval", "given": "Prajakta", "initials": "P"}, {"family": "Sood", "given": "Vikas", "initials": "V"}, {"family": "Nikouyan", "given": "Negin", "initials": "N"}, {"family": "Knudsen", "given": "Andreas D", "initials": "AD"}, {"family": "Vestad", "given": "Beate", "initials": "B"}, {"family": "H\u00f8gh", "given": "Julie", "initials": "J"}, {"family": "Hov", "given": "Johannes R", "initials": "JR"}, {"family": "Benfield", "given": "Thomas", "initials": "T"}, {"family": "Tr\u00f8seid", "given": "Marius", "initials": "M"}, {"family": "Pawar", "given": "Vinay", "initials": "V"}, {"family": "Rucevic", "given": "Marijana", "initials": "M"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1"}, {"family": "O'Mahony", "given": "Liam", "initials": "L"}, {"family": "Savai", "given": "Rajkumar", "initials": "R"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK"}, {"family": "Lourda", "given": "Magda", "initials": "M"}, {"family": "de Magalh\u00e3es", "given": "Jo\u00e3o Pedro", "initials": "JP"}, {"family": "Weiss", "given": "Siegfried", "initials": "S"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Varshney", "given": "Mukesh Kumar", "initials": "MK"}, {"family": "Karlsson", "given": "Annika C", "initials": "AC"}, {"family": "Syed", "given": "Yasir Ahmed", "initials": "YA"}, {"family": "Nielsen", "given": "Susanne D", "initials": "SD"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U", "orcid": "0000-0002-0844-3338", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f8094017c2a4d0a94d72813cab526f7.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "12", "issue": "16", "pages": "e2416453", "issn-l": null}, "abstract": "Risk stratification using multi-omics data deepens understanding of immunometabolism in successfully treated people with HIV (PWH) is inadequately explained. A personalized medicine approach integrating blood cell transcriptomics, plasma proteomics, and metabolomics is employed to identify the mechanisms of immunometabolic complications in prolonged treated PWH from the COCOMO cohort. Among the PWHs, 44% of PWH are at risk of experiencing immunometabolic complications identified using the network-based patient stratification method. Utilizing advanced machine learning techniques and a Bayesian classifier, five plasma protein biomarkers; Tubulin Folding Cofactor B (TBCB), Gamma-Glutamylcyclotransferase (GGCT), Taxilin Alpha (TXLNA), Pyridoxal Phosphate Binding Protein (PLPBP) and Large Tumor Suppressor Kinase 1 (LATS1) are identified as highly differentially abundant between healthy control (HC)-like and immunometabolically at-risk PWHs (all FDR<10-10). The personalized metabolic models predict metabolic perturbations, revealing disruptions in central carbon metabolic fluxes and host tryptophan metabolism in at-risk phenotype. Functional assays in primary cells and cortical forebrain organoids (FBOs) further validate this. Metabolic perturbations lead to persistent monocyte activation, thereby impairing their functions ex vivo. Furthermore, the chronic inflammatory plasma microenvironment contributes to synaptic dysregulation in FBOs. The endogenous plasma inflammatory microenvironment is responsible for chronic inflammation in treated immunometabolically complicated at-risk PWH who have a higher risk of cardiovascular and neuropsychiatric disorders.", "doi": "10.1002/advs.202416453", "pmid": "40013867", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12021100"}], "notes": [], "created": "2025-11-25T10:19:00.216Z", "modified": "2025-11-25T10:19:00.307Z"}, {"entity": "publication", "iuid": "061cf4f28b2e40c1bc8944cd8c3e49eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/061cf4f28b2e40c1bc8944cd8c3e49eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/061cf4f28b2e40c1bc8944cd8c3e49eb"}}, "title": "Folding of mRNA-DNA Origami for Controlled Translation and Viral Vector Packaging.", "authors": [{"family": "Seitz", "given": "Iris", "initials": "I"}, {"family": "Saarinen", "given": "Sharon", "initials": "S"}, {"family": "Wierzchowiecka", "given": "Julia", "initials": "J"}, {"family": "Kumpula", "given": "Esa-Pekka", "initials": "EP"}, {"family": "Shen", "given": "Boxuan", "initials": "B"}, {"family": "Cornelissen", "given": "Jeroen J L M", "initials": "JJLM"}, {"family": "Linko", "given": "Veikko", "initials": "V"}, {"family": "Huiskonen", "given": "Juha T", "initials": "JT"}, {"family": "Kostiainen", "given": "Mauri A", "initials": "MA", "orcid": "0000-0002-8282-2379", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ee9e43163b14b22acdf3613dbd18d89.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Adv Mater", "issn": "1521-4095", "volume": "37", "issue": "15", "pages": "e2417642", "issn-l": null}, "abstract": "mRNA is an important molecule in vaccine development and treatment of genetic disorders. Its capability to hybridize with DNA oligonucleotides in a programmable manner facilitates the formation of RNA-DNA origami structures, which can possess a well-defined morphology and serve as rigid supports for mRNA delivery. However, to date, comprehensive studies on the requirements for efficient folding of mRNA into distinct mRNA-DNA structures while preserving its translation functionality remain elusive. Here, the impact of design parameters on the folding of protein-encoding mRNA into mRNA-DNA origami structures is systematically investigated and the importance of the availability of ribosome-binding sequences on the translation efficiency is demonstrated. Furthermore, these hybrid structures are encapsulated inside virus capsids resulting in protecting them against nuclease degradation and also in enhancement of their cellular uptake. This multicomponent system therefore showcases a modular and versatile nanocarrier. The work provides valuable insight into the design of mRNA-DNA origami structures contributing to the development of mRNA-based gene delivery platforms.", "doi": "10.1002/adma.202417642", "pmid": "40012449", "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-13T09:37:43.422Z", "modified": "2025-11-13T09:37:43.506Z"}, {"entity": "publication", "iuid": "26b9ef3adace47b583a8720138aa1f04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26b9ef3adace47b583a8720138aa1f04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26b9ef3adace47b583a8720138aa1f04"}}, "title": "Fibromyalgia patients have altered lipid concentrations associated with disease symptom severity and anti-satellite glial cell IgG antibodies.", "authors": [{"family": "Jakobsson", "given": "Jenny E", "initials": "JE"}, {"family": "Menezes", "given": "Joana", "initials": "J"}, {"family": "Krock", "given": "Emerson", "initials": "E"}, {"family": "Hunt", "given": "Matthew A", "initials": "MA"}, {"family": "Carlsson", "given": "Henrik", "initials": "H"}, {"family": "Vaivade", "given": "Aina", "initials": "A"}, {"family": "Emami Khoonsari", "given": "Payam", "initials": "P"}, {"family": "Agalave", "given": "Nilesh M", "initials": "NM"}, {"family": "Sandstr\u00f6m", "given": "Angelica", "initials": "A"}, {"family": "Kadetoff", "given": "Diana", "initials": "D"}, {"family": "Tour Sohlin", "given": "Jeanette", "initials": "J"}, {"family": "Erngren", "given": "Ida", "initials": "I"}, {"family": "Al-Grety", "given": "Asma", "initials": "A"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Sandor", "given": "Katalin", "initials": "K"}, {"family": "Kosek", "given": "Eva", "initials": "E"}, {"family": "Svensson", "given": "Camilla I", "initials": "CI"}, {"family": "Kultima", "given": "Kim", "initials": "K"}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "J Pain", "issn": "1528-8447", "volume": "29", "pages": "105331", "issn-l": null}, "abstract": "Autoimmunity and immunoglobulin G (IgG) autoantibodies may contribute to pain in a subset of fibromyalgia (FM) patients. Previously, IgG from FM patients was found to induce pain-like behavior in mice and bind to satellite glial cells (anti-SGC IgG). The anti-SGC IgG levels were also associated with more severe symptomatology. Lipid metabolism in FM subjects is altered with lysophosphatidylcholines (LPCs) acting as pain mediators. The relationship between autoantibodies, lipid metabolism, and FM symptomatology remains unclear. Serum lipidomics with liquid chromatography mass spectrometry, anti-SGC IgG levels, and clinical measures were examined in 35 female FM subjects and 33 age- and body mass index-balanced healthy controls (HC). Fibromyalgia subjects with higher anti-SGC IgG levels experienced more intense pain than those with lower levels. Sixty-three lipids were significantly altered between FM subjects and HC or between FM subjects with severe (FM severe) and mild symptoms (FM mild). Compared to HC, FM subjects had lower concentrations of lipid species belonging to the classes LPC (n = 10), lysophosphatidylethanolamine (n = 7), phosphatidylcholine (n = 4), and triglyceride (n = 5), but higher concentrations of diglyceride (n = 3). Additionally, FM severe had higher LPC 19:0, 22:0, and 24:1 and lower sphingomyelin (n = 9) concentrations compared to FM mild. Positive associations were seen for LPC 22:0 and 24:1 with pain intensity and anti-SGC IgG levels in FM subjects. Taken together, these results suggest an association between altered lipid metabolism and autoimmune mechanisms in FM.", "doi": "10.1016/j.jpain.2025.105331", "pmid": "39922554", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1526-5900(25)00558-9"}], "notes": [], "created": "2025-11-21T12:09:30.182Z", "modified": "2025-11-21T12:09:30.222Z"}, {"entity": "publication", "iuid": "4d12b06a01ae4f7aa582051ac121185b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d12b06a01ae4f7aa582051ac121185b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d12b06a01ae4f7aa582051ac121185b"}}, "title": "Effects of Montelukast on Neuroinflammation in Parkinson's Disease: An Open Label Safety and Tolerability Trial with CSF Markers and [11C]PBR28 PET.", "authors": [{"family": "Wallin", "given": "Johan", "initials": "J", "orcid": "0000-0003-0490-9900", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f513ad777614e57a30ce641b9c436ae.json"}}, {"family": "Forsberg", "given": "Anton", "initials": "A", "orcid": "0000-0001-8790-3306", "researcher": {"href": "https://publications.scilifelab.se/researcher/e825af97d4ac433198d14d2c20826ed2.json"}}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Mov Disord", "issn": "1531-8257", "volume": "40", "issue": "4", "pages": "739-744", "issn-l": null}, "abstract": "Dysregulated leukotriene signaling is proposed to be involved in pathogenesis of Parkinson's disease (PD).\n\nThe objective was to examine the safety and tolerability of montelukast, a cysteinyl-leukotriene receptor1 and GPR17 antagonist, in patients with PD. Secondary outcomes were target engagement, effects on PD signs/symptoms, and central neuroinflammation.\n\nFifteen PD patients were recruited to a 12-week open-label trial of 20 mg bi-daily montelukast treatment. Patients underwent ratings with the Movement Disorder Society Unified Parkinson Disease Rating Scale (MDS-UPDRS), the Montreal Cognitive Assessment (MoCA), Beck's Depression Inventory (BDI), Parkinson's Disease Questionnaire-39 (PDQ-39), [11C]PBR28-PET, and lumbar punctures before and during montelukast treatment.\n\nAll patients completed the study. Three patients reported loose stool. No serious adverse events related to treatment were reported. MDS-UPDRS-Total scores improved by 6.9 points. Very low levels of montelukast were detected in all cerebrospinal fluid (CSF) samples and resulted in a reduction in inflammation/metabolism markers. [11C]PBR28 binding was lowered in high, but not mixed, affinity binders after montelukast.\n\nMontelukast crosses the blood-brain barrier at very low levels and is well tolerated and safe in PD patients. Preliminary effects on neuroinflammation and clinical scores motivate a future randomized controlled trial (RCT) in PD. \u00a9 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.", "doi": "10.1002/mds.30144", "pmid": "39912596", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12006882"}], "notes": [], "created": "2025-11-18T12:16:32.491Z", "modified": "2025-11-18T12:16:32.623Z"}, {"entity": "publication", "iuid": "4d18e85087514f59b370cda0f3182fae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d18e85087514f59b370cda0f3182fae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d18e85087514f59b370cda0f3182fae"}}, "title": "Dynamic networks connect the USP14 active site region with the proteasome interaction surface", "authors": [{"family": "Salomonsson", "given": "Johannes", "initials": "J", "orcid": "0000-0003-4810-3669", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcc65f9dd43440adb6da73997653fb20.json"}}, {"family": "Sj\u00f6strand", "given": "Linda", "initials": "L"}, {"family": "Eskilson", "given": "Arvid", "initials": "A"}, {"family": "Derbyshire", "given": "Dean", "initials": "D"}, {"family": "D'Arcy", "given": "P\u00e1draig", "initials": "P"}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M"}, {"family": "Ahlner", "given": "Alexandra", "initials": "A", "orcid": "0000-0001-7004-8251", "researcher": {"href": "https://publications.scilifelab.se/researcher/08cd17a1108045b5be32cd492a082453.json"}}], "type": "journal-article", "published": "2025-04-00", "journal": {"title": "Protein Sci.", "issn": "0961-8368", "volume": "34", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.1002/pro.70077", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:05:11.667Z", "modified": "2025-11-27T08:05:11.806Z"}, {"entity": "publication", "iuid": "ff0fdef4edde472b996e71389a31dadf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff0fdef4edde472b996e71389a31dadf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff0fdef4edde472b996e71389a31dadf"}}, "title": "Centennial-scale atmospheric CO2 rise increased photosynthetic efficiency in a tropical tree species.", "authors": [{"family": "Zwartsenberg", "given": "Sophie A", "initials": "SA", "orcid": "0000-0002-1610-6470", "researcher": {"href": "https://publications.scilifelab.se/researcher/401bed2dfb264407b73fed1b0cbb2fe3.json"}}, {"family": "Sterck", "given": "Frank J", "initials": "FJ", "orcid": "0000-0001-7559-6572", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e42dc45725d4731b9f6782200c2953f.json"}}, {"family": "Haddad", "given": "Lenny", "initials": "L", "orcid": "0009-0003-9821-783X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebec3fa5c2ab4c0e8730756d2bc7ab29.json"}}, {"family": "Schleucher", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0002-4815-3466", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad2a0d8c63a7453e9dda23cf94b9e202.json"}}, {"family": "Anten", "given": "Niels P R", "initials": "NPR", "orcid": "0000-0002-9097-0654", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ba0fe6329f643e7a22d4a624655ee74.json"}}, {"family": "Morales", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-6129-4570", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4eaa4c747304a9e9005c0f00534d2cd.json"}}, {"family": "Cernusak", "given": "Lucas A", "initials": "LA", "orcid": "0000-0002-7575-5526", "researcher": {"href": "https://publications.scilifelab.se/researcher/869ffc5eacdb422cb2ab89ea95417a7b.json"}}, {"family": "Medina-Vega", "given": "Jos\u00e9 A", "initials": "JA", "orcid": "0000-0001-5468-5605", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2b3d0cdd00a419eacad7d345737868f.json"}}, {"family": "Rahman", "given": "Mizanur", "initials": "M", "orcid": "0000-0001-9011-2011", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8a6e257fb2a402bb55860e0706a66bb.json"}}, {"family": "Vlam", "given": "Mart", "initials": "M", "orcid": "0000-0002-0038-6586", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b05d8512fa74f278b937e1eacdb4f58.json"}}, {"family": "Heinrich", "given": "Ingo", "initials": "I", "orcid": "0000-0001-5800-6999", "researcher": {"href": "https://publications.scilifelab.se/researcher/be70c14c4777408db7ad95ac62609705.json"}}, {"family": "Zuidema", "given": "Pieter A", "initials": "PA", "orcid": "0000-0001-8100-1168", "researcher": {"href": "https://publications.scilifelab.se/researcher/7531b33b4ada42f7b40e67618371aa45.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "246", "issue": "1", "pages": "131-143", "issn-l": "0028-646X"}, "abstract": "Tropical forests substantially influence the terrestrial carbon sink. Their contributions to the forest carbon sink may increase due to the stimulation of photosynthesis by rising atmospheric CO2 (Ca); however, the magnitude of this effect is poorly quantified for tropical canopy trees. We measured the ratio of two deuterium isotopomers of glucose derived from tree rings to estimate how photosynthetic efficiency (photorespiration-to-photosynthesis ratio) has responded to Ca rise at a centennial scale. Wood samples were obtained from Toona ciliata trees from three climatically distinct forests in Asia and Australia. We applied Bayesian mixed effect models to test how the isotopomer ratio changes with Ca, tree diameter (as a proxy for crown exposure), temperature, and precipitation. Across all sites, long-term Ca rise increased photosynthetic efficiency, likely due to increased photosynthesis and the concurrent suppression of photorespiration. Increasing tree size reduced photosynthetic efficiency, likely due to reduced leaf internal CO2 at higher irradiance and stronger hydraulic limitation. Associations of photosynthetic efficiency with temperature and precipitation were inconclusive. Our study reveals a centennial-scale association between photosynthetic efficiency and increasing Ca in canopy trees and provides a new and independent line of evidence for Ca-induced stimulation of photosynthetic efficiency in tropical forests.", "doi": "10.1111/nph.20358", "pmid": "39938475", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11883053"}], "notes": [], "created": "2025-06-11T13:33:22.303Z", "modified": "2025-10-17T13:03:52.373Z"}, {"entity": "publication", "iuid": "f44c3247c6294ee6a38e50b6c3afe7bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f44c3247c6294ee6a38e50b6c3afe7bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f44c3247c6294ee6a38e50b6c3afe7bc"}}, "title": "A multi-strategy antimicrobial discovery approach reveals new ways to treat Chlamydia.", "authors": [{"family": "\u00d6lander", "given": "Magnus", "initials": "M"}, {"family": "Rea V\u00e1zquez", "given": "Daniel", "initials": "D"}, {"family": "Meier", "given": "Karsten", "initials": "K"}, {"family": "Singh", "given": "Aakriti", "initials": "A"}, {"family": "Silva de Sousa", "given": "Amanda", "initials": "A"}, {"family": "Pu\u00e9rtolas-Balint", "given": "Fabiola", "initials": "F"}, {"family": "Milivojevic", "given": "Milica", "initials": "M"}, {"family": "Mooij", "given": "Lieke", "initials": "L"}, {"family": "Fredlund", "given": "Johanna", "initials": "J"}, {"family": "Calpe Bosch", "given": "Eduard", "initials": "E"}, {"family": "Ray\u00f3n D\u00edaz", "given": "Mar\u00eda", "initials": "M"}, {"family": "Lundgren", "given": "Moa", "initials": "M"}, {"family": "van der Wal", "given": "Karin", "initials": "K"}, {"family": "Zhu", "given": "Shaochun", "initials": "S"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Schroeder", "given": "Bjoern O", "initials": "BO"}, {"family": "Lohman", "given": "Jeremy R", "initials": "JR"}, {"family": "Sixt", "given": "Barbara S", "initials": "BS", "orcid": "0000-0002-5607-8902", "researcher": {"href": "https://publications.scilifelab.se/researcher/998ac876b31f45c5b10d36f0d10c7390.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "volume": "23", "issue": "4", "pages": "e3003123", "issn-l": "1544-9173"}, "abstract": "While the excessive use of broad-spectrum antibiotics is a major driver of the global antibiotic resistance crisis, more selective therapies remain unavailable for the majority of bacterial pathogens. This includes the obligate intracellular bacterial pathogens of the genus Chlamydia, which cause millions of urogenital, ocular, and respiratory infections each year. Conducting a comprehensive search of the chemical space for novel antichlamydial activities, we identified over 60 compounds that are chemically diverse, structurally distinct from known antibiotics, non-toxic to human cells, and highly potent in preventing the growth of Chlamydia trachomatis in cell cultures. Some blocked C. trachomatis development reversibly, while others eradicated both established and persistent infections in a bactericidal manner. The top molecules displayed compelling selectivity, yet broad activity against diverse Chlamydia strains and species, including both urogenital and ocular serovars of C. trachomatis, as well as Chlamydia muridarum and Chlamydia caviae. Some compounds also displayed synergies with clinically used antibiotics. Critically, we found the most potent antichlamydial compound to inhibit fatty acid biosynthesis via covalent binding to the active site of Chlamydia FabH, identifying a new mechanism of FabH inhibition and highlighting a possible way to selectively treat Chlamydia infections.", "doi": "10.1371/journal.pbio.3003123", "pmid": "40299795", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12040169"}, {"db": "pii", "key": "PBIOLOGY-D-25-00637"}], "notes": [], "created": "2026-02-23T09:07:47.582Z", "modified": "2026-02-23T09:07:47.690Z"}, {"entity": "publication", "iuid": "49398b063f5d4500a3dd373382da546a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49398b063f5d4500a3dd373382da546a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49398b063f5d4500a3dd373382da546a"}}, "title": "A genome-wide association study of imaging-defined atherosclerosis.", "authors": [{"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Lundmark", "given": "Per", "initials": "P", "orcid": "0009-0006-2334-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f30b1a2e60d646c4a0cc0be06ffe77dd.json"}}, {"family": "Chen", "given": "Qiao Sen", "initials": "QS", "orcid": "0000-0002-5864-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a.json"}}, {"family": "Bj\u00f6rnson", "given": "Elias", "initials": "E"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Adiels", "given": "Martin", "initials": "M"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y", "orcid": "0000-0003-1165-3595", "researcher": {"href": "https://publications.scilifelab.se/researcher/2869602ee77944d2b1a736638a76bb3a.json"}}, {"family": "Andersson", "given": "Therese", "initials": "T"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Carlh\u00e4ll", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Erlinge", "given": "David", "initials": "D"}, {"family": "Jernberg", "given": "Tomas", "initials": "T"}, {"family": "Landfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-5695-2276", "researcher": {"href": "https://publications.scilifelab.se/researcher/d85f85dce6c548fd9f36ac1540c9aff3.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Mannila", "given": "Maria", "initials": "M", "orcid": "0000-0001-6189-2901", "researcher": {"href": "https://publications.scilifelab.se/researcher/786397ffc6a54d3e8c54f5493fbb7aa2.json"}}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Pirazzi", "given": "Carlo", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ", "orcid": "0000-0003-1617-3179", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4b5d952d50c4801aa88c0c9ae0d5813.json"}}, {"family": "Gunnarsson", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-9474-6820", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed1a42fede5f4f6d87c20d6bb9f694de.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S", "orcid": "0000-0001-9225-1306", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13944767ad9446e885ce32ca88afebd.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}], "type": "journal article", "published": "2025-03-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2266", "issn-l": "2041-1723"}, "abstract": "Imaging-defined atherosclerosis represents an intermediate phenotype of atherosclerotic cardiovascular disease (ASCVD). Genome-wide association studies (GWAS) on directly measured coronary plaques using coronary computed tomography angiography (CCTA) are scarce. In the so far largest population-based cohort with CCTA data, we performed a GWAS on coronary plaque burden as determined by the segment involvement score (SIS) in 24,811 European individuals. We identified 20 significant independent genetic markers for SIS, three of which were found in loci not implicated in ASCVD before. Further GWAS on coronary artery calcification showed similar results to that of SIS, whereas a GWAS on ultrasound-assessed carotid plaques identified both shared and non-shared loci with SIS. In two-sample Mendelian randomization studies using SIS-associated markers in UK Biobank and CARDIoGRAMplusC4D, one extra coronary segment with atherosclerosis corresponded to 1.8-fold increased odds of myocardial infarction. This GWAS data can aid future studies of causal pathways in ASCVD.", "doi": "10.1038/s41467-025-57457-7", "pmid": "40164586", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11958696"}, {"db": "pii", "key": "10.1038/s41467-025-57457-7"}], "notes": [], "created": "2025-05-12T05:48:37.162Z", "modified": "2025-11-14T11:06:44.446Z"}, {"entity": "publication", "iuid": "647d53b18b37408db896d3a565fec76c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/647d53b18b37408db896d3a565fec76c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/647d53b18b37408db896d3a565fec76c"}}, "title": "The DNA methylation landscape of primary triple-negative breast cancer.", "authors": [{"family": "Aine", "given": "Mattias", "initials": "M", "orcid": "0000-0002-0851-5952", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec863fc84b064759b355272fa1be61ff.json"}}, {"family": "Nacer", "given": "Deborah F", "initials": "DF", "orcid": "0000-0002-7117-1371", "researcher": {"href": "https://publications.scilifelab.se/researcher/e484e25cfdf64d27842357355409dbfc.json"}}, {"family": "Arbajian", "given": "Elsa", "initials": "E", "orcid": "0000-0002-1484-0073", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9615e08a1a04fada47e805c27a29c61.json"}}, {"family": "Veerla", "given": "Srinivas", "initials": "S", "orcid": "0000-0001-7328-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/c203a0b3112f4f499ccc79db3e47b303.json"}}, {"family": "Karlsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-6974-5965", "researcher": {"href": "https://publications.scilifelab.se/researcher/016d7daf94304064a461e0df719112c5.json"}}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J", "orcid": "0000-0002-8466-9179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b8605b9a7c74b20986146f020cf4b8f.json"}}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fa1d04cb640858fe3534d04cd04d1.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications.scilifelab.se/researcher/127501d4e0854d14a4120acee9042bb7.json"}}, {"family": "Staaf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5254-5115", "researcher": {"href": "https://publications.scilifelab.se/researcher/07acbd7f211e4809a8195e2ccf5faf57.json"}}], "type": "journal article", "published": "2025-03-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "3041", "issn-l": "2041-1723"}, "abstract": "Triple-negative breast cancer (TNBC) is a clinically challenging and molecularly heterogenous breast cancer subgroup. Here, we investigate the DNA methylation landscape of TNBC. By analyzing tumor methylome profiles and accounting for the genomic context of CpG methylation, we divide TNBC into two epigenetic subtypes corresponding to a Basal and a non-Basal group, in which characteristic transcriptional patterns are correlated with DNA methylation of distal regulatory elements and epigenetic regulation of key steroid response genes and developmental transcription factors. Further subdivision of the Basal and non-Basal subtypes identifies subgroups transcending genetic and proposed TNBC mRNA subtypes, demonstrating widely differing immunological microenvironments, putative epigenetically-mediated immune evasion strategies, and a specific metabolic gene network in older patients that may be epigenetically regulated. Our study attempts to target the epigenetic backbone of TNBC, an approach that may inform future studies regarding tumor origins and the role of the microenvironment in shaping the cancer epigenome.", "doi": "10.1038/s41467-025-58158-x", "pmid": "40155623", "labels": {"Clinical Genomics Lund": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11953470"}, {"db": "pii", "key": "10.1038/s41467-025-58158-x"}], "notes": [], "created": "2025-04-14T12:30:37.267Z", "modified": "2025-09-08T06:57:25.392Z"}, {"entity": "publication", "iuid": "2cac06ed9ba246d490141086a39f3ee0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cac06ed9ba246d490141086a39f3ee0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cac06ed9ba246d490141086a39f3ee0"}}, "title": "Phylogeny of Palicoureeae (Rubiaceae) based on 353 low-copy nuclear genes - With particular focus on Hymenocoleus Robbr.", "authors": [{"family": "Thil\u00e9n", "given": "Lovisa", "initials": "L"}, {"family": "Lachenaud", "given": "Olivier", "initials": "O"}, {"family": "Thureborn", "given": "Olle", "initials": "O"}, {"family": "Razafimandimbison", "given": "Sylvain G", "initials": "SG"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}], "type": "journal article", "published": "2025-03-28", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "pages": "108338", "issn-l": "1055-7903"}, "abstract": "Members of the tribe Palicoureeae of the coffee family (Rubiaceae) have a complex taxonomic history and have been the focus of few modern systematic studies. The tribe comprises about 1,100 tropical species in ten genera. To investigate phylogeny, we used a target capture approach and the angiosperm-wide Angiosperms353 bait set to produce genomic data for a representative taxon sample of Palicoureeae, with particular focus on the African genus Hymenocoleus. Using coalescent-based inference methods, we find that Puffia gerrardii (recently separated from Geophila) is sister to Hymenocoleus. The deepest split in Hymenocoleus is highly affected by incomplete lineage sorting, possibly as a consequence of rapid speciation during the early evolution of the clade. Remaining interspecific relationships in Hymenocoleus could be confidently resolved and while Robbrecht's traditional subgeneric classification scheme based on floral features is not supported as reflecting evolution in the group, we find that several other features do, e.g. characters of pyrenes and involucral cups. Although not free of challenges, a strong advantage with our analytical approach is that gene tree heterogeneity can be taken into account. Including flanking regions yielded data sets that had the strongest power to reject polytomies and produced less gene tree error, resulting in species trees with higher normalised quartet scores and higher average support compared to trees inferred only from exon data. Presumably paralogous loci are often filtered out prior to species tree estimation but we find that they may contribute important phylogenetic information when using an inference method that actively accounts for them.", "doi": "10.1016/j.ympev.2025.108338", "pmid": "40158785", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(25)00055-7"}], "notes": [], "created": "2025-04-07T10:00:09.487Z", "modified": "2025-04-07T10:00:09.492Z"}, {"entity": "publication", "iuid": "80e90323a405495c8b65bcaea12d8d60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80e90323a405495c8b65bcaea12d8d60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80e90323a405495c8b65bcaea12d8d60"}}, "title": "PIP2-mediated oligomerization of the endosomal sodium/proton exchanger NHE9.", "authors": [{"family": "Kokane", "given": "Surabhi", "initials": "S"}, {"family": "Gulati", "given": "Ashutosh", "initials": "A", "orcid": "0000-0003-0960-994X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b2b0aa7260492c8141083762e08125.json"}}, {"family": "Meier", "given": "Pascal F", "initials": "PF"}, {"family": "Matsuoka", "given": "Rei", "initials": "R"}, {"family": "Pipatpolkai", "given": "Tanadet", "initials": "T", "orcid": "0000-0001-5396-4784", "researcher": {"href": "https://publications.scilifelab.se/researcher/b629d00aa88d4db4a51692bd594e4117.json"}}, {"family": "Albano", "given": "Giuseppe", "initials": "G"}, {"family": "Ho", "given": "Tin Manh", "initials": "TM", "orcid": "0000-0003-1608-2234", "researcher": {"href": "https://publications.scilifelab.se/researcher/72472dd6ef684f17ab462e5064b2203d.json"}}, {"family": "Delemotte", "given": "Lucie", "initials": "L", "orcid": "0000-0002-0828-3899", "researcher": {"href": "https://publications.scilifelab.se/researcher/2919e3b5cf0f466f980df8fd700bc306.json"}}, {"family": "Fuster", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7220-1803", "researcher": {"href": "https://publications.scilifelab.se/researcher/766aa106f9d6461e8f8e32a231b2ccc1.json"}}, {"family": "Drew", "given": "David", "initials": "D", "orcid": "0000-0001-8866-6349", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc19844f8147480fb0af2e437744131b.json"}}], "type": "journal article", "published": "2025-03-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "3055", "issn-l": "2041-1723"}, "abstract": "The strict exchange of Na+ for H+ ions across cell membranes is a reaction carried out in almost every cell. Na+/H+ exchangers that perform this task are physiological homodimers, and whilst the ion transporting domain is highly conserved, their dimerization differs. The Na+/H+ exchanger NhaA from Escherichia coli has a weak dimerization interface mediated by a \u03b2-hairpin domain and with dimer retention dependent on cardiolipin. Similarly, organellar Na+/H+ exchangers NHE6, NHE7 and NHE9 also contain \u03b2-hairpin domains and recent analysis of Equus caballus NHE9 indicated PIP2 lipids could bind at the dimer interface. However, structural validation of the predicted lipid-mediated oligomerization has been lacking. Here, we report cryo-EM structures of E. coli NhaA and E. caballus NHE9 in complex with cardiolipin and phosphatidylinositol-3,5-bisphosphate PI(3,5)P2 lipids binding at their respective dimer interfaces. We further show how the endosomal specific PI(3,5)P2 lipid stabilizes the NHE9 homodimer and enhances transport activity. Indeed, we show that NHE9 is active in endosomes, but not at the plasma membrane where the PI(3,5)P2 lipid is absent. Thus, specific lipids can regulate Na+/H+ exchange activity by stabilizing dimerization in response to either cell specific cues or upon trafficking to their correct membrane location.", "doi": "10.1038/s41467-025-58247-x", "pmid": "40155618", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11953442"}, {"db": "pii", "key": "10.1038/s41467-025-58247-x"}], "notes": [], "created": "2025-11-23T22:24:03.098Z", "modified": "2025-11-23T22:24:03.495Z"}, {"entity": "publication", "iuid": "e300a5100ec7443c9deaba850a878de7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e300a5100ec7443c9deaba850a878de7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e300a5100ec7443c9deaba850a878de7"}}, "title": "Metabolomic profiling of shade response and in silico analysis of PAL homologs imply the potential presence of bifunctional ammonia lyases in conifers.", "authors": [{"family": "Ranade", "given": "Sonali Sachin", "initials": "SS"}, {"family": "Garc\u00eda-Gil", "given": "Mar\u00eda Rosario", "initials": "MR", "orcid": "0000-0002-6834-6708", "researcher": {"href": "https://publications.scilifelab.se/researcher/774898d2b46f44cb8475be89ecd8b79d.json"}}], "type": "journal article", "published": "2025-03-28", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "2", "pages": "e70175", "issn-l": "0031-9317"}, "abstract": "Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.", "doi": "10.1111/ppl.70175", "pmid": "40148258", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11949857"}], "notes": [], "created": "2025-11-18T12:14:03.049Z", "modified": "2025-11-18T12:14:03.058Z"}, {"entity": "publication", "iuid": "e0d705c2a3ee47979f31a000531e4fd6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0d705c2a3ee47979f31a000531e4fd6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0d705c2a3ee47979f31a000531e4fd6"}}, "title": "Heritability and polygenic load for comorbid anxiety and depression.", "authors": [{"family": "Tabrizi", "given": "Fara", "initials": "F", "orcid": "0000-0003-4009-0090", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee28a29d54c344eebcb95a56e6707b8a.json"}}, {"family": "Ros\u00e9n", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Gr\u00f6nvall", "given": "Hampus", "initials": "H"}, {"family": "William-Olsson", "given": "Victor Rahimzadeh", "initials": "VR"}, {"family": "Arner", "given": "Erik", "initials": "E"}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Palm", "given": "Camilla", "initials": "C"}, {"family": "Larsson", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6851-3297", "researcher": {"href": "https://publications.scilifelab.se/researcher/21f2cca2f6b74c5393c0fc33bcf15ee6.json"}}, {"family": "Viktorin", "given": "Alexander", "initials": "A", "orcid": "0000-0003-2141-2816", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f02b9aad56348c28f639bf231748096.json"}}, {"family": "Bernhardsson", "given": "Jens", "initials": "J"}, {"family": "Bj\u00f6rkdahl", "given": "Johanna", "initials": "J"}, {"family": "Jansson", "given": "Billy", "initials": "B"}, {"family": "Sundin", "given": "\u00d6rjan", "initials": "\u00d6"}, {"family": "Zhou", "given": "Xuan", "initials": "X"}, {"family": "Speed", "given": "Doug", "initials": "D", "orcid": "0000-0002-0096-9765", "researcher": {"href": "https://publications.scilifelab.se/researcher/5144d83e395d43319b86e1af1e0b398b.json"}}, {"family": "\u00c5hs", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2025-03-27", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "volume": "15", "issue": "1", "pages": "98", "issn-l": "2158-3188"}, "abstract": "Anxiety and depression commonly occur together resulting in worse health outcomes than when they occur in isolation. We aimed to determine whether the genetic liability for comorbid anxiety and depression was greater than when anxiety or depression occurred alone. Data from 12,792 genotyped twins (ages 38-85) were analysed, including 1,986 complete monozygotic and 1,594 complete dizygotic pairs. Outcomes were prescription of antidepressant and anxiolytic drugs, as defined by the World Health Organization Anatomical Therapeutic Chemical Classification System (ATC) convention, for comorbid anxiety and depression (n = 1028), anxiety only (n = 718), and depression only (n = 484). Heritability of each outcome was estimated using twin modelling, and the influence of common genetic variation was assessed from polygenic scores (PGS) for depressive symptoms, anxiety, and 40 other traits. Heritability of comorbid anxiety and depression was 79% compared with 41% for anxiety and 50% for depression alone. The PGS for depressive symptoms likewise predicted more variation in comorbid anxiety and depression (adjusted odds ratio per SD PGS = 1.53, 95% CI = 1.43-1.63; \u0394R2 = 0.031, \u0394AUC = 0.044) than the other outcomes, with nearly identical results when comorbid anxiety and depression was defined by International Classification of Diseases (ICD) diagnoses (adjusted odds ratio per SD PGS = 1.70, 95% CI = 1.53-1.90; \u0394R2 = 0.036, \u0394AUC = 0.051). Individuals in the highest decile of PGS for depressive symptoms had over 5 times higher odds of being prescribed medication for comorbid anxiety and depression compared to those in the lowest decile. While results on a predominant role of depressive symptoms may have been biased by the size and heterogeneity of available data bases, they are consistent with the conclusion that genetic factors explain substantially more variation in comorbid anxiety and depression than anxiety or depression alone.", "doi": "10.1038/s41398-025-03325-3", "pmid": "40140358", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11947153"}, {"db": "pii", "key": "10.1038/s41398-025-03325-3"}], "notes": [], "created": "2025-11-28T10:44:51.862Z", "modified": "2025-11-28T10:44:52.088Z"}, {"entity": "publication", "iuid": "03ed3ceb3df04e84ab63b6b26dd7b251", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03ed3ceb3df04e84ab63b6b26dd7b251.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03ed3ceb3df04e84ab63b6b26dd7b251"}}, "title": "Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.", "authors": [{"family": "Doktorova", "given": "Milka", "initials": "M", "orcid": "0000-0003-4366-2242", "researcher": {"href": "https://publications.scilifelab.se/researcher/1011a29cebbe49ca884a7ee02d969e05.json"}}, {"family": "Symons", "given": "Jessica L", "initials": "JL"}, {"family": "Zhang", "given": "Xiaoxuan", "initials": "X"}, {"family": "Wang", "given": "Hong-Yin", "initials": "HY"}, {"family": "Schlegel", "given": "Jan", "initials": "J", "orcid": "0000-0003-3159-8079", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94351acc3934c3084f1ed0429a1879a.json"}}, {"family": "Lorent", "given": "Joseph H", "initials": "JH"}, {"family": "Heberle", "given": "Frederick A", "initials": "FA"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Lyman", "given": "Edward", "initials": "E"}, {"family": "Levental", "given": "Kandice R", "initials": "KR"}, {"family": "Levental", "given": "Ilya", "initials": "I", "orcid": "0000-0002-1206-9545", "researcher": {"href": "https://publications.scilifelab.se/researcher/aff0be08e1dd48e391dbf53b4b544ed8.json"}}], "type": "journal article", "published": "2025-03-26", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674"}, "abstract": "Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PMs). Using lipidomics, we report that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared with exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization.", "doi": "10.1016/j.cell.2025.02.034", "pmid": "40179882", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)00270-3"}], "notes": [], "created": "2025-04-09T20:41:35.973Z", "modified": "2025-07-11T12:00:18.796Z"}, {"entity": "publication", "iuid": "2ae5cc4ff3d946528ecb78f961464277", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ae5cc4ff3d946528ecb78f961464277.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ae5cc4ff3d946528ecb78f961464277"}}, "title": "Blood-based biomarkers of Alzheimer's disease and incident dementia in the community.", "authors": [{"family": "Grande", "given": "Giulia", "initials": "G", "orcid": "0000-0001-6312-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6fc0b0bad8243059965a2b828321c14.json"}}, {"family": "Valletta", "given": "Martina", "initials": "M", "orcid": "0000-0003-0139-8287", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa01849f48049c78eef04747ab1797a.json"}}, {"family": "Rizzuto", "given": "Debora", "initials": "D"}, {"family": "Xia", "given": "Xin", "initials": "X"}, {"family": "Qiu", "given": "Chengxuan", "initials": "C", "orcid": "0000-0003-1922-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/15238dd19bda48fcbf04b299a8368929.json"}}, {"family": "Orsini", "given": "Nicola", "initials": "N"}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Andersson", "given": "Sarah", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Winblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-0011-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/73185a13ca474153b66415e6a2dfff0f.json"}}, {"family": "Laukka", "given": "Erika J", "initials": "EJ"}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "Vetrano", "given": "Davide L", "initials": "DL", "orcid": "0000-0002-3099-4830", "researcher": {"href": "https://publications.scilifelab.se/researcher/06867644d5f14eef958737353517f53d.json"}}], "type": "journal article", "published": "2025-03-26", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "issn-l": "1078-8956"}, "abstract": "Evidence regarding the clinical validity of blood biomarkers of Alzheimer's disease (AD) in the general population is limited. We estimated the hazard and predictive performance of six AD blood biomarkers for incident all-cause and AD dementia-the ratio of amyloid-\u03b2 42 to amyloid-\u03b2 40 and levels of tau phosphorylated at T217 (p-tau217), tau phosphorylated at T181 (p-tau181), total tau, neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP)-in a cohort of 2,148 dementia-free older adults from Sweden, who were followed for up to 16 years. In multi-adjusted Cox regression models, elevated baseline levels of p-tau181, p-tau217, NfL, and GFAP were associated with a significantly increased hazard for all-cause and AD dementia, displaying a non-linear dose-response relationship. Elevated concentrations of p-tau181, p-tau217, NfL, and GFAP demonstrated strong predictive performance (area under the curve ranging from 70.9% to 82.6%) for 10-year all-cause and AD dementia, with negative predictive values exceeding 90% but low positive predictive values (PPVs). Combining p-tau217 with NfL or GFAP further improved prediction, with PPVs reaching 43%. Our findings suggest that these biomarkers have the potential to rule out impending dementia in community settings, but they might need to be combined with other biological or clinical markers to be used as screening tools.", "doi": "10.1038/s41591-025-03605-x", "pmid": "40140622", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41591-025-03605-x"}], "notes": [], "created": "2025-04-02T14:34:39.959Z", "modified": "2025-04-02T14:34:40.970Z"}, {"entity": "publication", "iuid": "1dc349ef9c3a452ea68af92df3a24d5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1dc349ef9c3a452ea68af92df3a24d5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1dc349ef9c3a452ea68af92df3a24d5b"}}, "title": "Scotch Pine Cones-Derived Hard Carbon as an Anode Material for Sodium-Ion Battery Applications.", "authors": [{"family": "Rao", "given": "Y Bhaskara", "initials": "YB"}, {"family": "Sundman", "given": "Ola", "initials": "O", "orcid": "0000-0002-1705-5249", "researcher": {"href": "https://publications.scilifelab.se/researcher/c15a15210b8a41e0826343602778bc6d.json"}}, {"family": "Holmboe", "given": "Michael", "initials": "M", "orcid": "0000-0003-3927-6197", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d069795b2434c7883f7017855bbb896.json"}}, {"family": "Tavajohi", "given": "Naser", "initials": "N", "orcid": "0000-0002-3973-0938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa5c356fc0524b31a9593284adf002a4.json"}}, {"family": "Ohlin", "given": "C Andr\u00e9", "initials": "CA", "orcid": "0000-0002-3804-6421", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc8a24c050c04953abf72381de7e9885.json"}}], "type": "journal article", "published": "2025-03-25", "journal": {"title": "ACS Omega", "issn": "2470-1343", "volume": "10", "issue": "11", "pages": "11158-11167", "issn-l": "2470-1343"}, "abstract": "A biobased anode material for sodium-ion batteries (SIBs) was prepared through the simple pyrolysis of Scotch pine cones (Pinus sylvestris, SPC), followed by a heteroatom doping modification. The resulting nitrogen-doped hard carbon exhibited a high reversible capacity of 273 mA\u00b7h\u00b7g-1 at a current density of 25 mA\u00b7g-1 compared to the undoped material (197 mA\u00b7h\u00b7g-1). X-ray diffraction analysis shows that the produced hard carbon from the biomass is highly amorphous in nature, and high-resolution transmission electron microscopy images reveal the presence of localized graphite-like structures that are found to be beneficial for the storage and transport of Na+ ions during charging/discharging. Experimental results demonstrated that the increased specific surface area (S BET = 424 m2\u00b7g-1), high micropore volume (0.177 cm3\u00b7g-1), and expanded interlayer spacing (>3.7 \u00c5) and a high Na+-ion diffusion coefficient (3.08 \u00d7 10-16 cm2\u00b7s-1) facilitated the diffusion of sodium ions, leading to a high capacity retention of 80% after 250 cycles for the SPC-N material over the undoped one, SPC (71%). This study highlights the potential of low-cost, widely available biobased Scotch pine cones as an alternative anode material to enhance the sustainability of SIB production.", "doi": "10.1021/acsomega.4c10363", "pmid": "40160790", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11948143"}], "notes": [], "created": "2025-10-30T12:06:03.272Z", "modified": "2025-10-30T12:06:03.595Z"}, {"entity": "publication", "iuid": "85c57e4cdd15436f887cf31addb56758", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85c57e4cdd15436f887cf31addb56758.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85c57e4cdd15436f887cf31addb56758"}}, "title": "Immunological and structural evaluation of the intranasally administrated CVB1 whole-virus and VLP vaccines.", "authors": [{"family": "Soppela", "given": "Saana", "initials": "S"}, {"family": "Plavec", "given": "Zlatka", "initials": "Z"}, {"family": "Gr\u00f6hn", "given": "Stina", "initials": "S"}, {"family": "Mustonen", "given": "Iiris", "initials": "I"}, {"family": "Jartti", "given": "Minne", "initials": "M"}, {"family": "Oikarinen", "given": "Sami", "initials": "S"}, {"family": "Laajala", "given": "Mira", "initials": "M"}, {"family": "Marjom\u00e4ki", "given": "Varpu", "initials": "V"}, {"family": "Butcher", "given": "Sarah J", "initials": "SJ"}, {"family": "Hankaniemi", "given": "Minna M", "initials": "MM"}], "type": "journal article", "published": "2025-03-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "10198", "issn-l": "2045-2322"}, "abstract": "Coxsackievirus B1 (CVB1) is a common cause of acute and chronic myocarditis, cardiomyopathy, and meningitis. CVBs replicate in mucosal membranes. Therefore, vaccines inducing robust mucosal immune responses are needed. We investigated the immunogenicity of virus-like particles (VLP) and inactivated virus vaccines for CVB1, administered to mice either subcutaneously or intranasally, formulated with and without commercial and an experimental adjuvant. In this study, epigallocatechin-3-gallate (EGCG) was used both as a potential adjuvant and as an inactivating agent. EGCG adjuvanted CVB1-VLP enhanced immunogenicity via the parenteral route, but not intranasally. EGCG-adjuvanted and non-adjuvanted CVB1-VLPs triggered an immune response after intranasal administration, although the response remained weak. Intranasal administration of formalin-inactivated virus elicited robust CVB1-specific humoral, cellular, and mucosal immune responses, but after EGCG-inactivation, the mucosal antibody response was lower than after formalin-inactivation. To identify the link between structure and mucosal immunogenicity, we solved the structures of CVB1-VLP and formalin-inactivated CVB1 virus at resolutions ranging from 2.15 to 4.1 \u00c5. The structural difference between VLP and formalin-inactivated CVB1 was the presence of the genome and cross-linked amino acid residues in the formalin-inactivated virus. Formalin-inactivated CVB1 vaccine shows promise for mucosal immunizations and the structural data supports the development of next-generation VLP-vaccines in the future.", "doi": "10.1038/s41598-025-94656-0", "pmid": "40133550", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11937443"}, {"db": "pii", "key": "10.1038/s41598-025-94656-0"}], "notes": [], "created": "2025-11-13T09:34:00.598Z", "modified": "2025-11-13T09:34:00.602Z"}, {"entity": "publication", "iuid": "c1da9377c9ef4f588decef70299d0c40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1da9377c9ef4f588decef70299d0c40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1da9377c9ef4f588decef70299d0c40"}}, "title": "Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity.", "authors": [{"family": "Fan", "given": "Chuannan", "initials": "C", "orcid": "0000-0001-8754-4913", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a665d568ce94fcbaaee270c6c7701a5.json"}}, {"family": "Wang", "given": "Qian", "initials": "Q", "orcid": "0000-0002-5196-4972", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4009e7b4ef0473a91c6e39b315e0f16.json"}}, {"family": "Krijger", "given": "Peter H L", "initials": "PHL", "orcid": "0000-0003-1702-348X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0cacf162ca643a68ea2bd723fa3a2b6.json"}}, {"family": "Cats", "given": "Davy", "initials": "D", "orcid": "0000-0001-9684-220X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23de688650944eca98ed9f9c1e8f19bb.json"}}, {"family": "Selle", "given": "Miriam", "initials": "M"}, {"family": "Khorosjutina", "given": "Olga", "initials": "O", "orcid": "0009-0001-0786-0260", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ada08b5ada04dfb8e948e0873ccf07d.json"}}, {"family": "Dhanjal", "given": "Soniya", "initials": "S"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Mei", "given": "Hailiang", "initials": "H"}, {"family": "de Laat", "given": "Wouter", "initials": "W", "orcid": "0000-0002-5603-0095", "researcher": {"href": "https://publications.scilifelab.se/researcher/4025d8f21a1f4f71a1a1e7d1f1afdc59.json"}}, {"family": "Ten Dijke", "given": "Peter", "initials": "P", "orcid": "0000-0002-7234-342X", "researcher": {"href": "https://publications.scilifelab.se/researcher/299812073080446a91fc6228efbdc1c5.json"}}], "type": "journal article", "published": "2025-03-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "2890"}, "abstract": "Enhancer RNAs (eRNAs) are a pivotal class of enhancer-derived non-coding RNAs that drive gene expression. Here we identify the SNAI1 enhancer RNA (SNAI1e; SCREEM2) as a key activator of SNAI1 expression and a potent enforcer of transforming growth factor-\u03b2 (TGF-\u03b2)/SMAD signaling in cancer cells. SNAI1e depletion impairs TGF-\u03b2-induced epithelial-mesenchymal transition (EMT), migration, in vivo extravasation, stemness, and chemotherapy resistance in breast cancer cells. SNAI1e functions as an eRNA to cis-regulate SNAI1 enhancer activity by binding to and strengthening the enrichment of the transcriptional co-activator bromodomain containing protein 4 (BRD4) at the local enhancer. SNAI1e selectively promotes the expression of SNAI1, which encodes the EMT transcription factor SNAI1. Furthermore, we reveal that SNAI1 interacts with and anchors the inhibitory SMAD7 in the nucleus, and thereby prevents TGF-\u03b2 type I receptor (T\u03b2RI) polyubiquitination and proteasomal degradation. Our findings establish SNAI1e as a critical driver of SNAI1 expression and TGF-\u03b2-induced cell plasticity.", "doi": "10.1038/s41467-025-58032-w", "pmid": "40133308", "labels": {"CRISPR Functional Genomics": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11937597"}, {"db": "pii", "key": "10.1038/s41467-025-58032-w"}], "notes": [], "created": "2025-03-27T09:27:46.634Z", "modified": "2026-03-18T09:38:07.353Z"}, {"entity": "publication", "iuid": "c25b47ed172f4104b9530aaeb0f8cc01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c25b47ed172f4104b9530aaeb0f8cc01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c25b47ed172f4104b9530aaeb0f8cc01"}}, "title": "Exploring NLRP3-related phenotypic fingerprints in human macrophages using Cell Painting assay.", "authors": [{"family": "Herring", "given": "Matthew", "initials": "M"}, {"family": "S\u00e4rndahl", "given": "Eva", "initials": "E"}, {"family": "Kotlyar", "given": "Oleksandr", "initials": "O"}, {"family": "Scherbak", "given": "Nikolai", "initials": "N"}, {"family": "Engwall", "given": "Magnus", "initials": "M"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Ejdeb\u00e4ck", "given": "Mikael", "initials": "M"}, {"family": "Persson", "given": "Alexander", "initials": "A"}, {"family": "Alijagic", "given": "Andi", "initials": "A"}], "type": "journal article", "published": "2025-03-21", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "28", "issue": "3", "pages": "111961", "issn-l": "2589-0042"}, "abstract": "Existing research has proven difficult to understand the interplay between upstream signaling events during NLRP3 inflammasome activation. Additionally, events downstream of inflammasome complex formation such as cytokine release and pyroptosis can exhibit variation, further complicating matters. Cell Painting has emerged as a prominent tool for unbiased evaluation of the effect of perturbations on cell morphological phenotypes. Using this technique, phenotypic fingerprints can be generated that reveal connections between phenotypes and possible modes of action. To the best of our knowledge, this was the first study that utilized Cell Painting on human THP-1 macrophages to generate phenotypic fingerprints in response to different endogenous and exogenous NLRP3 inflammasome triggers and to identify phenotypic features specific to NLRP3 inflammasome complex formation. Our results demonstrated that not only can Cell Painting generate morphological fingerprints that are NLRP3 trigger-specific but it can also identify cellular fingerprints associated with NLRP3 inflammasome activation.", "doi": "10.1016/j.isci.2025.111961", "pmid": "40040812", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11876907"}, {"db": "pii", "key": "S2589-0042(25)00221-4"}], "notes": [], "created": "2025-11-28T10:43:39.887Z", "modified": "2025-11-28T10:43:39.936Z"}, {"entity": "publication", "iuid": "067b61d871b748229c2cf96c89adeaa7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/067b61d871b748229c2cf96c89adeaa7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/067b61d871b748229c2cf96c89adeaa7"}}, "title": "A suitable strategy to find IAA metabolism mutants.", "authors": [{"family": "Casanova-S\u00e1ez", "given": "Rub\u00e9n", "initials": "R", "orcid": "0000-0001-5683-7051", "researcher": {"href": "https://publications.scilifelab.se/researcher/17868bb801534bd794ef1f5d2815a531.json"}}, {"family": "P\u011bn\u010d\u00edk", "given": "Ale\u0161", "initials": "A", "orcid": "0000-0002-1314-2249", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13dbbec35c441daa7ed84daa05cd6e7.json"}}, {"family": "Mu\u00f1oz-Viana", "given": "Rafael", "initials": "R", "orcid": "0000-0002-1363-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bd9a92a13fd4395aeae214b4930e55a.json"}}, {"family": "Brunoni", "given": "Federica", "initials": "F", "orcid": "0000-0003-1497-9419", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a28132c7a0e407da31e4d79698679c6.json"}}, {"family": "Pinto", "given": "Rui", "initials": "R", "orcid": "0000-0002-8527-4873", "researcher": {"href": "https://publications.scilifelab.se/researcher/58f5bd6ddde8458d927e78ef13efb67b.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Mateo-Bonmat\u00ed", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-2364-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1e96edf1a914d2f8ea8eb46c3ebacc4.json"}}], "type": "journal article", "published": "2025-03-21", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "2", "pages": "e70166", "issn-l": "0031-9317"}, "abstract": "Indole-3-acetic acid (IAA), the most common form of auxin, is involved in a great range of plant physiological processes. IAA is synthesized from the amino acid tryptophan and can be transported and inactivated in a myriad of ways. Despite intense research efforts, there are still dark corners in our comprehension of IAA metabolism and its interplays with other pathways. Genetic screens are a powerful tool for unbiasedly looking for new players in a given biological process. However, pleiotropism of auxin-related phenotypes and indirect effects make it necessary to incorporate additional screening steps to specifically find mutants affected in IAA homeostasis. We previously developed and validated a high-throughput methodology to simultaneously quantify IAA, key precursors, and inactive forms from as little as 10 mg of fresh tissue. We have carried out a genetic screening to identify mutants involved in IAA metabolism. Auxin reporters DR5pro:VENUS and 35Spro:DII-VENUS were EMS-mutagenized and subjected to a parallel morphological and reporter-signal pre-screen. We then obtained the auxin metabolite profile of 325 M3 selected lines and used multivariate data analysis to identify potential IAA-metabolism mutants. To test the screening design, we identified the causal mutations in three of the candidate lines by mapping-by-sequencing: dii365.3, dii571.1 and dr693. These carry new alleles of CYP83A1, MIAO, and SUPERROOT2, respectively, all of which have been previously involved in auxin homeostasis. Our results support the suitability of this approach to find new genes involved in IAA metabolism.", "doi": "10.1111/ppl.70166", "pmid": "40113441", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11925725"}], "notes": [], "created": "2025-11-18T12:07:26.876Z", "modified": "2025-11-18T12:07:27.054Z"}, {"entity": "publication", "iuid": "14386c68de7943c09413a06f0c389687", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14386c68de7943c09413a06f0c389687.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14386c68de7943c09413a06f0c389687"}}, "title": "A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness.", "authors": [{"family": "Schlesinger", "given": "D\u00f6rte", "initials": "D"}, {"family": "Dirks", "given": "Christopher", "initials": "C"}, {"family": "Navarro", "given": "Carmen", "initials": "C"}, {"family": "Lafranchi", "given": "Lorenzo", "initials": "L"}, {"family": "Spinner", "given": "Anna", "initials": "A"}, {"family": "Raja", "given": "Glancis Luzeena", "initials": "GL"}, {"family": "Mun-Sum Tong", "given": "Gregory", "initials": "G"}, {"family": "Eirich", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Martinez", "given": "Thomas Farid", "initials": "TF"}, {"family": "Els\u00e4sser", "given": "Simon Johannes", "initials": "SJ"}], "type": "journal article", "published": "2025-03-21", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "28", "issue": "3", "pages": "111884"}, "abstract": "The human genome contains thousands of potentially coding short open reading frames (sORFs). While a growing set of microproteins translated from these sORFs have been demonstrated to mediate important cellular functions, the majority remains uncharacterized. In our study, we performed a high-throughput CRISPR-Cas9 knock-out screen targeting 11,776 sORFs to identify microproteins essential for cancer cell line growth. We show that the CENPBD2P gene encodes a translated sORF and promotes cell fitness. We selected five additional candidate sORFs encoding microproteins between 11 and 63 amino acids in length for further functional assessment. Green fluorescent protein fusion constructs of these microproteins localized to distinct subcellular compartments, and the majority showed reproducible biochemical interaction partners. Studying the fitness and transcriptome of sORF knock-outs and complementation with the corresponding microprotein, we identify rescuable phenotypes while also illustrating the limitations and caveats of our pipeline for sORF functional screening and characterization.", "doi": "10.1016/j.isci.2025.111884", "pmid": "40124493", "labels": {"CRISPR Functional Genomics": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11929002"}, {"db": "pii", "key": "S2589-0042(25)00144-0"}], "notes": [], "created": "2025-04-30T17:31:37.359Z", "modified": "2025-11-14T11:06:08.650Z"}, {"entity": "publication", "iuid": "c08ec75bb9374481bc787b905027f244", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c08ec75bb9374481bc787b905027f244.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c08ec75bb9374481bc787b905027f244"}}, "title": "Structural recognition and stabilization of tyrosine hydroxylase by the J-domain protein DNAJC12.", "authors": [{"family": "Tai", "given": "Mary Dayne S", "initials": "MDS", "orcid": "0009-0001-5963-6500", "researcher": {"href": "https://publications.scilifelab.se/researcher/d95ad840fb1a4a22983760d11919ca21.json"}}, {"family": "Ochoa", "given": "Lissette", "initials": "L", "orcid": "0000-0002-9594-3735", "researcher": {"href": "https://publications.scilifelab.se/researcher/222f53a1a2b84d78a04fbede99a9aaad.json"}}, {"family": "Flydal", "given": "Marte I", "initials": "MI", "orcid": "0000-0002-4070-8367", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cf4e3c99fa0440493ad807ea4ac1927.json"}}, {"family": "Velasco-Carneros", "given": "Lorea", "initials": "L", "orcid": "0000-0002-1296-9498", "researcher": {"href": "https://publications.scilifelab.se/researcher/244afb211d2f42da8946c7b195dc6c31.json"}}, {"family": "Muntaner", "given": "Jimena", "initials": "J", "orcid": "0009-0004-8353-5007", "researcher": {"href": "https://publications.scilifelab.se/researcher/42cb2e2a21464f43bbcb861bcbc27819.json"}}, {"family": "Santiago", "given": "C\u00e9sar", "initials": "C", "orcid": "0000-0002-5149-1722", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c8faed11a1f4de888a4856dd8901ade.json"}}, {"family": "Gamiz-Arco", "given": "Gloria", "initials": "G", "orcid": "0000-0001-9883-3542", "researcher": {"href": "https://publications.scilifelab.se/researcher/e16fb372ba08475f94920126b37853ce.json"}}, {"family": "Moro", "given": "Fernando", "initials": "F", "orcid": "0000-0002-3568-3388", "researcher": {"href": "https://publications.scilifelab.se/researcher/0051632fb28940af8c0c6af28b4b9dc5.json"}}, {"family": "Jung-Kc", "given": "Kunwar", "initials": "K", "orcid": "0000-0002-6745-7318", "researcher": {"href": "https://publications.scilifelab.se/researcher/439702362d8348cabf95a37b6bdbc2ef.json"}}, {"family": "Gil-Cantero", "given": "David", "initials": "D", "orcid": "0000-0001-7761-2687", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca95e006d0e047f0a4dab1b5ec50a8c2.json"}}, {"family": "Marcilla", "given": "Miguel", "initials": "M", "orcid": "0000-0001-9171-5076", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e53d20e17f340228c3e57c0ce1c838c.json"}}, {"family": "Kallio", "given": "Juha P", "initials": "JP", "orcid": "0000-0003-3092-4012", "researcher": {"href": "https://publications.scilifelab.se/researcher/362f42627a1849bba4752e65c7c2e59c.json"}}, {"family": "Muga", "given": "Arturo", "initials": "A"}, {"family": "Valpuesta", "given": "Jos\u00e9 Mar\u00eda", "initials": "JM", "orcid": "0000-0001-7468-8053", "researcher": {"href": "https://publications.scilifelab.se/researcher/379b1cb40fdb48828d3779ef695297dd.json"}}, {"family": "Cu\u00e9llar", "given": "Jorge", "initials": "J", "orcid": "0000-0002-7789-807X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a55e6192356a4d4dafa8f149f18dc982.json"}}, {"family": "Martinez", "given": "Aurora", "initials": "A", "orcid": "0000-0003-1643-6506", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3e76064b5f8435fb0cbe3226743c5b2.json"}}], "type": "journal article", "published": "2025-03-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2755", "issn-l": "2041-1723"}, "abstract": "Pathogenic variants of the J-domain protein DNAJC12 cause parkinsonism, which is associated with a defective interaction of DNAJC12 with tyrosine hydroxylase (TH), the rate-limiting enzyme in dopamine biosynthesis. In this work, we characterize the formation of the TH:DNAJC12 complex, showing that DNAJC12 binding stabilizes both TH and the variant TH-p.R202H, associated with TH deficiency. This binding delays their time-dependent aggregation in an Hsp70-independent manner, while preserving TH activity and feedback regulatory inhibition by dopamine. DNAJC12 alone barely activates Hsc70 but synergistically stimulates Hsc70 ATPase activity when complexed with TH. Cryo-electron microscopy supported by crosslinking-mass spectroscopy reveals two DNAJC12 monomers bound per TH tetramer, each embracing one of the two regulatory domain dimers, leaving the active sites available for substrate, cofactor and inhibitory dopamine interaction. Our results also reveal the key role of the C-terminal region of DNAJC12 in TH binding, explaining the pathogenic mechanism of the DNAJC12 disease variant p.W175Ter.", "doi": "10.1038/s41467-025-57733-6", "pmid": "40113792", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11926245"}, {"db": "pii", "key": "10.1038/s41467-025-57733-6"}], "notes": [], "created": "2025-11-13T10:04:30.308Z", "modified": "2025-11-13T10:04:31.860Z"}, {"entity": "publication", "iuid": "0c0504235372472bbce50dd17656b923", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c0504235372472bbce50dd17656b923.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c0504235372472bbce50dd17656b923"}}, "title": "Serum microRNAs as peripheral markers of primary aldosteronism.", "authors": [{"family": "Makhnov", "given": "Nikita", "initials": "N"}, {"family": "Axling", "given": "Fredrik", "initials": "F"}, {"family": "Barazeghi", "given": "Elham", "initials": "E"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "\u00c5kerstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Hellman", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2025-03-20", "journal": {"title": "Front Endocrinol (Lausanne)", "issn": "1664-2392", "volume": "16", "pages": "1511096", "issn-l": null}, "abstract": "Primary aldosteronism (PA) is the principal cause of secondary hypertension; it leads to significantly elevated cardiovascular morbidity and mortality, but only a fraction of its cases ever get detected, partially due to diagnostic procedures that are difficult to perform and to interpret. More straightforward diagnostic methods are needed. Lateralized, or unilateral PA (uPA), is best treated by surgery. Bilateral PA (bPA) is treated medically.\n\nThe aim of our study was to explore microRNA (miRNA) in peripheral blood as markers of PA, uPA and bPA.\n\nIn groups of subjects with primary hypertension (HT, n = 11), bPA (n = 12), and uPA (n = 16), peripheral serum was used for isolation of total RNA, library preparation, and NGS sequencing to achieve a comparative analysis of miRNA expression. Five-fold cross-validation support vector machine learning (ML) models were employed to search for miRNA that could be used as markers of PA and its forms.\n\nIn our cohort of patients, the discovered combinations of miRNAs could, with a high level of accuracy, sensitivity, and specificity, characterize the difference between HT and PA, as well as between a combined group of HT + bPA vs. uPA. The differentiating parameters were moderately good for comparison of bPA vs. uPA.\n\nWithin our patient cohort, and using ML, the study identified distinctly different miRNA profiles between HT and PA, as well as between bPA and uPA. Further validation studies may lead to the emergence of a new tool for clinical diagnostics of PA.", "doi": "10.3389/fendo.2025.1511096", "pmid": "40182638", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11967191"}], "notes": [], "created": "2025-11-26T14:14:03.691Z", "modified": "2025-11-26T14:14:03.706Z"}, {"entity": "publication", "iuid": "d1d1ed8922b843f183791a890740a5ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1d1ed8922b843f183791a890740a5ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1d1ed8922b843f183791a890740a5ab"}}, "title": "mRNA extracted from frozen buffy coat samples stored long term in tubes with no RNA preservative shows promise for downstream sequencing analyses.", "authors": [{"family": "Bovinder Ylitalo", "given": "Erik", "initials": "E"}, {"family": "Vidman", "given": "Linda", "initials": "L", "orcid": "0000-0002-5012-4074", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6dbd6309a64dd5a6e24f542ff25d25.json"}}, {"family": "Harlid", "given": "Sophia", "initials": "S"}, {"family": "Van Guelpen", "given": "Bethany", "initials": "B"}], "type": "journal article", "published": "2025-03-19", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "3", "pages": "e0318834", "issn-l": "1932-6203"}, "abstract": "Transcriptomics is an important OMICs method that is often unavailable in biobank research. Frozen blood samples are routinely collected and stored in medical biobanks, but transcriptional studies have been limited due to technical difficulties of extracting high-quality RNA from blood frozen in standard tubes (without RNA preservatives). We aimed to determine whether biobanked buffy coat samples stored at -80\u00b0C for up to 23 years could be successfully used for mRNA sequencing. We used a CryoXtract CXT 350 to remove frozen sample cores, which were immersed in RNA preservative during thawing prior to RNA extraction. RNA sequencing was then performed on extractions from pooled samples as well as from 23 buffy coat samples from prospective colorectal cancer cases and 23 matched controls included in the population-based, prospective Northern Sweden Health and Disease Study (NSHDS). For all samples, two library preparation methods were used (Illumina TruSeq Stranded mRNA poly-A selection and Illumina Stranded Total RNA with Ribo-Zero Globin). RNA yields of over 1 \u00b5g were obtained from the majority of NSHDS samples (mean = 2.57 \u00b5g), and over 92% of samples had RIN values of \u2265 6, indicating suitability for downstream analyses. In conclusion, we developed a method for successfully extracting and sequencing high-quality mRNA from frozen buffy coat samples stored long term in tubes with no RNA preservative.", "doi": "10.1371/journal.pone.0318834", "pmid": "40106499", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11922291"}, {"db": "pii", "key": "PONE-D-24-19421"}], "notes": [], "created": "2025-11-28T10:54:03.508Z", "modified": "2025-11-28T10:54:03.560Z"}, {"entity": "publication", "iuid": "f971c5ac1eee407e8f0a6ea9a6805b1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f971c5ac1eee407e8f0a6ea9a6805b1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f971c5ac1eee407e8f0a6ea9a6805b1b"}}, "title": "The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle.", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Chisausky", "given": "Jacob", "initials": "J"}, {"family": "Galindo-Pellicena", "given": "\u00c1ngeles M", "initials": "\u00c1M"}, {"family": "Iriarte", "given": "Eneko", "initials": "E"}, {"family": "Cortes Gardyn", "given": "Oscar", "initials": "O", "orcid": "0000-0001-7685-3980", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d3ec08f74ef47ebbab08a298b2da649.json"}}, {"family": "Eusebi", "given": "Paulina G", "initials": "PG"}, {"family": "Garc\u00eda-Gonz\u00e1lez", "given": "Rebeca", "initials": "R"}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I"}, {"family": "Moreno-Garc\u00eda", "given": "Marta", "initials": "M", "orcid": "0000-0002-6735-9355", "researcher": {"href": "https://publications.scilifelab.se/researcher/31bc572fc9d740699fab5fb59977d5b3.json"}}, {"family": "Alday", "given": "Alfonso", "initials": "A"}, {"family": "Rojo", "given": "Manuel", "initials": "M"}, {"family": "P\u00e9rez", "given": "Amalia", "initials": "A"}, {"family": "Tejedor Rodr\u00edguez", "given": "Cristina", "initials": "C"}, {"family": "Garc\u00eda Mart\u00ednez de Lagr\u00e1n", "given": "I\u00f1igo", "initials": "I"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Carretero", "given": "Jos\u00e9-Miguel", "initials": "JM"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Smith", "given": "Colin", "initials": "C"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}], "type": "journal article", "published": "2025-03-19", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "13", "issn-l": "2050-084X"}, "abstract": "Cattle (Bos taurus) play an important role in the life of humans in the Iberian Peninsula not just as a food source but also in cultural events. When domestic cattle were first introduced to Iberia, wild aurochs (Bos primigenius) were still present, leaving ample opportunity for mating (whether intended by farmers or not). Using a temporal bioarchaeological dataset covering eight millennia, we trace gene flow between the two groups. Our results show frequent hybridisation during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry in domestic cattle remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (~20%) continues into modern Western European breeds including Iberian cattle selected for aggressiveness and fighting ability. This study illuminates the genomic impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.", "doi": "10.7554/eLife.93076", "pmid": "40106345", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11922504"}, {"db": "pii", "key": "93076"}, {"db": "SRA", "key": "PRJNA838078"}, {"db": "Dryad", "key": "10.5061/dryad.f2d1q"}], "notes": [], "created": "2025-11-21T14:24:17.213Z", "modified": "2025-11-21T14:24:17.614Z"}, {"entity": "publication", "iuid": "5dd2c482172c4bfebbef112fd7f32a78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5dd2c482172c4bfebbef112fd7f32a78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5dd2c482172c4bfebbef112fd7f32a78"}}, "title": "Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost.", "authors": [{"family": "Clouard", "given": "Camille", "initials": "C", "orcid": "0009-0006-3654-6525", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd4bd5b6f553465d98cf8c3075b107fb.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications.scilifelab.se/researcher/c300f2900aff429d8a3bbc72ee006df7.json"}}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "15", "issue": "3", "issn-l": "2160-1836"}, "abstract": "Conducting genomic selection (GS) in plant breeding programs can substantially speed up the development of new varieties. GS provides more reliable insights when it is based on dense marker data, in which the rare variants can be particularly informative. Despite the availability of new technologies, the cost of large-scale genotyping remains a major limitation to the implementation of GS. We suggest to combine pooled genotyping with population-based imputation as a cost-effective computational strategy for genotyping SNPs. Pooling saves genotyping tests and has proven to accurately capture the rare variants that are usually missed by imputation. In this study, we investigate adding iterative coupling to a joint model of pooling and imputation that we have previously proposed. In each iteration, the imputed genotype probabilities serve as feedback input for adjusting the per-sample prior genotype probabilities, before running a new imputation based on these adjusted data. This flexible setup indirectly imposes consistency between the imputed genotypes and the pooled observations. We demonstrate that repeated cycles of feedback can take advantage of the strengths in both pooling and imputation when an appropriate set of reference haplotypes is available for imputation. The iterations improve greatly upon the initial genotype predictions, achieving very high genotype accuracy for both low- and high-frequency variants. We enhance the average concordance from 94.5% to 98.4% at limited computational cost and without requiring any additional genotype testing.", "doi": "10.1093/g3journal/jkaf010", "pmid": "39847531", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11917477"}, {"db": "pii", "key": "7976924"}], "notes": [], "created": "2025-11-28T10:49:10.699Z", "modified": "2025-11-28T10:49:10.753Z"}, {"entity": "publication", "iuid": "eed9d79d809f4d5d864e6170b1dcfc20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eed9d79d809f4d5d864e6170b1dcfc20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eed9d79d809f4d5d864e6170b1dcfc20"}}, "title": "Titanium micro-particles are commonly found in soft tissues surrounding dental implants.", "authors": [{"family": "Dionigi", "given": "Carlotta", "initials": "C", "orcid": "0000-0002-4195-0729", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ee57750bddd48a3a323e397c64ba435.json"}}, {"family": "Nagy", "given": "Gyula", "initials": "G", "orcid": "0000-0003-3172-5736", "researcher": {"href": "https://publications.scilifelab.se/researcher/07c27d64291549dca9eda3709cbab30d.json"}}, {"family": "Derks", "given": "Jan", "initials": "J"}, {"family": "Ichioka", "given": "Yuki", "initials": "Y"}, {"family": "Tomasi", "given": "Cristiano", "initials": "C", "orcid": "0000-0002-3610-6574", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3067facfa6743db83d011e510fcddcf.json"}}, {"family": "Larsson", "given": "Lena", "initials": "L"}, {"family": "Primetzhofer", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5815-3742", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeed8e1ab76842eab7f052f57abcd960.json"}}, {"family": "Berglundh", "given": "Tord", "initials": "T", "orcid": "0000-0001-5864-6398", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d29bd79b2914b47b00a0c1005b30b43.json"}}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "78", "issn-l": null}, "abstract": "Dental implants are one of the most frequently used medical devices for therapeutic purposes in dentistry. Peri-implantitis is a severe, microbial biofilm-associated condition, characterized by inflammation in peri-implant soft tissues and destruction of supporting bone. It has been suggested that metal particles originating from the implant may influence the local host response to microbial biofilms.\n\nSoft tissue biopsies were collected from implant sites with and without peri-implantitis in 21 patients. Micro Proton-induced X-ray Emission (\u00b5-PIXE) analysis was used to localize, quantify and characterize titanium micro-particles within tissues. RNA sequencing was performed to evaluate potential associations between titanium micro-particles and gene expression profiles in peri-implantitis lesions.\n\nTitanium micro-particles are consistent findings in soft tissues surrounding dental implants. Their occurrence varies across patients but not between sites with and without peri-implantitis within the same individual. Most particles reside in a 2-mm wide tissue portion close to the implant/tissue interface. The time in function of the implants does not influence the volumetric density of titanium micro-particles, while implant systems do. Fourteen differentially expressed genes are identified when comparing peri-implantitis samples with high and low densities of titanium micro-particles. The gene-set enrichment analysis reveals functions related to the regulation of the immune response and epithelial development.\n\nThe present results indicate that titanium micro-particles are commonly found in tissues surrounding dental implants and are not associated with the occurrence of peri-implantitis.", "doi": "10.1038/s43856-025-00756-3", "pmid": "40102654", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service", "Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11920262"}, {"db": "pii", "key": "10.1038/s43856-025-00756-3"}], "notes": [], "created": "2025-07-08T13:53:22.922Z", "modified": "2025-11-05T13:50:37.870Z"}, {"entity": "publication", "iuid": "7da5d2be4acf47fa8c81d9873c0265e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7da5d2be4acf47fa8c81d9873c0265e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7da5d2be4acf47fa8c81d9873c0265e5"}}, "title": "The Role of Caspase-1 and Caspase-4 in Modulating Gingival Epithelial Cell Responses to Aggregatibacter actinomycetemcomitans Infection.", "authors": [{"family": "Demirel", "given": "Kartheyaene Jayaprakash", "initials": "KJ"}, {"family": "Neves Guimaraes", "given": "Alessandra", "initials": "A", "orcid": "0000-0002-1291-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cb4149b660e4e2d83857c316b789e08.json"}}, {"family": "Demirel", "given": "Isak", "initials": "I"}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "Pathogens", "issn": "2076-0817", "volume": "14", "issue": "3", "issn-l": null}, "abstract": "Periodontitis is a chronic inflammatory disease characterized by bacterial infection and immune dysregulation. Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) is a key pathogen linked to disease progression. Caspase-1 and caspase-4 regulate inflammasome activation and cytokine release, yet their roles in gingival epithelial immunity remain unclear. The aim of this study was to elucidate the involvement of caspase-1 and caspase-4 in regulating the immune response to A. actinomycetemcomitans infection in gingival epithelial cells. Human gingival epithelial cells (Ca9-22) and caspase-1- and caspase-4-deficient cells were infected with A. actinomycetemcomitans for 24 h. Inflammatory mediator release was analyzed using Olink proteomics. Bacterial colonization and invasion were assessed using fluorescence-based assays and gentamicin protection assays. Caspase-1- and caspase-4-deficient cells showed significantly altered cytokine and chemokine profiles after infection with A. actinomycetemcomitans, showing reduced IL-17C and IL-18 release. We also found an increased release of TGF-\u03b1 and LIF from caspase-4-deficient cells, along with elevated levels of the chemokines IL-8, CXCL9, and CXCL10. Additionally, both caspase-1- and caspase-4-deficient cells showed increased bacterial colonization and invasion, particularly in caspase-4-deficient cells. These findings suggest that caspase-1 and caspase-4 play distinct yet essential roles in gingival epithelial immunity, regulating cytokine release, barrier integrity, and defense against A. actinomycetemcomitans colonization.", "doi": "10.3390/pathogens14030295", "pmid": "40137780", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11945752"}, {"db": "pii", "key": "pathogens14030295"}], "notes": [], "created": "2025-11-25T19:23:06.594Z", "modified": "2025-11-25T19:23:06.649Z"}, {"entity": "publication", "iuid": "71be5efa49b74b6ba458b37ce5b5b7ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71be5efa49b74b6ba458b37ce5b5b7ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71be5efa49b74b6ba458b37ce5b5b7ba"}}, "title": "Laparoscopic lavage in a purulent peritonitis model: impact on inflammatory proteins.", "authors": [{"family": "Sinclair", "given": "Erik", "initials": "E"}, {"family": "Magnusson", "given": "Maria K", "initials": "MK"}, {"family": "Angenete", "given": "Eva", "initials": "E"}, {"family": "Prytz", "given": "Mattias", "initials": "M"}, {"family": "Tasselius", "given": "Viktor", "initials": "V"}, {"family": "\u00d6hman", "given": "Lena", "initials": "L"}, {"family": "Haglind", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "Eur J Med Res", "issn": "2047-783X", "volume": "30", "issue": "1", "pages": "180", "issn-l": null}, "abstract": "Laparoscopic lavage is an effective, safe, and feasible treatment in patients with perforated diverticulitis with purulent peritonitis. Laparoscopic lavage was introduced without any detailed knowledge regarding the mechanisms of action. The aim of this study was to validate the reproducibility of an animal model of purulent peritonitis and to study the effect of laparoscopic lavage on inflammatory proteins in this model.\n\nForty rats, divided into eight groups (n = 5) were operated. Six groups underwent cecal ligation and puncture (CLP) causing peritonitis and two groups underwent sham surgery. Three CLP and one sham group received laparoscopic lavage, while the remaining groups acted as time-matched controls. Samples of abdominal fluid and blood were collected after 1, 2 or 3 h and analyzed regarding 92 inflammatory proteins using Olink Target 96 Mouse exploratory panel.\n\nAnimals with peritonitis had higher levels of inflammatory proteins such as CCL3, IL17A and IL6 in abdominal fluid and serum compared to sham. The groups treated with laparoscopic lavage had lower levels of inflammatory proteins in both abdominal fluid and serum compared with untreated peritonitis groups, results were most distinct sampled after one hour.\n\nOur animal model is reproducible, and mimics perforated diverticulitis with purulent peritonitis with increased levels of inflammatory proteins in abdominal fluid and serum. The levels of several inflammatory proteins were lower following laparoscopic lavage treatment perhaps indicating the physiological effect of laparoscopic lavage. This model can be used to further explore the mechanisms involved in peritonitis and laparoscopic lavage treatment.", "doi": "10.1186/s40001-025-02445-2", "pmid": "40102905", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11917159"}, {"db": "pii", "key": "10.1186/s40001-025-02445-2"}], "notes": [], "created": "2025-11-25T19:23:08.671Z", "modified": "2025-11-25T19:23:08.700Z"}, {"entity": "publication", "iuid": "fd6b36b9b7954640a91eda229981e7a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd6b36b9b7954640a91eda229981e7a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd6b36b9b7954640a91eda229981e7a4"}}, "title": "Computational drug repurposing: approaches, evaluation of in silico resources and case studies.", "authors": [{"family": "Tanoli", "given": "Ziaurrehman", "initials": "Z", "orcid": "0000-0003-2435-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/313c5ea401cf4c178d088e587d9f288f.json"}}, {"family": "Fern\u00e1ndez-Torras", "given": "Adri\u00e0", "initials": "A"}, {"family": "\u00d6zcan", "given": "Umut Onur", "initials": "UO", "orcid": "0000-0002-7317-1682", "researcher": {"href": "https://publications.scilifelab.se/researcher/263b2b77f07a473db81d4e1bf628bbaf.json"}}, {"family": "Kushnir", "given": "Aleksandr", "initials": "A"}, {"family": "Nader", "given": "Kristen Michelle", "initials": "KM", "orcid": "0009-0002-1068-0831", "researcher": {"href": "https://publications.scilifelab.se/researcher/28b9535c8a1a41fcb2b50677151dc92c.json"}}, {"family": "Gadiya", "given": "Yojana", "initials": "Y", "orcid": "0000-0002-7683-0452", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda537ad863640fbbe1b3e85e05092bb.json"}}, {"family": "Fiorenza", "given": "Laura", "initials": "L"}, {"family": "Ianevski", "given": "Aleksandr", "initials": "A", "orcid": "0000-0002-7780-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/438e80f3668b41c08d75618faabb285d.json"}}, {"family": "V\u00e4h\u00e4-Koskela", "given": "Markus", "initials": "M", "orcid": "0000-0001-7764-7820", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5c55c58b0f64591878356ab8c1a3ff4.json"}}, {"family": "Miihkinen", "given": "Mitro", "initials": "M", "orcid": "0000-0001-6822-3647", "researcher": {"href": "https://publications.scilifelab.se/researcher/782f144499194829a67e53d90af357bd.json"}}, {"family": "Seemab", "given": "Umair", "initials": "U"}, {"family": "Leinonen", "given": "Henri", "initials": "H", "orcid": "0000-0002-0388-832X", "researcher": {"href": "https://publications.scilifelab.se/researcher/08beef151ecb47978cc70e49d428d039.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Tampere", "given": "Marianna", "initials": "M"}, {"family": "Kalman", "given": "Adelinn", "initials": "A"}, {"family": "Ballante", "given": "Flavio", "initials": "F", "orcid": "0000-0002-4831-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/20429d2a46f4479a9c262875794a3a9d.json"}}, {"family": "Benfenati", "given": "Emilio", "initials": "E"}, {"family": "Saunders", "given": "Gary", "initials": "G"}, {"family": "Potdar", "given": "Swapnil", "initials": "S"}, {"family": "G\u00f3mez Garc\u00eda", "given": "Ismael", "initials": "I"}, {"family": "Garc\u00eda-Serna", "given": "Ricard", "initials": "R"}, {"family": "Talarico", "given": "Carmine", "initials": "C"}, {"family": "Beccari", "given": "Andrea Rosario", "initials": "AR", "orcid": "0000-0001-6830-2695", "researcher": {"href": "https://publications.scilifelab.se/researcher/a834a85c9dfd4cd69fe9578b05bfdb92.json"}}, {"family": "Schaal", "given": "Wesley", "initials": "W"}, {"family": "Polo", "given": "Andrea", "initials": "A"}, {"family": "Costantini", "given": "Susan", "initials": "S"}, {"family": "Cabri", "given": "Enrico", "initials": "E"}, {"family": "Jacobs", "given": "Marc", "initials": "M", "orcid": "0000-0003-4153-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/2057ce10fc4a40c28d6c99ddbca2da22.json"}}, {"family": "Saarela", "given": "Jani", "initials": "J"}, {"family": "Budillon", "given": "Alfredo", "initials": "A", "orcid": "0000-0002-6330-6053", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aa51cfd215b44aaa4fd2c262c84c13a.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Xhaard", "given": "Henri", "initials": "H"}, {"family": "Quintana", "given": "Jordi", "initials": "J"}, {"family": "Mestres", "given": "Jordi", "initials": "J", "orcid": "0000-0002-5202-4501", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b0fe21b221a4723bff492055fa6061b.json"}}, {"family": "Gribbon", "given": "Philip", "initials": "P"}, {"family": "Ussi", "given": "Anton E", "initials": "AE"}, {"family": "Lo", "given": "Donald C", "initials": "DC"}, {"family": "de Kort", "given": "Martin", "initials": "M", "orcid": "0000-0002-7264-5436", "researcher": {"href": "https://publications.scilifelab.se/researcher/016a2e73e1254b84aeb5898e8a026f1b.json"}}, {"family": "Wennerberg", "given": "Krister", "initials": "K", "orcid": "0000-0002-1352-4220", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a447e220e144c63a907f9c824ccc9da.json"}}, {"family": "Fratelli", "given": "Maddalena", "initials": "M", "orcid": "0000-0002-1769-3427", "researcher": {"href": "https://publications.scilifelab.se/researcher/a159ec26402b411dac5d5081a64f36cb.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Aittokallio", "given": "Tero", "initials": "T", "orcid": "0000-0002-0886-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/47e0db692d16440ea6779948c188713a.json"}}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "Nat Rev Drug Discov", "issn": "1474-1784", "issn-l": "1474-1776"}, "abstract": "Repurposing of existing drugs for new indications has attracted substantial attention owing to its potential to accelerate drug development and reduce costs. Hundreds of computational resources such as databases and predictive platforms have been developed that can be applied for drug repurposing, making it challenging to select the right resource for a specific drug repurposing project. With the aim of helping to address this challenge, here we overview computational approaches to drug repurposing based on a comprehensive survey of available in silico resources using a purpose-built drug repurposing ontology that classifies the resources into hierarchical categories and provides application-specific information. We also present an expert evaluation of selected resources and three drug repurposing case studies implemented within the Horizon Europe REMEDi4ALL project to demonstrate the practical use of the resources. This comprehensive Review with expert evaluations and case studies provides guidelines and recommendations on the best use of various in silico resources for drug repurposing and establishes a basis for a sustainable and extendable drug repurposing web catalogue.", "doi": "10.1038/s41573-025-01164-x", "pmid": "40102635", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41573-025-01164-x"}], "notes": [], "created": "2025-06-04T12:37:06.655Z", "modified": "2025-10-17T13:04:26.771Z"}, {"entity": "publication", "iuid": "3f77b47c2c9d4cb4b7c69ccd9596688c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f77b47c2c9d4cb4b7c69ccd9596688c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f77b47c2c9d4cb4b7c69ccd9596688c"}}, "title": "A chromosome-level genome assembly of the European green toad (Bufotes viridis).", "authors": [{"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P", "orcid": "0000-0001-6737-1488", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6abe040b284d67b11f45db1e58540e.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Choi", "given": "Eunkyoung", "initials": "E", "orcid": "0009-0007-7147-9468", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4255b0cdeec4f43885e730affd1246b.json"}}, {"family": "Ciofi", "given": "Claudio", "initials": "C", "orcid": "0000-0001-8537-8659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15012e62daf4c28b3c101550f460d35.json"}}, {"family": "Diedericks", "given": "Genevieve", "initials": "G", "orcid": "0000-0001-7700-8906", "researcher": {"href": "https://publications.scilifelab.se/researcher/7506eb0e88da4e4da970947289df5c4c.json"}}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA", "orcid": "0000-0003-1427-8946", "researcher": {"href": "https://publications.scilifelab.se/researcher/93fd5ac3fe64467d9e617b2bf14fea71.json"}}, {"family": "Einarsd\u00f3ttir", "given": "El\u00edsabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "F\u00f6rs\u00e4ter", "given": "Kristofer", "initials": "K", "orcid": "0009-0009-7670-215X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2e8576dc5354bef84f13f2e6a3fc1b6.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}}, {"family": "Jons\u00e4ll", "given": "Linnea", "initials": "L", "orcid": "0009-0004-6729-0185", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9c8f571a5be4dfeb7ebf5b35f4b4ae7.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Laurila", "given": "Anssi", "initials": "A", "orcid": "0000-0001-8090-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b55d6c459ef448c992a37db2a02c3ea.json"}}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG", "orcid": "0000-0002-9212-4590", "researcher": {"href": "https://publications.scilifelab.se/researcher/991f0492e152466f8f02cb6b7365ca6b.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Natali", "given": "Chiara", "initials": "C", "orcid": "0000-0002-0293-171X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df472019f49541f3bd455f1d8b1aea91.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Svardal", "given": "Hannes", "initials": "H", "orcid": "0000-0001-7866-7313", "researcher": {"href": "https://publications.scilifelab.se/researcher/4aee397f0ff64641a9c2033d56c6effb.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J", "orcid": "0000-0002-5840-779X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1eb3c1903f4a97a4c585a2dee3b05f.json"}}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "15", "issue": "3", "pages": null}, "abstract": "The European green toad (Bufotes viridis) is geographically widely distributed. While the species global conservation status is labeled as of least concern by the IUCN, it is declining in many parts of its range where populations are fragmented and isolated. A high-quality reference genome is an important resource for conservation genomic researchers who are trying to understand and interpret the genomic signals of population decline, inbreeding, and the accumulation of deleterious mutations. Here, we assembled and annotated a chromosome-level reference genome for B. viridis as part of the European Reference Genome Atlas pilot project. The genome assembly, with a size of \u223c3.89 Gb consists of 11 chromosomes and an additional 2,096 unplaced scaffolds. The final assembly had a scaffold N50 value of 478.39 Mb and covered 90.4% single copy tetrapod orthologs, and 46.7% repetitive elements. Finally, a total of 23,830 protein-coding genes matching a known gene, together with 56,974 mRNAs were predicted. This high-quality reference genome will benefit amphibian evolutionary genomics research and enable conservation genetic studies to inform practical conservation work on this species.", "doi": "10.1093/g3journal/jkaf002", "pmid": "39969399", "labels": {"NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11917475"}, {"db": "pii", "key": "8024180"}], "notes": [], "created": "2025-02-28T07:50:03.734Z", "modified": "2025-11-21T12:40:15.314Z"}, {"entity": "publication", "iuid": "6d6022e4a7f44f05adf49a56b8dce29d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d6022e4a7f44f05adf49a56b8dce29d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d6022e4a7f44f05adf49a56b8dce29d"}}, "title": "NQO1\u2010Responsive Prodrug for in Cellulo Release of Cytochalasin B as Cancer Cell\u2010Targeted Migrastatic", "authors": [{"family": "Kagho", "given": "Mervic D", "initials": "MD", "orcid": "0000-0003-3714-7738", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0d7812a50e942f09ec2df8bb7d6e287.json"}}, {"family": "Schmidt", "given": "Katharina", "initials": "K", "orcid": "0000-0003-1512-1748", "researcher": {"href": "https://publications.scilifelab.se/researcher/9127b79482d64c53acf2b175e32079f9.json"}}, {"family": "Lambert", "given": "Christopher", "initials": "C"}, {"family": "Jia", "given": "Lili", "initials": "L"}, {"family": "Venkatakrishnan", "given": "Vignesh", "initials": "V", "orcid": "0000-0001-5671-1547", "researcher": {"href": "https://publications.scilifelab.se/researcher/24ce056b14f54c83beffc5aa6e7a5066.json"}}, {"family": "Mehr", "given": "Luisa", "initials": "L"}, {"family": "Bylund", "given": "Johan", "initials": "J", "orcid": "0000-0002-9094-6478", "researcher": {"href": "https://publications.scilifelab.se/researcher/782377f783314bcdb2d2c6d9be4532de.json"}}, {"family": "Rottner", "given": "Klemens", "initials": "K", "orcid": "0000-0003-4244-4198", "researcher": {"href": "https://publications.scilifelab.se/researcher/272d787b62ee4e6b80920ec6d1a8e456.json"}}, {"family": "Stadler", "given": "Marc", "initials": "M", "orcid": "0000-0002-7284-8671", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd617bba3c524e3092538ea086715b62.json"}}, {"family": "Stradal", "given": "Theresia E B", "initials": "TEB", "orcid": "0000-0002-0352-9474", "researcher": {"href": "https://publications.scilifelab.se/researcher/7981da95069947799a3deccfad2de025.json"}}, {"family": "Klahn", "given": "Philipp", "initials": "P", "orcid": "0000-0003-4713-2345", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c6f067dc85a4e12b3593401e34e36d6.json"}}], "type": "journal-article", "published": "2025-03-17", "journal": {"title": "Small", "issn": "1613-6810", "issn-l": null}, "abstract": null, "doi": "10.1002/smll.202410861", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:06:23.561Z", "modified": "2025-11-27T08:06:24.718Z"}, {"entity": "publication", "iuid": "06ad0fb25bc94a7da35d862c094f74a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06ad0fb25bc94a7da35d862c094f74a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06ad0fb25bc94a7da35d862c094f74a8"}}, "title": "Human jejunal enteroids for studies of epithelial drug transport and metabolism", "authors": [{"family": "Ceylan", "given": "Merve", "initials": "M"}, {"family": "Tzioufa", "given": "Foteini", "initials": "F", "orcid": "0009-0006-6884-6821", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea7581291cc147d5a814abc0a80b91a4.json"}}, {"family": "Di Martino", "given": "Maria Letizia", "initials": "ML", "orcid": "0000-0002-9491-4000", "researcher": {"href": "https://publications.scilifelab.se/researcher/708eae058cb3494f8407574a666a16f0.json"}}, {"family": "Hammar", "given": "Rebekkah", "initials": "R", "orcid": "0000-0001-5740-0353", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d8e872219e74a5d90adc8047b1e476e.json"}}, {"family": "Lopes", "given": "Ana C C", "initials": "ACC"}, {"family": "Eriksson", "given": "Jens", "initials": "J", "orcid": "0000-0002-8945-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/b94e7f542841474d86d53aa48958f870.json"}}, {"family": "Vo", "given": "Dinh Son", "initials": "DS", "orcid": "0009-0000-4180-8231", "researcher": {"href": "https://publications.scilifelab.se/researcher/03968401df594760a9df66791cdc05b2.json"}}, {"family": "Sundbom", "given": "Magnus", "initials": "M", "orcid": "0000-0002-6243-2859", "researcher": {"href": "https://publications.scilifelab.se/researcher/a54316faa45947bd92615d27a38c2b87.json"}}, {"family": "Skogar", "given": "Martin", "initials": "M"}, {"family": "Hellstr\u00f6m", "given": "Per M", "initials": "PM"}, {"family": "Webb", "given": "Dominic Luc", "initials": "DL", "orcid": "0000-0002-6979-9194", "researcher": {"href": "https://publications.scilifelab.se/researcher/868fca24b48f440eb2417acdb04e73d3.json"}}, {"family": "Karlgren", "given": "Maria", "initials": "M", "orcid": "0000-0003-4500-0170", "researcher": {"href": "https://publications.scilifelab.se/researcher/34f36303d2f9406f8bf50eefd41c544c.json"}}, {"family": "Gardner", "given": "Iain", "initials": "I"}, {"family": "Lundquist", "given": "Patrik", "initials": "P", "orcid": "0000-0002-7458-7882", "researcher": {"href": "https://publications.scilifelab.se/researcher/f44b798ddc81465f89907c7ef52eb206.json"}}, {"family": "Hjelmqvist", "given": "Daisy", "initials": "D", "orcid": "0000-0002-2126-4385", "researcher": {"href": "https://publications.scilifelab.se/researcher/c02e61f71d0a4f1d9c39c804b9f5b808.json"}}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}, {"family": "Hubert", "given": "Madlen", "initials": "M", "orcid": "0000-0002-5908-9535", "researcher": {"href": "https://publications.scilifelab.se/researcher/48acd1c7795b45919bba57a5a9817ea7.json"}}, {"family": "Artursson", "given": "Per", "initials": "P", "orcid": "0000-0002-3708-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/31575936c2714e1eb2f35c12df9a65a8.json"}}], "type": "posted-content", "published": "2025-03-17", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.03.17.643545", "pmid": null, "labels": {"Cryo-EM": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [], "notes": [], "created": "2025-10-29T14:38:08.332Z", "modified": "2025-12-18T19:17:29.703Z"}, {"entity": "publication", "iuid": "d0227fdc5b3843deb2096267d97646b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d0227fdc5b3843deb2096267d97646b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d0227fdc5b3843deb2096267d97646b6"}}, "title": "Targeting TUBG1 in RB1\u2010negative tumors", "authors": [{"family": "Lindstr\u00f6m", "given": "Lisa", "initials": "L", "orcid": "0009-0008-4510-4635", "researcher": {"href": "https://publications.scilifelab.se/researcher/1091020b47274bfcb2f03a329057d7ae.json"}}, {"family": "Zhou", "given": "Jingkai", "initials": "J", "orcid": "0000-0002-9867-3486", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dc6dcbd404c47eca422a2167085492e.json"}}, {"family": "Villoutreix", "given": "Bruno O", "initials": "BO", "orcid": "0000-0002-6456-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/faac02c89da248e4b2b393614365c304.json"}}, {"family": "Malycheva", "given": "Darina", "initials": "D"}, {"family": "Otrocka", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-2139-8236", "researcher": {"href": "https://publications.scilifelab.se/researcher/f60f84f70b744033b0c94b6d24e1c405.json"}}, {"family": "Gustavsson", "given": "Anna\u2010Lena", "initials": "A", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T", "orcid": "0000-0002-8145-7808", "researcher": {"href": "https://publications.scilifelab.se/researcher/e13df787cb884549bcf333aba4e6f010.json"}}, {"family": "Bliman", "given": "David", "initials": "D", "orcid": "0000-0003-0487-8366", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e29451fca1644f3a6fd2bd4bbff9594.json"}}, {"family": "Shameem", "given": "Muhammad Anwar", "initials": "MA", "orcid": "0000-0001-6173-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c7fb16605874dfe93c1343f6ab32e67.json"}}, {"family": "Straw", "given": "Megan", "initials": "M"}, {"family": "Riesbeck", "given": "Kristian", "initials": "K", "orcid": "0000-0001-6274-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/d757ccad30b043748c8fe48a7308210c.json"}}, {"family": "Olsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-7107-3472", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3e5a72515bf44e98f43d4690c6e577e.json"}}, {"family": "Alvarado\u2010Kristensson", "given": "Maria", "initials": "M", "orcid": "0000-0003-0598-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ee81797eff452fa037821f293d8673.json"}}], "type": "journal-article", "published": "2025-03-15", "journal": {"title": "The FASEB Journal", "issn": "0892-6638", "volume": "39", "issue": "5", "issn-l": "0892-6638"}, "abstract": null, "doi": "10.1096/fj.202403180rr", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-04-23T10:27:30.624Z", "modified": "2025-10-17T13:04:26.785Z"}, {"entity": "publication", "iuid": "db7bafd701444e32b52fe11feea86f7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db7bafd701444e32b52fe11feea86f7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db7bafd701444e32b52fe11feea86f7b"}}, "title": "Sox9 and nuclear factor I transcription factors regulate the timing of neurogenesis and ependymal maturation in dopamine progenitors.", "authors": [{"family": "Lahti", "given": "Laura", "initials": "L", "orcid": "0000-0003-2929-1975", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ee35dc36f440d197afe3cd433d64ca.json"}}, {"family": "Volakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Yaghmaeian Salmani", "given": "Behzad", "initials": "B", "orcid": "0000-0002-4221-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb9b5976d0b34622aff0e9a564b3ae54.json"}}, {"family": "Tiklov\u00e1", "given": "Katar\u00edna", "initials": "K", "orcid": "0000-0002-9529-4552", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bbad41b8ed42268b71014ce111d247.json"}}, {"family": "Kee", "given": "Nigel", "initials": "N", "orcid": "0000-0002-7095-0760", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa213cf47c30423e8be78d0e8968b0b3.json"}}, {"family": "Lund\u00e9n-Miguel", "given": "Hilda", "initials": "H"}, {"family": "Werkman", "given": "Maarten", "initials": "M", "orcid": "0009-0000-6880-0897", "researcher": {"href": "https://publications.scilifelab.se/researcher/0eecf2c25f464784bf84003d051279ba.json"}}, {"family": "Piper", "given": "Michael", "initials": "M", "orcid": "0000-0002-6759-2560", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f040420470a4f11852954781cd23c15.json"}}, {"family": "Gronostajski", "given": "Richard", "initials": "R", "orcid": "0000-0003-4264-208X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff92d5fdb7fe4967a3f1af62077ef82e.json"}}, {"family": "Perlmann", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4821-8036", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c8dc93c324455b93aa392fcbb67315.json"}}], "type": "journal article", "published": "2025-03-15", "journal": {"title": "Development", "issn": "1477-9129", "issn-l": "0950-1991", "volume": "152", "issue": "6", "pages": null}, "abstract": "Correct timing of neurogenesis is crucial for generating the correct number and subtypes of glia and neurons in the embryo, and for preventing tumours and stem cell depletion in the adults. Here, we analyse how the midbrain dopamine (mDA) neuron progenitors transition into cell cycle arrest (G0) and begin to mature into ependymal cells. Comparison of mDA progenitors from different embryonic stages revealed upregulation of the genes encoding Sox9 and nuclear factor I transcription factors during development. Their conditional inactivation in the early embryonic midbrain led to delayed G0 entry and ependymal maturation in the entire midbrain ventricular zone, reduced gliogenesis and increased generation of neurons, including mDA neurons. In contrast, their inactivation in late embryogenesis did not result in mitotic re-entry, suggesting that these factors are necessary for G0 induction, but not for its maintenance. Our characterisation of adult ependymal cells by single-cell RNA sequencing and histology show that mDA-progenitor-derived cells retain several progenitor features but also secrete neuropeptides and contact neighbouring cells and blood vessels, indicating that these cells may form part of the circumventricular organ system.", "doi": "10.1242/dev.204421", "pmid": "39995267", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "367503"}], "notes": [], "created": "2025-04-07T09:04:57.491Z", "modified": "2025-11-28T10:53:42.874Z"}, {"entity": "publication", "iuid": "ae58c2f2b2de41cfa09cec10f2b828d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae58c2f2b2de41cfa09cec10f2b828d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae58c2f2b2de41cfa09cec10f2b828d8"}}, "title": "Deciphering the phenotypic, inflammatory, and endocrine disrupting impacts of e-waste plastic-associated chemicals.", "authors": [{"family": "Alijagic", "given": "Andi", "initials": "A"}, {"family": "Seilitz", "given": "Fredric S\u00f6dergren", "initials": "FS"}, {"family": "Bredberg", "given": "Anna", "initials": "A"}, {"family": "Hakonen", "given": "Aron", "initials": "A"}, {"family": "Larsson", "given": "Maria", "initials": "M"}, {"family": "Selin", "given": "Erica", "initials": "E"}, {"family": "Sj\u00f6berg", "given": "Viktor", "initials": "V"}, {"family": "Kotlyar", "given": "Oleksandr", "initials": "O"}, {"family": "Scherbak", "given": "Nikolai", "initials": "N"}, {"family": "Repsilber", "given": "Dirk", "initials": "D"}, {"family": "K\u00e4rrman", "given": "Anna", "initials": "A"}, {"family": "Wang", "given": "Thanh", "initials": "T"}, {"family": "S\u00e4rndahl", "given": "Eva", "initials": "E"}, {"family": "Engwall", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2025-03-15", "journal": {"title": "Environ. Res.", "issn": "1096-0953", "volume": "269", "pages": "120929", "issn-l": "0013-9351"}, "abstract": "As the volume of plastic waste from electrical and electronic equipment (WEEE) continues to rise, a significant portion is disposed of in the environment, with only a small fraction being recycled. Both disposal and recycling pose unknown health risks that require immediate attention. Existing knowledge of WEEE plastic toxicity is limited and mostly relies on epidemiological data and association studies, with few insights into the underlying toxicity mechanisms. Therefore, this study aimed to perform comprehensive chemical screening and mechanistic toxicological assessment of WEEE plastic-associated chemicals. Chemical analysis, utilizing suspect screening based on high-resolution mass spectrometry, along with quantitative target chemical analysis, unveiled numerous hazardous compounds including polyaromatic compounds, organophosphate flame retardants, phthalates, benzotriazoles, etc. Toxicity endpoints included perturbation of morphological phenotypes using the Cell Painting assay, inflammatory response, oxidative stress, and endocrine disruption. Results demonstrated that WEEE plastic chemicals altered the phenotypes of the cytoskeleton, endoplasmic reticulum, and mitochondria in a dose-dependent manner. In addition, WEEE chemicals induced inflammatory responses in resting macrophages and altered inflammatory responses in lipopolysaccharide-primed macrophages. Furthermore, WEEE chemicals activated the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway, indicating oxidative stress, and the aryl hydrocarbon receptor (AhR). Endocrine disruption was also observed through the activation of estrogenic receptor-\u03b1 (ER-\u03b1) and the induction of anti-androgenic activity. The findings show that WEEE plastic-associated chemicals exert effects in multiple subcellular sites, via different receptors and mechanisms. Thus, an integrated approach employing both chemical and toxicological methods is essential for comprehensive assessment of the toxicity mechanisms and cumulative chemical burden of WEEE plastic-associated chemicals.", "doi": "10.1016/j.envres.2025.120929", "pmid": "39862959", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0013-9351(25)00180-X"}], "notes": [], "created": "2025-11-28T10:43:09.232Z", "modified": "2025-11-28T10:43:09.256Z"}, {"entity": "publication", "iuid": "7352c8aca5214ed1878a95ee46d195ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7352c8aca5214ed1878a95ee46d195ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7352c8aca5214ed1878a95ee46d195ab"}}, "title": "Dietary patterns and blood-based biomarkers of Alzheimer's disease in cognitively intact older adults: Findings from a population-based study.", "authors": [{"family": "Mrhar", "given": "Anja", "initials": "A"}, {"family": "Carballo-Casla", "given": "Adri\u00e1n", "initials": "A"}, {"family": "Grande", "given": "Giulia", "initials": "G", "orcid": "0000-0001-6312-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6fc0b0bad8243059965a2b828321c14.json"}}, {"family": "Valletta", "given": "Martina", "initials": "M", "orcid": "0000-0003-0139-8287", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa01849f48049c78eef04747ab1797a.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "Gregori\u010d Kramberger", "given": "Milica", "initials": "M"}, {"family": "Kuhar", "given": "Ale\u0161", "initials": "A"}, {"family": "Winblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-0011-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/73185a13ca474153b66415e6a2dfff0f.json"}}, {"family": "Calder\u00f3n-Larra\u00f1aga", "given": "Amaia", "initials": "A"}, {"family": "Vetrano", "given": "Davide Liborio", "initials": "DL", "orcid": "0000-0002-3099-4830", "researcher": {"href": "https://publications.scilifelab.se/researcher/06867644d5f14eef958737353517f53d.json"}}], "type": "journal article", "published": "2025-03-14", "journal": {"title": "J Prev Alzheimers Dis", "issn": "2426-0266", "pages": "100124", "issn-l": null}, "abstract": "Diet can impact cognitive aging, but comprehensive data from human studies is lacking and the underlying biological mechanisms are still not fully understood.\n\nTo investigate the associations between two dietary patterns consistently linked to inflammation and brain health [the Mediterranean diet (MDS) and inflammatory potential of diet (EDII)] and five blood-based biomarkers of Alzheimer\u00b4s disease (AD) in a sample of dementia-free community-dwelling older adults.\n\nWe used cross-sectional data from the Swedish National Study on Aging and Care in Kungsholmen (SNAC-K).\n\nParticipants who were institutionalized, had dementia or Parkinson's disease, or had missing data on diet and/or biomarkers were excluded. Our study sample consisted of 1907 adults \u226560 years old.\n\nAdherence to the MDS and EDII was assessed using a validated food frequency questionnaire. T-tau, p-tau181, A\u03b2 42/40, NfL, and GFAP were measured in serum. Associations were estimated through quantile regression models at the 25th, 50th, and 75th percentiles of the biomarkers' levels, and were adjusted for potential confounders and stratified by sex, age, and APOE-e4 genotype.\n\nIn the whole sample, higher adherence to the MDS was associated with lower levels of p-tau181 at the 50th and 75th percentiles [\u03b2 (95% CI) per 1-SD increment = -0.028 (-0.053, -0.002) and -0.036 (-0.072, -0.001), respectively], while higher adherence to the EDII was associated with higher levels of NfL at the 75th percentile [\u03b2 (95% CI) per 1-SD increment =0.031 (0.008, 0.053)]. Associations with other biomarkers were only apparent at lower levels of their distribution. Subgroup analyses showed: 1) a stronger inverse association between the MDS and p-tau181 in APOE-e4 carriers than non-carriers, and 2) an inverse association of the MDS with GFAP only in participants \u226578 years.\n\nDiet seems to be associated with biomarkers of AD pathology in cognitively intact older adults. Some associations were more apparent in the presence of genetic predisposition for AD or advanced age.", "doi": "10.1016/j.tjpad.2025.100124", "pmid": "40089420", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2274-5807(25)00068-8"}], "notes": [], "created": "2025-04-02T14:35:17.246Z", "modified": "2025-04-03T08:26:38.025Z"}, {"entity": "publication", "iuid": "fd4905a14c1844bf8c1f8909a2103c09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd4905a14c1844bf8c1f8909a2103c09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd4905a14c1844bf8c1f8909a2103c09"}}, "title": "2024 OME-NGFF workflows hackathon", "authors": [{"family": "L\u00fcthi", "given": "Joel", "initials": "J", "orcid": "0000-0003-3023-170X", "researcher": {"href": "https://publications.scilifelab.se/researcher/57c7a89f6c7143eb949ce4b0e5c89adf.json"}}, {"family": "Albert", "given": "Marvin", "initials": "M"}, {"family": "Anita", "given": "Liviu", "initials": "L"}, {"family": "Babalola", "given": "Kola", "initials": "K"}, {"family": "Bennett", "given": "Davis", "initials": "D"}, {"family": "Bogovic", "given": "John A", "initials": "JA"}, {"family": "Cerrone", "given": "Lorenzo", "initials": "L"}, {"family": "Dornier", "given": "R\u00e9my", "initials": "R"}, {"family": "Eglinger", "given": "Jan", "initials": "J"}, {"family": "Galinova", "given": "Vera", "initials": "V"}, {"family": "Gerber", "given": "Reto", "initials": "R", "orcid": "0000-0001-5414-8906", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c1376a1d5b54a6c9a901b9f624c0612.json"}}, {"family": "Gros", "given": "Oane", "initials": "O"}, {"family": "Hahmann", "given": "Stefan", "initials": "S"}, {"family": "Hess", "given": "Max", "initials": "M"}, {"family": "Hornbachner", "given": "Ruth", "initials": "R"}, {"family": "Horyslavets", "given": "Dmytro", "initials": "D"}, {"family": "Huxford", "given": "Rachael", "initials": "R"}, {"family": "Krentzel", "given": "Daniel", "initials": "D", "orcid": "0000-0002-6234-7259", "researcher": {"href": "https://publications.scilifelab.se/researcher/db794929e7744ac49bb12e39490fcba2.json"}}, {"family": "LI", "given": "Tong", "initials": "T", "orcid": "0000-0002-8240-4476", "researcher": {"href": "https://publications.scilifelab.se/researcher/20d115ec11454392809f05f518cc06b5.json"}}, {"family": "Marconato", "given": "Luca", "initials": "L"}, {"family": "McCormick", "given": "Matthew", "initials": "M", "orcid": "0000-0001-9475-3756", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad31630d4b384a13b8e3ee31d90aece6.json"}}, {"family": "Moos", "given": "Franziska", "initials": "F"}, {"family": "Mroz", "given": "Filip", "initials": "F"}, {"family": "\u00d6zdemir", "given": "Bugra", "initials": "B"}, {"family": "Pavie", "given": "Benjamin", "initials": "B"}, {"family": "Perlman", "given": "Eric", "initials": "E"}, {"family": "Schulz", "given": "Maximilian", "initials": "M"}, {"family": "Schwarz", "given": "Leonardo", "initials": "L"}, {"family": "Spitz", "given": "Hannes M", "initials": "HM"}, {"family": "Stansby", "given": "David", "initials": "D"}, {"family": "Steffen", "given": "Fabio", "initials": "F"}, {"family": "Stoma", "given": "Szymon", "initials": "S"}, {"family": "Sturzenegger", "given": "Flurin", "initials": "F"}, {"family": "Vierdag", "given": "Wouter Michiel", "initials": "WM", "orcid": "0000-0003-1666-5421", "researcher": {"href": "https://publications.scilifelab.se/researcher/b08b46ab6bab4cbd8a6e72be1c1b2f47.json"}}, {"family": "Windhager", "given": "Jonas", "initials": "J"}, {"family": "Yamauchi", "given": "Kevin", "initials": "K"}, {"family": "Zubarev", "given": "Igor", "initials": "I"}, {"family": "Moore", "given": "Josh", "initials": "J", "orcid": "0000-0003-4028-811X", "researcher": {"href": "https://publications.scilifelab.se/researcher/18cb52a735fd44ce844af5968836bf87.json"}}, {"family": "Rzepka", "given": "Norman", "initials": "N"}, {"family": "Tischer", "given": "Christian", "initials": "C"}, {"family": "Ulman", "given": "Vladimir", "initials": "V"}, {"family": "Uhlmann", "given": "Virginie", "initials": "V"}], "type": "posted-content", "published": "2025-03-14", "journal": {"title": "OSF", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.37044/osf.io/5uhwz_v2", "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T12:58:13.570Z", "modified": "2025-12-18T19:22:37.818Z"}, {"entity": "publication", "iuid": "87b7ae2910fe4078a07ec298cbfaae7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87b7ae2910fe4078a07ec298cbfaae7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87b7ae2910fe4078a07ec298cbfaae7c"}}, "title": "Above-Filter Digestion Proteomics reveals drug targets and localizes ligand binding site", "authors": [{"family": "Sokolova", "given": "Bohdana", "initials": "B"}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85179acfa7e4916ad40ae478d6dcc0a.json"}}, {"family": "Jafari", "given": "Maryam", "initials": "M"}, {"family": "Lyu", "given": "Hezheng", "initials": "H", "orcid": "0009-0008-7995-6473", "researcher": {"href": "https://publications.scilifelab.se/researcher/de932cbcb2c341f7a6544104026c7b1c.json"}}, {"family": "Lovera", "given": "Silvia", "initials": "S"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Zubarev", "given": "Roman", "initials": "R", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "posted-content", "published": "2025-03-13", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.03.11.642584", "pmid": null, "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2025-11-25T16:34:50.393Z", "modified": "2025-12-18T19:19:00.493Z"}, {"entity": "publication", "iuid": "c5b4d283a9414611bfeae71de58abe32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5b4d283a9414611bfeae71de58abe32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5b4d283a9414611bfeae71de58abe32"}}, "title": "Genetic liability for anxiety and treatment response to the monoamine stabilizer OSU6162 in alcohol dependence: a retrospective secondary analysis.", "authors": [{"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Khemiri", "given": "Lotfi", "initials": "L"}, {"family": "Guterstam", "given": "Joar", "initials": "J"}, {"family": "Franck", "given": "Johan", "initials": "J"}, {"family": "Jayaram-Lindstr\u00f6m", "given": "Nitya", "initials": "N"}, {"family": "Melas", "given": "Philippe A", "initials": "PA"}], "type": "journal article", "published": "2025-03-12", "journal": {"title": "Pharmacol Rep", "issn": "2299-5684", "issn-l": null}, "abstract": "OSU6162, a monoamine stabilizer, has demonstrated efficacy in reducing alcohol and anxiety-related behaviors in preclinical settings. In a previous randomized, double-blind, placebo-controlled trial involving patients with alcohol dependence (AD), OSU6162 significantly reduced craving for alcohol but did not alter drinking behaviors. This retrospective secondary analysis explores whether genetic predispositions related to AD and associated traits might influence the response to OSU6162 treatment in original trial participants.\n\nPolygenic risk scores (PRSs) were calculated for 48 AD patients using PRSice-2 and genome-wide association study (GWAS) data for (i) alcohol use disorder and alcohol consumption, (ii) problematic alcohol use, (iii) drinks per week, (iv) major depression, and (v) anxiety (case-control comparisons and quantitative anxiety factor scores). Linear regression analyses, adjusted for population stratification, assessed interaction effects between PRSs and treatment type (OSU6162 or placebo) on various clinical outcomes.\n\nSignificant interactions were found between treatment type and anxiety factor score PRS at the genome-wide significance threshold. In the OSU6162-treated group, a higher anxiety PRS was associated with reductions in the number of drinks consumed (FDR = 0.0017), percentage of heavy drinking days (FDR = 0.0060), and percentage of drinking days (FDR = 0.0017), with a trend toward reduced blood phosphatidylethanol (PEth) levels (FDR = 0.068). These associations were absent in the placebo group.\n\nThese preliminary findings suggest that anxiety PRS may help predict response to OSU6162 treatment in AD. Further research with larger cohorts and more comprehensive genetic data is needed to confirm these results and advance personalized medicine approaches for alcohol use disorder.", "doi": "10.1007/s43440-025-00707-8", "pmid": "40069537", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s43440-025-00707-8"}], "notes": [], "created": "2025-03-31T07:45:02.876Z", "modified": "2025-03-31T07:45:03.018Z"}, {"entity": "publication", "iuid": "b9a52931d3d74346a7d1d9534c62ab91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9a52931d3d74346a7d1d9534c62ab91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9a52931d3d74346a7d1d9534c62ab91"}}, "title": "A clinical prostate biopsy dataset with undetected cancer.", "authors": [{"family": "Chelebian", "given": "Eduard", "initials": "E", "orcid": "0000-0001-6852-6605", "researcher": {"href": "https://publications.scilifelab.se/researcher/278694af6d7e499f9432c6523da24f25.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "J\u00e4remo", "given": "Helena", "initials": "H"}, {"family": "Andersson", "given": "Pernilla", "initials": "P"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Bergh", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2025-03-11", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "423", "issn-l": "2052-4463"}, "abstract": "Prostate cancer is a heterogeneous disease showing variability both among individuals and within a patient. While most cases are indolent, aggressive tumors require early intervention. Accurately predicting tumor behavior is challenging, contributing to overdiagnosis but also undertreatment. Current imaging methods may miss the most malignant areas, leading to biopsies often capturing non-malignant prostate tissue even if cancer is present elsewhere in the organ. This non-malignant tissue, however, holds potential as a source for novel diagnostic and prognostic markers. Our clinical dataset comprises men with raised prostate-specific antigen but whose initial prostate needle biopsies only contained benign tissue. Half of the paired patients remained cancer-free for over eight years, while the others were diagnosed with prostate cancer within 30 months of follow-up. We share these initial benign biopsies to enable the exploration of morphological changes in non-malignant tissue and the potential for improved diagnostic accuracy in the early identification of patients with prostate cancer.", "doi": "10.1038/s41597-025-04758-7", "pmid": "40069192", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11897396"}, {"db": "pii", "key": "10.1038/s41597-025-04758-7"}], "notes": [], "created": "2025-11-25T12:53:53.705Z", "modified": "2025-11-25T12:53:53.733Z"}, {"entity": "publication", "iuid": "3448380f4dca4f2c9218130e25c03172", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3448380f4dca4f2c9218130e25c03172.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3448380f4dca4f2c9218130e25c03172"}}, "title": "Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation.", "authors": [{"family": "Kistler", "given": "Logan", "initials": "L", "orcid": "0000-0002-5730-5986", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7f9fed415ac4818b28b9854af1cd996.json"}}, {"family": "de Oliveira Freitas", "given": "Fabio", "initials": "F", "orcid": "0000-0002-1242-6119", "researcher": {"href": "https://publications.scilifelab.se/researcher/70f51b4d4c8a4f0b96e76565d21cf168.json"}}, {"family": "Gutaker", "given": "Rafal M", "initials": "RM", "orcid": "0000-0001-9226-879X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fd4f6274b604cd786fb41b41ab65d13.json"}}, {"family": "Maezumi", "given": "S Yoshi", "initials": "SY", "orcid": "0000-0002-4333-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/71b2aba560e24fbd8fb3c706304ea872.json"}}, {"family": "Ramos-Madrigal", "given": "Jazm\u00edn", "initials": "J", "orcid": "0000-0002-1661-7991", "researcher": {"href": "https://publications.scilifelab.se/researcher/31e1ca5ba0dc44fbbb8106beab9e4e44.json"}}, {"family": "Simon", "given": "Marcelo F", "initials": "MF", "orcid": "0000-0002-5732-1716", "researcher": {"href": "https://publications.scilifelab.se/researcher/e25bce0105914ce1a7346a2c0543420d.json"}}, {"family": "Mendoza F", "given": "J Moises", "initials": "JM", "orcid": "0000-0003-1835-7051", "researcher": {"href": "https://publications.scilifelab.se/researcher/09f3e77a361a41d1ae8e6c36248ca7cd.json"}}, {"family": "Drovetski", "given": "Sergei V", "initials": "SV", "orcid": "0000-0002-1832-5597", "researcher": {"href": "https://publications.scilifelab.se/researcher/133195ffac4f44a6a020cb2926316cb1.json"}}, {"family": "Loiselle", "given": "Hope", "initials": "H", "orcid": "0000-0002-6197-4752", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bb9a722e5bd42429281694720bd9ae9.json"}}, {"family": "de Oliveira", "given": "Eder Jorge", "initials": "EJ", "orcid": "0000-0001-8992-7459", "researcher": {"href": "https://publications.scilifelab.se/researcher/6734816913324f93b622c552c8285a7d.json"}}, {"family": "Vieira", "given": "Eduardo Alano", "initials": "EA", "orcid": "0000-0003-4931-3895", "researcher": {"href": "https://publications.scilifelab.se/researcher/fddd391a36e44014bb46559b5e3b482e.json"}}, {"family": "Carvalho", "given": "Luiz Joaquim Castelo Branco", "initials": "LJCB"}, {"family": "Ellis Perez", "given": "Marina", "initials": "M", "orcid": "0009-0000-1271-536X", "researcher": {"href": "https://publications.scilifelab.se/researcher/020a3d5f06724a8ca3b30682d84c5615.json"}}, {"family": "Lin", "given": "Audrey T", "initials": "AT", "orcid": "0000-0003-2505-1480", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f1f6e691ce04fd396757c4918535cc2.json"}}, {"family": "Liu", "given": "Hsiao-Lei", "initials": "H"}, {"family": "Miller", "given": "Rachel", "initials": "R", "orcid": "0009-0006-9322-2930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0caea54e94e948de803f092ec62d480d.json"}}, {"family": "Przelomska", "given": "Natalia A S", "initials": "NAS", "orcid": "0000-0001-9207-4565", "researcher": {"href": "https://publications.scilifelab.se/researcher/8de86c85c2ac47e398e8cd0175fcda35.json"}}, {"family": "Ratan", "given": "Aakrosh", "initials": "A", "orcid": "0000-0002-0782-3056", "researcher": {"href": "https://publications.scilifelab.se/researcher/da8fc51b280d4283b7ce57ef8063600d.json"}}, {"family": "Wales", "given": "Nathan", "initials": "N", "orcid": "0000-0003-0359-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c5af47529d418eb93ba5e51eeee86e.json"}}, {"family": "Wann", "given": "Kevin", "initials": "K", "orcid": "0009-0005-1045-3833", "researcher": {"href": "https://publications.scilifelab.se/researcher/f355d3d4244346b98228fdb85ed8e030.json"}}, {"family": "Zhang", "given": "Shuya", "initials": "S", "orcid": "0009-0008-7061-7627", "researcher": {"href": "https://publications.scilifelab.se/researcher/e62a05ea897644338e66ec5af2db1052.json"}}, {"family": "Garc\u00eda", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-1128-9941", "researcher": {"href": "https://publications.scilifelab.se/researcher/878832e786334905817869afbb67e8b5.json"}}, {"family": "Valenzuela", "given": "Daniela", "initials": "D", "orcid": "0000-0001-7318-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/28e80dc46b654a9daeb81a8e212e8077.json"}}, {"family": "Rothhammer", "given": "Francisco", "initials": "F"}, {"family": "Santoro", "given": "Calogero M", "initials": "CM"}, {"family": "Domic", "given": "Alejandra I", "initials": "AI", "orcid": "0000-0003-0762-3967", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbc5a934524147c39c493caa59cd79fc.json"}}, {"family": "Capriles", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0001-6046-0939", "researcher": {"href": "https://publications.scilifelab.se/researcher/54d972de19d04c9c828afa2a43b4d24f.json"}}, {"family": "Allaby", "given": "Robin G", "initials": "RG", "orcid": "0000-0001-5046-002X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6cf7900088744c6b2270d8bbea4ff94.json"}}], "type": "journal article", "published": "2025-03-07", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "387", "issue": "6738", "pages": "eadq0018"}, "abstract": "Manioc-also called cassava and yuca-is among the world's most important crops, originating in South America in the early Holocene. Domestication for its starchy roots involved a near-total shift from sexual to clonal propagation, and almost all manioc worldwide is now grown from stem cuttings. In this work, we analyze 573 new and published genomes, focusing on traditional varieties from the Americas and wild relatives from herbaria, to reveal the effects of this shift to clonality. We observe kinship over large distances, maintenance of high genetic diversity, intergenerational heterozygosity enrichment, and genomic mosaics of identity-by-descent haploblocks that connect all manioc worldwide. Interviews with Indigenous traditional farmers in the Brazilian Cerrado illuminate how traditional management strategies for sustaining, diversifying, and sharing the gene pool have shaped manioc diversity.", "doi": "10.1126/science.adq0018", "pmid": "40048537", "labels": {"Ancient DNA": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-03-10T08:05:58.525Z", "modified": "2025-11-21T18:14:52.315Z"}, {"entity": "publication", "iuid": "5d8481ffcfb0478cb49fb65a406e33f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d8481ffcfb0478cb49fb65a406e33f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d8481ffcfb0478cb49fb65a406e33f3"}}, "title": "Continuous map of early hematopoietic stem cell differentiation across human lifetime.", "authors": [{"family": "Komic", "given": "Hana", "initials": "H", "orcid": "0000-0001-5209-393X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e58a972d4a584a0886d0a64c7966cb2a.json"}}, {"family": "Schmachtel", "given": "Tessa", "initials": "T"}, {"family": "Simoes", "given": "Catia", "initials": "C"}, {"family": "K\u00fclp", "given": "Marius", "initials": "M", "orcid": "0000-0002-6594-8412", "researcher": {"href": "https://publications.scilifelab.se/researcher/673d10466a874f31a0be9fe2162d8311.json"}}, {"family": "Yu", "given": "Weijia", "initials": "W", "orcid": "0000-0001-8471-3048", "researcher": {"href": "https://publications.scilifelab.se/researcher/6663774d48534299b5bc56d45db1f817.json"}}, {"family": "Jolly", "given": "Adrien", "initials": "A", "orcid": "0000-0002-2609-5621", "researcher": {"href": "https://publications.scilifelab.se/researcher/bba8ced4f36d4dcd8035149d9c5fe32e.json"}}, {"family": "Nilsson", "given": "Malin S", "initials": "MS", "orcid": "0000-0002-0981-2617", "researcher": {"href": "https://publications.scilifelab.se/researcher/83fab5fb78c043e9affbbabd7a4d43e8.json"}}, {"family": "Gonzalez", "given": "Carmen", "initials": "C", "orcid": "0009-0001-3074-9229", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6ee53d6ea9447bbd8ec7e595e2fe89.json"}}, {"family": "Prosper", "given": "Felipe", "initials": "F", "orcid": "0000-0001-6115-8790", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa428789689a41f396098ee1edd3f8da.json"}}, {"family": "Bonig", "given": "Halvard", "initials": "H"}, {"family": "Paiva", "given": "Bruno", "initials": "B", "orcid": "0000-0003-1977-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf6f4d344b54bcab428014c4191cf27.json"}}, {"family": "Thor\u00e9n", "given": "Fredrik B", "initials": "FB", "orcid": "0000-0003-2167-7451", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e8a4846c6f44c0793f4cb5d73b66de6.json"}}, {"family": "Rieger", "given": "Michael A", "initials": "MA", "orcid": "0000-0002-4158-5872", "researcher": {"href": "https://publications.scilifelab.se/researcher/753728d6825443299274a4c5dfdacd75.json"}}], "type": "journal article", "published": "2025-03-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2287", "issn-l": "2041-1723"}, "abstract": "Uncovering early gene network changes of human hematopoietic stem cells (HSCs) leading to differentiation induction is of utmost importance for therapeutic manipulation. We employed single cell proteo-transcriptomic sequencing to FACS-enriched bone marrow hematopoietic stem and progenitor cells (HSPCs) from 15 healthy donors. Pseudotime analysis reveals four major differentiation trajectories, which remain consistent upon aging, with an early branching point into megakaryocyte-erythroid progenitors. However, young donors suggest a more productive differentiation from HSPCs to committed progenitors of all lineages. tradeSeq analysis depicts continuous changes in gene expression of HSPC-related genes (DLK1, ADGRG6), and provides a roadmap of gene expression at the earliest branching points. We identify CD273/PD-L2 to be highly expressed in a subfraction of immature multipotent HSPCs with enhanced quiescence. Functional experiments confirm the immune-modulatory function of CD273/PD-L2 on HSPCs in regulating T-cell activation and cytokine release. Here, we present a molecular map of early HSPC differentiation across human life.", "doi": "10.1038/s41467-025-57096-y", "pmid": "40055319", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11889232"}, {"db": "pii", "key": "10.1038/s41467-025-57096-y"}], "notes": [], "created": "2025-04-07T10:01:27.833Z", "modified": "2025-11-28T10:45:24.290Z"}, {"entity": "publication", "iuid": "53004388459e465ab3c59b47d352f040", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53004388459e465ab3c59b47d352f040.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53004388459e465ab3c59b47d352f040"}}, "title": "Systems-level immunomonitoring in children with solid tumors to enable precision medicine.", "authors": [{"family": "Chen", "given": "Qi", "initials": "Q", "orcid": "0000-0002-5864-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a.json"}}, {"family": "Zhao", "given": "Binbin", "initials": "B", "orcid": "0000-0002-5560-6750", "researcher": {"href": "https://publications.scilifelab.se/researcher/22329dc812fc4684acce02c18ae6fa18.json"}}, {"family": "Tan", "given": "Ziyang", "initials": "Z", "orcid": "0000-0001-5958-2584", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd87015d70fb4f71a9c5c40a22b84d4e.json"}}, {"family": "Hedberg", "given": "Gustav", "initials": "G"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Negrini", "given": "Erika", "initials": "E"}, {"family": "P\u00e1ez", "given": "Laura Pi\u00f1ero", "initials": "LP"}, {"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f9c2cfec48e4c4d8e9bc528a02d489b.json"}}, {"family": "James", "given": "Anna", "initials": "A"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mike\u0161", "given": "Jarom\u00edr", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Bernhardsson", "given": "Anna Karin", "initials": "AK"}, {"family": "Reitzner", "given": "Stefan Markus", "initials": "SM", "orcid": "0000-0003-0151-2780", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ca59c30b2e45459eb3638c65b452b3.json"}}, {"family": "von Walden", "given": "Ferdinand", "initials": "F"}, {"family": "O'Neill", "given": "Olivia", "initials": "O"}, {"family": "Barcenilla", "given": "Hugo", "initials": "H", "orcid": "0000-0002-7255-362X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0f0d6085e774a0fbdc1ad8d6eea3c23.json"}}, {"family": "Wang", "given": "Chunlin", "initials": "C"}, {"family": "Davis", "given": "Mark M", "initials": "MM"}, {"family": "Carlson", "given": "Lena-Maria", "initials": "LM"}, {"family": "Pal", "given": "Niklas", "initials": "N"}, {"family": "Blomgren", "given": "Klas", "initials": "K", "orcid": "0000-0002-0476-7271", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb3b554177d481ebc9d4aa0f3b1fbc4.json"}}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "Herold", "given": "Nikolas", "initials": "N", "orcid": "0000-0001-9468-4543", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2af6f17f76457680908c36693f2de5.json"}}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Kogner", "given": "Per", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications.scilifelab.se/researcher/e963274b921a4a2c8263f509334d4e22.json"}}, {"family": "Ljungblad", "given": "Linda", "initials": "L"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2025-03-06", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "188", "issue": "5", "pages": "1425-1440.e11", "issn-l": "0092-8674"}, "abstract": "Cancer is the leading cause of death from disease in children. Survival depends not only on surgery, cytostatic drugs, and radiation but also on systemic immune responses. Factors influencing these immune responses in children of different ages and tumor types are unknown. Novel immunotherapies can enhance anti-tumor immune responses, but few children have benefited, and markers of effective responses are lacking. Here, we present a systems-level analysis of immune responses in 191 children within a population-based cohort with diverse tumors and reveal that age and tumor type shape immune responses differently. Systemic inflammation and cytotoxic T cell responses correlate with tumor mutation rates and immune cell infiltration. Clonally expanded T cell responses are rarely detected in blood or tumors at diagnosis but are sometimes elicited during treatment. Expanded T cells are similarly regulated in children and adults with more immunogenic cancers. This research aims to facilitate the development of precision immunotherapies for children with cancer.", "doi": "10.1016/j.cell.2024.12.014", "pmid": "39837329", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Affinity Proteomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(24)01427-2"}], "notes": [], "created": "2025-01-30T10:50:10.864Z", "modified": "2025-11-28T10:42:05.786Z"}, {"entity": "publication", "iuid": "a2b369b29d704e429e7d6fc25ebcdee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b369b29d704e429e7d6fc25ebcdee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b369b29d704e429e7d6fc25ebcdee7"}}, "title": "Genetic Origins of the Kiritimati Population from Central-Eastern Micronesia.", "authors": [{"family": "Larena", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8799-7645", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d580f1f3e584c809f5f22d7355f154f.json"}}, {"family": "Chowdhury", "given": "Afifa Enam", "initials": "AE", "orcid": "0009-0000-8509-0276", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d3db9785b2f47fd93c5d4a23d8b2ced.json"}}, {"family": "Kels", "given": "Ma Junaliah Tuazon", "initials": "MJT", "orcid": "0000-0002-8730-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/083b0316d97f4be3a43126d01f9a173e.json"}}, {"family": "T\u00e4tte", "given": "Kai", "initials": "K", "orcid": "0000-0002-4753-8954", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44e6836c0144dac85f38f1054520e44.json"}}, {"family": "Metspalu", "given": "Mait", "initials": "M", "orcid": "0000-0003-3099-9161", "researcher": {"href": "https://publications.scilifelab.se/researcher/0557a5b67af948ee8e47473a8ee621d7.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Garcia-Bertrand", "given": "Ralph", "initials": "R", "orcid": "0000-0003-3011-9822", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e0cd4c1175c444c912c1a6db7f44665.json"}}, {"family": "Herrera", "given": "Rene J", "initials": "RJ", "orcid": "0000-0002-5119-4381", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cd8305c817e4adabe92faeebb02fe6e.json"}}], "type": "journal article", "published": "2025-03-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "17", "issue": "3", "issn-l": "1759-6653"}, "abstract": "The migration of Austronesian-speaking populations through Oceania has intrigued researchers for decades. The Kiribati islands, situated along the boundaries of Micronesia and Polynesia, provide a crucial link in this migration. We analyzed the genome-wide data of the Kiritimati population of Kiribati to uncover their genetic origins and connections with other Oceanian groups. Our study reveals that the Kiritimati population primarily exhibits Remote Oceanian-related ancestry associated with ancient Lapita and present-day Polynesian populations. In addition, our identity-by-descent analysis identifies populations from the coastal southern Philippines as their closest relatives in Island Southeast Asia. The genetic links between Kiritimati, ancient Lapita, and modern Polynesians underscore the shared ancestry and continuous gene flow across these regions. This genetic continuity and ongoing links are supported by linguistic and cultural evidence, illustrating a complex history of migration and admixture in Oceania.", "doi": "10.1093/gbe/evaf046", "pmid": "40065639", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11937891"}, {"db": "pii", "key": "8069057"}], "notes": [], "created": "2025-09-08T07:15:27.954Z", "modified": "2025-11-14T11:07:53.391Z"}, {"entity": "publication", "iuid": "9d6d948275cd4670b61bb0b58d65f8c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d6d948275cd4670b61bb0b58d65f8c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d6d948275cd4670b61bb0b58d65f8c9"}}, "title": "Fungal Pathogens Associated with Tomicus Species in European Forests: Regional Variations and Impacts on Forest Health.", "authors": [{"family": "Davydenko", "given": "Kateryna", "initials": "K", "orcid": "0000-0001-6077-8533", "researcher": {"href": "https://publications.scilifelab.se/researcher/898e62ced79a48108cbbfa50ce1f1657.json"}}, {"family": "Baturkin", "given": "Denys", "initials": "D", "orcid": "0000-0002-6061-9863", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7a64391d27e476ca0580f30f891cad3.json"}}, {"family": "Dyshko", "given": "Valentyna", "initials": "V"}, {"family": "Lazarevi\u0107", "given": "Jelena", "initials": "J", "orcid": "0000-0002-9460-7342", "researcher": {"href": "https://publications.scilifelab.se/researcher/68dde8362e4944388ee89bf5fa442512.json"}}, {"family": "Mar\u010diulynas", "given": "Adas", "initials": "A", "orcid": "0000-0003-3039-7945", "researcher": {"href": "https://publications.scilifelab.se/researcher/fee3bbac17cf4d7197e2ebaaa185ff4f.json"}}, {"family": "Elfstrand", "given": "Malin", "initials": "M", "orcid": "0000-0002-0214-5284", "researcher": {"href": "https://publications.scilifelab.se/researcher/2957dac173f4495a9245f0d8a9750606.json"}}, {"family": "Vasaitis", "given": "Rimvydas", "initials": "R", "orcid": "0000-0001-9349-4625", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ecd677a4b3f4f0ba4e2dafa6f0e8643.json"}}, {"family": "Menkis", "given": "Audrius", "initials": "A", "orcid": "0000-0002-6545-8907", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d4d16d281344b9f9cf2c3c27fb40f06.json"}}], "type": "journal article", "published": "2025-03-06", "journal": {"title": "Insects", "issn": "2075-4450", "volume": "16", "issue": "3", "issn-l": null}, "abstract": "Pinus species are extensively abundant in Europe and, as pioneer trees, prominently influence local ecology. However, pine forests in Lithuania, Montenegro, and Ukraine have been significantly damaged by pine bark beetles (Tomicus sp.), which are closely associated with ophiostomatoid and other pathogenic fungi. This study aimed to identify the diversity of ophiostomatoid and other fungi associated with Tomicus sp. in these three countries. Fungi were isolated from beetles and identified. High-throughput sequencing of ITS2 rDNA yielded 285,828 reads, of which 91,141 high-quality reads were retained, representing 561 fungal operational taxonomic units (OTUs). The most important groups of fungi included ophiostomatoids, yeasts, and plant pathogens. While the fungal communities associated with Tomicus spp. were influenced more by environmental factors than by beetle species, the presence of known pathogens such as Ophiostoma spp. indicates that Tomicus spp. could play a significant role in dispersing harmful fungi. Although the virulence of these fungi may vary, their association with potentially pathogenic species suggests that Tomicus spp. may contribute to forest health decline, especially if environmental conditions or host susceptibility change.", "doi": "10.3390/insects16030277", "pmid": "40266754", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11943276"}, {"db": "pii", "key": "insects16030277"}], "notes": [], "created": "2025-08-19T13:55:28.251Z", "modified": "2025-08-19T13:55:28.582Z"}, {"entity": "publication", "iuid": "59ebc9f2f08d46dcafe5fe8d76317dbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59ebc9f2f08d46dcafe5fe8d76317dbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59ebc9f2f08d46dcafe5fe8d76317dbf"}}, "title": "Genomic characterization of the HER2-enriched intrinsic molecular subtype in primary ER-positive HER2-negative breast cancer.", "authors": [{"family": "Hohmann", "given": "Lennart", "initials": "L", "orcid": "0000-0002-0281-7140", "researcher": {"href": "https://publications.scilifelab.se/researcher/b605a3b893a24a238b5bb6eddd27b672.json"}}, {"family": "Sigurjonsdottir", "given": "Kristin", "initials": "K"}, {"family": "Campos", "given": "Ana Bosch", "initials": "AB"}, {"family": "Nacer", "given": "Deborah F", "initials": "DF", "orcid": "0000-0002-7117-1371", "researcher": {"href": "https://publications.scilifelab.se/researcher/e484e25cfdf64d27842357355409dbfc.json"}}, {"family": "Veerla", "given": "Srinivas", "initials": "S", "orcid": "0000-0001-7328-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/c203a0b3112f4f499ccc79db3e47b303.json"}}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Reddy", "given": "Poojaswini Thimmaraya", "initials": "PT", "orcid": "0009-0009-7743-4986", "researcher": {"href": "https://publications.scilifelab.se/researcher/868440eeaf364b28aa186eb24b37e2d8.json"}}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J", "orcid": "0000-0002-8466-9179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b8605b9a7c74b20986146f020cf4b8f.json"}}, {"family": "Nordborg", "given": "Nicklas", "initials": "N"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fa1d04cb640858fe3534d04cd04d1.json"}}, {"family": "Memari", "given": "Yasin", "initials": "Y"}, {"family": "Black", "given": "Daniella", "initials": "D"}, {"family": "Bowden", "given": "Ramsay", "initials": "R", "orcid": "0000-0003-1138-4452", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b6effa9663145dabd83b3ced199385c.json"}}, {"family": "Davies", "given": "Helen R", "initials": "HR", "orcid": "0000-0001-6381-3664", "researcher": {"href": "https://publications.scilifelab.se/researcher/e02b6738c9e140858456e24cef5d6b42.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications.scilifelab.se/researcher/127501d4e0854d14a4120acee9042bb7.json"}}, {"family": "Nik-Zainal", "given": "Serena", "initials": "S", "orcid": "0000-0001-5054-1727", "researcher": {"href": "https://publications.scilifelab.se/researcher/af746cf472144e1699ee12fa08921c1d.json"}}, {"family": "Staaf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5254-5115", "researcher": {"href": "https://publications.scilifelab.se/researcher/07acbd7f211e4809a8195e2ccf5faf57.json"}}], "type": "journal article", "published": "2025-03-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2208", "issn-l": "2041-1723"}, "abstract": "ER-positive/HER2-negative (ERpHER2n) breast cancer classified as PAM50 HER2-enriched (ERpHER2n-HER2E) represents a small high-risk patient subgroup. In this study, we investigate genomic, transcriptomic, and clinical features of ERpHER2n-HER2E breast tumors using two primary ERpHER2n cohorts comprising a total of 5640 patients. We show that ERpHER2n-HER2E tumors exhibit aggressive clinical features and poorer clinical outcomes compared to Luminal A and Luminal B tumors. Furthermore, ERpHER2n-HER2E breast cancer does not consist of misclassified or HER2-low cases, has little impact of ERBB2, is highly proliferative and less ER dependent than other luminal subtypes. It is not an obvious biological entity but is nevertheless associated with potentially targetable molecular features, notably a high immune response and high FGFR4 expression. Strikingly, molecular features that define the HER2E subtype in luminal disease are also consistent in HER2-positive disease, including an epigenetic mechanism for high FGFR4 expression in breast cancer.", "doi": "10.1038/s41467-025-57419-z", "pmid": "40044693", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11882987"}, {"db": "pii", "key": "10.1038/s41467-025-57419-z"}], "notes": [], "created": "2025-09-08T07:15:25.268Z", "modified": "2025-09-08T07:15:25.630Z"}, {"entity": "publication", "iuid": "7b6d68bef27c42ccbf33580e86f46cdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b6d68bef27c42ccbf33580e86f46cdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b6d68bef27c42ccbf33580e86f46cdf"}}, "title": "Antisense-mediated regulation of exon usage in the elastic spring region of Titin modulates sarcomere function.", "authors": [{"family": "Celik", "given": "Selvi", "initials": "S", "orcid": "0000-0001-7032-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da057ac725d4fb0bdbaddbc06a8ea64.json"}}, {"family": "Hyrefelt", "given": "Ludvig", "initials": "L"}, {"family": "Czuba", "given": "Tomasz", "initials": "T"}, {"family": "Li", "given": "Yuan", "initials": "Y"}, {"family": "Assis", "given": "Juliana", "initials": "J", "orcid": "0000-0001-5995-8684", "researcher": {"href": "https://publications.scilifelab.se/researcher/09d17153a55c4eeaba108c7ecfb8fa3a.json"}}, {"family": "Martinez", "given": "Julia", "initials": "J"}, {"family": "Johansson", "given": "Markus", "initials": "M"}, {"family": "Andr\u00e9", "given": "Oscar", "initials": "O"}, {"family": "Synnergren", "given": "Jane", "initials": "J"}, {"family": "Sandstedt", "given": "Joakim", "initials": "J", "orcid": "0000-0002-6458-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/070e186990424c4b83225eb93efc2a66.json"}}, {"family": "Nordenfelt", "given": "Pontus", "initials": "P", "orcid": "0000-0002-9481-9951", "researcher": {"href": "https://publications.scilifelab.se/researcher/7aa3418ab23a4ec48c037d6d6ddea5b5.json"}}, {"family": "Vukusic", "given": "Kristina", "initials": "K", "orcid": "0000-0002-4243-0565", "researcher": {"href": "https://publications.scilifelab.se/researcher/342e325123674e74963ae7c4dd307874.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG", "orcid": "0000-0001-6285-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e50df6bb7f4194a52546dbd5652e84.json"}}, {"family": "Gidl\u00f6f", "given": "Olof", "initials": "O", "orcid": "0000-0002-7402-3139", "researcher": {"href": "https://publications.scilifelab.se/researcher/83f5453e507041b995e0d69a74540c24.json"}}], "type": "journal article", "published": "2025-03-05", "journal": {"title": "Cardiovasc. Res.", "issn": "1755-3245", "issn-l": "0008-6363"}, "abstract": "Alternative splicing of Titin (TTN) I-band exons produce protein isoforms with variable size and elasticity, but the mechanisms whereby TTN splice factors regulate exon usage and thereby determining cardiomyocyte passive stiffness and diastolic function, is not well understood. Non-coding RNA transcripts from the antisense strand of protein-coding genes have been shown to regulate alternative splicing of the sense gene. The TTN gene locus harbours >80 natural antisense transcripts (NATs) with unknown function in the human heart. The aim of this study was to determine if TTN antisense transcripts play a role in alternative splicing of TTN.\n\nRNA-sequencing and RNA in situ hybridization (ISH) of cardiac tissue from heart failure patients (HF), unused donor hearts and human iPS-derived cardiomyocytes (iPS-CMs) were used to determine the expression and localization of TTN NATs. Live cell imaging was used to analyze the effect of NATs on sarcomere properties. RNA ISH, immunofluorescence was performed in iPS-CMs to study the interaction between NATs, TTN mRNA and splice factor protein RBM20.We found that TTN-AS1-276 was the predominant TTN NAT in the human heart and that it was upregulated in HF. Knock down of TTN-AS1-276 in human iPS-CMs resulted in decreased interaction between the splicing factor RBM20 and TTN pre-mRNA, decreased TTN I-band exon skipping, and markedly lower expression of the less compliant TTN isoform N2B. The effect on TTN exon usage was independent of sense-antisense exon overlap and polymerase II elongation rate. Furthermore, knockdown resulted in longer sarcomeres with preserved alignment, improved fractional shortening and relaxation times.\n\nWe demonstrate a role for TTN-AS1-276 in facilitating alternative splicing of TTN and regulating sarcomere properties. This transcript could constitute a target for improving cardiac passive stiffness and diastolic function in conditions such as heart failure with preserved ejection fraction.", "doi": "10.1093/cvr/cvaf037", "pmid": "40042822", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "8052712"}], "notes": [], "created": "2025-03-31T07:47:55.441Z", "modified": "2025-04-03T08:26:49.969Z"}, {"entity": "publication", "iuid": "1372078a962f47209ae67af8d5b0982f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1372078a962f47209ae67af8d5b0982f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1372078a962f47209ae67af8d5b0982f"}}, "title": "PopGLen-a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods.", "authors": [{"family": "Nolen", "given": "Zachary J", "initials": "ZJ", "orcid": "0000-0001-8146-8016", "researcher": {"href": "https://publications.scilifelab.se/researcher/a44940fda05d493e8297bfe1220458f3.json"}}], "type": "journal article", "published": "2025-03-04", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "41", "issue": "3", "issn-l": "1367-4803"}, "abstract": "PopGLen is a Snakemake workflow for performing population genomic analyses within a genotype-likelihood framework, integrating steps for raw sequence processing of both historical and modern DNA, quality control, multiple filtering schemes, and population genomic analysis. Currently, the population genomic analyses included allow for estimating linkage disequilibrium, kinship, genetic diversity, genetic differentiation, population structure, inbreeding, and allele frequencies. Through Snakemake, it is highly scalable, and all steps of the workflow are automated, with results compiled into an HTML report. PopGLen provides an efficient, customizable, and reproducible option for analyzing population genomic datasets across a wide variety of organisms.\n\nPopGLen is available under GPLv3 with code, documentation, and a tutorial at https://github.com/zjnolen/PopGLen. An example HTML report using the tutorial dataset is included in the Supplementary Material.", "doi": "10.1093/bioinformatics/btaf105", "pmid": "40067089", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11932725"}, {"db": "pii", "key": "8069456"}], "notes": [], "created": "2025-10-30T13:24:23.421Z", "modified": "2025-11-28T10:48:39.840Z"}, {"entity": "publication", "iuid": "914ba3f9eb6f4bed942f6cabc548b913", "links": {"self": {"href": "https://publications.scilifelab.se/publication/914ba3f9eb6f4bed942f6cabc548b913.json"}, "display": {"href": "https://publications.scilifelab.se/publication/914ba3f9eb6f4bed942f6cabc548b913"}}, "title": "Unraveling the role of early coeliac disease diagnosis in the risk of developing immune-mediated renal diseases.", "authors": [{"family": "De Luca", "given": "Francesco", "initials": "F"}, {"family": "Nilsson", "given": "Staffan", "initials": "S"}, {"family": "Truv\u00e9", "given": "Katarina", "initials": "K", "orcid": "0000-0002-2449-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c36d2ff5111435aa23416cdfc359b2d.json"}}, {"family": "Kuhn", "given": "Hans-Georg", "initials": "HG"}, {"family": "Ejesk\u00e4r", "given": "Katarina", "initials": "K", "orcid": "0000-0001-8962-0860", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c79e724c1954cf39f5511f7a6021513.json"}}, {"family": "Haraldsson", "given": "B\u00f6rje", "initials": "B"}, {"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-0504-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcf3474dc7054c598cbe3a195deb8a1b.json"}}], "type": "journal article", "published": "2025-03-03", "journal": {"title": "BMC Gastroenterol", "issn": "1471-230X", "volume": "25", "issue": "1", "pages": "125", "issn-l": null}, "abstract": "coeliac disease (CD) is an inflammatory condition of the small intestine caused by immunological intolerance towards dietary gluten. Associations between CD and other autoimmune disorders have been extensively reported. However, the risk in CD patients of developing immune-mediated renal diseases (IMRDs) as a function of the duration of exposure to gluten remains uncharacterized.\n\nwe used data from the Swedish national patient register to retrospectively construct two subcohorts of CD patients by either years before or after CD diagnosis, matched by sex and age to reference individuals (ratio 1:6). Adopting cox regressions, we assessed the risk in CD to develop IMRDs.\n\nwe found that unrecognized CD patients had a higher risk to develop the majority of the IMRDs here investigated compared with matched reference individuals. Following a CD diagnosis, the risk was reduced in eight of the twelve IMRDs. Furthermore, if patients were diagnosed with CD earlier in childhood they showed less or no increased risk to develop IMRDs compared with reference individuals. CD patients diagnosed by the age of 15 had an overall 12% increased risk of developing any IMRD, (HR: 1.12; CI = 1.02, 1.24; p < 0.02), as those with a CD diagnosis between 16 and 30 years of age had a 60% increased risk of developing IMRD (HR: 1.61; CI = 1.36, 1.91; p < 0.001).\n\nOur data show that individuals diagnosed with CD at an earlier age have a lower risk of developing immune-mediated kidney conditions.", "doi": "10.1186/s12876-025-03705-5", "pmid": "40025438", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11874109"}, {"db": "pii", "key": "10.1186/s12876-025-03705-5"}], "notes": [], "created": "2025-07-08T13:52:51.209Z", "modified": "2025-11-04T11:53:51.029Z"}, {"entity": "publication", "iuid": "838b09dc81044f33a0064562140064a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/838b09dc81044f33a0064562140064a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/838b09dc81044f33a0064562140064a7"}}, "title": "Influence of apolipoprotein E genotype on the proteomic profile in cerebral microdialysis after human severe traumatic brain injury: a prospective observational study.", "authors": [{"family": "Lindblad", "given": "Caroline", "initials": "C", "orcid": "0000-0003-4952-8597", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac6cf98ab3694a248df6ac1a46e36e94.json"}}, {"family": "Klang", "given": "Andrea", "initials": "A", "orcid": "0000-0002-5975-0960", "researcher": {"href": "https://publications.scilifelab.se/researcher/a77785bb6ab64971a57eb6f717fef623.json"}}, {"family": "Bark", "given": "David", "initials": "D"}, {"family": "Bellotti", "given": "Cristina", "initials": "C", "orcid": "0000-0002-3999-2807", "researcher": {"href": "https://publications.scilifelab.se/researcher/37014ab6032b4daf9a1397ba88438169.json"}}, {"family": "H\u00e5nell", "given": "Anders", "initials": "A"}, {"family": "Enblad", "given": "Per", "initials": "P"}, {"family": "Lew\u00e9n", "given": "Anders", "initials": "A"}, {"family": "Rostami", "given": "Elham", "initials": "E", "orcid": "0000-0003-1218-6247", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4e5d32d3023425c9940f1eb1ed876b4.json"}}], "type": "journal article", "published": "2025-03-03", "journal": {"title": "Brain Commun", "issn": "2632-1297", "volume": "7", "issue": "2", "pages": "fcaf096", "issn-l": null}, "abstract": "Patient-tailored treatment, also known as precision-medicine, has been emphasized as a prioritized area in traumatic brain injury research. In fact, pre-injury patient genetic factors alone account for almost 26% of outcome prediction variance following traumatic brain injury. Among implicated genetic variants single-nucleotide polymorphism in apolipoprotein E has been linked to worse prognosis following traumatic brain injury, but the underlying mechanism is still unknown. We hypothesized that apolipoprotein E genotype would affect the levels of pathophysiology-driving structural, or inflammatory, proteins in cerebral microdialysate following severe traumatic brain injury. We conducted a prospective observational study of patients with severe traumatic brain injury treated with invasive neuromonitoring including cerebral microdialysis at Uppsala University Hospital. All patients were characterized regarding apolipoprotein E genotype. Utilizing fluid- and plate-based antibody arrays, we quantified 101 proteins (of which 89 were eligible for analysis) in cerebral microdialysate at 1 day and 3 days following trauma. Statistical analysis included clustering techniques, as well as uni- and multi-variate linear mixed modelling. In total, 26 patients were included, and all relevant genotypes of apolipoprotein E were represented in the data. Among all proteins tested, 41 proteins showed a time-dependent expression level. There was a weak clustering tendency in the data, and not primarily to genotype, either depicted through t-distributed stochastic neighbour embedding or hierarchical clustering. Using linear mixed models, two proteins [the inflammatory protein CD300 molecule like family member f (CLM-1) and the neurotrophic protein glial-derived neurotrophic factor family receptor \u03b11] were found to have protein levels concomitantly dependent upon time and genotype, albeit this effect was not seen following multiple testing corrections. Apart from amyloid-\u03b2-40 (A\u03b2) and Microtubule-associated protein tau, neither A\u03b2 peptide levels nor the A\u03b242/40 ratio were seen related to time from trauma or apolipoprotein E genotype. This is the first study in clinical severe traumatic brain injury examining the influence of apolipoprotein E genotype on microdialysate protein expression. Protein levels in cerebral microdialysate following trauma are seen to be strongly dependent on time from trauma, corroborating previous work on protein expression longitudinally following traumatic brain injury. We also identified protein expression level alterations dependent on apolipoprotein E genotype, which might indicate that apolipoprotein E affects ongoing pathophysiology in the injured brain at the proteomic level.", "doi": "10.1093/braincomms/fcaf096", "pmid": "40109561", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11920868"}, {"db": "pii", "key": "fcaf096"}], "notes": [], "created": "2025-11-25T19:23:10.793Z", "modified": "2025-11-25T19:23:11.026Z"}, {"entity": "publication", "iuid": "95cbfa77bb344c08bf41cb612bea42f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95cbfa77bb344c08bf41cb612bea42f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95cbfa77bb344c08bf41cb612bea42f1"}}, "title": "Genome-wide association study and Mendelian randomization analyses reveal insights into bladder cancer etiology.", "authors": [{"family": "Larsson", "given": "Susanna C", "initials": "SC", "orcid": "0000-0003-0118-0341", "researcher": {"href": "https://publications.scilifelab.se/researcher/afe4b220a6c547e6aac27a10c5024a23.json"}}, {"family": "Chen", "given": "Jie", "initials": "J", "orcid": "0000-0002-4029-4192", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dbfd7fc4a2d4fe38a244f78cf48dce2.json"}}, {"family": "Ruan", "given": "Xixian", "initials": "X", "orcid": "0000-0002-4937-9168", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d92ee22a384cb0bc5a7bcdccb83d0e.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0001-6880-2577", "researcher": {"href": "https://publications.scilifelab.se/researcher/360d5c60409d415f8c6957d9e3373cd0.json"}}, {"family": "Yuan", "given": "Shuai", "initials": "S", "orcid": "0000-0001-5055-5627", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a51e0853b654cdcb2d42ebc5d73b52a.json"}}], "type": "journal article", "published": "2025-03-03", "journal": {"title": "JNCI Cancer Spectr", "issn": "2515-5091", "volume": "9", "issue": "2", "issn-l": null}, "abstract": "The causes of bladder cancer are not completely understood. Our objective was to identify blood proteins and modifiable causal risk factors for bladder cancer by combining genome-wide association study (GWAS) and Mendelian randomization (MR) analyses.\n\nWe first performed a GWAS meta-analysis of 6984 bladder cancer case patients and 708 432 control individuals from 3 European databases. Next, we conducted 2-sample MR and colocalization analyses using data from the present GWAS and published GWAS meta-analyses on plasma proteins and modifiable factors.\n\nGenome-wide association study meta-analysis uncovered 17 bladder cancer susceptibility loci, of which 3 loci were novel. Genes were enriched in pathways related to the metabolic and catabolic processes of xenobiotics and cellular detoxification. Proteome-wide MR analysis based on cis-acting genetic variants revealed that higher plasma levels of glutathione S-transferases were strongly associated with a reduced risk of bladder cancer. There is strong evidence of colocalization between GSTM1 and bladder cancer. Finally, multivariable MR analyses of suspected risk factors for bladder cancer revealed independent causal associations between smoking and adiposity, particularly abdominal obesity, and risk of bladder cancer.\n\nFindings from this large-scale GWAS and multivariable MR analyses highlight the key role of detoxification processes, particularly glutathione S-transferase 1, as well as smoking and abdominal obesity in bladder cancer etiology.", "doi": "10.1093/jncics/pkaf014", "pmid": "39898788", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11950924"}, {"db": "pii", "key": "7997273"}], "notes": [], "created": "2025-11-28T10:49:53.296Z", "modified": "2025-11-28T10:49:53.391Z"}, {"entity": "publication", "iuid": "1489ac4c0e85434b87a47f5d5cf048d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1489ac4c0e85434b87a47f5d5cf048d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1489ac4c0e85434b87a47f5d5cf048d5"}}, "title": "Decreased levels and function of dendritic cells in blood and airways predict COVID-19 severity.", "authors": [{"family": "\u00d6sterberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Falck-Jones", "given": "Sara", "initials": "S"}, {"family": "Vangeti", "given": "Sindhu", "initials": "S"}, {"family": "\u00c5hlberg", "given": "Eric", "initials": "E"}, {"family": "Yu", "given": "Meng", "initials": "M"}, {"family": "Granja", "given": "Diana", "initials": "D"}, {"family": "Snik", "given": "Marijn E", "initials": "ME"}, {"family": "Falck-Jones", "given": "Ryan", "initials": "R"}, {"family": "Barros", "given": "Guilherme Wf", "initials": "GW"}, {"family": "Charles", "given": "Afandi", "initials": "A"}, {"family": "Lepzien", "given": "Rico", "initials": "R"}, {"family": "Johansson", "given": "Niclas", "initials": "N"}, {"family": "Holmes", "given": "Tyson H", "initials": "TH"}, {"family": "Maecker", "given": "Holden", "initials": "H"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Bell", "given": "Max", "initials": "M"}, {"family": "F\u00e4rnert", "given": "Anna", "initials": "A"}, {"family": "Smed-S\u00f6rensen", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-03-03", "journal": {"title": "Clin Transl Immunology", "issn": "2050-0068", "volume": "14", "issue": "3", "pages": "e70026", "issn-l": null}, "abstract": "Monocytes and dendritic cells (DCs) are essential players in the immune response to infections, involved in shaping innate and adaptive immunity. However, a complete understanding of their specific roles in respiratory infections, including SARS-CoV-2, remains elusive.\n\nTo investigate the dynamics of monocytes and DCs in blood as well as the upper and lower airways, we sampled 147 patients with varying degree of COVID-19 severity longitudinally during the spring of 2020.\n\nUsing flow cytometry, proteomics and in vitro TLR stimulation, we found differences in the distribution and function of monocytes and DCs in patients compared with controls, and importantly, reduced levels of DCs in both blood and airways. In fact, lower frequencies of cDC2s (Lin- HLA-DR+ CD1c+) early after symptom onset predicted subsequent severe disease, and depletion of DC subsets lasted longer in patients with more severe disease. In contrast, severe COVID-19 was associated with increased frequencies of activated monocytes in the lower, but not the upper, airways. Proteomic analysis showed that monocyte and DC-related cytokines in plasma and airways associated with disease severity. During convalescence, cell frequencies and responses to TLR ligands normalised in blood, except for persistently low plasmacytoid DCs.\n\nOur study reveals a distinct pattern of recruitment of monocytes but not DCs to the airways during severe COVID-19. Instead, decreased levels of DCs in both blood and airways were found, possibly contributing to more severe COVID-19. The connection between low blood DCs early in disease course and more severe outcomes provides insight into COVID-19 immunopathology, with possible therapeutic implications.", "doi": "10.1002/cti2.70026", "pmid": "40041475", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11873541"}, {"db": "pii", "key": "CTI270026"}], "notes": [], "created": "2025-03-31T07:54:01.461Z", "modified": "2025-03-31T07:54:01.467Z"}, {"entity": "publication", "iuid": "7da6de55f455454581bf8a799b9e198a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7da6de55f455454581bf8a799b9e198a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7da6de55f455454581bf8a799b9e198a"}}, "title": "Applying machine learning to high-dimensional proteomics datasets for the identification of Alzheimer's disease biomarkers.", "authors": [{"family": "Ivarsson Orrelid", "given": "Christoffer", "initials": "C"}, {"family": "Rosberg", "given": "Oscar", "initials": "O"}, {"family": "Weiner", "given": "Sophia", "initials": "S"}, {"family": "Johansson", "given": "Fredrik D", "initials": "FD"}, {"family": "Gobom", "given": "Johan", "initials": "J"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Mwai", "given": "Newton", "initials": "N"}, {"family": "Stempfle", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2025-03-03", "journal": {"title": "Fluids Barriers CNS", "issn": "2045-8118", "volume": "22", "issue": "1", "pages": "23", "issn-l": null}, "abstract": "This study explores the application of machine learning to high-dimensional proteomics datasets for identifying Alzheimer's disease (AD) biomarkers. AD, a neurodegenerative disorder affecting millions worldwide, necessitates early and accurate diagnosis for effective management.\n\nWe leverage Tandem Mass Tag (TMT) proteomics data from the cerebrospinal fluid (CSF) samples from the frontal cortex of patients with idiopathic normal pressure hydrocephalus (iNPH), a condition often comorbid with AD, with rare access to both lumbar and ventricular samples. Our methodology includes extensive data preprocessing to address batch effects and missing values, followed by the use of the Synthetic Minority Over-sampling Technique (SMOTE) for data augmentation to overcome the small sample size. We apply linear, and non-linear machine learning models, and ensemble methods, to compare iNPH patients with and without biomarker evidence of AD pathology ( or A \u03b2 - T - ) in a classification task. A \u03b2 + T +\n\nWe present a machine learning workflow for working with high-dimensional TMT proteomics data that addresses their inherent data characteristics. Our results demonstrate that batch effect correction has no or minor impact on the models' performance and robust feature selection is critical for model stability and performance, especially in the high-dimensional proteomics data setting for AD diagnostics. The results further indicated that removing features with missing values produced stronger models than imputing them, and the batch effect had minimal impact on the models Our best-performing disease-progression detection model, a random forest, achieves an AUC of 0.84 (\u00b1 0.03).\n\nWe identify several novel protein biomarkers candidates, such as FABP3 and GOT1, with potential diagnostic value for AD pathology detection, suggesting the necessity of different biomarkers for AD diagnoses for patients with iNPH, and considering different biomarkers for ventricular and lumbar CSF samples. This work underscores the importance of a meticulous machine learning process in enhancing biomarker discovery. Our study also provides insights in translating biomarkers from other central nervous system diseases like iNPH, and both ventricular and lumbar CSF samples for biomarker discovery, providing a foundation for future research and clinical applications.", "doi": "10.1186/s12987-025-00634-z", "pmid": "40033432", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11874791"}, {"db": "pii", "key": "10.1186/s12987-025-00634-z"}], "notes": [], "created": "2025-11-28T10:53:00.149Z", "modified": "2025-11-28T10:53:00.157Z"}, {"entity": "publication", "iuid": "b4d27c0d48ac4143a49b87b646b8f03d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4d27c0d48ac4143a49b87b646b8f03d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4d27c0d48ac4143a49b87b646b8f03d"}}, "title": "Indole-3-propionic acid promotes hepatic stellate cells inactivation.", "authors": [{"family": "Ilha", "given": "Mariana", "initials": "M"}, {"family": "Sehgal", "given": "Ratika", "initials": "R"}, {"family": "Matilainen", "given": "Johanna", "initials": "J"}, {"family": "Rilla", "given": "Kirsi", "initials": "K"}, {"family": "Kaminska", "given": "Dorota", "initials": "D"}, {"family": "Gandhi", "given": "Shrey", "initials": "S"}, {"family": "M\u00e4nnist\u00f6", "given": "Ville", "initials": "V"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}, {"family": "Romeo", "given": "Stefano", "initials": "S"}, {"family": "Pajukanta", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Pirinen", "given": "Eija", "initials": "E"}, {"family": "Virtanen", "given": "Kirsi A", "initials": "KA"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Vaittinen", "given": "Maija", "initials": "M", "orcid": "0000-0002-7423-557X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4df504651a54e8bae68022d8ce7f89a.json"}}, {"family": "Pihlajam\u00e4ki", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2025-03-01", "journal": {"title": "J Transl Med", "issn": "1479-5876", "volume": "23", "issue": "1", "pages": "253", "issn-l": "1479-5876"}, "abstract": "We have previously reported that the serum levels of gut-derived tryptophan metabolite indole-3-propionic acid (IPA) are lower in individuals with liver fibrosis. Now, we explored the transcriptome and DNA methylome associated with serum IPA levels in human liver from obese individuals together with IPA effects on shifting the hepatic stellate cell (HSC) phenotype to inactivation in vitro.\n\nA total of 116 obese individuals without type 2 diabetes (T2D) (age 46.8 \u00b1 9.3 years; BMI: 42.7 \u00b1 5.0 kg/m2) from the Kuopio OBesity Surgery (KOBS) study undergoing bariatric surgery were included. Circulating IPA levels were measured using LC-MS, liver transcriptomics with total RNA-sequencing and DNA methylation with Infinium HumanMethylation450 BeadChip. Human hepatic stellate cells (LX-2) where used for in vitro experiments.\n\nSerum IPA levels were associated with the expression of liver genes enriched for apoptosis, mitophagy and longevity pathways in the liver. AKT serine/threonine kinase 1 (AKT1) was the shared and topmost interactive gene from the liver transcript and DNA methylation profile. IPA treatment induced apoptosis, reduced mitochondrial respiration as well as modified cell morphology, and mitochondrial dynamics by modulating the expression of genes known to regulate fibrosis, apoptosis, and survival in LX-2 cells.\n\nIn conclusion, these data support that IPA has a plausible therapeutic effect and may induce apoptosis and the HSC phenotype towards the inactivation state, extending the possibilities to suppress hepatic fibrogenesis by interfering with HSC activation and mitochondrial metabolism.", "doi": "10.1186/s12967-025-06266-z", "pmid": "40025530", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11871697"}, {"db": "pii", "key": "10.1186/s12967-025-06266-z"}], "notes": [], "created": "2025-10-30T13:30:46.601Z", "modified": "2025-10-30T13:30:46.745Z"}, {"entity": "publication", "iuid": "1ed57cee75824ec0a43c626f80dac7e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ed57cee75824ec0a43c626f80dac7e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ed57cee75824ec0a43c626f80dac7e7"}}, "title": "Blood-Based Epigenetic Biomarkers Associated With Incident Chronic Kidney Disease in Individuals With Type 2 Diabetes.", "authors": [{"family": "Marchiori", "given": "Marian", "initials": "M"}, {"family": "Maguolo", "given": "Alice", "initials": "A", "orcid": "0000-0002-8921-2012", "researcher": {"href": "https://publications.scilifelab.se/researcher/cac232a66c6745f7b74d2b52ec0d007a.json"}}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Maziarz", "given": "Marlena", "initials": "M"}, {"family": "Martinell", "given": "Mats", "initials": "M"}, {"family": "Gomez", "given": "Maria F", "initials": "MF"}, {"family": "Ahlqvist", "given": "Emma", "initials": "E"}, {"family": "Garc\u00eda-Calz\u00f3n", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1249-4795", "researcher": {"href": "https://publications.scilifelab.se/researcher/76aa68910e0f427e853c8e7db7b17332.json"}}, {"family": "Ling", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-0587-7154", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7c1ea934034c4db99f31a5a9b04691.json"}}], "type": "journal article", "published": "2025-03-01", "journal": {"title": "Diabetes", "issn": "1939-327X", "volume": "74", "issue": "3", "pages": "439-450", "issn-l": "0012-1797"}, "abstract": "There is an increasing need for new biomarkers to improve prediction of chronic kidney disease (CKD) in individuals with type 2 diabetes (T2D). We aimed to identify blood-based epigenetic biomarkers associated with incident CKD and develop a methylation risk score (MRS) predicting CKD in individuals with newly diagnosed T2D. DNA methylation was analyzed epigenome wide in blood from 487 individuals with newly diagnosed T2D, of whom 88 developed CKD during an 11.5-year follow-up. Weighted Cox regression was used to associate methylation with incident CKD. Weighted logistic models and cross-validation (k = 5) were performed to test whether the MRS could predict CKD. Methylation at 37 sites was associated with CKD development based on a false discovery rate of <5% and absolute methylation differences of \u22655% between individuals with incident CKD and those free of CKD during follow-up. Notably, 15 genes annotated to these sites, e.g., TGFBI, SHISA3, and SLC43A2 (encoding LAT4), have been linked to CKD or related risk factors, including blood pressure, BMI, and estimated glomerular filtration rate. Using an MRS including 37 sites and cross-validation for prediction of CKD, we generated receiver operating characteristic (ROC) curves with an area under the curve (AUC) of 0.82 for the MRS and AUC of 0.87 for the combination of MRS and clinical factors. Importantly, ROC curves including the MRS had significantly better AUCs versus the one only including clinical factors (AUC = 0.72). The combined epigenetic biomarker had high accuracy in identifying individuals free of future CKD (negative predictive value of 94.6%). We discovered a high-performance epigenetic biomarker for predicting CKD, encouraging its potential role in precision medicine, risk stratification, and targeted prevention in T2D.\n\nThere is an increasing need for new biomarkers to improve the prediction and prevention of chronic kidney disease (CKD) in individuals with type 2 diabetes (T2D), a leading cause of morbidity and mortality in this population. We investigated whether new blood-based epigenetic biomarkers predict incident CKD in individuals with newly diagnosed T2D. We discovered a novel blood-based epigenetic biomarker, composed of a combination of a methylation risk score and clinical factors, capable of predicting CKD during an 11.5-year follow-up (area under the curve of 0.87, negative predictive value of 94.6%) in individuals with newly diagnosed T2D. The epigenetic biomarker could provide a valuable tool for early risk stratification and prevention of CKD in individuals with newly diagnosed T2D, supporting its future use for precision medicine.", "doi": "10.2337/db24-0483", "pmid": "39715581", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11842608"}, {"db": "pii", "key": "157641"}], "notes": [], "created": "2025-10-30T13:38:03.879Z", "modified": "2025-10-30T13:38:04.234Z"}, {"entity": "publication", "iuid": "86224b9927024f2dbe91734530bc518a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86224b9927024f2dbe91734530bc518a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86224b9927024f2dbe91734530bc518a"}}, "title": "Time-Resolved Hierarchical Modeling Highlights Metabolites Influencing Productivity and Cell Death in Chinese Hamster Ovary Cells.", "authors": [{"family": "Eriksson", "given": "Andreas", "initials": "A", "orcid": "0009-0009-7323-192X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9ea928d916c48a68e0e996bf3dc76d7.json"}}, {"family": "Richelle", "given": "Anne", "initials": "A"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Scholze", "given": "Steffi", "initials": "S"}, {"family": "Pijeaud", "given": "Shanti", "initials": "S"}, {"family": "Antti", "given": "Henrik", "initials": "H"}, {"family": "Zehe", "given": "Christoph", "initials": "C"}, {"family": "Surowiec", "given": "Izabella", "initials": "I", "orcid": "0009-0002-3709-2458", "researcher": {"href": "https://publications.scilifelab.se/researcher/22e6f70588334990bb3eddc2c48b8d9c.json"}}, {"family": "Jonsson", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0001-8357-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd630ff903db4a61af5bf65a46c9c098.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Biotechnol J", "issn": "1860-7314", "volume": "20", "issue": "3", "pages": "e202400624", "issn-l": "1860-6768"}, "abstract": "Biopharmaceuticals are medical compounds derived from biological sources and are often manufactured by living cells, primarily Chinese hamster ovary (CHO) cells. CHO cells display variation among cell clones, leading to growth and productivity differences that influence the product's quantity and quality. The biological and environmental factors behind these differences are not fully understood. To identify metabolites with a consistent relationship to productivity or cell death over time, we analyzed the extracellular metabolome of 11 CHO clones with different growth and productivity characteristics over 14 days. However, in bioreactor processes, metabolic profiles and process variables are both strongly time-dependent, confounding the metabolite-process variable relationship. To address this, we customized an existing hierarchical approach for handling time dependency to highlight metabolites with a consistent correlation to a process variable over a selected timeframe. We benchmarked this new method against conventional orthogonal partial least squares (OPLS) models. Our hierarchical method highlighted several metabolites consistently related to productivity or cell death that the conventional method missed. These metabolites were biologically relevant; most were known already, but some that had not been reported in CHO literature before, such as 3-methoxytyrosine and succinyladenosine, had ties to cell death in studies with other cell types. The metabolites showed an inverse relationship with the response variables: those positively correlated with productivity were typically negatively correlated with the death rate, or vice versa. For both productivity and cell death, the citrate cycle and adjacent pathways (pyruvate, glyoxylate, pantothenate) were among the most important. In summary, we have proposed a new method to analyze time-dependent omics data in bioprocess production. This approach allowed us to identify metabolites tied to cell death and productivity that were not detected with traditional models.", "doi": "10.1002/biot.202400624", "pmid": "40065671", "labels": {"Swedish NMR Centre": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11894446"}], "notes": [], "created": "2025-06-11T13:34:21.410Z", "modified": "2026-02-27T08:32:11.278Z"}, {"entity": "publication", "iuid": "4fe3addb33484cff817d889e07006e21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4fe3addb33484cff817d889e07006e21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4fe3addb33484cff817d889e07006e21"}}, "title": "The Federated European Genome-Phenome Archive as a global network for sharing human genomics data.", "authors": [{"family": "D'Altri", "given": "Teresa", "initials": "T"}, {"family": "Freeberg", "given": "Mallory Ann", "initials": "MA", "orcid": "0000-0003-2949-3921", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2f4de47af2449838f18ab027c4c80cb.json"}}, {"family": "Curwin", "given": "Amy J", "initials": "AJ", "orcid": "0000-0003-1086-2483", "researcher": {"href": "https://publications.scilifelab.se/researcher/e75c84e221f840f3bf39d62b333f6b63.json"}}, {"family": "Alonso", "given": "Ana", "initials": "A"}, {"family": "Freitas", "given": "Ana T", "initials": "AT", "orcid": "0000-0002-2997-5990", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda2f09713a547a786efeb3e522e19db.json"}}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S", "orcid": "0000-0002-0309-604X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00b9296cc37341aaad61ee4e028b204e.json"}}, {"family": "Gadelha", "given": "Luiz", "initials": "L", "orcid": "0000-0002-8122-9522", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe171bd11f9f4e62bf5bdbba0effe182.json"}}, {"family": "Hagwall", "given": "Anna", "initials": "A"}, {"family": "Hovig", "given": "Eivind", "initials": "E", "orcid": "0000-0002-9103-1077", "researcher": {"href": "https://publications.scilifelab.se/researcher/c940d1465ef34485a962799da848a798.json"}}, {"family": "Kerry", "given": "Giselle", "initials": "G"}, {"family": "Kirli", "given": "Koray", "initials": "K"}, {"family": "Kochel", "given": "Krzysztof", "initials": "K", "orcid": "0009-0006-0772-3916", "researcher": {"href": "https://publications.scilifelab.se/researcher/b06f697bc387473fb05f6b4d2b9f5d86.json"}}, {"family": "Kohlbacher", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1739-4598", "researcher": {"href": "https://publications.scilifelab.se/researcher/8125bfb10c2c437ca20dabc5990d5e16.json"}}, {"family": "Korbel", "given": "Jan O", "initials": "JO"}, {"family": "Leinonen", "given": "Jaakko", "initials": "J", "orcid": "0000-0001-6537-8520", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ca1d05760fa4784ad3576e8d05608d5.json"}}, {"family": "Marciniak", "given": "Blazej", "initials": "B", "orcid": "0000-0003-1571-1473", "researcher": {"href": "https://publications.scilifelab.se/researcher/740bf05e343d4cdbbc77bf367e2488d6.json"}}, {"family": "Oliveira", "given": "Jorge S", "initials": "JS"}, {"family": "Petersen", "given": "Kjell", "initials": "K"}, {"family": "Silva", "given": "M\u00e1rio J", "initials": "MJ", "orcid": "0000-0002-5452-6185", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a2ee355a92c4d3081ccf9dd27604cd6.json"}}, {"family": "Stegle", "given": "Oliver", "initials": "O", "orcid": "0000-0002-8818-7193", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a6c75c25ae47488dd8404778db3067.json"}}, {"family": "Valencia", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-8937-6789", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7c49c33a0bb4c89a6cc55c69f20ded7.json"}}, {"family": "Viklund", "given": "Johan", "initials": "J"}, {"family": "Guigo", "given": "Roderic", "initials": "R", "orcid": "0000-0002-5738-4477", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcfd9721e5014d6dbdfa4aefada6890e.json"}}, {"family": "Parkinson", "given": "Helen", "initials": "H"}, {"family": "Navarro", "given": "Arcadi", "initials": "A", "orcid": "0000-0003-2162-8246", "researcher": {"href": "https://publications.scilifelab.se/researcher/c541642111d94cb8a682b1ff8bea41ac.json"}}, {"family": "Rambla", "given": "Jordi", "initials": "J", "orcid": "0000-0001-9091-257X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3db73bd679a04f62b5139db846bab9ff.json"}}, {"family": "Keane", "given": "Thomas M", "initials": "TM", "orcid": "0000-0001-7532-6898", "researcher": {"href": "https://publications.scilifelab.se/researcher/f62e6fce65544e96b541290ec6b7ccac.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "57", "issue": "3", "pages": "481-485", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/s41588-025-02101-9", "pmid": "40033058", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-025-02101-9"}], "notes": [], "created": "2025-11-21T13:20:58.831Z", "modified": "2025-11-21T13:21:00.305Z"}, {"entity": "publication", "iuid": "ca71d7f357f64f549fe916f1e8354fbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca71d7f357f64f549fe916f1e8354fbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca71d7f357f64f549fe916f1e8354fbb"}}, "title": "Structure of the MUC5AC VWD3 assembly responsible for the formation of net-like mucin polymers.", "authors": [{"family": "Trillo-Muyo", "given": "Sergio", "initials": "S", "orcid": "0000-0002-3135-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e6b6b830e9145a2ae3e6c10895acbee.json"}}, {"family": "Ermund", "given": "Anna", "initials": "A", "orcid": "0000-0002-3233-043X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8215eeb434f84deaafa2f9f198bfb2bc.json"}}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC", "orcid": "0000-0002-1900-1869", "researcher": {"href": "https://publications.scilifelab.se/researcher/44b3815603154322a6dac16f2fc1c1e9.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "EMBO Rep.", "issn": "1469-3178", "volume": "26", "issue": "6", "pages": "1457-1471", "issn-l": "1469-221X"}, "abstract": "Gel-forming mucins MUC5AC and MUC5B constitute the main structural component of the mucus in the respiratory system. Secreted mucins interact specifically with each other and other molecules giving mucus specific properties. We determined the cryoEM structures of the wild type D3 assembly of the human MUC5AC mucin and the structural single nucleotide polymorphisms (SNP) variants Arg996Gln and Arg1201Trp that affect intermolecular interactions. Our structures explain the MUC5AC N-terminal non-covalent oligomerization after secretion. The D3 assembly forms covalent dimers that can appear in two alternative conformations, open and closed, where the closed conformation dimers interact through an arginine-rich loop in the TIL3 domain to form tetramers. Our study provides a model to explain MUC5AC net-like structures and how the two SNPs will affect mucus organization, something that might affect lung and other diseases.", "doi": "10.1038/s44319-025-00395-8", "pmid": "40016425", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11933400"}, {"db": "pii", "key": "10.1038/s44319-025-00395-8"}], "notes": [], "created": "2025-11-13T12:43:47.758Z", "modified": "2025-11-13T12:43:47.811Z"}, {"entity": "publication", "iuid": "102376536a794e47bd95561fb7f4f946", "links": {"self": {"href": "https://publications.scilifelab.se/publication/102376536a794e47bd95561fb7f4f946.json"}, "display": {"href": "https://publications.scilifelab.se/publication/102376536a794e47bd95561fb7f4f946"}}, "title": "Structural Variants in COL1A1 and COL1A2 in Osteogenesis Imperfecta.", "authors": [{"family": "Batkovskyte", "given": "Dominyka", "initials": "D", "orcid": "0000-0002-0492-1259", "researcher": {"href": "https://publications.scilifelab.se/researcher/017749b78ac540a6b2a36303130606f2.json"}}, {"family": "Swolin-Eide", "given": "Diana", "initials": "D"}, {"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A"}, {"family": "S\u00e6ther", "given": "Kristine Bilgrav", "initials": "KB"}, {"family": "Thunstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "\u00c5str\u00f6m", "given": "Eva", "initials": "E"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Am. J. Med. Genet. A", "issn": "1552-4833", "pages": "e63935", "volume": "197", "issue": "3", "issn-l": "1552-4825"}, "abstract": "Osteogenesis Imperfecta (OI) is a heterogeneous skeletal dysplasia characterized by bone fragility, skeletal deformities, and short stature. Most commonly, it is caused by autosomal dominant variants in the type I collagen genes, COL1A1 or COL1A2. Type I collagen is the main protein of the extracellular matrix in the skeleton and changes in its structure or quantity may lead to OI. 85%-90% of OI cases occur due to sequence variants in type I collagen genes, while OI caused by structural abnormalities in type I collagen genes is less common. In most cases, haploinsufficiency of type I collagen is associated with a milder OI phenotype. Large genomic deletions often involve several genes within the same chromosomal region, leading to microdeletion syndromes with OI features. Here, we report eight Swedish patients from five unrelated families with OI due to structural variants in the COL1A1 and COL1A2 genes. One patient with OI type III had a complex rearrangement with a deletion and duplication event in COL1A2, leading to reduced COL1A2 expression. Three other patients from two different families with OI type I had whole gene deletions involving COL1A1. In one family, three affected individuals with OI type I had a small intragenic deletion of exons 11-12 in COL1A2. One patient had a 2.1 Mb de novo deletion encompassing COL1A1 and DLX3 genes and features of OI and tricho-dento-osseous syndrome. Overall, this study highlights the importance of investigating gene dosage abnormalities in patients with OI and further delineates clinical and genetic variability of OI caused by structural variants in type I collagen genes.", "doi": "10.1002/ajmg.a.63935", "pmid": "39513464", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-26T12:47:44.136Z", "modified": "2025-11-18T20:44:25.168Z"}, {"entity": "publication", "iuid": "aeb04606dd804999ad7eeda50801fa80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aeb04606dd804999ad7eeda50801fa80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aeb04606dd804999ad7eeda50801fa80"}}, "title": "Somatic CAG repeat expansion in blood associates with biomarkers of neurodegeneration in Huntington's disease decades before clinical motor diagnosis.", "authors": [{"family": "Scahill", "given": "Rachael I", "initials": "RI"}, {"family": "Farag", "given": "Mena", "initials": "M", "orcid": "0000-0002-0679-0117", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80e5f0ebb00498f8dbf2fb4518e459a.json"}}, {"family": "Murphy", "given": "Michael J", "initials": "MJ"}, {"family": "Hobbs", "given": "Nicola Z", "initials": "NZ"}, {"family": "Leocadi", "given": "Michela", "initials": "M"}, {"family": "Langley", "given": "Christelle", "initials": "C", "orcid": "0000-0001-5061-2820", "researcher": {"href": "https://publications.scilifelab.se/researcher/f12932ef6d674608b4da04d09836770c.json"}}, {"family": "Knights", "given": "Harry", "initials": "H"}, {"family": "Ciosi", "given": "Marc", "initials": "M", "orcid": "0000-0002-7663-4080", "researcher": {"href": "https://publications.scilifelab.se/researcher/11d89a99b658483ea65d11c2f0af96c1.json"}}, {"family": "Fayer", "given": "Kate", "initials": "K"}, {"family": "Nakajima", "given": "Mitsuko", "initials": "M"}, {"family": "Thackeray", "given": "Olivia", "initials": "O"}, {"family": "Gobom", "given": "Johan", "initials": "J", "orcid": "0000-0001-6193-6193", "researcher": {"href": "https://publications.scilifelab.se/researcher/add4c0c68cff447383c1f0184e2be943.json"}}, {"family": "R\u00f6nnholm", "given": "John", "initials": "J"}, {"family": "Weiner", "given": "Sophia", "initials": "S", "orcid": "0009-0000-2298-220X", "researcher": {"href": "https://publications.scilifelab.se/researcher/501cabeaaa3649ffa111f9c445065fed.json"}}, {"family": "Hassan", "given": "Yara R", "initials": "YR"}, {"family": "Ponraj", "given": "Nehaa K P", "initials": "NKP", "orcid": "0009-0002-9576-5753", "researcher": {"href": "https://publications.scilifelab.se/researcher/c15cb959adaa4dd69f9fcfecfde82336.json"}}, {"family": "Estevez-Fraga", "given": "Carlos", "initials": "C", "orcid": "0000-0001-6855-1093", "researcher": {"href": "https://publications.scilifelab.se/researcher/a358aae32ce141f081748a37bc1d361c.json"}}, {"family": "Parker", "given": "Christopher S", "initials": "CS"}, {"family": "Malone", "given": "Ian B", "initials": "IB"}, {"family": "Hyare", "given": "Harpreet", "initials": "H"}, {"family": "Long", "given": "Jeffrey D", "initials": "JD", "orcid": "0000-0001-7181-9652", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cbb5cdb954a4f0ea50cb27c0ffd31ed.json"}}, {"family": "Heslegrave", "given": "Amanda", "initials": "A"}, {"family": "Sampaio", "given": "Cristina", "initials": "C", "orcid": "0000-0002-7052-9079", "researcher": {"href": "https://publications.scilifelab.se/researcher/e977513b61bf47b5a81489c74ad612e4.json"}}, {"family": "Zhang", "given": "Hui", "initials": "H", "orcid": "0000-0002-5426-2140", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4da907c8afe4858b02b4914520bcf5b.json"}}, {"family": "Robbins", "given": "Trevor W", "initials": "TW", "orcid": "0000-0003-0642-5977", "researcher": {"href": "https://publications.scilifelab.se/researcher/9accce3ce1c54ce18f8557dedc1dbf15.json"}}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Wild", "given": "Edward J", "initials": "EJ", "orcid": "0000-0002-6921-7887", "researcher": {"href": "https://publications.scilifelab.se/researcher/25781990d57a455c8a5e2332669cea0b.json"}}, {"family": "Rees", "given": "Geraint", "initials": "G", "orcid": "0000-0002-9623-7007", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfba7a08558246cdb7259d79344a4f80.json"}}, {"family": "Rowe", "given": "James B", "initials": "JB", "orcid": "0000-0001-7216-8679", "researcher": {"href": "https://publications.scilifelab.se/researcher/4211255a53fd4ce5a2903f8b3fa75dcb.json"}}, {"family": "Sahakian", "given": "Barbara J", "initials": "BJ", "orcid": "0000-0001-7352-1745", "researcher": {"href": "https://publications.scilifelab.se/researcher/522cd4149c914cd19da7e78852526bbd.json"}}, {"family": "Monckton", "given": "Darren G", "initials": "DG", "orcid": "0000-0002-8298-8264", "researcher": {"href": "https://publications.scilifelab.se/researcher/a982cf9a4bf946c497765c5953230788.json"}}, {"family": "Langbehn", "given": "Douglas R", "initials": "DR"}, {"family": "Tabrizi", "given": "Sarah J", "initials": "SJ", "orcid": "0000-0003-2716-2045", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b5169e345e3411587abd10613f57d1d.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "volume": "31", "issue": "3", "pages": "807-818", "issn-l": "1078-8956"}, "abstract": "Huntington's disease (HD) is an autosomal dominant neurodegenerative disease with the age at which characteristic symptoms manifest strongly influenced by inherited HTT CAG length. Somatic CAG expansion occurs throughout life and understanding the impact of somatic expansion on neurodegeneration is key to developing therapeutic targets. In 57 HD gene expanded (HDGE) individuals, ~23 years before their predicted clinical motor diagnosis, no significant decline in clinical, cognitive or neuropsychiatric function was observed over 4.5 years compared with 46 controls (false discovery rate (FDR) > 0.3). However, cerebrospinal fluid (CSF) markers showed very early signs of neurodegeneration in HDGE with elevated neurofilament light (NfL) protein, an indicator of neuroaxonal damage (FDR = 3.2 \u00d7 10-12), and reduced proenkephalin (PENK), a surrogate marker for the state of striatal medium spiny neurons (FDR = 2.6 \u00d7 10-3), accompanied by brain atrophy, predominantly in the caudate (FDR = 5.5 \u00d7 10-10) and putamen (FDR = 1.2 \u00d7 10-9). Longitudinal increase in somatic CAG repeat expansion ratio (SER) in blood was a significant predictor of subsequent caudate (FDR = 0.072) and putamen (FDR = 0.148) atrophy. Atypical loss of interruption HTT repeat structures, known to predict earlier age at clinical motor diagnosis, was associated with substantially faster caudate and putamen atrophy. We provide evidence in living humans that the influence of CAG length on HD neuropathology is mediated by somatic CAG repeat expansion. These critical mechanistic insights into the earliest neurodegenerative changes will inform the design of preventative clinical trials aimed at modulating somatic expansion. ClinicalTrials.gov registration: NCT06391619 .", "doi": "10.1038/s41591-024-03424-6", "pmid": "39825149", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11922752"}, {"db": "pii", "key": "10.1038/s41591-024-03424-6"}, {"db": "ClinicalTrials.gov", "key": "NCT06391619"}], "notes": [], "created": "2025-02-11T14:14:37.115Z", "modified": "2025-11-20T17:41:58.894Z"}, {"entity": "publication", "iuid": "da5fad8eadab40d6b0c59925d1429184", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da5fad8eadab40d6b0c59925d1429184.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da5fad8eadab40d6b0c59925d1429184"}}, "title": "Single drop turbulent breakup in the anisotropic turbulence inside a high-pressure homogenizer scale-up model", "authors": [{"family": "Olad", "given": "Peyman", "initials": "P", "orcid": "0000-0002-1695-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a3f23b64c10446086be9f85814dd338.json"}}, {"family": "H\u00e5kansson", "given": "Andreas", "initials": "A", "orcid": "0000-0002-0002-661X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44bf9c0aa604a8b80927bb04e10b493.json"}}], "type": "journal-article", "published": "2025-03-00", "journal": {"title": "International Journal of Multiphase Flow", "issn": "0301-9322", "volume": "184", "pages": "105077", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ijmultiphaseflow.2024.105077", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:43:29.480Z", "modified": "2025-11-28T10:43:29.637Z"}, {"entity": "publication", "iuid": "988e47264ea04cbfba6dca9fd6973eb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/988e47264ea04cbfba6dca9fd6973eb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/988e47264ea04cbfba6dca9fd6973eb8"}}, "title": "Plasma Alkylresorcinols Is an Objective Biomarker for Gluten Intake in Young Children.", "authors": [{"family": "Af Segerstad", "given": "Elin M H\u00e5rd", "initials": "EMH"}, {"family": "Ericson-Hallstr\u00f6m", "given": "Emelie", "initials": "E"}, {"family": "Bokstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Armeni", "given": "Marina", "initials": "M"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Andr\u00e9n Aronsson", "given": "Carin", "initials": "C"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "J. Nutr.", "issn": "1541-6100", "volume": "155", "issue": "3", "pages": "985-993", "issn-l": "0022-3166"}, "abstract": "Alkylresorcinols are a well-established biomarker for whole-grain intake. There is evidence suggesting that total plasma alkylresorcinol concentration may also be used as a biomarker for gluten intake in adults.\n\nThe aim of this study was to evaluate if total alkylresorcinol concentration is a valid biomarker for gluten intake in young children.\n\nNonfasting plasma alkylresorcinol concentrations were analyzed by normal-phase ultrahigh-pressure liquid chromatography-tandem mass spectrometry in 65 children aged 18 mo included in a randomized controlled trial. The intervention group was following a gluten-free diet (n = 21, 31.3%), whereas the diet was unrestricted in the control group (n = 44, 65.7%). Alkylresorcinol concentrations in the 65 children were validated against simultaneously collected 3-d food records estimating total gluten intake.\n\nGluten intake in controls was median 5.8 grams/d (IQR: 2.8-9.4, max 17.1) compared with 0.0 g/d (IQR: 0.0-0.0, max 0.7, P < 0.001) in the intervention group. In the control group, wheat accounted for mean 85% (SD: 0.1) of the gluten intake. The intervention group had lower alkylresorcinol levels (median: 7.2 nmol/L; IQR: 4.0-10.5) compared with controls (median: 269; IQR: 116-505 nmol/L, P < 0.001). The correlation between alkylresorcinol concentrations and gluten intake was \u03c1 = 0.68 (P < 0.001). Alkylresorcinol concentrations increased by 35.7% [95% confidence interval (CI): 25.9, 46.2, P < 0.001] for every g/d increase of gluten intake. The Cohen's weighted kappa between quartiles of alkylresorcinol and gluten intake was 0.73 (95% CI: 0.59, 0.86).\n\nAlkylresorcinol concentrations increased with gluten intake in young nonfasting children. The findings suggest that alkylresorcinol concentrations may be a useful biomarker for gluten intake in young children. This trial was registered at clinicaltrials.gov as NCT03562221.", "doi": "10.1016/j.tjnut.2025.01.020", "pmid": "39880171", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11934242"}, {"db": "pii", "key": "S0022-3166(25)00027-6"}, {"db": "ClinicalTrials.gov", "key": "NCT03562221"}], "notes": [], "created": "2025-11-27T11:23:54.366Z", "modified": "2025-11-27T11:23:54.379Z"}, {"entity": "publication", "iuid": "3b66cf23e23e44c58c134c7834269f8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b66cf23e23e44c58c134c7834269f8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b66cf23e23e44c58c134c7834269f8a"}}, "title": "Modeling of Disease Progression of Type 2 Diabetes Using Real-World Data: Quantifying Competing Risks of Morbidity and Mortality.", "authors": [{"family": "Kunina", "given": "Hanna", "initials": "H", "orcid": "0009-0000-0512-545X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece6ec4138cf479ea9cfa05510540db3.json"}}, {"family": "Franz\u00e9n", "given": "Stefan", "initials": "S", "orcid": "0000-0002-9640-0927", "researcher": {"href": "https://publications.scilifelab.se/researcher/513bc805359f41eb96ff937c0a609b99.json"}}, {"family": "Kjellsson", "given": "Maria C", "initials": "MC", "orcid": "0000-0003-3531-9452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f141039b41a84acf9599dfee7dcc3396.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "CPT Pharmacometrics Syst Pharmacol", "issn": "2163-8306", "volume": "14", "issue": "3", "pages": "606-615", "issn-l": null}, "abstract": "Type 2 diabetes (T2D) is a progressive metabolic disorder that could be an underlying cause of long-term complications that increase mortality. The assessment of the probability of such events could be essential for mortality risk management. This work aimed to establish a framework for risk predictions of macrovascular complications (MVC) and diabetic kidney disease (DKD) in patients with T2D, using real-world data from the Swedish National Diabetes Registry (NDR), in the presence of mortality as a competing risk. The study consisted of 41,517 patients with T2D registered in NDR between 2005 and 2013. At inclusion, patients were newly diagnosed (T2D < 1 year) and had no prior evidence of DKD or MVC. Using three-quarters of the data, a five-state multistate model was established to describe competing events of MVC, DKD, a combination thereof, and the terminal state, death. Two hypotheses were investigated: (1) the risk of MVC and DKD are mutually independent, and (2) mortality is independent of morbidities. At the end of the study, the majority of individuals remained in uncomplicated T2D; however, the probability of transition to complications and death increased over time. The mortality hazard depended on the presence of morbidities and was quantified as a life expectancy decreased by 5.0, 9.7, and 12.2 years for MVC, DKD, and the combined morbidity, respectively, compared to uncomplicated T2D. An established framework with a five-state model incorporating competing events was shown to be a useful tool for comorbidities risk assessment in newly diagnosed patients with T2D.", "doi": "10.1002/psp4.13301", "pmid": "39825570", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11919267"}], "notes": [], "created": "2025-11-28T10:40:47.299Z", "modified": "2025-11-28T10:40:47.462Z"}, {"entity": "publication", "iuid": "dd56467030644e0e8dbd5f6d944de7b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd56467030644e0e8dbd5f6d944de7b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd56467030644e0e8dbd5f6d944de7b5"}}, "title": "Mild-to-moderate psoriasis is associated with subclinical inflammation in the duodenum and a tendency of disturbed intestinal barrier.", "authors": [{"family": "Lundquist", "given": "Patrik", "initials": "P"}, {"family": "Hagforsen", "given": "Eva", "initials": "E"}, {"family": "Wagner", "given": "Michael", "initials": "M"}, {"family": "Alimohammadi", "given": "Mohammad", "initials": "M"}, {"family": "Melo", "given": "Fabio Rabelo", "initials": "FR"}, {"family": "Pejler", "given": "Gunnar", "initials": "G"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Carlson", "given": "Marie", "initials": "M"}, {"family": "Rollman", "given": "Ola", "initials": "O"}, {"family": "Lampinen", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Biochim Biophys Acta Mol Basis Dis", "issn": "1879-260X", "volume": "1871", "issue": "3", "pages": "167634", "issn-l": null}, "abstract": "Psoriasis is a chronic skin disease occasionally associated with abdominal symptoms and IBD. We aimed to characterize intestinal immune cells and the integrity of the intestinal barrier in psoriasis. Biopsies from the duodenum and colon were analyzed by flow cytometry and immunohistochemistry for the presence and activation status of different immune cell populations. Intestinal permeability was measured using Ussing chambers. Proinflammatory markers were analyzed in fecal and blood samples using ELISA. The intestinal level of inflammatory mediators was assessed using a multiplex proximity extension assay. We found an increased density of intestinal eosinophils, mast cells, macrophages, and CD8+ T-cells in psoriasis; eosinophils, macrophages, and CD8+ T-cells expressed activation markers. Half of the psoriasis patients showed increased permeability across the duodenum, correlating with increased mucosal IL-17A, IL-13, IL-2, and IL-20, and with gastrointestinal symptoms. Our findings reveal that psoriasis is associated with low-grade intestinal inflammation, which may contribute to abdominal symptoms in these patients and possibly set the stage for the development of intestinal disease.", "doi": "10.1016/j.bbadis.2024.167634", "pmid": "39706352", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "S0925-4439(24)00628-8"}], "notes": [], "created": "2025-11-25T09:13:24.586Z", "modified": "2025-11-25T09:13:24.589Z"}, {"entity": "publication", "iuid": "d89c90552d974d6ea6979a3c189833fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d89c90552d974d6ea6979a3c189833fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d89c90552d974d6ea6979a3c189833fe"}}, "title": "Intraneuronal A\u03b2 accumulation causes tau hyperphosphorylation via endolysosomal leakage.", "authors": [{"family": "Gao", "given": "Yang", "initials": "Y", "orcid": "0000-0002-7733-5365", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3c1d375765a41e0b0a7d2c0af9cb4ff.json"}}, {"family": "Wang", "given": "Lisha", "initials": "L"}, {"family": "Doeswijk", "given": "Tosca", "initials": "T"}, {"family": "Winblad", "given": "Bengt", "initials": "B"}, {"family": "Schedin-Weiss", "given": "Sophia", "initials": "S"}, {"family": "Tjernberg", "given": "Lars O", "initials": "LO", "orcid": "0000-0001-6889-4950", "researcher": {"href": "https://publications.scilifelab.se/researcher/35d7bd25361f4e08a7223926311b399a.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Alzheimers Dement", "issn": "1552-5279", "volume": "21", "issue": "3", "pages": "e70091", "issn-l": null}, "abstract": "Alzheimer's disease (AD) is characterized by amyloid beta (A\u03b2) peptide plaques and intracellular neurofibrillary tangles formed by hyperphosphorylated tau. Many attempts have been made to clarify the link between A\u03b2 and tau in the pathogenesis, but conclusive data describing a pathway for this connection are still lacking.\n\nWe developed a neuronal model of A\u03b2-induced toxicity and studied downstream effects of intraneuronal A\u03b242 accumulation on tau hyperphosphorylation using confocal microscopy and live cell imaging.\n\nA\u03b242 added to the medium was endocytosed into neurons, inducing the formation of endolysosomal protofibrils and endolysosomal leakage, which in turn promoted tau hyperphosphorylation. Asparaginyl endopeptidase (AEP) was released from the disrupted lysosomes, and inhibition of this peptidase activity reduced tau hyperphosphorylation.\n\nThe data suggest a mechanism of AD in which A\u03b242 accumulates and aggregates gradually in neurons over time, leading to endolysosomal leakage and release of AEP, which subsequently triggers tau hyperphosphorylation.\n\nA\u03b242 endocytosis leads to its endolysosomal accumulation in neurons over time. A\u03b242 polymerizes into protofibrils and causes endolysosomal leakage. Tau hyperphosphorylation is induced by endolysosomal asparagine endopeptidase leakage. Tau hyperphosphorylation is inhibited by an asparagine endopeptidase inhibitor.", "doi": "10.1002/alz.70091", "pmid": "40145397", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11947758"}], "notes": [], "created": "2026-06-11T12:35:12.376Z", "modified": "2026-06-11T12:35:30.496Z"}, {"entity": "publication", "iuid": "b5e92260b7eb4e89a6a71c678e822438", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5e92260b7eb4e89a6a71c678e822438.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5e92260b7eb4e89a6a71c678e822438"}}, "title": "In-Depth Analysis of Disease Manifestations in Antineutrophil Cytoplasmic Antibody-Associated Vasculitides Identifies Distinct Clinical Phenotypes.", "authors": [{"family": "Lindberg", "given": "Hanna", "initials": "H"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Hellbacher", "given": "Erik", "initials": "E"}, {"family": "Norling", "given": "Olof", "initials": "O"}, {"family": "Berglin", "given": "Ewa", "initials": "E"}, {"family": "Stegmayr", "given": "Bernd", "initials": "B"}, {"family": "Baslund", "given": "Bo", "initials": "B"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Haukeland", "given": "Hilde", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A"}, {"family": "Weiner", "given": "Maria", "initials": "M"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Segelmark", "given": "M\u00e5rten", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Mohammad", "given": "Aladdin J", "initials": "AJ"}, {"family": "Sv\u00e4rd", "given": "Anna", "initials": "A"}, {"family": "Pullerits", "given": "Rille", "initials": "R"}, {"family": "Herlitz", "given": "Hans", "initials": "H"}, {"family": "S\u00f6derbergh", "given": "Annika", "initials": "A"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "ACR Open Rheumatol", "issn": "2578-5745", "volume": "7", "issue": "3", "pages": "e70009", "issn-l": null}, "abstract": "The antineutrophil cytoplasmic antibody (ANCA)-associated vasculitides are heterogeneous disorders. The aim of this study was to identify and characterize subgroups of patients based on sex, ANCA, age at diagnosis, and organ involvement.\n\nIn total, 1,167 patients with granulomatosis with polyangiitis (GPA) or microscopic polyangiitis (MPA) were retrospectively recruited to the study. Data including cumulative involvement of 10 different organ systems, end-stage kidney disease (ESKD), sex, proteinase (PR) 3-ANCA, myeloperoxidase (MPO)-ANCA, age at diagnosis, disease duration, and relapse were obtained from medical records. Clinical variables were analyzed for associations with sex, age at diagnosis, and relapse using logistic regression analysis. Thirteen clinical variables were included in hierarchical cluster analyses using the Ward method.\n\nIn patients with GPA, PR3-ANCA, renal and pulmonary involvement, and ESKD were significantly associated with male sex, whereas MPO-ANCA was associated with female sex. Patients with GPA who were younger than 32 years of age at diagnosis were significantly more often females and had more ear-nose-throat involvement than patients older than 32 years. In patients with MPA, female patients were significantly younger at diagnosis than male patients. Relapse was significantly associated with young age at diagnosis and pulmonary involvement in GPA and with musculoskeletal involvement in MPA. Hierarchical cluster analyses identified five and seven patient clusters among individuals with GPA and MPA, respectively. PR3-/MPO-ANCA defined the largest clusters, whereas heart, gastrointestinal, and central nervous system involvement were hallmarks for three clusters for both patients with GPA and MPA.\n\nSex, age at diagnosis, and specific organ involvements define clinically relevant subgroups among patients with ANCA-associated vasculitides.", "doi": "10.1002/acr2.70009", "pmid": "40033657", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11876290"}], "notes": [], "created": "2025-11-17T10:12:19.867Z", "modified": "2025-11-17T10:12:19.927Z"}, {"entity": "publication", "iuid": "52422faa8797490593fd60de4fdc11f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52422faa8797490593fd60de4fdc11f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52422faa8797490593fd60de4fdc11f6"}}, "title": "Importance of individual residues in hydrophobic patch PLVIVGL (1481-1487) in FV-Short for synergistic TFPI\u03b1 cofactor activity with protein S, an alanine-scanning study: AlphaFold-mediated prediction of FV-Short/TFPI\u03b1/protein S trimolecular complex structure.", "authors": [{"family": "Dahlb\u00e4ck", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Tran", "given": "Sinh", "initials": "S"}, {"family": "Draczkowski", "given": "Piotr", "initials": "P"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "J. Thromb. Haemost.", "issn": "1538-7836", "issn-l": null, "volume": "23", "issue": "3", "pages": "849-862"}, "abstract": "In the splice variant factor (F)V-Short, 702 residues are deleted from the B domain, resulting in exposure of an acid region (AR2; 1493-1537) that binds TFPI\u03b1. FV-Short and protein S serve as synergistic TFPI\u03b1 cofactors in inhibition of FXa. In the preAR2 region, a hydrophobic patch PLVIVGL (1481-1487) is crucial for synergistic TFPI\u03b1-cofactor activity and assembly of FV-Short, TFPI\u03b1, and protein S.\r\n\r\nTo elucidate the importance of individual residues in the PLVIVGL patch for synergism between FV-Short and protein S as TFPI\u03b1 cofactors.\r\n\r\nAn alanine scanning of the hydrophobic patch was performed in which 7 FV-Short variants were created. The synergistic TFPI\u03b1-cofactor activity was analyzed by FXa inhibition and a microtiter-based assay tested binding between the proteins. AlphaFold 3 was used to predict protein-protein interactions between FV-Short, protein S, and TFPI\u03b1.\r\n\r\nFive of the 7 variants (V1483A, I1484A, V1485A, G1486A, and L1487A) demonstrated decreased synergistic TFPI\u03b1 cofactor activity; in particular, G1486A and L1487A were severely affected. Neither wild-type FV-Short nor any of the mutants bound protein S in the absence of TFPI\u03b1. In the presence of TFPI\u03b1, wild-type FV-Short, P1481A, L1482A, and V1485A bound protein S, whereas V1483A, I1484A, G1486A, and L1487A did not. AlphaFold predicted an interaction between the hydrophobic patch in FV-Short and a hydrophobic patch in protein S involving residues 268-276 and 422-426.\r\n\r\nIndividual residues (V1483, I1484, G1486, and L1487) in the hydrophobic patch are demonstrated to be important for the synergistic TFPI\u03b1-cofactor activity and for the assembly of a trimolecular FXa-inhibitory complex.", "doi": "10.1016/j.jtha.2024.11.013", "pmid": "39617184", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1538-7836(24)00703-7"}], "notes": [], "created": "2025-10-25T10:13:42.245Z", "modified": "2025-11-25T09:04:02.191Z"}, {"entity": "publication", "iuid": "4f4d1f7839b6467eb6f4d7b6b2564378", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f4d1f7839b6467eb6f4d7b6b2564378.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f4d1f7839b6467eb6f4d7b6b2564378"}}, "title": "Genomic prediction of bone strength in laying hens using different sources of information.", "authors": [{"family": "Sallam", "given": "M", "initials": "M"}, {"family": "Wall", "given": "H", "initials": "H"}, {"family": "Wilson", "given": "P W", "initials": "PW"}, {"family": "Andersson", "given": "B", "initials": "B"}, {"family": "Schmutz", "given": "M", "initials": "M"}, {"family": "Benavides", "given": "C", "initials": "C"}, {"family": "Checa", "given": "M", "initials": "M"}, {"family": "Sanchez-Rodriguez", "given": "E", "initials": "E"}, {"family": "Rodriguez-Navarro", "given": "A B", "initials": "AB"}, {"family": "Kindmark", "given": "A", "initials": "A"}, {"family": "Dunn", "given": "I C", "initials": "IC"}, {"family": "de Koning", "given": "D-J", "initials": "DJ"}, {"family": "Johnsson", "given": "M", "initials": "M"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Animal", "issn": "1751-732X", "volume": "19", "issue": "3", "pages": "101452", "issn-l": null}, "abstract": "Bone damage in laying hens remains a significant welfare concern in the egg industry. Breeding companies rely on selective cross-breeding of purebred birds to produce commercial hybrids, which farmers raise for table-egg production. Genomic prediction is a potential tool to improve bone quality in laying hens. Because commercial layers are crossbred and kept in different environments than pure lines, the question arises whether to use within-line purebred selection or whether to use crossbred data. While selection based on pure line data is common, achieving optimal bone strength in hybrids may require incorporating hybrid data to account for heterosis and housing-specific effects. This study aims to evaluate how combining pure line and hybrid data could affect the accuracy of breeding values for bone strength. Genotypes and phenotypes were available from two types of white hybrids (Bovans White and Lohmann Selected Leghorn Classic) housed in two housing systems (furnished cages and floor housing). This resulted in four hybrid-housing combinations (n \u223c 220 for each). Tibia strength and genotypes for pure breeding lines of White Leghorn (WL, n = 947) and Rhode Island Red (RIR, n = 924) were also included. Each of the hybrid-housing combinations and pure lines was fitted separately into (1) single-trait Genomic Best Linear Unbiased Prediction (GBLUP), then simultaneously via multitrait GBLUP, (2) within hybrids across housing, (3) across hybrids within housing, (4) across hybrids and housing, (5) the latter in combination with WL and/or RIR data. Including hybrid data slightly increased the accuracy of the genomic estimated breeding value (GEBV) of other hybrids, but not that of pure lines. Pure line data increased the GEBV accuracy of hybrids over and above that of combining hybrid information. Combining data from two pure lines improved the GEBV accuracy of both. In comparison to the combination of data across lines and/or houses, combining tibia strength and BW within-lines increased tibia strength GEBV accuracy. The maximum GEBV accuracy obtained for tibia strength ranged from 0.42 to 0.65 for hybrids and from 0.63 to 0.78 for pure lines. Further study is required to test whether modelling the interactions of genotype by environment could help to breed hybrids for specific housing systems.", "doi": "10.1016/j.animal.2025.101452", "pmid": "40043590", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S1751-7311(25)00035-7"}], "notes": [], "created": "2025-09-08T06:53:11.259Z", "modified": "2025-09-08T06:53:11.308Z"}, {"entity": "publication", "iuid": "94b833e1cf11498a8be10d219e3db160", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94b833e1cf11498a8be10d219e3db160.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94b833e1cf11498a8be10d219e3db160"}}, "title": "Genome Sequence Resources from Three Isolates of the Apple Canker Pathogen Neonectria ditissima Infecting Forest Trees", "authors": [{"family": "Bourras", "given": "Salim", "initials": "S", "orcid": "0000-0003-0855-5433", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6b49cf30d404c7ab7bbbe30bda39d1c.json"}}, {"family": "V\u00e9l\u00ebz", "given": "Heriberto", "initials": "H"}, {"family": "Ihrmark", "given": "Katarina", "initials": "K"}, {"family": "Corrales Guti\u00e9rrez", "given": "Miguel \u00c1ngel", "initials": "M\u00c1"}, {"family": "Elfstrand", "given": "Malin", "initials": "M", "orcid": "0000-0002-0214-5284", "researcher": {"href": "https://publications.scilifelab.se/researcher/2957dac173f4495a9245f0d8a9750606.json"}}, {"family": "Garkava-Gustavsson", "given": "Larisa", "initials": "L"}, {"family": "Falk", "given": "Kerstin Dalman", "initials": "KD"}], "type": "journal-article", "published": "2025-03-00", "journal": {"title": "PhytoFrontiers\u2122", "issn": "2690-5442", "volume": "5", "issue": "1", "pages": "117-119", "issn-l": null}, "abstract": null, "doi": "10.1094/phytofr-05-24-0055-a", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T06:54:44.172Z", "modified": "2025-09-08T06:54:44.391Z"}, {"entity": "publication", "iuid": "1420057903e04d48827b5eceffb27b71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1420057903e04d48827b5eceffb27b71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1420057903e04d48827b5eceffb27b71"}}, "title": "Effect of broccoli sprout extract and baseline gut microbiota on fasting blood glucose in prediabetes: a randomized, placebo-controlled trial.", "authors": [{"family": "Dwibedi", "given": "Chinmay", "initials": "C", "orcid": "0000-0001-6416-4440", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b0dbf807be449da1856c0c018f13a3.json"}}, {"family": "Axelsson", "given": "Annika S", "initials": "AS"}, {"family": "Abrahamsson", "given": "Birgitta", "initials": "B"}, {"family": "Fahey", "given": "Jed W", "initials": "JW"}, {"family": "Asplund", "given": "Olof", "initials": "O"}, {"family": "Hansson", "given": "Ola", "initials": "O"}, {"family": "Ahlqvist", "given": "Emma", "initials": "E"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V", "orcid": "0000-0002-9150-4233", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ddf7701aaf4c01b160f2a1c596dc6f.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Rosengren", "given": "Anders H", "initials": "AH", "orcid": "0000-0002-9333-5736", "researcher": {"href": "https://publications.scilifelab.se/researcher/5053b8428d9042b2a0284f2213fbbe42.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Nat Microbiol", "issn": "2058-5276", "volume": "10", "issue": "3", "pages": "681-693", "issn-l": "2058-5276"}, "abstract": "More effective treatments are needed for impaired fasting glucose or glucose intolerance, known as prediabetes. Sulforaphane is an isothiocyanate that reduces hepatic gluconeogenesis in individuals with type 2 diabetes and is well tolerated when provided as a broccoli sprout extract (BSE). Here we report a randomized, double-blind, placebo-controlled trial in which drug-naive individuals with prediabetes were treated with BSE (n = 35) or placebo (n = 39) once daily for 12 weeks. The primary outcome was a 0.3 mmol l-1 reduction in fasting blood glucose compared with placebo from baseline to week 12. Gastro-intestinal side effects but no severe adverse events were observed in response to treatment. BSE did not meet the prespecified primary outcome, and the overall effect in individuals with prediabetes was a 0.2 mmol l-1 reduction in fasting blood glucose (95% confidence interval -0.44 to -0.01; P = 0.04). Exploratory analyses to identify subgroups revealed that individuals with mild obesity, low insulin resistance and reduced insulin secretion had a pronounced response (0.4 mmol l-1 reduction) and were consequently referred to as responders. Gut microbiota analysis further revealed an association between baseline gut microbiota and pathophysiology and that responders had a different gut microbiota composition. Genomic analyses confirmed that responders had a higher abundance of a Bacteroides-encoded transcriptional regulator required for the conversion of the inactive precursor to bioactive sulforaphane. The abundance of this gene operon correlated with sulforaphane serum concentration. These findings suggest a combined influence of host pathophysiology and gut microbiota on metabolic treatment response, and exploratory analyses need to be confirmed in future trials. ClinicalTrials.gov registration: NCT03763240 .", "doi": "10.1038/s41564-025-01932-w", "pmid": "39929977", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11879859"}, {"db": "pii", "key": "10.1038/s41564-025-01932-w"}, {"db": "ClinicalTrials.gov", "key": "NCT03763240"}], "notes": [], "created": "2025-11-28T10:46:27.072Z", "modified": "2025-11-28T10:46:27.196Z"}, {"entity": "publication", "iuid": "39441d60527c41cea325c6e6103afacf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39441d60527c41cea325c6e6103afacf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39441d60527c41cea325c6e6103afacf"}}, "title": "Discovery of Cis-Regulatory Mechanisms via Non-Coding Mutations in Acute Lymphoblastic Leukemia.", "authors": [{"family": "Ayd\u0131n", "given": "Efe", "initials": "E"}, {"family": "Woodward", "given": "Eleanor L", "initials": "EL"}, {"family": "Dushime", "given": "Gladys Telliam", "initials": "GT"}, {"family": "Gunnarsson", "given": "Rebeqa", "initials": "R"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H", "orcid": "0000-0001-8703-1173", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a75300e8c346858ce8dd8f64ecae85.json"}}, {"family": "Moura-Castro", "given": "Larissa H", "initials": "LH", "orcid": "0000-0001-9063-5592", "researcher": {"href": "https://publications.scilifelab.se/researcher/d326f608c7744622a92cc73768f23afb.json"}}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Johansson", "given": "Bertil", "initials": "B"}, {"family": "Paulsson", "given": "Kajsa", "initials": "K", "orcid": "0000-0001-7950-222X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2033b23811f1432c90ad860dd993e7a8.json"}}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Genes Chromosomes Cancer", "issn": "1098-2264", "volume": "64", "issue": "3", "pages": "e70045", "issn-l": "1045-2257"}, "abstract": "The non-coding genome, constituting 98% of human DNA, remains largely unexplored, yet holds potential for identifying new biomarkers and therapeutic targets in acute lymphoblastic leukemia (ALL). In this study, we conducted a systematic analysis of recurrent somatic non-coding single nucleotide variants (SNVs) in pediatric B-cell precursor (BCP) ALL. We leveraged whole genome sequencing (WGS) data from 345 pediatric BCP ALL cases, representing all major genetic subtypes and identified 346 mutational hotspots that harbored somatic SNVs in at least three cases. Through the integration of paired RNA sequencing along with published ChIP-seq and ATAC-seq data, we found 128 non-coding hotspots associated with differentially expressed genes nearby, which were enriched for cis-regulatory elements, demonstrating the effectiveness of multi-omics integration in distinguishing pathogenic mutations from passengers. We identified one mutational hotspot that was associated with increased expression of the leukemia-associated gene NRAS in three primary ALLs. Micro-C analysis in the leukemia cell line demonstrated interactions between the hotspot region and NRAS regulatory elements. Dual luciferase assays indicated that the mutations disrupted regulatory interactions and CRISPR-mediated deletion of the region significantly upregulated NRAS, confirming the hypothesized regulatory link. Altogether, we provide new insights into the functional roles of non-coding mutations in leukemia.", "doi": "10.1002/gcc.70045", "pmid": "40145864", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11949094"}], "notes": [], "created": "2025-11-06T09:12:42.571Z", "modified": "2025-11-06T09:12:42.739Z"}, {"entity": "publication", "iuid": "dd900ce5536d4217ba7a3b0f11bf6b36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd900ce5536d4217ba7a3b0f11bf6b36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd900ce5536d4217ba7a3b0f11bf6b36"}}, "title": "Comparative gene expression pattern of immune-related genes using dual-color RT-MLPA in the lesions of cutaneous leishmaniasis caused by L. major and L. tropica.", "authors": [{"family": "Masoudzadeh", "given": "Nasrin", "initials": "N"}, {"family": "Ait Kbaich", "given": "Mouad", "initials": "M"}, {"family": "van Veen", "given": "Suzanne", "initials": "S"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "C Haks", "given": "Marielle", "initials": "M"}, {"family": "Persson", "given": "Josefine", "initials": "J"}, {"family": "Mashayekhi Goyonlo", "given": "Vahid", "initials": "V"}, {"family": "Hadifar", "given": "Shima", "initials": "S"}, {"family": "Erfanian Salim", "given": "Reza", "initials": "R"}, {"family": "Mhaidi", "given": "Idris", "initials": "I"}, {"family": "Riyad", "given": "Myriam", "initials": "M"}, {"family": "Akarid", "given": "Khadija", "initials": "K"}, {"family": "M Harandi", "given": "Ali", "initials": "A"}, {"family": "Hm Ottenhoff", "given": "Tom", "initials": "T"}, {"family": "Lemrani", "given": "Meryem", "initials": "M"}, {"family": "Rafati", "given": "Sima", "initials": "S", "orcid": "0000-0002-7221-1320", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffd9442ba99f414ea54bd670c8453e8e.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "PLoS Negl Trop Dis", "issn": "1935-2735", "volume": "19", "issue": "3", "pages": "e0012812", "issn-l": "1935-2727"}, "abstract": "Cutaneous leishmaniasis (CL) is the most prevalent type of leishmaniasis disease and causes skin lesions, mainly ulcers, on exposed parts of the body. The Americas, Mediterranean basin, Middle East, and Central Asia account for approximately 95% of all CL cases. Leishmania (L.) major and L. tropica are the most significant species causing CL. A better understanding of the molecular mechanisms of CL caused by Leishmania parasite species in patients' skin lesions may help inform intervention approaches. Using dual-color reverse transcriptase multiplex ligation-dependent probe amplification (dcRT-MLPA), we evaluated the expression of 144 host immune-related genes in lesions from CL patients infected with two Leishmania species, L. major and L. tropica, in Morocco and Iran, respectively. Distinct gene expression patterns were identified in the lesions of patients infected with L. major and L. tropica. The results revealed that L. tropica-infected patients had rather more significant gene expression than L. major-infected patients relative to healthy volunteers. However, CD14 and IFI6 (interferon alpha inducible protein 6), were two common genes expressed in the lesions of patients infected with L. major and L. tropica. Our analysis revealed that gene expression changes related to the IFN signaling pathway were significant in both lesion groups. This research advances our understanding of the host immune response to zoonotic and anthroponotic leishmaniasis and shows immune transcript signatures in the skin lesions of CL patients infected with L. major and L. tropica. These findings can inform further investigation into the processes underpinning immunity and immunopathology of CL caused by L. major and L. tropica.", "doi": "10.1371/journal.pntd.0012812", "pmid": "40100809", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11918365"}, {"db": "pii", "key": "PNTD-D-24-00402"}], "notes": [], "created": "2025-07-08T13:55:43.500Z", "modified": "2025-11-04T11:37:05.277Z"}, {"entity": "publication", "iuid": "3f1de7a0b2cd41d5a9d11a02ffc1c93f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f1de7a0b2cd41d5a9d11a02ffc1c93f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f1de7a0b2cd41d5a9d11a02ffc1c93f"}}, "title": "Commonly prescribed multi-medication therapies exert sex-specific effects on Alzheimer's disease pathology and metabolomic profiles in AppNL-G-F mice: Implications for personalized therapeutics in aging.", "authors": [{"family": "Eroli", "given": "Francesca", "initials": "F"}, {"family": "Johnell", "given": "Kristina", "initials": "K"}, {"family": "Acararicin", "given": "Zeynep", "initials": "Z"}, {"family": "Tsagkogianni", "given": "Christina", "initials": "C"}, {"family": "Zerial", "given": "Stefania", "initials": "S"}, {"family": "Lancia", "given": "Saverio", "initials": "S"}, {"family": "Latorre-Leal", "given": "Maria", "initials": "M"}, {"family": "Alanko", "given": "Vilma", "initials": "V"}, {"family": "Hilmer", "given": "Sarah N", "initials": "SN"}, {"family": "Matton", "given": "Anna", "initials": "A"}, {"family": "Wastesson", "given": "Jonas W", "initials": "JW"}, {"family": "Cedazo-Minguez", "given": "Angel", "initials": "A"}, {"family": "Maioli", "given": "Silvia", "initials": "S"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Alzheimers Dement", "issn": "1552-5279", "volume": "21", "issue": "3", "pages": "e70081", "issn-l": null}, "abstract": "Polypharmacy is common among older adults and people with dementia. Multi-medication therapy poses risks of harm but also targets comorbidities and risk factors associated with dementia, offering therapeutic potential.\n\nWe evaluated the effects of two polypharmacy regimens and monotherapies on male and female AppNL-G-F knock-in mice. We assessed functional, emotional, and cognitive outcomes;amyloid pathology; and serum metabolomics profiles.\n\nA combination of metoprolol, simvastatin, aspirin, paracetamol, and citalopram improved memory, reduced amyloid burden and neuroinflammation, and modulated AD-associated metabolomic signatures in male mice, with negligible effects in female mice. Substituting two cardiovascular drugs impacted emotional domains but worsened memory, predominantly in female mice. In males, monotherapies could not explain the combination effects, suggesting drug synergy, whereas in female mice, certain monotherapy effects were lost when combined.\n\nThis study uncovers the sex-specific effects of polypharmacy in an AD model, identifying mechanisms and biomarkers that can guide gender-specific use of medicines in dementia prevention and management.\n\nTwo polypharmacy combinations show sex-specific effects on AD pathology and serum metabolomic profiles. Metoprolol+simvastatin+aspirin+paracetamol+citalopram improves memory and amyloid pathology in male mice. Replacing metoprolol and simvastatin with enalapril and atorvastatin eliminates benefits in male mice and impairs memory in female mice. Selected monotherapies produce sex-specific effects but only partially explain the outcomes of the combinations. Metabolomic pathways in serum indicate possible mechanisms and biomarkers for evaluating the effectiveness and safety of personalized therapies in aging and dementia.", "doi": "10.1002/alz.70081", "pmid": "40145346", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11947741"}], "notes": [], "created": "2025-11-18T12:07:34.066Z", "modified": "2025-11-18T12:07:36.222Z"}, {"entity": "publication", "iuid": "35f8f501e005484788d085fd0b0a9d6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35f8f501e005484788d085fd0b0a9d6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35f8f501e005484788d085fd0b0a9d6f"}}, "title": "Closed and open structures of the eukaryotic magnesium channel Mrs2 reveal the auto-ligand-gating regulation mechanism.", "authors": [{"family": "Li", "given": "Ping", "initials": "P", "orcid": "0000-0002-7364-3301", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cc17e1d61cb498b88038a9f5dfa6aff.json"}}, {"family": "Liu", "given": "Shiyan", "initials": "S"}, {"family": "Wallerstein", "given": "Johan", "initials": "J"}, {"family": "Villones", "given": "Rhiza Lyne E", "initials": "RLE"}, {"family": "Huang", "given": "Peng", "initials": "P"}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}, {"family": "Meloni", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4976-1401", "researcher": {"href": "https://publications.scilifelab.se/researcher/24f1558274e845e7a7351c62d8f627fe.json"}}, {"family": "Lu", "given": "Kefeng", "initials": "K", "orcid": "0000-0001-8200-9380", "researcher": {"href": "https://publications.scilifelab.se/researcher/d38d6efdc9744554b14b3370196467b8.json"}}, {"family": "Steen Jensen", "given": "Kristine", "initials": "K", "orcid": "0000-0001-9174-8361", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b573ed9dbd440c6b4cda217120ff974.json"}}, {"family": "Liin", "given": "Sara I", "initials": "SI", "orcid": "0000-0001-8493-0114", "researcher": {"href": "https://publications.scilifelab.se/researcher/e82a591108f24dcabf50779d88fc8844.json"}}, {"family": "Gourdon", "given": "Pontus", "initials": "P", "orcid": "0000-0002-8631-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dc6cdbbcab048fab7a65df6cb796aab.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "32", "issue": "3", "pages": "491-501", "issn-l": "1545-9985"}, "abstract": "The CorA/Mrs2 family of pentameric proteins are cardinal for the influx of Mg2+ across cellular membranes, importing the cation to mitochondria in eukaryotes. Yet, the conducting and regulation mechanisms of permeation remain elusive, particularly for the eukaryotic Mrs2 members. Here, we report closed and open Mrs2 cryo-electron microscopy structures, accompanied by functional characterization. Mg2+ flux is permitted by a narrow pore, gated by methionine and arginine residues in the closed state. Transition between the conformations is orchestrated by two pairs of conserved sensor-serving Mg2+-binding sites in the mitochondrial matrix lumen, located in between monomers. At lower levels of Mg2+, these ions are stripped, permitting an alternative, symmetrical shape, maintained by the RDLR motif that replaces one of the sensor site pairs in the open conformation. Thus, our findings collectively establish the molecular basis for selective Mg2+ influx of Mrs2 and an auto-ligand-gating regulation mechanism.", "doi": "10.1038/s41594-024-01432-1", "pmid": "39609652", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11919701"}, {"db": "pii", "key": "10.1038/s41594-024-01432-1"}], "notes": [], "created": "2024-11-29T18:28:28.359Z", "modified": "2025-10-25T10:16:19.762Z"}, {"entity": "publication", "iuid": "457d855f29f74d89929c33a7f0fed43b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/457d855f29f74d89929c33a7f0fed43b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/457d855f29f74d89929c33a7f0fed43b"}}, "title": "Cardio-metabolic-related plasma proteins reveal biological links between cardiovascular diseases and fragility fractures: a cohort and Mendelian randomisation investigation.", "authors": [{"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Zheng", "given": "Rui", "initials": "R"}, {"family": "Baron", "given": "John A", "initials": "JA"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Wolk", "given": "Alicja", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "H\u00f6ijer", "given": "Jonas", "initials": "J"}, {"family": "Brunius", "given": "Carl", "initials": "C"}, {"family": "Warensj\u00f6 Lemming", "given": "Eva", "initials": "E"}, {"family": "Titova", "given": "Olga E", "initials": "OE"}, {"family": "Svennblad", "given": "Bodil", "initials": "B"}, {"family": "Larsson", "given": "Susanna C", "initials": "SC"}, {"family": "Yuan", "given": "Shuai", "initials": "S"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Brooke", "given": "Hannah L", "initials": "HL"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "113", "pages": "105580", "issn-l": "2352-3964"}, "abstract": "How cardiovascular diseases (CVD) predispose to a higher risk of fragility fractures is not well understood. Both contribute to significant components of disease burden and health expenditure. Poor bone quality, central obesity, sarcopenia, falls, and low grip strength are independent risk factors for hip and other fragility fractures and also for CVD and early death.\n\nWe used proteomics and a cohort design combined with Mendelian randomisation analysis to understand shared mechanisms for developing CVD and fragility fractures, two significant sources of disease burden and health expenditure. We primarily aimed to discover and replicate the association of 274 cardio-metabolic-related proteins with future rates of hip and any fracture in two separate population-based cohorts, with a total of 12,314 women and men.\n\nThe average age at baseline was 68 years in the discovery cohort of women and 74 years in the mixed-sex replication cohort. During 100,619 person-years of follow-up, 2168 had any fracture, and 538 had a hip fracture. Our analysis resulted in 24 cardiometabolic proteins associated with fracture risk: 20 with hip fracture, 9 with any fracture, and 5 with both. The associations remained even if protein concentrations were measured from specimens taken during preclinical stages of cardio-metabolic diseases, and 19 associations remained after adjustment for bone mineral density. Twenty-two of the proteins were associated with total body fat mass or lean body mass. Mendelian randomisation (MR) analysis supported causality since genetically predicted levels of SOST (Sclerostin), CCDC80 (Coiled-coil domain-containing protein 80), NT-proBNP (N-terminal prohormone brain natriuretic peptide), and BNP (Brain natriuretic peptide) were associated with risk of hip fracture. MR analysis also revealed a possible negative impact on bone mineral density (BMD) by genetically predicted higher levels of SOST, CCDC80, and TIMP4 (Metalloproteinase inhibitor 4). The MR association with BMD was positive for PTX3 (Pentraxin-related protein) and SPP1 (Osteopontin). Genetically predicted higher concentrations of SOST and lower concentrations of SPP1 also conferred a higher risk of falls and lowered grip strength. The genetically determined concentration of nine proteins influenced fat mass, and one influenced lean body mass.\n\nThese data reveal biological links between cardiovascular diseases and fragility fractures. The proteins should be further evaluated as shared targets for developing pharmacological interventions to prevent fractures and cardiovascular disease.\n\nThe study was supported by funding from the Swedish Research Council (https://www.vr.se; grants No. 2015-03257, 2017-00644, 2017-06100, and 2019-01291 to Karl Micha\u00eblsson) and funding from Olle Engkvist Byggm\u00e4stares stiftelse (SOEB).", "doi": "10.1016/j.ebiom.2025.105580", "pmid": "39919333", "labels": {"Affinity Proteomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11848109"}, {"db": "pii", "key": "S2352-3964(25)00024-6"}], "notes": [], "created": "2025-11-25T19:21:08.458Z", "modified": "2025-11-28T10:42:48.747Z"}, {"entity": "publication", "iuid": "e65ee69679804c9db4f4b460585bd4d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e65ee69679804c9db4f4b460585bd4d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e65ee69679804c9db4f4b460585bd4d7"}}, "title": "Ultra-Sensitive Detection of Bacterial Spores via SERS.", "authors": [{"family": "Segervald", "given": "Jonas", "initials": "J", "orcid": "0009-0002-9248-5748", "researcher": {"href": "https://publications.scilifelab.se/researcher/283c709a8ce74c118e3e1710814fb018.json"}}, {"family": "Malyshev", "given": "Dmitry", "initials": "D", "orcid": "0000-0002-0496-6692", "researcher": {"href": "https://publications.scilifelab.se/researcher/a36e950e3dd143339cf3d246a63ab117.json"}}, {"family": "\u00d6berg", "given": "Rasmus", "initials": "R", "orcid": "0000-0002-0168-0197", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23b2e0213244a598ab42d29c9dbea24.json"}}, {"family": "Z\u00e4ll", "given": "Erik", "initials": "E"}, {"family": "Jia", "given": "Xueen", "initials": "X"}, {"family": "W\u00e5gberg", "given": "Thomas", "initials": "T", "orcid": "0000-0002-5080-8273", "researcher": {"href": "https://publications.scilifelab.se/researcher/1614ac6527654be8b0e15fd079cb4233.json"}}, {"family": "Andersson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9835-3263", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe860af5d944447086cbf2d00e3beb3e.json"}}], "type": "journal article", "published": "2025-02-28", "journal": {"title": "ACS Sens.", "issn": "2379-3694", "volume": "10", "issue": "2", "pages": "1237-1248", "issn-l": "2379-3694"}, "abstract": "Bacterial spores are highly resilient and capable of surviving extreme conditions, making them a persistent threat in contexts such as disease transmission, food safety, and bioterrorism. Their ability to withstand conventional sterilization methods necessitates rapid and accurate detection techniques to effectively mitigate the risks they present. In this study, we introduce a surface-enhanced Raman spectroscopy (SERS) approach for detecting Bacillus thuringiensis spores by targeting calcium dipicolinate acid (CaDPA), a biomarker uniquely associated with bacterial spores. Our method uses probe sonication to disrupt spores, releasing their CaDPA, which is then detected by SERS on drop-dried supernatant mixed with gold nanorods. This simple approach enables the selective detection of CaDPA, distinguishing it from other spore components and background noise. We demonstrate detection of biogenic CaDPA from concentrations as low as 103 spores/mL, with sensitivity reaching beyond CaDPA levels of a single spore. Finally, we show the method's robustness by detecting CaDPA from a realistic sample of fresh milk mixed with spores. These findings highlight the potential of SERS as a sensitive and specific technique for bacterial spore detection, with implications for fields requiring rapid and reliable spore identification.", "doi": "10.1021/acssensors.4c03151", "pmid": "39847439", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11877637"}], "notes": [], "created": "2025-01-30T11:37:25.468Z", "modified": "2025-11-03T12:41:02.712Z"}, {"entity": "publication", "iuid": "c130f0ff51454fccb12fbb55363f71e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c130f0ff51454fccb12fbb55363f71e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c130f0ff51454fccb12fbb55363f71e4"}}, "title": "Therapeutic Potential of STE20-Type Kinase STK25 Inhibition for the Prevention and Treatment of Metabolically Induced Hepatocellular Carcinoma.", "authors": [{"family": "Xia", "given": "Ying", "initials": "Y"}, {"family": "Caputo", "given": "Mara", "initials": "M"}, {"family": "Andersson", "given": "Emma", "initials": "E"}, {"family": "Asiedu", "given": "Bernice", "initials": "B"}, {"family": "Zhang", "given": "Jingjing", "initials": "J"}, {"family": "Hou", "given": "Wei", "initials": "W"}, {"family": "Amrutkar", "given": "Manoj", "initials": "M"}, {"family": "Cansby", "given": "Emmelie", "initials": "E"}, {"family": "Gul", "given": "Nadia", "initials": "N"}, {"family": "Gemmink", "given": "Anne", "initials": "A"}, {"family": "Myers", "given": "Caitlyn", "initials": "C"}, {"family": "Aghajan", "given": "Mariam", "initials": "M"}, {"family": "Booten", "given": "Sheri", "initials": "S"}, {"family": "Hoy", "given": "Andrew J", "initials": "AJ"}, {"family": "H\u00e4rtlova", "given": "Anetta", "initials": "A"}, {"family": "Lindahl", "given": "Per", "initials": "P"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A"}, {"family": "Schaart", "given": "Gert", "initials": "G"}, {"family": "Hesselink", "given": "Matthijs K C", "initials": "MKC"}, {"family": "Peter", "given": "Andreas", "initials": "A"}, {"family": "Murray", "given": "Sue", "initials": "S"}, {"family": "Mahlapuu", "given": "Margit", "initials": "M"}], "type": "journal article", "published": "2025-02-28", "journal": {"title": "Cellular and Molecular Gastroenterology and Hepatology", "issn": "2352-345X", "volume": "19", "issue": "7", "pages": "101485", "issn-l": "2352-345X"}, "abstract": "Hepatocellular carcinoma (HCC) is a rapidly growing malignancy with high mortality. Recently, metabolic dysfunction-associated steatohepatitis (MASH) has emerged as a major HCC catalyst; however, signals driving transition of MASH to HCC remain elusive and treatment options are limited. Herein, we investigated the role of STE20-type kinase STK25, a critical regulator of hepatocellular lipotoxic milieu and MASH susceptibility, in the initiation and progression of MASH-related HCC.\n\nThe clinical relevance of STK25 in HCC was assessed in publicly available datasets and by RT-qPCR and proximity ligation assay in a validation cohort. The functional significance of STK25 silencing in human hepatoma cells was evaluated in vitro and in a subcutaneous xenograft mouse model. The therapeutic potential of STK25 antagonism was examined in a mouse model of MASH-driven HCC, induced by a single diethylnitrosamine injection combined with a high-fat diet.\n\nAnalysis of public databases and in-house cohorts revealed that STK25 expression in human liver biopsies positively correlated with HCC incidence and severity. The in vitro silencing of STK25 in human hepatoma cells suppressed proliferation, migration, and invasion with efficacy comparable to that achieved by anti-HCC drugs sorafenib or regorafenib. STK25 knockout in human hepatoma cells also blocked tumor formation and growth in a subcutaneous xenograft mouse model. Furthermore, pharmacologic inhibition of STK25 with antisense oligonucleotides-administered systemically or hepatocyte-specifically-efficiently mitigated the development and exacerbation of hepatocarcinogenesis in a mouse model of MASH-driven HCC.\n\nThis study underscores STK25 antagonism as a promising therapeutic strategy for the prevention and treatment of HCC in the context of MASH.", "doi": "10.1016/j.jcmgh.2025.101485", "pmid": "40024534", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12022666"}, {"db": "pii", "key": "S2352-345X(25)00026-8"}], "notes": [], "created": "2025-11-05T13:58:47.588Z", "modified": "2025-11-05T13:58:47.594Z"}, {"entity": "publication", "iuid": "5e9bfb4d2aac4d3b827631ccd1bfd299", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e9bfb4d2aac4d3b827631ccd1bfd299.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e9bfb4d2aac4d3b827631ccd1bfd299"}}, "title": "Human adaptation in the Andes Mountains", "authors": [{"family": "De Loma", "given": "Jessica", "initials": "J"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Tirado", "given": "Noemi", "initials": "N"}, {"family": "Ascui", "given": "Franz", "initials": "F"}, {"family": "Parada", "given": "Luis A", "initials": "LA"}, {"family": "Gardon", "given": "Jacques", "initials": "J"}, {"family": "Schlebusch", "given": "Carina", "initials": "C"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal-article", "published": "2025-02-28", "journal": {"title": "Hum Popul Genet Genom", "issn": "2770-5005", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.47248/hpgg2505010002", "pmid": null, "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T06:53:08.875Z", "modified": "2025-11-19T08:10:24.832Z"}, {"entity": "publication", "iuid": "7e61a1bb95354373a3a6f1dd1b5438bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e61a1bb95354373a3a6f1dd1b5438bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e61a1bb95354373a3a6f1dd1b5438bb"}}, "title": "Characterization and description of Clostridium filamentum ETTB, a novel gut bacterium with TLR5 modulating properties", "authors": [{"family": "Makki", "given": "Kassem", "initials": "K", "orcid": "0000-0002-7488-3411", "researcher": {"href": "https://publications.scilifelab.se/researcher/471da96cf7324c0bb45f8d2fb6b66fbc.json"}}, {"family": "Martino", "given": "Maria Elena", "initials": "ME"}, {"family": "Alberdi", "given": "Antton", "initials": "A"}, {"family": "Aizpurua", "given": "Ostaizka", "initials": "O"}, {"family": "Quagliariello", "given": "Andrea", "initials": "A"}, {"family": "Olsson", "given": "Lisa", "initials": "L"}, {"family": "Clasen", "given": "Sara", "initials": "S"}, {"family": "J\u00f6nsson", "given": "Johanna", "initials": "J"}, {"family": "Brolin", "given": "Harald", "initials": "H"}, {"family": "Dwibedi", "given": "Chinmay", "initials": "C", "orcid": "0000-0001-6416-4440", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b0dbf807be449da1856c0c018f13a3.json"}}, {"family": "Yang", "given": "Gaohua", "initials": "G"}, {"family": "Favero", "given": "Chiara", "initials": "C"}, {"family": "Bergh", "given": "Per Olof", "initials": "PO"}, {"family": "Schnupf", "given": "Pamela", "initials": "P"}, {"family": "Ley", "given": "Ruth", "initials": "R"}, {"family": "Khan", "given": "Muhammad Tanweer", "initials": "MT"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V", "orcid": "0000-0002-9150-4233", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ddf7701aaf4c01b160f2a1c596dc6f.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4871-8818", "researcher": {"href": "https://publications.scilifelab.se/researcher/1689878e0c5542d08d3e2d5043a6ce5c.json"}}], "type": "posted-content", "published": "2025-02-28", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.02.28.640726", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-05T13:54:11.274Z", "modified": "2025-12-18T19:19:32.052Z"}, {"entity": "publication", "iuid": "a0c095fc5e9e48d295cd22a998627f16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0c095fc5e9e48d295cd22a998627f16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0c095fc5e9e48d295cd22a998627f16"}}, "title": "Interpreting mammalian synonymous site conservation in light of the unwanted transcript hypothesis.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6be89ad73a14d66a3b9439efc9c4099.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2025-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2007", "issn-l": "2041-1723"}, "abstract": "Mammalian genomes are biased towards GC bases at third codon positions, likely due to a GC-biased ancestral genome and the selectively neutral recombination-related process of GC-biased gene conversion. The unwanted transcript hypothesis posits that this high GC content at synonymous sites may be beneficial for protecting against spurious transcripts, particularly in species with low effective population sizes. Utilising a 240 placental mammal genome alignment and single-base resolution conservation scores, we interpret sequence conservation at mammalian four-fold degenerate sites in this context and find evidence in support of the unwanted transcript hypothesis, including a strong GC bias, high conservation at sites relating to exon splicing, less human genetic variation at conserved four-fold degenerate sites, and conservation of sites important for epigenetic regulation of developmental genes. Additionally, we show that high conservation of four-fold degenerate sites in essential developmental genes, including homeobox genes, likely relates to the low mutation rates experienced by these genes.", "doi": "10.1038/s41467-025-57179-w", "pmid": "40011430", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11865589"}, {"db": "pii", "key": "10.1038/s41467-025-57179-w"}], "notes": [], "created": "2025-11-28T10:45:29.590Z", "modified": "2025-11-28T10:45:29.691Z"}, {"entity": "publication", "iuid": "e56cef1073d44c8eb0a86a421a968ac2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e56cef1073d44c8eb0a86a421a968ac2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e56cef1073d44c8eb0a86a421a968ac2"}}, "title": "Detection and genetic characterization of equine viruses in Sweden using viral metagenomics.", "authors": [{"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "K\u00e4llse", "given": "Annika", "initials": "A"}, {"family": "Riihim\u00e4ki", "given": "Miia", "initials": "M"}], "type": "journal article", "published": "2025-02-27", "journal": {"title": "BMC Vet Res", "issn": "1746-6148", "volume": "21", "issue": "1", "pages": "119", "issn-l": null}, "abstract": "Viral infections pose a significant challenge to the equine population, compromising welfare and causing substantial economic losses for the global equine industry. While numerous equine viral pathogens have been identified, many suspected viral infections remain undiagnosed. This highlights the need for further identification and characterization of viruses circulating within the equine population. In this study, we utilized viral metagenomics to investigate viruses present in serum samples and nasal swabs collected from horses in Sweden. The primary focus was on horses presenting with fever, although control horses were also included for comparison.\n\nThe viral metagenomic analysis identified several viruses in the investigated samples. Among nasal swabs, the majority of the viral reads were classified as various equine herpesvirues (EHVs), mainly EHV-2 and EHV-5. Other viruses in nasal swabs include but are not limited to EHV-4, Torque teno equus virus 1 (TTeqV1) and equine copiparvovirus (eqCopV). Both TTeqV1 and eqCopV were also detected in the serum samples together with equine circovirus and equine pegivirus. A number of the detected viruses were further genetically characterized and were shown to display high sequence similarity to viruses from the US and/or China. qPCR screening of a selected number of the detected viruses revealed a rather low detection rate (1.6%-9.4%) in individual horses.\n\nThis study identified several viruses that circulate in the horse population in Sweden, some of which have not been previously detected in Sweden or Europe. Furthermore, the complete or nearly complete genomes of several of these viruses have been genetically characterized. These new data provide a valuable foundation for developing improved detection assays and conducting larger prevalence studies to assess the potential impact of these viruses on the equine population. Such efforts could ultimately contribute to enhanced equine welfare.", "doi": "10.1186/s12917-025-04613-2", "pmid": "40011862", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11866639"}, {"db": "pii", "key": "10.1186/s12917-025-04613-2"}], "notes": [], "created": "2025-11-28T10:52:44.929Z", "modified": "2025-11-28T10:52:44.938Z"}, {"entity": "publication", "iuid": "fc055e8837224d21859377ef3fb0f37f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc055e8837224d21859377ef3fb0f37f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc055e8837224d21859377ef3fb0f37f"}}, "title": "Comprehensive genetic variant analysis reveals combination of KRAS and LRP1B as a predictive biomarker of response to immunotherapy in patients with non-small cell lung cancer.", "authors": [{"family": "Eklund", "given": "Ella A", "initials": "EA"}, {"family": "Svensson", "given": "Johanna", "initials": "J"}, {"family": "N\u00e4slund", "given": "Louise Stauber", "initials": "LS"}, {"family": "Yhr", "given": "Maria", "initials": "M"}, {"family": "Sayin", "given": "Sama I", "initials": "SI"}, {"family": "Wiel", "given": "Clotilde", "initials": "C"}, {"family": "Aky\u00fcrek", "given": "Levent M", "initials": "LM"}, {"family": "Torstensson", "given": "Per", "initials": "P"}, {"family": "Sayin", "given": "Volkan I", "initials": "VI"}, {"family": "Hallqvist", "given": "Andreas", "initials": "A"}, {"family": "Raghavan", "given": "Sukanya", "initials": "S"}, {"family": "Rohlin", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-02-27", "journal": {"title": "J. Exp. Clin. Cancer Res.", "issn": "1756-9966", "volume": "44", "issue": "1", "pages": "75", "issn-l": "1756-9966"}, "abstract": "In non-small cell lung cancer (NSCLC), the rapid advancement of predictive genetic testing of tumors by identifying specific pathogenic driver variants has significantly improved treatment guidance. However, immune checkpoint blockade (ICB) is typically administered to patients with tumors in the absence of such driver variants. Since only about 30% of patients will respond to ICB treatment, identifying novel genetic biomarkers of clinical response is crucial and will improve treatment decisions. This prospective clinical study aims to combine molecular biology, advanced bioinformatics and clinical data on response to treatment with ICB from a prospective cohort of NSCLC patients to identify single or combination of genetic variants in the tumor that can serve as predictive biomarkers of clinical response.\n\nIn this prospective bi-center clinical study, we performed next-generation sequencing (NGS) of 597 cancer-associated genes in a prospective cohort of 49 patients as the final cohort analyzed, with stage III or IV NSCLC, followed by establishment of an in-house developed bioinformatics-based molecular classification method that integrates, interprets and evaluates data from multiple databases and variant prediction tools. Overall survival (OS) and progression-free survival (PFS) were analyzed for selected candidate genes and variants identified using our novel methodology including molecular tools, databases and clinical information.\n\nOur novel molecular interpretation and classification method identified high impact variants in frequently altered genes KRAS, LRP1B, and TP53. Analysis of these genes as single predictive biomarkers in ICB-treated patients revealed that the presence of likely pathogenic variants and variants of unclear significance in LRP1B was associated with improved OS (p = 0.041). Importantly, further analysis of variant combinations in the tumor showed that co-occurrence of KRAS and LRP1B variants significantly improved OS (p = 0.003) and merged PFS (p = 0.008). Notably, the triple combination of variants in KRAS, LRP1B, and TP53 positively impacted both OS (p = 0.026) and merged PFS (p = 0.003).\n\nThis study suggests that combination of the LRP1B and KRAS variants identified through our novel molecular classification scheme leads to better outcomes following ICB treatment in NSCLC. The addition of TP53 improves the outcome even further. To our knowledge, this is the first report indicating that harboring a combination of KRAS, LRP1B, and TP53 variants can significantly enhance the response to ICB, suggesting a novel predictive biomarker combination for NSCLC patients.", "doi": "10.1186/s13046-025-03342-6", "pmid": "40011914", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11866712"}, {"db": "pii", "key": "10.1186/s13046-025-03342-6"}], "notes": [], "created": "2025-07-08T13:54:20.556Z", "modified": "2025-11-04T11:34:56.412Z"}, {"entity": "publication", "iuid": "fcaf83e14171434292e517ec5c5af2a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcaf83e14171434292e517ec5c5af2a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcaf83e14171434292e517ec5c5af2a8"}}, "title": "Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening.", "authors": [{"family": "Vaivade", "given": "Aina", "initials": "A"}, {"family": "Erngren", "given": "Ida", "initials": "I", "orcid": "0000-0001-7867-9525", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8a16aaaf5194acba6b8649690a101d8.json"}}, {"family": "Carlsson", "given": "Henrik", "initials": "H", "orcid": "0000-0001-5558-6641", "researcher": {"href": "https://publications.scilifelab.se/researcher/de9581804a0b4b22991b34ebe89e9017.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Emami Khoonsari", "given": "Payam", "initials": "P"}, {"family": "Noui", "given": "Yassine", "initials": "Y", "orcid": "0000-0002-0513-7546", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e4b7066daf4084b24fdbbac41e3c9e.json"}}, {"family": "Al-Grety", "given": "Asma", "initials": "A"}, {"family": "\u00c5kerfeldt", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Gallo", "given": "Valentina", "initials": "V"}, {"family": "Larsson", "given": "Anders Olof", "initials": "AO"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Hedstr\u00f6m", "given": "Anna Karin", "initials": "AK", "orcid": "0000-0002-6612-4749", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4a1c4b315cd4a09b8f98a87b6cd2fba.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Burman", "given": "Joachim", "initials": "J", "orcid": "0000-0002-7045-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b9b82661abc49baaeac34bfcfc45321.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}], "type": "journal article", "published": "2025-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2014", "issn-l": "2041-1723"}, "abstract": "Exposure to per- and polyfluorinated substances (PFAS) and hydroxylated polychlorinated biphenyls (OH-PCBs) is associated with adverse human health effects, including immunosuppression. It is unknown if these substances can affect the course of autoimmune diseases. This study was based on 907 individuals with multiple sclerosis (MS) and 907 matched controls, where the MS cases were followed longitudinally using the Swedish MS register. We demonstrate sex- and disease-specific differences in serum PFAS concentrations between individuals with MS and controls. Moreover, two OH-PCBs (4-OH-CB187 and 3-OH-CB153) are associated with an increased risk of developing multiple sclerosis, regardless of sex and immigration status. With a clinical follow-up time of up to 18 years, an increase in serum concentrations of perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS), and perfluorodecanoic acid (PFDA) decreases the risk of confirmed disability worsening in both sexes, as well as perfluoroheptanesulfonic acid (PFHpS) and perfluorononanoic acid (PFNA), only in males with MS. These results show previously unknown associations between OH-PCBs and the risk of developing MS, as well as the inverse associations between PFAS exposure and the risk of disability worsening in MS.", "doi": "10.1038/s41467-025-57172-3", "pmid": "40016224", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-57172-3"}], "notes": [], "created": "2025-03-01T11:13:17.025Z", "modified": "2025-03-24T08:20:33.179Z"}, {"entity": "publication", "iuid": "42d2bb44130c40a9a57616496fc17474", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42d2bb44130c40a9a57616496fc17474.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42d2bb44130c40a9a57616496fc17474"}}, "title": "Yellow barley xan-m mutants are deficient in the motor unit SECA1 of the SEC1 translocase system.", "authors": [{"family": "Stuart", "given": "David", "initials": "D"}, {"family": "Ivanova", "given": "Anastasiia", "initials": "A"}, {"family": "Zakhrabekova", "given": "Shakhira", "initials": "S"}, {"family": "Hansson", "given": "Mats", "initials": "M", "orcid": "0000-0002-0168-9968", "researcher": {"href": "https://publications.scilifelab.se/researcher/63440c24a3874af18614b26ac550e5cc.json"}}], "type": "journal article", "published": "2025-02-26", "journal": {"title": "Planta", "issn": "1432-2048", "volume": "261", "issue": "4", "pages": "68", "issn-l": "0032-0935"}, "abstract": "Chloroplast protein transport depends on the SEC1 translocase. Barley xan-m mutants, deficient in SECA1, lack chlorophyll and die as seedlings. Their yellow phenotype indicates that carotenoid chemistry is less SEC1-dependent. Chloroplast proteins encoded by genes located in the cell nucleus need to be transported across up to three chloroplast membranes to find its correct location. SEC1 is one of the major translocase systems. In plants, SEC1 consists of three proteins (SECA1, SECY1 and SECE1) and transports substrate proteins over the thylakoid membrane. SECA1 is an ATPase that delivers the substrate protein to the SECY1-SECE1 channel. In the present study, we analyzed five allelic barley xan-m mutants, which had been isolated between 1925 and 1957. The mutants belong to a larger collection of barley mutants deficient in chlorophyll biosynthesis and chloroplast development. Mutations in the xan-m gene are recessive and result in a yellow phenotype due to lack of chlorophyll and presence of carotenoids. Mutant seedlings die after approximately 10 days. We identified the defective gene in the xan-m mutants by a variant of bulk segregant analysis. The gene xan-m is an orthologue of SECA1 in Arabidopsis. Previously, only genes related to chlorophyll biosynthesis have been identified in the collection of barley xan mutants. The yellow phenotype of the mutants demonstrates that proteins responsible for carotenoid biosynthesis and storage are not or less dependent on an intact SEC1 translocase.", "doi": "10.1007/s00425-025-04654-9", "pmid": "40009246", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11865152"}, {"db": "pii", "key": "10.1007/s00425-025-04654-9"}], "notes": [], "created": "2025-09-08T06:54:56.835Z", "modified": "2025-11-14T11:05:42.039Z"}, {"entity": "publication", "iuid": "31cc2ec2f8a34c93b6d17050bec2d830", "links": {"self": {"href": "https://publications.scilifelab.se/publication/31cc2ec2f8a34c93b6d17050bec2d830.json"}, "display": {"href": "https://publications.scilifelab.se/publication/31cc2ec2f8a34c93b6d17050bec2d830"}}, "title": "Single-cell analysis of aplastic anemia reveals a convergence of NK and NK-like CD8+ T cells with a disease-associated TCR signature.", "authors": [{"family": "Lundgren", "given": "Sofie", "initials": "S", "orcid": "0000-0003-3146-9816", "researcher": {"href": "https://publications.scilifelab.se/researcher/3838050baa4847c5ad8edcd02b3b54e2.json"}}, {"family": "Huuhtanen", "given": "Jani", "initials": "J", "orcid": "0000-0003-2750-4033", "researcher": {"href": "https://publications.scilifelab.se/researcher/f982fef263e644799e27df3f31083d6c.json"}}, {"family": "Ker\u00e4nen", "given": "Mikko", "initials": "M", "orcid": "0000-0001-8027-499X", "researcher": {"href": "https://publications.scilifelab.se/researcher/065055dc206c4749b64c08e7414875b1.json"}}, {"family": "Feng", "given": "Xingmin", "initials": "X", "orcid": "0000-0001-8018-2366", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecf564243b464d919b534c054c6e5fee.json"}}, {"family": "Patel", "given": "Bhavisha A", "initials": "BA", "orcid": "0000-0002-2974-7701", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f42376804c4437fb68895915f369d39.json"}}, {"family": "Ryland", "given": "Georgina L", "initials": "GL", "orcid": "0000-0002-4990-0961", "researcher": {"href": "https://publications.scilifelab.se/researcher/891952aec8b442e1af79388838e73e05.json"}}, {"family": "Fox", "given": "Lucy C", "initials": "LC", "orcid": "0000-0002-3855-8232", "researcher": {"href": "https://publications.scilifelab.se/researcher/827f9263f0734c7ab1b757bc35758862.json"}}, {"family": "Bravo-Perez", "given": "Carlos", "initials": "C", "orcid": "0000-0001-9794-7847", "researcher": {"href": "https://publications.scilifelab.se/researcher/4260758112534ceba7efe94660a0a43e.json"}}, {"family": "Clemente", "given": "Michael", "initials": "M"}, {"family": "Kerr", "given": "Cassandra", "initials": "C"}, {"family": "Walldin", "given": "Gunilla", "initials": "G", "orcid": "0009-0005-6663-6540", "researcher": {"href": "https://publications.scilifelab.se/researcher/24fb888d0212421eaa2353ed6cc31ac7.json"}}, {"family": "Dufva", "given": "Olli", "initials": "O"}, {"family": "Zaimoku", "given": "Yoshitaka", "initials": "Y", "orcid": "0000-0002-4108-5245", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9bc97e77a35491197fa901757bd92f0.json"}}, {"family": "Tuononen", "given": "Tiina", "initials": "T", "orcid": "0009-0007-6677-3064", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c764c4bf7746fc9c6c468a51a5db52.json"}}, {"family": "Myllym\u00e4ki", "given": "Mikko", "initials": "M", "orcid": "0000-0002-8194-7356", "researcher": {"href": "https://publications.scilifelab.se/researcher/071c21748567437393dfb1b7c3bedad4.json"}}, {"family": "Ebeling", "given": "Freja", "initials": "F", "orcid": "0000-0002-7921-089X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5318f08e1aff4e988f961f1c7806d1bb.json"}}, {"family": "Jokinen", "given": "Emmi", "initials": "E", "orcid": "0000-0002-0060-6868", "researcher": {"href": "https://publications.scilifelab.se/researcher/8392afc052914d47ab93466ba898cbc8.json"}}, {"family": "Heinonen", "given": "Markus", "initials": "M", "orcid": "0000-0002-7741-2279", "researcher": {"href": "https://publications.scilifelab.se/researcher/8733ddf664b2445188aed518dab08873.json"}}, {"family": "Kasanen", "given": "Tiina", "initials": "T", "orcid": "0000-0002-5408-1948", "researcher": {"href": "https://publications.scilifelab.se/researcher/06fb270832244566bfc649d43f7e718c.json"}}, {"family": "Klievink", "given": "Jay", "initials": "J", "orcid": "0000-0002-4081-5840", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdad6fd259c749a5b3a770ae47c770cf.json"}}, {"family": "L\u00e4hteenm\u00e4ki", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6773-2677", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0cb9da3e4cb4430a779d4d4185e6652.json"}}, {"family": "Jaatinen", "given": "Taina", "initials": "T", "orcid": "0000-0001-7783-6189", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b981dc2e49a4731abc5ac1ee7bbfecf.json"}}, {"family": "Kyt\u00f6l\u00e4", "given": "Sari", "initials": "S", "orcid": "0000-0003-1649-8993", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e0b29c15c24626b529b3b1cab1ca1a.json"}}, {"family": "Siitonen", "given": "Sanna", "initials": "S", "orcid": "0009-0001-2241-6731", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c6a7c0c04f3451086c3b32d74da6ffa.json"}}, {"family": "Dulau-Florea", "given": "Alina", "initials": "A", "orcid": "0000-0003-3512-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/480fa59b41ab400d8eca304bf23c3332.json"}}, {"family": "Braylan", "given": "Raul", "initials": "R", "orcid": "0000-0001-6733-5161", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1ec596e60c542238a5ada29bb62fc51.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}, {"family": "Nakao", "given": "Shinji", "initials": "S", "orcid": "0000-0002-9674-624X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab2d147043454ff2b403f70bd60136e6.json"}}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-7839-3743", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf8d52e24234fa8b348ad08f58d1d48.json"}}, {"family": "Maciejewski", "given": "Jaroslaw P", "initials": "JP"}, {"family": "Blombery", "given": "Piers", "initials": "P"}, {"family": "Young", "given": "Neal S", "initials": "NS"}, {"family": "L\u00e4hdesm\u00e4ki", "given": "Harri", "initials": "H"}, {"family": "Mustjoki", "given": "Satu", "initials": "S", "orcid": "0000-0002-0816-8241", "researcher": {"href": "https://publications.scilifelab.se/researcher/03cdbac477284e7093121bc3d35a6dfb.json"}}], "type": "journal article", "published": "2025-02-26", "journal": {"title": "Sci Transl Med", "issn": "1946-6242", "volume": "17", "issue": "787", "pages": "eadl6758", "issn-l": "1946-6234"}, "abstract": "Immune aplastic anemia (AA) is a life-threatening bone marrow failure disorder driven by an autoimmune T cell attack against hematopoietic stem and progenitor cells (HSPCs). However, the exact autoantigen targets and role of other immune cells in the pathogenesis of AA are unknown. Here, we analyzed a cohort of 218 patients with AA using single-cell RNA and T cell receptor (TCR) \u03b1\u03b2 sequencing, TCR\u03b2 sequencing, flow cytometry, and plasma cytokine profiling. We identified natural killer (NK) cells and CD8+ terminally differentiated effector T (TEMRA) cells expressing NK receptors with AA-associated TCR\u03b2 motifs as the most dysregulated immune cell populations in AA bone marrow. Functional coculture experiments using primary HSPCs and immune cells showed that NK cells cannot kill HSPCs alone but may sensitize HSPCs to CD8+ T cell-mediated killing through production of interferons. Furthermore, HSPCs induced activation of T cell clones with CD8+ TEMRA NK-like phenotype in coculture. Our results reveal a convergent phenotype of innate and adaptive immune cells that may drive AA.", "doi": "10.1126/scitranslmed.adl6758", "pmid": "40009697", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:37:23.304Z", "modified": "2025-09-08T11:37:24.704Z"}, {"entity": "publication", "iuid": "8f813a953a47489dbce089b11fc24f50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f813a953a47489dbce089b11fc24f50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f813a953a47489dbce089b11fc24f50"}}, "title": "Duplexed CeTEAM drug biosensors reveal determinants of PARP inhibitor selectivity in cells.", "authors": [{"family": "Pires", "given": "Maria J", "initials": "MJ"}, {"family": "Alam", "given": "Seher", "initials": "S"}, {"family": "Lovric", "given": "Alen", "initials": "A"}, {"family": "Fabbrizi", "given": "Emanuele", "initials": "E"}, {"family": "Rotili", "given": "Dante", "initials": "D"}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}, {"family": "Valerie", "given": "Nicholas C K", "initials": "NCK", "orcid": "0000-0002-9423-964X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d90c5a1f924c8b97409934dec74b0b.json"}}], "type": "journal article", "published": "2025-02-26", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "pages": "108361", "issn-l": "0021-9258"}, "abstract": "Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) targeting PARP1 and PARP2 have revolutionized cancer therapy by selectively killing cancer cells with defective DNA repair. However, achieving PARP1 or PARP2-selective inhibitors is difficult due to structural homology. Selectivity profiling is typically done with purified proteins, but these lack the complexity of intracellular environments and could therefore be inaccurate. Here, we duplex PARP1 L713F-GFP and PARP2 L269A-mCherry cellular target engagement by accumulation of mutant (CeTEAM) drug biosensors to systematically characterize binding and cell cycle alterations of 27 PARPi. Our results reveal that most PARPi are equipotent for both PARPs, including the next-generation drug, senaparib. However, benzimidazole carboxamide (niraparib) derivatives demonstrated PARP1-selective tendencies, while pthalazinones (olaparib) favored PARP2. AZD5305, a reported PARP1-selective inhibitor with characteristics of both series, was the exception and appears \u223c1600-fold more potent towards PARP1. In agreement with current understanding, we see that trapping-associated S/G2-phase transitions positively correlate with PARP1/2 binding potency, while some potent binders, such as veliparib, did not - likely reflecting their allosteric influence on DNA retention. We also assessed the effect of the PARP1/2 active site component, histone PARylation factor 1 (HPF1), on intracellular PARPi binding and see that HPF1 depletion elicits slight deviations in apparent binding potency, while contributing additively to trapping-like phenotypes. The PARP1/2 CeTEAM platform thus provides a structural roadmap for the development of selective PARPi and should facilitate the discovery of targeted therapies. Furthermore, our results highlight that multiplexing CeTEAM biosensors and layered genetic perturbations can systematically profile determinants of intracellular drug selectivity.", "doi": "10.1016/j.jbc.2025.108361", "pmid": "40021124", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(25)00210-8"}], "notes": [], "created": "2025-03-14T14:15:13.223Z", "modified": "2025-10-17T13:04:26.850Z"}, {"entity": "publication", "iuid": "15fcc6be822e4aa68cd5cbc970867939", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15fcc6be822e4aa68cd5cbc970867939.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15fcc6be822e4aa68cd5cbc970867939"}}, "title": "Structure of the T=13 capsid of infectious pancreatic necrosis virus (IPNV)-a salmonid birnavirus.", "authors": [{"family": "Munke", "given": "Anna", "initials": "A", "orcid": "0000-0002-5510-2245", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd6d8030171420190aa65f3eb1ac4bd.json"}}, {"family": "Ahmed Abdelrahim Gamil", "given": "Amr", "initials": "A"}, {"family": "Mikalsen", "given": "Aase B", "initials": "AB", "orcid": "0000-0001-6367-9629", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3f7fbaf8774430ba38bb79a66e40a77.json"}}, {"family": "Wang", "given": "Han", "initials": "H"}, {"family": "Evensen", "given": "\u00d8ystein", "initials": "\u00d8", "orcid": "0000-0003-3538-3657", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd35b9aea23f463787ed9a78ae800906.json"}}, {"family": "Okamoto", "given": "Kenta", "initials": "K", "orcid": "0000-0002-4858-1196", "researcher": {"href": "https://publications.scilifelab.se/researcher/9302e76f16a04afdbb72f00c805bffa4.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "J. Virol.", "issn": "1098-5514", "pages": "e0145424", "volume": "99", "issue": "2", "issn-l": "0022-538X"}, "abstract": "Birnaviruses infect a broad range of vertebrate hosts, including fish and birds, and cause substantial economic losses in the fishery and livestock industries. The infectious pancreatic necrosis virus (IPNV), an aquabirnavirus, specifically infects salmonids. While structures on T=1 subviral particles of the birnaviruses, including IPNV, have been studied, structural insights into the infectious T=13 particles have been limited to the infectious bursal disease virus (IBDV), an avibirnavirus. Determining the capsid structure of the T=13 particle of IPNV is crucial for advancing knowledge of its antigenicity, capsid assembly, and possible functional structures. Here, the capsid structure of the IPNV L5 strain has been determined at a resolution of 2.75 \u00c5. The overall structure resembles the T=13 IBDV structure, with notable differences in the surface loops on the P domain of the VP2 capsid protein essential for antigenicity and virulence. Additionally, previously undescribed structural features have been identified, including the C-terminal regions of the VP2 subunits within the pentagonal assembly unit at each 5-fold axis, which interlock with adjacent VP2 subunits. This interlocking, together with class-averaged projections of triangular and pentagonal units, suggests that the pentagonal unit formation could be important for a correct T=13 particle assembly, preventing the formation of T=1 subviral particles. Furthermore, positively charged residues in obstructed capsid pores at each 5-fold axis are speculated to facilitate intraparticle genome synthesis of IPNV.IMPORTANCEAquabirnaviruses cause deadly infectious diseases in salmonid fish, posing significant challenges for both wild and farmed fish populations. The most prevalent aquabirnavirus worldwide is the infectious pancreatic necrosis virus, whose multifunctional capsid is critical to its infection, replication, and maturation. Previously, research has focused on the structure of the virus' non-infectious subviral capsid. In this study, however, the first structure of the large, infectious, and functional form of the capsid has been determined. This new capsid structure reveals functional motifs that were previously unclear in the non-infectious capsid. These motifs are believed to be essential for the virus' replication and particle assembly, making them promising targets for developing strategies to control virus proliferation.", "doi": "10.1128/jvi.01454-24", "pmid": "39817769", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11853034"}], "notes": [], "created": "2025-01-20T09:02:04.842Z", "modified": "2025-11-13T10:40:54.346Z"}, {"entity": "publication", "iuid": "229f504c7e6941e88c6f4ae750d0bbcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/229f504c7e6941e88c6f4ae750d0bbcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/229f504c7e6941e88c6f4ae750d0bbcf"}}, "title": "Digital sequencing is improved by using structured unique molecular identifiers.", "authors": [{"family": "Micallef", "given": "Peter", "initials": "P"}, {"family": "Santamar\u00eda", "given": "Manuel Luna", "initials": "ML"}, {"family": "Escobar", "given": "Mandy", "initials": "M"}, {"family": "Andersson", "given": "Daniel", "initials": "D"}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T"}, {"family": "Mouhanna", "given": "Pia", "initials": "P"}, {"family": "Filges", "given": "Stefan", "initials": "S"}, {"family": "Johansson", "given": "Gustav", "initials": "G"}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "Vannas", "given": "Christoffer", "initials": "C"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "26", "issue": "1", "pages": "37", "issn-l": "1474-7596"}, "abstract": "Digital sequencing uses unique molecular identifiers (UMIs) to correct for polymerase induced errors and amplification biases. Here, we design 19 different structured UMIs to minimize the capacity of primers to form non-specific PCR products during library construction using SiMSen-Seq, a PCR-based digital sequencing approach with flexible multiplexing capabilities suitable for tumor-informed mutation analysis. All structured UMI designs demonstrate enhanced assay performance compared with an unstructured reference UMI. The best performing structured UMI design shows significant improvements in all tested aspects of assay and sequencing performance with the ability to reliable detect low variant allele frequencies.", "doi": "10.1186/s13059-025-03504-x", "pmid": "40001095", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11853513"}, {"db": "pii", "key": "10.1186/s13059-025-03504-x"}], "notes": [], "created": "2025-09-08T06:54:47.020Z", "modified": "2025-09-08T06:54:47.088Z"}, {"entity": "publication", "iuid": "7de26605147e4edb8845e6c78bddd3aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7de26605147e4edb8845e6c78bddd3aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7de26605147e4edb8845e6c78bddd3aa"}}, "title": "DNA methylation patterns contribute to changes of cellular differentiation pathways in leukocytes with LOY from patients with Alzheimer\u00b4s disease.", "authors": [{"family": "J\u0105kalski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-5481-9148", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4411ec776b94c89b0444bd8d49672ca.json"}}, {"family": "Bruhn-Olszewska", "given": "Bo\u017cena", "initials": "B", "orcid": "0000-0003-2141-0247", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa96509bbe94834858aee3c16d41b97.json"}}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Siedlar", "given": "Maciej", "initials": "M"}, {"family": "Baran", "given": "Jaros\u0142aw", "initials": "J"}, {"family": "W\u0119glarczyk", "given": "Kazimierz", "initials": "K"}, {"family": "Jaszczynski", "given": "Janusz", "initials": "J"}, {"family": "Ry\u015b", "given": "Janusz", "initials": "J"}, {"family": "Gedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Filipowicz", "given": "Natalia", "initials": "N"}, {"family": "Klich-R\u0105czka", "given": "Alicja", "initials": "A"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "Cell. Mol. Life Sci.", "issn": "1420-9071", "volume": "82", "issue": "1", "pages": "93", "issn-l": "1420-682X"}, "abstract": "Alzheimer's disease (AD) is a common and increasing societal problem due to the extending human lifespan. In males, loss of chromosome Y (LOY) in leukocytes is strongly associated with AD. We studied here DNA methylation and RNA expression in sorted monocytes and granulocytes with and without LOY from male AD patients. Through multi-omic analysis, we identified new candidate genes along with those previously associated with AD. Global analyses of DNA methylation in samples with LOY vs. normal state showed that hypomethylation dominated both in granulocytes and monocytes. Our findings highlight LOY-related differences in DNA methylation that occur in gene regulatory regions. Specifically, we observed alterations in key genes involved in leukocyte differentiation: FLI1, involved in early hematopoiesis; RUNX1, essential for blood cell development; RARA, regulating gene expression in response to retinoic acid; CANX, crucial for protein folding; CEBPB, a transcription factor important for immune responses; and MYADM, implicated in cell adhesion and migration. Moreover, protein-protein interaction analysis in granulocytes identified that products of two of these genes, CANX and CEBPB, are key hub proteins. This research underscores the potential of multi-omic approach in pure hematopoietic cell populations to uncover the molecular underpinnings of AD. Finally, our results link previous analysis showing impact of LOY on leukocyte differentiation, LOY-associated transcriptional dysregulation and GWAS studies of LOY.", "doi": "10.1007/s00018-025-05618-8", "pmid": "39998604", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11861481"}, {"db": "pii", "key": "10.1007/s00018-025-05618-8"}], "notes": [], "created": "2025-09-08T06:57:22.526Z", "modified": "2025-09-08T07:12:23.743Z"}, {"entity": "publication", "iuid": "82da1c79ab3d480f8ef86647b089b801", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82da1c79ab3d480f8ef86647b089b801.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82da1c79ab3d480f8ef86647b089b801"}}, "title": "Aberrant growth and expansion in Penium margaritaceum triggered by disruption of microtubules and the cell wall.", "authors": [{"family": "LoRicco", "given": "Josephine G", "initials": "JG", "orcid": "0000-0002-1550-2463", "researcher": {"href": "https://publications.scilifelab.se/researcher/edbbb3add76a4370b4037d1aaa8132dc.json"}}, {"family": "Malone", "given": "Stuart", "initials": "S"}, {"family": "Becker", "given": "Abigail", "initials": "A"}, {"family": "Xue", "given": "Nichole", "initials": "N"}, {"family": "Bagdan", "given": "Kaylee", "initials": "K", "orcid": "0000-0002-5060-4270", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f069d44c6094291a5452952b4209e66.json"}}, {"family": "Eastman", "given": "Anika", "initials": "A"}, {"family": "Sgambettera", "given": "Gabriel", "initials": "G"}, {"family": "Winegrad", "given": "Aaron", "initials": "A"}, {"family": "Gibeau", "given": "Benjamin", "initials": "B"}, {"family": "Bauer", "given": "Lindsay", "initials": "L"}, {"family": "Epstein", "given": "Ruby", "initials": "R"}, {"family": "Domozych", "given": "David S", "initials": "DS", "orcid": "0000-0001-8800-0061", "researcher": {"href": "https://publications.scilifelab.se/researcher/389412e319244f48955e4aeeac9ec616.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "76", "issue": "4", "pages": "961-979", "issn-l": "0022-0957"}, "abstract": "Penium margaritaceum, a unicellular zygnematophyte (Streptophyta), was employed to elucidate changes in cell expansion when cells were challenged with the fungal pectinolytic enzyme, pectate lyase, and/or the microtubule-disrupting agent, amiprophos-methyl (APM). Microtubule disruption by APM resulted in significant swelling at expansion zones. These swollen zones provided an easy marker for the location of expansion zones, particularly in cells with altered cell wall pectin. Short-term treatment with pectate lyase showed pectin degradation primarily at the isthmus expansion zone and two satellite bands, corresponding to the location of future expansion in daughter cells. When the homogalacturonan lattice of the cell wall was removed by treatment with pectate lyase during long treatments, cell division was maintained, but daughter cell products were considerably smaller. Treatment of cells with a mixture of both pectate lyase and APM resulted in a distinct phenotype, consisting of 'dumbbell'-shaped cells, as APM-induced swelling occurs at the novel expansion centers exposed by pectate lyase treatment. These cells also presented other curious alterations, including an extensive, chloroplast-free cytoplasmic zone at the center of the cell, a septum containing \u03b2-glycan, arabinogalactan and homogalacturonan epitopes, unique stacks of endoplasmic reticulum, displaced Golgi bodies, and an extensive network of vacuoles. These results provide insight into the importance of cell wall integrity in defining the location of cell growth and division in P. margaritaceum. Understanding these processes in a unicellular zygnematophyte may provide insights into steps involved in the evolution of land plants.", "doi": "10.1093/jxb/erae387", "pmid": "39269031", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "7756302"}], "notes": [], "created": "2024-11-15T12:08:05.360Z", "modified": "2025-11-05T13:54:08.964Z"}, {"entity": "publication", "iuid": "1ff33641093042958cf2612e484a087c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ff33641093042958cf2612e484a087c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ff33641093042958cf2612e484a087c"}}, "title": "A long-distance inhibitory system regulates haustoria numbers in parasitic plants.", "authors": [{"family": "Kokla", "given": "Anna", "initials": "A"}, {"family": "Leso", "given": "Martina", "initials": "M", "orcid": "0000-0003-4192-8027", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ec4323cecc7419a8bcf1b8bd98c58e6.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J"}, {"family": "W\u00e4rdig", "given": "Cecilia", "initials": "C"}, {"family": "Hayashi", "given": "Marina", "initials": "M"}, {"family": "Nishii", "given": "Naoshi", "initials": "N"}, {"family": "Tsuchiya", "given": "Yuichiro", "initials": "Y"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Melnyk", "given": "Charles W", "initials": "CW", "orcid": "0000-0003-3251-800X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd60bb90f97b42ca902c63ca66fbc96f.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "8", "pages": "e2424557122", "issn-l": "0027-8424"}, "abstract": "The ability of parasitic plants to withdraw nutrients from their hosts depends on the formation of an infective structure known as the haustorium. How parasites regulate their haustoria numbers is poorly understood, and here, we uncovered that existing haustoria in the facultative parasitic plants Phtheirospermum japonicum and Parentucellia viscosa suppressed the formation of new haustoria located on distant roots. Using Phtheirospermum, we found that this effect depended on the formation of mature haustoria and could be induced through the application of external nutrients. To understand the molecular basis of this root plasticity, we analyzed hormone response and found that existing infections upregulated cytokinin-responsive genes first at the haustoria and then more distantly in Phtheirospermum shoots. We observed that infections increased endogenous cytokinin levels in Phtheirospermum roots and shoots, and this increase appeared relevant since local treatments with exogenous cytokinins blocked the formation of both locally and distantly formed haustoria. In addition, local overexpression of a cytokinin-degrading enzyme in Phtheirospermum prevented this systemic interhaustoria repression and increased haustoria numbers locally. We propose that a long-distance signal produced by haustoria negatively regulates future haustoria, and in Phtheirospermum, such a signaling system is mediated by a local increase in cytokinin to regulate haustoria numbers and balance nutrient acquisition.", "doi": "10.1073/pnas.2424557122", "pmid": "39964721", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11874510"}], "notes": [], "created": "2025-11-18T12:13:53.745Z", "modified": "2025-11-18T12:13:53.824Z"}, {"entity": "publication", "iuid": "9a3465e3abdf475bb8a8318061d787de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a3465e3abdf475bb8a8318061d787de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a3465e3abdf475bb8a8318061d787de"}}, "title": "Lessons learnt from strain types, milking order, and mastitis pathogen transmission", "authors": [{"family": "Woudstra", "given": "Svenja", "initials": "S"}, {"family": "Gussmann", "given": "Maya Katrin", "initials": "MK"}, {"family": "Marina", "given": "Hector", "initials": "H"}, {"family": "Hansson", "given": "Ida", "initials": "I"}, {"family": "Kirkeby", "given": "Carsten Thure", "initials": "CT"}, {"family": "Kr\u00f6mker", "given": "Volker", "initials": "V"}, {"family": "Nielsen", "given": "Per Peetz", "initials": "PP"}, {"family": "Ren", "given": "Keni", "initials": "K"}, {"family": "R\u00f6nneg\u00e5rd", "given": "Lars", "initials": "L"}], "type": "journal-article", "published": "2025-02-24", "journal": {"title": "Front. Anim. Sci.", "issn": "2673-6225", "volume": "6", "issn-l": null}, "abstract": null, "doi": "10.3389/fanim.2025.1556831", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:54:23.898Z", "modified": "2025-11-28T10:54:23.901Z"}, {"entity": "publication", "iuid": "c99bc8e1a31143e2bd7fd1ef3ba8ab01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c99bc8e1a31143e2bd7fd1ef3ba8ab01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c99bc8e1a31143e2bd7fd1ef3ba8ab01"}}, "title": "Dissecting the properties of circulating IgG against streptococcal pathogens through a combined systems antigenomics-serology workflow", "authors": [{"family": "Gomez Toledo", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-2103-7158", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e9d9a5e2dc148c9bcdc07f2b4a17ebc.json"}}, {"family": "Chowdhury", "given": "Sounak", "initials": "S"}, {"family": "Hjortswang", "given": "Elisabeth", "initials": "E", "orcid": "0009-0003-9932-1751", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fcf5002d49b458f81cea775594e63fb.json"}}, {"family": "Sorrentino", "given": "James T", "initials": "JT"}, {"family": "Lewis", "given": "Nathan E", "initials": "NE", "orcid": "0000-0001-7700-3654", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8b8fb6dee874a178dd5c9d10d280982.json"}}, {"family": "Bl\u00e4ckberg", "given": "Anna", "initials": "A"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S", "orcid": "0000-0002-7694-285X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6416b323664f4126b70067193d7b8347.json"}}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S", "orcid": "0000-0003-4646-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfae5f64ec9d45e282cdfd038539fe25.json"}}, {"family": "Izadi", "given": "Arman", "initials": "A", "orcid": "0000-0002-0262-1017", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d6f1927cfc643818a0a3a1b8602af14.json"}}, {"family": "Olofsson", "given": "Berit", "initials": "B", "orcid": "0009-0009-0602-2183", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ad483473b044b7dbc7e6c61ef1c0a73.json"}}, {"family": "Nordenfelt", "given": "Pontus", "initials": "P", "orcid": "0000-0002-9481-9951", "researcher": {"href": "https://publications.scilifelab.se/researcher/7aa3418ab23a4ec48c037d6d6ddea5b5.json"}}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L", "orcid": "0000-0001-9885-9312", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e99f34fb854beb8d810b05fe941057.json"}}, {"family": "Rasmussen", "given": "Magnus", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad3c999da10c41e4a3afda2718815083.json"}}], "type": "journal-article", "published": "2025-02-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": null}, "abstract": null, "doi": "10.1038/s41467-025-57170-5", "pmid": null, "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-12-01T13:27:44.561Z", "modified": "2025-03-24T08:20:48.298Z"}, {"entity": "publication", "iuid": "fcbdbb2263e146be9fc848a187e93293", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcbdbb2263e146be9fc848a187e93293.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcbdbb2263e146be9fc848a187e93293"}}, "title": "Phage parasites targeting phage homologous recombinases provide antiviral immunity.", "authors": [{"family": "Debiasi-Anders", "given": "Gianluca", "initials": "G", "orcid": "0000-0003-0545-6579", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc915806f12e4653b8c28e751615f951.json"}}, {"family": "Qiao", "given": "Cuncun", "initials": "C", "orcid": "0000-0002-2642-3672", "researcher": {"href": "https://publications.scilifelab.se/researcher/adec2227b1f54401821231561e11d27e.json"}}, {"family": "Salim", "given": "Amrita", "initials": "A"}, {"family": "Li", "given": "Na", "initials": "N"}, {"family": "Mir-Sanchis", "given": "Ignacio", "initials": "I", "orcid": "0000-0002-6536-0045", "researcher": {"href": "https://publications.scilifelab.se/researcher/10c03ba1d83b4fbe8515cf2989b62149.json"}}], "type": "journal article", "published": "2025-02-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "1889", "issn-l": "2041-1723"}, "abstract": "Bacteria often carry multiple genes encoding anti-phage defense systems, clustered in defense islands and phage satellites. Various unrelated anti-phage defense systems target phage-encoded homologous recombinases (HRs) through unclear mechanisms. Here, we show that the phage satellite SaPI2, which does not encode orthodox anti-phage defense systems, provides antiviral immunity mediated by Stl2, the SaPI2-encoded transcriptional repressor. Stl2 targets and inhibits phage-encoded HRs, including Sak and Sak4, two HRs from the Rad52-like and Rad51-like superfamilies. Remarkably, apo Stl2 forms a collar of dimers oligomerizing as closed rings and as filaments, mimicking the quaternary structure of its targets. Stl2 decorates both Sak rings and Sak4 filaments. The oligomerization of Stl2 as a collar of dimers is necessary for its inhibitory activity both in vitro and in vivo. Our results shed light on the mechanisms underlying antiviral immunity against phages carrying divergent HRs.", "doi": "10.1038/s41467-025-57156-3", "pmid": "39987160", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11846896"}, {"db": "pii", "key": "10.1038/s41467-025-57156-3"}], "notes": [], "created": "2025-11-17T11:37:49.359Z", "modified": "2025-11-17T11:37:49.605Z"}, {"entity": "publication", "iuid": "631321ade8c64aee894b30aeb0022924", "links": {"self": {"href": "https://publications.scilifelab.se/publication/631321ade8c64aee894b30aeb0022924.json"}, "display": {"href": "https://publications.scilifelab.se/publication/631321ade8c64aee894b30aeb0022924"}}, "title": "Insights into metabolic changes during epidermal differentiation as revealed by multiphoton microscopy with fluorescence lifetime imaging.", "authors": [{"family": "Malak", "given": "Monika", "initials": "M"}, {"family": "Qian", "given": "Chen", "initials": "C"}, {"family": "James", "given": "Jeemol", "initials": "J"}, {"family": "Nair", "given": "Syam", "initials": "S"}, {"family": "Grantham", "given": "Julie", "initials": "J"}, {"family": "Ericson", "given": "Marica B", "initials": "MB"}], "type": "journal article", "published": "2025-02-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "6377", "issn-l": "2045-2322"}, "abstract": "Rapid developments in the field of organotypic cultures have generated a growing need for effective and non-invasive methods for quality control during tissue development. In this study, we correlate metabolic changes with epidermal differentiation and demonstrate that multiphoton microscopy with fluorescence lifetime imaging (MPM-FLIM) can be applied to monitor epidermal differentiation of keratinocytes with respect to proliferative and differentiated states. In a 2D keratinocyte tissue culture model, increased expression of differentiation markers keratin-1 and keratin-10 was induced with calcium supplementation. An accompanying shift from glycolysis to mitochondrial respiration was detected in metabolic flux assays. Analysis of MPM-FLIM images acquired at 750 nm and 900 nm excitation revealed a decreased relative fraction of intracellular NADH and FAD after high calcium treatment, consistent with increased oxidative phosphorylation. Epidermal differentiation could be monitored over a 96 h period. Discrimination analysis based on k-means clustering generated clusters that correlated well with the duration of high Ca2+ treatment, suggesting that MPM-FLIM can provide useful parameters for monitoring keratinocyte differentiation.", "doi": "10.1038/s41598-025-90101-4", "pmid": "39984626", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11845624"}, {"db": "pii", "key": "10.1038/s41598-025-90101-4"}], "notes": [], "created": "2025-11-05T13:54:13.831Z", "modified": "2025-11-05T13:54:13.868Z"}, {"entity": "publication", "iuid": "e09133a40d7145b18f9bb8facb4dc96c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e09133a40d7145b18f9bb8facb4dc96c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e09133a40d7145b18f9bb8facb4dc96c"}}, "title": "Comprehensive Gene Expression Analysis in Papillary Thyroid Carcinoma Reveals a Transcriptional Profile Associated with Reduced Radioiodine Avidity.", "authors": [{"family": "Condello", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4569-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/09be613118f743bd992bba237b61ceb4.json"}}, {"family": "Marchettini", "given": "Carlotta", "initials": "C"}, {"family": "Ihre-Lundgren", "given": "Catharina", "initials": "C"}, {"family": "Nilsson", "given": "Joachim N", "initials": "JN", "orcid": "0000-0001-7496-9189", "researcher": {"href": "https://publications.scilifelab.se/researcher/47b5460e0a2444c49675506d7f028784.json"}}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC", "orcid": "0000-0002-5945-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb660e24421749d4acaaf6e9a90042f8.json"}}], "type": "journal article", "published": "2025-02-21", "journal": {"title": "Endocr. Pathol.", "issn": "1559-0097", "volume": "36", "issue": "1", "pages": "4", "issn-l": "1046-3976"}, "abstract": "Papillary thyroid carcinoma (PTC) is the most common form of well-differentiated thyroid cancer (WDTC) and generally has a favorable prognosis. However, subsets of these tumors can metastasize, leading to aggressive disease progression and poorer clinical outcomes. Radioactive iodine (RAI) therapy is routinely given in the adjuvant setting following thyroidectomy and lymph node dissection for WDTC. Nevertheless, its therapeutic efficacy is limited to tumors with high iodine avidity. Early post-surgical classification of thyroid cancers as either iodine-avid or refractory is crucial for enabling more personalized and effective treatment strategies. In this study, we aimed to identify transcriptomic determinants associated with RAI refractoriness (RAI-R) to improve prognostication. We collected clinicopathologic data and conducted RNA-seq on 36 tissue samples (18 high-avidity and 18 low-avidity), each uniquely characterized by ex vivo iodine concentration measurements taken directly from surgical specimens. Whole-transcriptomic analysis identified 63 differentially expressed genes, with six (S100A4, CRTC2, ANO1, WWTR1, DEPTOR, MT1G) showing consistent deregulation. The expression of ANO1, an established iodine transporter at the apical membrane of the thyroid follicular cells, correlated significantly with iodine avidity (r = 0.54). Validation via RT-qPCR confirmed differential expression trends. Gene ontology and pathway enrichment analyses highlighted thyroid hormone synthesis, PI3K-AKT, and MAPK signaling pathways as key regulators of RAI avidity. A refined multivariate predictive model incorporating ANO1 mRNA expression, histological subtypes, and sample type demonstrated strong predictive performance (adjusted R2 = 0.55). These findings suggest ANO1 as a promising biomarker for predicting iodine avidity in thyroid cancer.", "doi": "10.1007/s12022-025-09849-0", "pmid": "39982585", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11845550"}, {"db": "pii", "key": "10.1007/s12022-025-09849-0"}], "notes": [], "created": "2025-05-12T05:46:47.965Z", "modified": "2025-09-08T07:13:03.100Z"}, {"entity": "publication", "iuid": "031dd715561244629454ed59ab2b7d5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/031dd715561244629454ed59ab2b7d5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/031dd715561244629454ed59ab2b7d5c"}}, "title": "The beneficial effects of a probiotic mix on bone and lean mass are dependent on the diet in female mice.", "authors": [{"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Lawenius", "given": "Lina", "initials": "L"}, {"family": "Jiang", "given": "Yiwen", "initials": "Y"}, {"family": "Horkeby", "given": "Karin", "initials": "K"}, {"family": "Wu", "given": "Jianyao", "initials": "J"}, {"family": "Nilsson", "given": "Karin H", "initials": "KH"}, {"family": "Koskela", "given": "Antti", "initials": "A"}, {"family": "Tuukkanen", "given": "Juha", "initials": "J"}, {"family": "Mov\u00e9rare-Skrtic", "given": "Sofia", "initials": "S"}, {"family": "Henning", "given": "Petra", "initials": "P"}, {"family": "Sj\u00f6gren", "given": "Klara", "initials": "K"}], "type": "journal article", "published": "2025-02-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "6182", "issn-l": "2045-2322"}, "abstract": "Bone mass and lean mass decrease with age and these changes are associated with increased fracture risk and sarcopenia. Previous studies demonstrated that a probiotic mixture of Lacticaseibacillus paracasei DSM13434, Lactiplantibacillus plantarum DSM 15312 and DSM 15313 (L. Mix) prevents bone loss in ovariectomized (ovx) female mice. The purpose of the present study is to test if the beneficial effect of L. Mix is modified by the diet. Female mice were fed either a high-fat (HFD, 60% kcal from fat) or a low-fat (LFD, 10% kcal from fat) diet and subjected to either sham or ovx surgery and treated with L. Mix for 12 weeks. L. Mix treatment increased total body bone mineral density (p \u2264 0.01), by increasing cortical bone area, and total body lean mass (p = 0.035) in mice on LFD but not in mice on HFD. Metagenome sequencing of cecal content showed that L. Mix treatment increased the relative abundance of Lacticaseibacillus paracasei and, Lactiplantibacillus plantarum, demonstrating successful treatment. In addition, the probiotic treatment affected the overall gut microbiota composition and functionality. These findings demonstrate that the L. Mix in combination with a healthy diet is beneficial for musculoskeletal health in female mice.", "doi": "10.1038/s41598-025-91056-2", "pmid": "39979617", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11842756"}, {"db": "pii", "key": "10.1038/s41598-025-91056-2"}], "notes": [], "created": "2025-07-08T13:56:17.822Z", "modified": "2025-11-04T11:37:45.596Z"}, {"entity": "publication", "iuid": "017ea3a81ce94808ab8f3f0ccf95d952", "links": {"self": {"href": "https://publications.scilifelab.se/publication/017ea3a81ce94808ab8f3f0ccf95d952.json"}, "display": {"href": "https://publications.scilifelab.se/publication/017ea3a81ce94808ab8f3f0ccf95d952"}}, "title": "Structural basis of ATP release and ion selectivity in Pannexin1 channels", "authors": [{"family": "Zhang", "given": "Qingyang", "initials": "Q"}, {"family": "Wang", "given": "Junjie", "initials": "J"}, {"family": "Gaullier", "given": "Guillaume", "initials": "G", "orcid": "0000-0003-3405-6021", "researcher": {"href": "https://publications.scilifelab.se/researcher/26bde2020c164cff8216338fb2d6d652.json"}}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications.scilifelab.se/researcher/085cca6e87fb4639b720b0e5c8c1da2a.json"}}, {"family": "Blikstad", "given": "Cecilia", "initials": "C"}, {"family": "Dahl", "given": "Gerhard", "initials": "G"}, {"family": "Barro-Soria", "given": "Rene", "initials": "R"}, {"family": "Mim", "given": "Carsten", "initials": "C", "orcid": "0000-0001-6402-8270", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5919b7026fd4229b2593106ee0a727d.json"}}], "type": "posted-content", "published": "2025-02-20", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.02.17.638584", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-13T13:57:07.639Z", "modified": "2025-12-18T19:19:56.746Z"}, {"entity": "publication", "iuid": "41afeeccb52b4070923d6c4d9c505ea1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41afeeccb52b4070923d6c4d9c505ea1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41afeeccb52b4070923d6c4d9c505ea1"}}, "title": "Ancient DNA HLA typing reveals significant shifts in frequency in Europe since the Neolithic.", "authors": [{"family": "Plascencia", "given": "Alan God\u00ednez", "initials": "AG"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "S\u00e1nchez-Quinto", "given": "Federico", "initials": "F"}], "type": "journal article", "published": "2025-02-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "6161", "issn-l": "2045-2322"}, "abstract": "Computational HLA typing has surged as a cost-effective strategy to uncover questions regarding the evolution of the HLA system, enabling immunogenic characterization from ancient DNA (aDNA) data. Nevertheless, it remains to be seen whether these methods are suitable for analyzing aDNA generated without target-enrichment. To investigate this, we evaluated the performance of five HLA typing tools using present-day data with simulated profiles typical of aDNA, as well as from high-coverage aDNA genomes downsampled at different read depths. We found that characterization of Class I genes at the first field resolution is feasible at read depths as low as 2x, where it retains an accuracy of \u2248 80%. Next, we used this insight to characterize HLA evolution in Europe from 154 ancient genomes by detecting allele frequency changes throughout distinct prehistoric European populations. We observed important shifts in alleles associated with infectious and autoimmune diseases, most of which are found by contrasting the HLA landscape of Neolithic Farmers to that of present-day. Interestingly, several of these observations are in line with findings that have been previously reported by target-enrichment-based studies. Our results highlight the feasibility of applying HLA typing on shotgun aDNA data to examine the evolution of this loci during important transitions.", "doi": "10.1038/s41598-024-82449-w", "pmid": "39979344", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11842861"}, {"db": "pii", "key": "10.1038/s41598-024-82449-w"}], "notes": [], "created": "2025-11-28T10:46:54.368Z", "modified": "2025-11-28T10:46:54.377Z"}, {"entity": "publication", "iuid": "d9bc92127ecf49ce8f19dabdd5e631a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9bc92127ecf49ce8f19dabdd5e631a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9bc92127ecf49ce8f19dabdd5e631a1"}}, "title": "Age-Dependent Pleomorphism in Mycobacterium monacense Cultures.", "authors": [{"family": "Ramesh", "given": "Malavika", "initials": "M", "orcid": "0000-0002-2353-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e679c292f1904ecbb1dece92d5513d26.json"}}, {"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK", "orcid": "0000-0002-8810-6066", "researcher": {"href": "https://publications.scilifelab.se/researcher/711dae7f552146ac95d209bc8efab54e.json"}}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF", "orcid": "0009-0006-8579-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5d1d0f6732d4dee869861d57ce02cd7.json"}}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2025-02-20", "journal": {"title": "Microorganisms", "issn": "2076-2607", "volume": "13", "issue": "3", "issn-l": "2076-2607"}, "abstract": "Changes in cell shape have been shown to be an integral part of the mycobacterial life cycle; however, systematic investigations into its patterns of pleomorphic behaviour in connection with stages or conditions of growth are scarce. We have studied the complete growth cycle of Mycobacterium monacense cultures, a Non-Tuberculous Mycobacterium (NTM), in solid as well as in liquid media. We provide data showing changes in cell shape from rod to coccoid and occurrence of refractive cells ranging from Phase Grey to phase Bright (PGB) in appearance upon ageing. Changes in cell shape could be correlated to the bi-phasic nature of the growth curves for M. monacense (and the NTM Mycobacterium boenickei) as measured by the absorbance of liquid cultures while growth measured by colony-forming units (CFU) on solid media showed a uniform exponential growth. Based on the complete M. monacense genome we identified genes involved in cell morphology, and analyses of their mRNA levels revealed changes at different stages of growth. One gene, dnaK_3 (encoding a chaperone), showed significantly increased transcript levels in stationary phase cells relative to exponentially growing cells. Based on protein domain architecture, we identified that the DnaK_3 N-terminus domain is an MreB-like homolog. Endogenous overexpression of M. monacense dnaK_3 in M. monacense was unsuccessful (appears to be lethal) while exogenous overexpression in Mycobacterium marinum resulted in morphological changes with an impact on the frequency of appearance of PGB cells. However, the introduction of an anti-sense \"gene\" targeting the M. marinum dnaK_3 did not show significant effects. Using dnaK_3-lacZ reporter constructs we also provide data suggesting that the morphological differences could be due to differences in the regulation of dnaK_3 in the two species. Together these data suggest that, although its regulation may vary between mycobacterial species, the dnaK_3 might have a direct or indirect role in the processes influencing mycobacterial cell shape.", "doi": "10.3390/microorganisms13030475", "pmid": "40142368", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11946739"}, {"db": "pii", "key": "microorganisms13030475"}], "notes": [], "created": "2025-08-19T13:27:17.755Z", "modified": "2025-09-08T07:17:25.329Z"}, {"entity": "publication", "iuid": "d6b6473e8ba241aba65ecf65773c1ac4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6b6473e8ba241aba65ecf65773c1ac4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6b6473e8ba241aba65ecf65773c1ac4"}}, "title": "Toward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open.", "authors": [{"family": "Tredup", "given": "Claudia", "initials": "C", "orcid": "0000-0001-6518-3344", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9598692f92a42cbbac352bda93085c8.json"}}, {"family": "Ackloo", "given": "Suzanne", "initials": "S", "orcid": "0000-0002-9696-1839", "researcher": {"href": "https://publications.scilifelab.se/researcher/95141c024a414c3aaa53daf781433e87.json"}}, {"family": "Beck", "given": "Hartmut", "initials": "H"}, {"family": "Brown", "given": "Peter J", "initials": "PJ"}, {"family": "Bullock", "given": "Alex N", "initials": "AN", "orcid": "0000-0001-6757-0436", "researcher": {"href": "https://publications.scilifelab.se/researcher/68163f1d336e4ad4818d6b2cdbfeaf0e.json"}}, {"family": "Ciulli", "given": "Alessio", "initials": "A", "orcid": "0000-0002-8654-1670", "researcher": {"href": "https://publications.scilifelab.se/researcher/d36e64e6af894ca28c2d4592896b0ae0.json"}}, {"family": "Dikic", "given": "Ivan", "initials": "I", "orcid": "0000-0001-8156-9511", "researcher": {"href": "https://publications.scilifelab.se/researcher/d81061feaa3a49b4a4859566c7542e72.json"}}, {"family": "Edfeldt", "given": "Kristina", "initials": "K", "orcid": "0000-0002-0550-1133", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf9c3d4af5dd4a538513a6648486f5eb.json"}}, {"family": "Edwards", "given": "Aled M", "initials": "AM"}, {"family": "Elkins", "given": "Jonathan M", "initials": "JM"}, {"family": "Farin", "given": "Henner F", "initials": "HF", "orcid": "0000-0003-1558-5366", "researcher": {"href": "https://publications.scilifelab.se/researcher/7301a4e75e33404cb68b91154af0075f.json"}}, {"family": "Fon", "given": "Edward A", "initials": "EA", "orcid": "0000-0002-5520-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/503836b6aa764c888988ce730a9386f2.json"}}, {"family": "Gstaiger", "given": "Matthias", "initials": "M"}, {"family": "G\u00fcnther", "given": "Judith", "initials": "J"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL"}, {"family": "H\u00e4berle", "given": "Sandra", "initials": "S"}, {"family": "Isigkeit", "given": "Laura", "initials": "L", "orcid": "0000-0002-0168-1093", "researcher": {"href": "https://publications.scilifelab.se/researcher/a14d651c3033499f8e72e47860413968.json"}}, {"family": "Huber", "given": "Kilian V M", "initials": "KVM", "orcid": "0000-0002-1103-5300", "researcher": {"href": "https://publications.scilifelab.se/researcher/8386d4f361df45ee863e5fca46eb875b.json"}}, {"family": "Kotschy", "given": "Andras", "initials": "A", "orcid": "0000-0002-7675-3864", "researcher": {"href": "https://publications.scilifelab.se/researcher/9853686b9acb4d86898a872b10bfdfc9.json"}}, {"family": "Kr\u00e4mer", "given": "Oliver", "initials": "O"}, {"family": "Leach", "given": "Andrew R", "initials": "AR"}, {"family": "Marsden", "given": "Brian D", "initials": "BD"}, {"family": "Matsui", "given": "Hisanori", "initials": "H"}, {"family": "Merk", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5359-8128", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3adffe811c743bda016dfe7d25c8bec.json"}}, {"family": "Montel", "given": "Florian", "initials": "F"}, {"family": "Mulder", "given": "Monique P C", "initials": "MPC", "orcid": "0000-0001-5386-7132", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f56d7418ec94a44a274fe83b5586f8d.json"}}, {"family": "M\u00fcller", "given": "Susanne", "initials": "S", "orcid": "0000-0003-2402-4157", "researcher": {"href": "https://publications.scilifelab.se/researcher/addee378115f41cba3e59d223e8276df.json"}}, {"family": "Owen", "given": "Dafydd R", "initials": "DR", "orcid": "0000-0003-3106-7809", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc3e57270832497f8996b1cd583031d6.json"}}, {"family": "Proschak", "given": "Ewgenij", "initials": "E"}, {"family": "R\u00f6hm", "given": "Sandra", "initials": "S"}, {"family": "Stolz", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-3340-439X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b40ffdc8fcf497499fa4ba93a530b8d.json"}}, {"family": "Sundstr\u00f6m", "given": "Michael", "initials": "M"}, {"family": "von Delft", "given": "Frank", "initials": "F", "orcid": "0000-0003-0378-0017", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c50d3e370c34cba9d9ce376273fd5fc.json"}}, {"family": "Willson", "given": "Timothy M", "initials": "TM"}, {"family": "Arrowsmith", "given": "Cheryl H", "initials": "CH"}, {"family": "Knapp", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5995-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4d84c40612d48f280d4ead25558d835.json"}}], "type": "editorial", "published": "2025-02-19", "journal": {"title": "RSC Med Chem", "issn": "2632-8682", "issn-l": null, "volume": "16", "issue": "2", "pages": "457-464"}, "abstract": "Target 2035 is a global initiative that seeks to identify a pharmacological modulator of most human proteins by the year 2035. As part of an ongoing series of annual updates of this initiative, we summarise here the efforts of the EUbOPEN project whose objectives and results are making a strong contribution to the goals of Target 2035. EUbOPEN is a public-private partnership with four pillars of activity: (1) chemogenomic library collections, (2) chemical probe discovery and technology development for hit-to-lead chemistry, (3) profiling of bioactive compounds in patient-derived disease assays, and (4) collection, storage and dissemination of project-wide data and reagents. The substantial outputs of this programme include a chemogenomic compound library covering one third of the druggable proteome, as well as 100 chemical probes, both profiled in patient derived assays, as well as hundreds of data sets deposited in existing public data repositories and a project-specific data resource for exploring EUbOPEN outputs.", "doi": "10.1039/d4md00735b", "pmid": "39618964", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11605244"}, {"db": "pii", "key": "d4md00735b"}], "notes": [], "created": "2024-12-16T09:06:27.733Z", "modified": "2025-10-17T13:04:26.868Z"}, {"entity": "publication", "iuid": "c1b67296b16347f48ac41930064ca6be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1b67296b16347f48ac41930064ca6be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1b67296b16347f48ac41930064ca6be"}}, "title": "Temporal dynamics of airborne fungi in Swedish forest nurseries.", "authors": [{"family": "Larsson", "given": "Rebecca", "initials": "R", "orcid": "0000-0002-5261-7390", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2fab759f00549cfaf3417d98e691323.json"}}, {"family": "Menkis", "given": "Audrius", "initials": "A", "orcid": "0000-0002-6545-8907", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d4d16d281344b9f9cf2c3c27fb40f06.json"}}, {"family": "Olson", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0001-8998-6096", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a79139c2b94d9f97cf038e1cab8c03.json"}}], "type": "journal article", "published": "2025-02-19", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "volume": "91", "issue": "2", "pages": "e0130624", "issn-l": "0099-2240"}, "abstract": "In Sweden, reforestation of managed forests relies predominantly on planting nursery-produced tree seedlings. However, the intense production using containerized cultivation systems (e.g., high seedling density, irrigation from above, regular fertilization) creates favorable conditions for fungal infections. Despite the harmful role of diseases in forest nurseries, the origin and dispersal factors of fungal pathogens remain largely unknown. A better understanding of the airborne spread of pathogens could improve the prediction of fungal infection, ultimately optimizing preventative methods and decreasing the use of fungicides. This study investigated the temporal dynamics of airborne fungi in forest nurseries, with a focus on fungal pathogens. Airborne fungi were monitored in four Swedish forest nurseries over two growing seasons using spore traps and high-throughput sequencing. Fungal pathogens were identified using bioinformatics and quantified with quantitative PCR. Results showed strong temporal shifts of airborne fungal diversity and community composition following the growing seasons. The airborne spread included high abundances of important fungal pathogens (e.g., Cladosporium sp., Botrytis cinerea, Alternaria sp., Sydowia polyspora, and Melampsora populnea) with individual temporal and spatial variations. In general, the deposited spore loads of nursery pathogens correlated positively with increased temperature and negatively with higher precipitation. This was expressed the strongest for Cladosporium sp., Alternaria sp., and M. populnea, which suggests a higher availability of fungal inoculum in warm and dry periods. This study highlights the influence of seasonality on the temporal dynamics of economically important fungal pathogens in Swedish forest nurseries, which should be considered in the development of a local decision support system.IMPORTANCEFungal diseases in forest nurseries have significant environmental and economic impacts on the tree seedling production. This study highlights the role of seasonality in the airborne spread of fungal pathogens in Swedish forest nurseries. By analyzing airborne fungal spores using advanced sequencing and monitoring techniques, key fungal pathogens and their dispersal patterns over two growing seasons were identified. The findings indicate that warmer, drier periods may increase the spread of fungal pathogens, emphasizing the need for targeted preventative measures. Understanding these temporal dynamics can help optimize the use of fungicides in forest nurseries, thereby promoting more sustainable and environmentally friendly management practices. This research provides valuable insights for improving disease management in forest nurseries, ultimately supporting sustainable tree seedling production.", "doi": "10.1128/aem.01306-24", "pmid": "39817739", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11837532"}], "notes": [], "created": "2025-03-07T09:41:43.999Z", "modified": "2025-03-07T09:41:44.362Z"}, {"entity": "publication", "iuid": "d2c5072fe8644c0b8b5297199b1fd0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2c5072fe8644c0b8b5297199b1fd0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2c5072fe8644c0b8b5297199b1fd0e5"}}, "title": "Measuring plasma membrane fluidity using confocal microscopy.", "authors": [{"family": "Carravilla", "given": "Pablo", "initials": "P", "orcid": "0000-0001-6592-7630", "researcher": {"href": "https://publications.scilifelab.se/researcher/b791a8068a724c179b731f0446b1737a.json"}}, {"family": "Andronico", "given": "Luca", "initials": "L"}, {"family": "Schlegel", "given": "Jan", "initials": "J", "orcid": "0000-0003-3159-8079", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94351acc3934c3084f1ed0429a1879a.json"}}, {"family": "Urem", "given": "Yagmur B", "initials": "YB", "orcid": "0009-0008-5053-2191", "researcher": {"href": "https://publications.scilifelab.se/researcher/78c952b0962443199c9be0ce64d48e4e.json"}}, {"family": "Sjule", "given": "Ellen", "initials": "E", "orcid": "0000-0003-0166-2826", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e0fd8926ef843a0a8db936df7209107.json"}}, {"family": "Ragaller", "given": "Franziska", "initials": "F", "orcid": "0000-0002-4148-262X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ead87aca17f476b9febf3f020567c4b.json"}}, {"family": "Weber", "given": "Florian", "initials": "F", "orcid": "0000-0002-8946-1377", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d4b9aaf4b7041cdbf1d99f3a0d833f2.json"}}, {"family": "Gurdap", "given": "Cenk O", "initials": "CO", "orcid": "0000-0002-5327-2523", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e3e5501e8d84f46884f1001367ab262.json"}}, {"family": "Ascioglu", "given": "Yavuz", "initials": "Y"}, {"family": "Sych", "given": "Taras", "initials": "T", "orcid": "0000-0002-7330-9063", "researcher": {"href": "https://publications.scilifelab.se/researcher/d104a7d8096b4a4ab2a9fe618489fc7e.json"}}, {"family": "Lorent", "given": "Joseph", "initials": "J"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}], "type": "journal article", "published": "2025-02-19", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "issn-l": null}, "abstract": "Membrane fluidity is a crucial parameter for cellular physiology. Recent evidence suggests that fluidity varies between cell types and states and in diseases. As membrane fluidity has gradually become an important consideration in cell biology and biomedicine, it is essential to have reliable and quantitative ways to measure it in cells. In the past decade, there has been substantial progress both in chemical probes and in imaging tools to make membrane fluidity measurements easier and more reliable. We have recently established a robust pipeline, using confocal imaging and new environment-sensitive probes, that has been successfully used for several studies. Here we present our detailed protocol for membrane fluidity measurement, from labeling to imaging and image analysis. The protocol takes ~4 h and requires basic expertise in cell culture, wet lab and microscopy.", "doi": "10.1038/s41596-024-01122-8", "pmid": "39972239", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41596-024-01122-8"}], "notes": [], "created": "2025-03-11T12:49:46.696Z", "modified": "2025-03-24T08:20:58.620Z"}, {"entity": "publication", "iuid": "374916d5866340bd9a5d6c4801db1717", "links": {"self": {"href": "https://publications.scilifelab.se/publication/374916d5866340bd9a5d6c4801db1717.json"}, "display": {"href": "https://publications.scilifelab.se/publication/374916d5866340bd9a5d6c4801db1717"}}, "title": "Virtual fragment screening for DNA repair inhibitors in vast chemical space.", "authors": [{"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d46047fab4247caaeecf31be6da987f.json"}}, {"family": "Vo", "given": "Duc Duy", "initials": "DD"}, {"family": "Scaletti", "given": "Emma R", "initials": "ER"}, {"family": "Wiita", "given": "Elis\u00e9e", "initials": "E"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Wallner", "given": "Olov", "initials": "O"}, {"family": "Davies", "given": "Jonathan", "initials": "J"}, {"family": "Ko\u0161enina", "given": "Sara", "initials": "S", "orcid": "0000-0001-7893-0249", "researcher": {"href": "https://publications.scilifelab.se/researcher/9370d4ecf19c438bb205c43c23f94f26.json"}}, {"family": "Meng", "given": "Liuzhen", "initials": "L"}, {"family": "Long", "given": "Maeve", "initials": "M"}, {"family": "Mortusewicz", "given": "Oliver", "initials": "O", "orcid": "0000-0002-4290-4994", "researcher": {"href": "https://publications.scilifelab.se/researcher/b62a88fc39a54906a40e28e679c9f624.json"}}, {"family": "Masuyer", "given": "Geoffrey", "initials": "G", "orcid": "0000-0002-9527-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/41dcc0806dba4a56bb04725812f3a000.json"}}, {"family": "Ballante", "given": "Flavio", "initials": "F", "orcid": "0000-0002-4831-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/20429d2a46f4479a9c262875794a3a9d.json"}}, {"family": "Michel", "given": "Maurice", "initials": "M"}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Kalder\u00e9n", "given": "Christina", "initials": "C"}, {"family": "Warpman Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Tarnovskiy", "given": "Andrii V", "initials": "AV"}, {"family": "Radchenko", "given": "Dmytro S", "initials": "DS", "orcid": "0000-0001-5444-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/df4077c366bc4f4a8b422762c0be9cfe.json"}}, {"family": "Moroz", "given": "Yurii S", "initials": "YS", "orcid": "0000-0001-6073-002X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8586d3b69b4782bed34192411a02e5.json"}}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9805d4f39cc48f79a6e6ba076917021.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T"}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7d91087358e46e38bb1b7110dc0b214.json"}}], "type": "journal article", "published": "2025-02-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "1741", "issn-l": "2041-1723"}, "abstract": "Fragment-based screening can catalyze drug discovery by identifying novel scaffolds, but this approach is limited by the small chemical libraries studied by biophysical experiments and the challenging optimization process. To expand the explored chemical space, we employ structure-based docking to evaluate orders-of-magnitude larger libraries than those used in traditional fragment screening. We computationally dock a set of 14 million fragments to 8-oxoguanine DNA glycosylase (OGG1), a difficult drug target involved in cancer and inflammation, and evaluate 29 highly ranked compounds experimentally. Four of these bind to OGG1 and X-ray crystallography confirms the binding modes predicted by docking. Furthermore, we show how fragment elaboration using searches among billions of readily synthesizable compounds identifies submicromolar inhibitors with anti-inflammatory and anti-cancer effects in cells. Comparisons of virtual screening strategies to explore a chemical space of 1022 compounds illustrate that fragment-based design enables enumeration of all molecules relevant for inhibitor discovery. Virtual fragment screening is hence a highly efficient strategy for navigating the rapidly growing combinatorial libraries and can serve as a powerful tool to accelerate drug discovery efforts for challenging therapeutic targets.", "doi": "10.1038/s41467-025-56893-9", "pmid": "39966348", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11836371"}, {"db": "pii", "key": "10.1038/s41467-025-56893-9"}], "notes": [], "created": "2025-11-28T10:45:18.822Z", "modified": "2025-11-28T10:45:19.246Z"}, {"entity": "publication", "iuid": "f28f6a98aeeb4c36a667374a906d634e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f28f6a98aeeb4c36a667374a906d634e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f28f6a98aeeb4c36a667374a906d634e"}}, "title": "Impact of glucose and propionic acid on even and odd chain fatty acid profiles of oleaginous yeasts.", "authors": [{"family": "Bonzanini", "given": "Veronica", "initials": "V"}, {"family": "Haddad Momeni", "given": "Majid", "initials": "M"}, {"family": "Olofsson", "given": "Kim", "initials": "K"}, {"family": "Olsson", "given": "Lisbeth", "initials": "L"}, {"family": "Geijer", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2025-02-18", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "25", "issue": "1", "pages": "79", "issn-l": "1471-2180"}, "abstract": "Odd chain fatty acids (OCFAs) are gaining attention for their valuable medical and nutritional applications. Microbial fermentation offers a sustainable and environmentally friendly alternative for OCFA production compared to traditional extraction or chemical synthesis methods. To achieve an economically feasible OCFA production process, it is essential to identify and develop microbial cell factories capable of producing OCFAs with high titers and yields.\n\nWe selected 19 yeast species, including both oleaginous yeasts and representatives from the Ascomycota and Basidiomycota phyla, based on their known or potential ability to produce OCFAs. These species were screened under various growth conditions to evaluate their OCFA production potential. In glucose-based, nitrogen-limited media, the strains produced fatty acids to varying extents, with OCFAs comprising 0.5-5% of the total fatty acids. When using the OCFAs precursor propionic acid as the sole carbon source, only eight strains exhibited growth, with tolerance to propionic acid concentrations between 5 and 29 g/L. The strains also displayed varying efficiencies in converting propionic acid into fatty acids, yielding between 0.16 and 1.22 g/L of fatty acids, with OCFAs constituting 37-89% of total fatty acids. Among the top performing strains, Cutaneotrichosporon oleaginosus produced the highest OCFA titers and yields (0.94 g/L, 0.07 g/g), Yarrowia lipolytica demonstrated superior growth rates even at elevated propionic acid concentrations, and Rhodotorula toruloides achieved the highest proportion of OCFAs relative to total fatty acids (89%).\n\nOur findings highlight the diverse capacities of the selected yeast species for OCFA production, identifying several promising strains for further optimization as microbial cell factories in sustainable OCFA production processes.", "doi": "10.1186/s12866-025-03788-w", "pmid": "39966733", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11834278"}, {"db": "pii", "key": "10.1186/s12866-025-03788-w"}], "notes": [], "created": "2025-11-27T11:28:40.091Z", "modified": "2025-11-27T11:28:40.099Z"}, {"entity": "publication", "iuid": "aec477d8498f4dcab84fdaedd3b9dea8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aec477d8498f4dcab84fdaedd3b9dea8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aec477d8498f4dcab84fdaedd3b9dea8"}}, "title": "Circular RNA circASH1L(4,5) protects microRNA-129-5p from target-directed microRNA degradation in human skin wound healing.", "authors": [{"family": "Wang", "given": "Qizhang", "initials": "Q"}, {"family": "Niu", "given": "Guanglin", "initials": "G"}, {"family": "Liu", "given": "Zhuang", "initials": "Z"}, {"family": "Toma", "given": "Maria A", "initials": "MA"}, {"family": "Geara", "given": "Jennifer", "initials": "J"}, {"family": "Bian", "given": "Xiaowei", "initials": "X"}, {"family": "Zhang", "given": "Letian", "initials": "L"}, {"family": "Piipponen", "given": "Minna", "initials": "M"}, {"family": "Li", "given": "Dongqing", "initials": "D"}, {"family": "Wang", "given": "Aoxue", "initials": "A"}, {"family": "Sommar", "given": "Pehr", "initials": "P"}, {"family": "Xu Land\u00e9n", "given": "Ning", "initials": "N"}], "type": "journal article", "published": "2025-02-18", "journal": {"title": "Br J Dermatol", "issn": "1365-2133", "volume": "192", "issue": "3", "pages": "468-480", "issn-l": null}, "abstract": "Skin wound healing involves a complex gene expression programme that remains largely undiscovered in humans. Circular RNAs (circRNAs) and microRNAs (miRNAs) are key players in this process.\n\nTo understand the functions and potential interactions of circRNAs and miRNAs in human skin wound healing.\n\nCircRNA, linear RNA and miRNA expression in human acute and chronic wounds were analysed with RNA sequencing and quantitative reverse transcription polymerase chain reaction. The roles of circASH1L(4,5) and miR-129-5p were studied in human primary keratinocytes (proliferation and migration assays, microarray analysis) and ex vivo wound models (histological analysis). The interaction between circASH1L(4,5) and miR-129-5p was examined using luciferase reporter and RNA pulldown assays.\n\nWe identified circASH1L(4,5) and its interaction with miR-129-5p, both of which increased during human skin wound healing. Unlike typical miRNA sponging, circASH1L enhanced miR-129 stability and silencing activity by protecting it from target-directed degradation triggered by NR6A1 mRNA. Transforming growth factor-\u03b2 signalling - crucial in wound healing - promoted circASH1L expression while suppressing NR6A1, thereby increasing the abundance of miR-129 at the post-transcriptional level. CircASH1L and miR-129 enhanced keratinocyte migration and proliferation, crucial processes for the re-epithelialization of human wounds.\n\nOur study uncovered a novel role for circRNAs as protectors of miRNAs and highlights the importance of regulated miRNA degradation in skin wound healing.", "doi": "10.1093/bjd/ljae405", "pmid": "39422230", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7826154"}], "notes": [], "created": "2025-02-28T14:17:10.000Z", "modified": "2025-02-28T14:17:10.004Z"}, {"entity": "publication", "iuid": "db0102f308044e068375eaab4e78dc48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db0102f308044e068375eaab4e78dc48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db0102f308044e068375eaab4e78dc48"}}, "title": "An Evolutionary Mosaic Challenges Traditional Monitoring of a Foundation Species in a Coastal Environment-The Baltic Fucus vesiculosus.", "authors": [{"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}, {"family": "Kinnby", "given": "Alexandra", "initials": "A"}, {"family": "Le Moan", "given": "Alan", "initials": "A", "orcid": "0000-0002-9124-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/609a745ce1fb42fea85cc8d55db25acf.json"}}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Piarulli", "given": "Stefania", "initials": "S"}, {"family": "Pinder", "given": "Matthew I M", "initials": "MIM", "orcid": "0000-0003-4407-0214", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6d9f52178249f3995c3d276fbc2728.json"}}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Knutsen", "given": "Halvor", "initials": "H", "orcid": "0000-0002-7627-7634", "researcher": {"href": "https://publications.scilifelab.se/researcher/a822f994fed046018a713105bc5e03a0.json"}}, {"family": "Johannesson", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-0176-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/a376951d80cd405183f4ff8606df8bbc.json"}}], "type": "journal article", "published": "2025-02-17", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17699", "issn-l": "0962-1083"}, "abstract": "During periods of environmental change, genetic diversity in foundation species is critical for ecosystem function and resilience, but it remains overlooked in environmental monitoring. In the Baltic Sea, a key species for monitoring is the brown seaweed Fucus vesiculosus, which forms sublittoral 3D habitats providing shelter and food for fish and invertebrates. Ecological distribution models predict a significant loss of Baltic F. vesiculosus due to ocean warming, unless populations can adapt. Genetic variation and recombination during sexual reproduction are essential for adaptation, but studies have revealed large-scale clonal reproduction within the Baltic Sea. We analysed genome-wide single nucleotide polymorphism (SNP) data from the east Atlantic, the \"Transition zone,\" and the Baltic Sea, and found a mosaic of divergent lineages in the Baltic Sea, contrasting an outside dominance of a few genetic groups. We determined that the previously described endemic species Fucus radicans is predominantly a large female clone of F. vesiculosus in its northern Baltic distribution. In the two Estonian sites, however, individuals earlier referred to as F. radicans are sexually and reproductively isolated from Baltic F. vesiculosus, revealing a separate lineage that may have diverged long before the formation of the Baltic Sea. Monitoring Baltic Fucus without considering this genetic complexity will fail to prioritise populations with adaptive potential to new climate conditions. From our genomic data, we can extract informative and diagnostic genetic markers that differentiate major genetic entities. Such a SNP panel will provide a straightforward tool for spatial and temporal monitoring and informing management decisions and actions.", "doi": "10.1111/mec.17699", "pmid": "39957665", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:26:56.214Z", "modified": "2025-11-07T07:26:56.376Z"}, {"entity": "publication", "iuid": "9cffa610a5254003956c5dedb591e1d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9cffa610a5254003956c5dedb591e1d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9cffa610a5254003956c5dedb591e1d0"}}, "title": "Microbial communities in slow sand filters for drinking water treatment adapt to organic matter altered by ozonation.", "authors": [{"family": "Rosenqvist", "given": "Tage", "initials": "T"}, {"family": "Hilding", "given": "Johanna", "initials": "J"}, {"family": "Suarez", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5988-4048", "researcher": {"href": "https://publications.scilifelab.se/researcher/86cadb16f7cf45eca8030af1a8ae860e.json"}}, {"family": "Paul", "given": "Catherine J", "initials": "CJ", "orcid": "0000-0003-0323-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c169e96b18c403b9c18228126e6fd8d.json"}}], "type": "journal article", "published": "2025-02-15", "journal": {"title": "Water Res.", "issn": "1879-2448", "issn-l": "0043-1354", "volume": "270", "issue": null, "pages": "122843"}, "abstract": "Changing natural organic matter quality from anthropogenic activity and stricter requirements for micropollutant removal challenges existing systems for drinking water production. Ozonation of water followed by biofiltration, such as passage through a slow sand filter (SSF), is a partial solution. Biofiltration relies on biofilms (microbial communities within extracellular matrices). However, the effects of ozonation on SSF microbial communities are unknown. In this study, genome-resolved and read-based metagenomics were used to compare the microbial communities of two full-scale SSFs employing conventional pre-treatment to a 20 m2 SSF operated in parallel with ozonation as additional pre-treatment. The SSF microbial community receiving ozonated water was less diverse than those receiving non-ozonated water. Families Hyphomicrobiaceae, Acetobacteraceae, Sphingomonadaceae and Burkholderiaceae were more abundant when ozone was used, as were genes for metabolism of single-carbon organic compounds. Conversely, genes for metabolism of aromatic compounds and fatty acids were less abundant. Metagenome assembled genomes associated with the non-ozonated SSFs were enriched with several glycoside hydrolases, while those associated with the ozonated SSF were enriched with genes for 1-2 carbon compound metabolism. No indications of increased microbial risk (pathogens or antibiotic resistance genes) were detected as a consequence of ozonation. This study shows how microbial communities of SSFs adapt to changes in organic matter quality, highlighting the key role of biofilters for production of safe and sustainable drinking water in a changing climate.", "doi": "10.1016/j.watres.2024.122843", "pmid": "39612821", "labels": {"Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0043-1354(24)01742-1"}], "notes": [], "created": "2025-02-28T14:13:29.572Z", "modified": "2025-05-27T08:38:18.414Z"}, {"entity": "publication", "iuid": "12fa1b73f76d40158b12fc385a35aa1f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12fa1b73f76d40158b12fc385a35aa1f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12fa1b73f76d40158b12fc385a35aa1f"}}, "title": "Methodological aspects of investigating the resistome in pig farm environments.", "authors": [{"family": "Ladyhina", "given": "Valeriia", "initials": "V"}, {"family": "Rajala", "given": "Elisabeth", "initials": "E"}, {"family": "Sternberg-Lewerin", "given": "Susanna", "initials": "S"}, {"family": "Nasirzadeh", "given": "Leila", "initials": "L"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-02-13", "journal": {"title": "J Microbiol Methods", "issn": "1872-8359", "issn-l": null, "volume": "230-231", "issue": null, "pages": "107103"}, "abstract": "A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.", "doi": "10.1016/j.mimet.2025.107103", "pmid": "39954816", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0167-7012(25)00019-3"}], "notes": [], "created": "2025-03-18T07:11:00.806Z", "modified": "2025-09-08T07:13:09.538Z"}, {"entity": "publication", "iuid": "67fe70a7254545e7b2be4a509f5ff479", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479"}}, "title": "Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.", "authors": [{"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Mujica", "given": "Endrina", "initials": "E"}, {"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Jenseit", "given": "Anne", "initials": "A"}, {"family": "Evcimen", "given": "Bade", "initials": "B"}, {"family": "Metzendorf", "given": "Christoph", "initials": "C"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Loos", "given": "Ruth Jf", "initials": "RJ"}, {"family": "Vienberg", "given": "Sara Gry", "initials": "SG"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}], "type": "journal article", "published": "2025-02-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "5408"}, "abstract": "Hundreds of loci have been robustly associated with obesity-related traits, but functional characterization of candidate genes remains a bottleneck. Aiming to systematically characterize candidate genes for a role in accumulation of lipids in adipocytes and other cardiometabolic traits, we developed a pipeline using CRISPR/Cas9, non-invasive, semi-automated fluorescence imaging and deep learning-based image analysis in live zebrafish larvae. Results from a dietary intervention show that 5 days of overfeeding is sufficient to increase the odds of lipid accumulation in adipocytes by 10 days post-fertilization (dpf, n = 275). However, subsequent experiments show that across 12 to 16 established obesity genes, 10 dpf is too early to detect an effect of CRISPR/Cas9-induced mutations on lipid accumulation in adipocytes (n = 1014), and effects on food intake at 8 dpf (n = 1127) are inconsistent with earlier results from mammals. Despite this, we observe effects of CRISPR/Cas9-induced mutations on ectopic accumulation of lipids in the vasculature (sh2b1 and sim1b) and liver (bdnf); as well as on body size (pcsk1, pomca, irs1); whole-body LDLc and/or total cholesterol content (irs2b and sh2b1); and pancreatic beta cell traits and/or glucose content (pcsk1, pomca, and sim1a). Taken together, our results illustrate that CRISPR/Cas9- and image-based experiments in zebrafish larvae can highlight direct effects of obesity genes on cardiometabolic traits, unconfounded by their - not yet apparent - effect on excess adiposity.", "doi": "10.1038/s41598-025-89823-2", "pmid": "39948378", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11825957"}, {"db": "pii", "key": "10.1038/s41598-025-89823-2"}], "notes": [], "created": "2025-09-08T11:37:27.351Z", "modified": "2025-11-28T10:47:20.122Z"}, {"entity": "publication", "iuid": "c3eadc8419634a3683d40848bbed6238", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3eadc8419634a3683d40848bbed6238.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3eadc8419634a3683d40848bbed6238"}}, "title": "Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae).", "authors": [{"family": "Cauz-Santos", "given": "Luiz Augusto", "initials": "LA"}, {"family": "da Costa", "given": "Zirlane Portugal", "initials": "ZP"}, {"family": "Sader", "given": "Mariela Anal\u00eda", "initials": "MA"}, {"family": "van den Berg", "given": "C\u00e1ssio", "initials": "C"}, {"family": "Vieira", "given": "Maria Lucia Carneiro", "initials": "MLC"}], "type": "journal article", "published": "2025-02-13", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "25", "issue": "1", "pages": "192", "issn-l": "1471-2229"}, "abstract": "Chloroplasts are essential organelles in plants and eukaryotic algae, responsible for photosynthesis, fatty acid synthesis, amino acid production, and stress responses. The genus Passiflora, known for its species diversity and dynamic chloroplast (cp) genome evolution, serves as an excellent model for studying structural variations. This study investigates evolutionary relationships within Passiflora by sequencing 11 new chloroplast genomes, assessing selective pressures on cp genes, and comparing plastid and nuclear phylogenies. Passiflora cp genomes showed significant variations in size, gene content, and structure, ranging from 132,736 to 163,292 base pairs, especially in Decaloba. Structural rearrangements and species-specific repeat patterns were identified. Selective pressure tests revealed significant adaptive evolution in certain lineages, with several genes, including clpP and petL, under positive selection. Phylogenetic analyses confirmed the monophyly of subgenera Astrophea, Passiflora, and Decaloba, while Deidamioides appeared polyphyletic. Nuclear phylogenetic analysis based on 35S rDNA sequences supported the monophyly of Astrophea but showed inconsistencies within subgenus Passiflora compared to cp genome data. This study highlights the evolutionary complexity of Passiflora cp genomes, demonstrating significant structural variations and adaptive evolution. The findings underscore the effectiveness of plastid phylogenomics in resolving phylogenetic relationships and provide insights into adaptive mechanisms shaping cp genome diversity in angiosperms.", "doi": "10.1186/s12870-025-06210-9", "pmid": "39948451", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11823247"}, {"db": "pii", "key": "10.1186/s12870-025-06210-9"}], "notes": [], "created": "2025-08-19T13:23:20.848Z", "modified": "2025-08-19T13:23:20.852Z"}, {"entity": "publication", "iuid": "b69e3a293cb74fbc9c8c46ecf0a78fbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b69e3a293cb74fbc9c8c46ecf0a78fbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b69e3a293cb74fbc9c8c46ecf0a78fbb"}}, "title": "Imaging Single Particle Profiler to Study Nanoscale Bioparticles Using Conventional Confocal Microscopy.", "authors": [{"family": "Sych", "given": "Taras", "initials": "T", "orcid": "0000-0002-7330-9063", "researcher": {"href": "https://publications.scilifelab.se/researcher/d104a7d8096b4a4ab2a9fe618489fc7e.json"}}, {"family": "G\u00f6rgens", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-9198-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea5f85e2c23a4515a39a2fa23d665a99.json"}}, {"family": "Steiner", "given": "Lo\u00efc", "initials": "L", "orcid": "0000-0001-6640-3513", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef6ac5c6f9324434b11fc1cccd0a9027.json"}}, {"family": "Gucluler", "given": "Gozde", "initials": "G"}, {"family": "Huge", "given": "Ylva", "initials": "Y"}, {"family": "Alamdari", "given": "Farhood", "initials": "F"}, {"family": "Johansson", "given": "Markus", "initials": "M"}, {"family": "Aljabery", "given": "Firas", "initials": "F"}, {"family": "Sherif", "given": "Amir", "initials": "A", "orcid": "0000-0002-3675-3050", "researcher": {"href": "https://publications.scilifelab.se/researcher/e27ad5d3def147849d4821d86075c3d2.json"}}, {"family": "Gabrielsson", "given": "Susanne", "initials": "S", "orcid": "0000-0003-1771-1346", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d446cb52d7e4a01ad8478a9cfe22ae1.json"}}, {"family": "El Andaloussi", "given": "Samir", "initials": "S", "orcid": "0000-0003-4468-9113", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd1036a42043441da3e444f4eac58010.json"}}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}], "type": "journal article", "published": "2025-02-12", "journal": {"title": "Nano Lett.", "issn": "1530-6992", "volume": "25", "issue": "6", "pages": "2173-2180", "issn-l": "1530-6984"}, "abstract": "Single particle profiling (SPP) is a unique methodology to study nanoscale bioparticles such as liposomes, lipid nanoparticles, extracellular vesicles, and lipoproteins in a single particle and high throughput manner. The initial version requires the single photon counting modules for data acquisition, which limits its adoptability. Here, we present imaging-based SPP (iSPP) that can be performed by imaging a spot over time in the common imaging mode with confocal detectors. We also provide user-friendly software with a graphical user interface to analyze such data and give quantitative insights on the content and properties of nanoscale bioparticles. We use iSPP to decipher lipid-protein interactions, membrane modifications by drugs, and the heterogeneity of extracellular vesicles isolated from cell lines and human urine. This easily applicable modality of the single particle profiler will facilitate nanoscale bioparticle research in laboratories with access to any confocal microscope.", "doi": "10.1021/acs.nanolett.4c05117", "pmid": "39878336", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11827106"}], "notes": [], "created": "2025-03-11T12:50:21.409Z", "modified": "2025-03-24T08:21:15.353Z"}, {"entity": "publication", "iuid": "dcfeee20dac44d149e7456edf098d297", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcfeee20dac44d149e7456edf098d297.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcfeee20dac44d149e7456edf098d297"}}, "title": "Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.", "authors": [{"family": "Brown", "given": "Thomas", "initials": "T"}, {"family": "Mishra", "given": "Ketan", "initials": "K"}, {"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Iarovenko", "given": "Svetlana", "initials": "S"}, {"family": "Subramanian", "given": "Elaiyaraja", "initials": "E"}, {"family": "Araus", "given": "Alberto Joven", "initials": "AJ"}, {"family": "Petzold", "given": "Andreas", "initials": "A"}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29dd3593b894c5e9d233da6049d59e8.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}, {"family": "Rikk", "given": "Lennart", "initials": "L"}, {"family": "Suzuki", "given": "Miyuki", "initials": "M"}, {"family": "Suzuki", "given": "Ken-Ichi T", "initials": "KT"}, {"family": "Hayashi", "given": "Toshinori", "initials": "T"}, {"family": "Toyoda", "given": "Atsushi", "initials": "A"}, {"family": "Oliveira", "given": "Catarina R", "initials": "CR"}, {"family": "Osipova", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-6769-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900.json"}}, {"family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}}, {"family": "Yun", "given": "Maximina H", "initials": "MH"}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "researcher": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}}], "type": "journal article", "published": "2025-02-12", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "issn-l": null, "volume": "5", "issue": "2", "pages": "100761"}, "abstract": "Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.3 Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. Utilizing this assembly, we demonstrate conserved synteny as well as genetic rearrangements, such as in the major histocompatibility complex locus. We provide evidence suggesting that intronic repeat elements drive newt-specific circular RNA (circRNA) biogenesis and show their regeneration-specific expression. We also present a comprehensive in-depth annotation and chromosomal mapping of microRNAs, highlighting genomic expansion profiles as well as a distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs, and adult regeneration and provide key resources for addressing developmental, regenerative, and evolutionary principles.", "doi": "10.1016/j.xgen.2025.100761", "pmid": "39874962", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11872487"}, {"db": "pii", "key": "S2666-979X(25)00017-5"}], "notes": [], "created": "2025-01-30T10:51:47.306Z", "modified": "2025-11-14T11:06:23.898Z"}, {"entity": "publication", "iuid": "ab8fa0c345a2433995ebac47f3ad0b58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab8fa0c345a2433995ebac47f3ad0b58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab8fa0c345a2433995ebac47f3ad0b58"}}, "title": "Rare and common single nucleotide variants in childhood-onset systemic lupus erythematosus.", "authors": [{"family": "Sayadi", "given": "Ahmed", "initials": "A", "orcid": "0000-0002-5662-9145", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f74f301499b4f888e0ac7c5161ae161.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML", "orcid": "0000-0002-8454-1351", "researcher": {"href": "https://publications.scilifelab.se/researcher/d162e060954d420e825884f254886dcd.json"}}, {"family": "ImmunoArray Development Consortium", "given": "", "initials": ""}, {"family": "DISSECT Consortium", "given": "", "initials": ""}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": " DISSECT Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2025-02-11", "journal": {"title": "Lupus Sci Med", "issn": "2053-8790", "volume": "12", "issue": "1", "issn-l": "2053-8790"}, "abstract": "SLE is a systemic autoimmune disease with a large number of common risk gene variants, but several rare gene variants can cause monogenic SLE. The relationship between common and rare variants in SLE is unclear. We therefore investigated the occurrence of rare deleterious variants in patients with childhood-onset SLE (cSLE) and adult-onset SLE (aSLE) and compared the frequency of these variants with their individual SLE polygenic risk score (PRS).\n\nTargeted sequencing of 1832 gene regions, including coding regions of 31 genes associated with monogenic SLE, was performed in 958 patients with SLE and 1026 healthy individuals. A total of 116 patients with SLE had disease onset before the age of 18 (cSLE). An SLE common variant PRS was created from 37 SLE genome-wide association study single nucleotide variants (SNVs).\n\nRare coding deleterious SNVs (RD SNVs) were observed in 23 of the monogenic SLE-associated genes. Six per cent of patients with cSLE, compared with 3.2% of controls and 4.6% of patients with aSLE, carried rare deleterious alleles. In cSLE, RD SNVs were observed in the C1S, DDX58, IFIH1, IKZF1, RNASEH2A and C8A genes. A PRS analysis showed that patients with cSLE with any of these gene variants had a similar average PRS as control individuals.\n\nRD SNVs were observed in a small proportion of cSLE and carriers of these RD SNVs had a PRS similar to healthy individuals, suggesting the importance of rare coding heterozygous variants in driving disease risk in a subset of children with SLE.", "doi": "10.1136/lupus-2024-001436", "pmid": "39933823", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "12/1/e001436"}], "notes": [], "created": "2025-02-12T13:49:33.306Z", "modified": "2025-03-24T08:21:29.400Z"}, {"entity": "publication", "iuid": "59c6a9db7d8d4f358f854245b00ff172", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59c6a9db7d8d4f358f854245b00ff172.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59c6a9db7d8d4f358f854245b00ff172"}}, "title": "Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats.", "authors": [{"family": "Yang", "given": "Hong", "initials": "H", "orcid": "0009-0002-0414-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52bdf7cbd1745e3a4578f17322c83f1.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Shi", "given": "Mengnan", "initials": "M"}, {"family": "Kiliclioglu", "given": "Metin", "initials": "M"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolar", "given": "Ismail", "initials": "I"}, {"family": "Tozlu", "given": "\u00d6zlem \u00d6zdemir", "initials": "\u00d6\u00d6"}, {"family": "Baba", "given": "Cem", "initials": "C"}, {"family": "Yuksel", "given": "Nursena", "initials": "N"}, {"family": "Yildirim", "given": "Serkan", "initials": "S"}, {"family": "Iqbal", "given": "Shazia", "initials": "S"}, {"family": "Sebhaoui", "given": "Jihad", "initials": "J"}, {"family": "Hac\u0131muftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Uhlen", "given": "Matthias", "initials": "M"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2025-02-11", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "13", "issn-l": "2050-084X"}, "abstract": "Excessive consumption of sucrose, in the form of sugar-sweetened beverages, has been implicated in the pathogenesis of metabolic dysfunction-associated fatty liver disease (MAFLD) and other related metabolic syndromes. The c-Jun N-terminal kinase (JNK) pathway plays a crucial role in response to dietary stressors, and it was demonstrated that the inhibition of the JNK pathway could potentially be used in the treatment of MAFLD. However, the intricate mechanisms underlying these interventions remain incompletely understood given their multifaceted effects across multiple tissues. In this study, we challenged rats with sucrose-sweetened water and investigated the potential effects of JNK inhibition by employing network analysis based on the transcriptome profiling obtained from hepatic and extrahepatic tissues, including visceral white adipose tissue, skeletal muscle, and brain. Our data demonstrate that JNK inhibition by JNK-IN-5A effectively reduces the circulating triglyceride accumulation and inflammation in rats subjected to sucrose consumption. Coexpression analysis and genome-scale metabolic modeling reveal that sucrose overconsumption primarily induces transcriptional dysfunction related to fatty acid and oxidative metabolism in the liver and adipose tissues, which are largely rectified after JNK inhibition at a clinically relevant dose. Skeletal muscle exhibited minimal transcriptional changes to sucrose overconsumption but underwent substantial metabolic adaptation following the JNK inhibition. Overall, our data provides novel insights into the molecular basis by which JNK inhibition exerts its metabolic effect in the metabolically active tissues. Furthermore, our findings underpin the critical role of extrahepatic metabolism in the development of diet-induced steatosis, offering valuable guidance for future studies focused on JNK-targeting for effective treatment of MAFLD.", "doi": "10.7554/eLife.98427", "pmid": "39932177", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11813226"}, {"db": "pii", "key": "98427"}, {"db": "GEO", "key": "GSE282954"}], "notes": [], "created": "2025-11-28T10:54:50.019Z", "modified": "2025-11-28T10:54:50.040Z"}, {"entity": "publication", "iuid": "cec32d91927047408b5b7f7d57722a0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cec32d91927047408b5b7f7d57722a0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cec32d91927047408b5b7f7d57722a0c"}}, "title": "MUC5B modulation of early oral biofilm glucose metabolism", "authors": [{"family": "Robertsson", "given": "Carolina", "initials": "C"}, {"family": "Davies", "given": "Julia", "initials": "J"}, {"family": "Svens\u00e4ter", "given": "Gunnel", "initials": "G"}, {"family": "Nord", "given": "Anders Bay", "initials": "AB"}, {"family": "Norrstr\u00f6m", "given": "Niclas", "initials": "N"}, {"family": "Wickstr\u00f6m", "given": "Claes", "initials": "C"}], "type": "journal-article", "published": "2025-02-11", "journal": {"title": "Front Oral Health", "issn": "2673-4842", "volume": "6", "issn-l": null}, "abstract": null, "doi": "10.3389/froh.2025.1516025", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:01:52.945Z", "modified": "2025-11-27T08:01:52.960Z"}, {"entity": "publication", "iuid": "1a5ce794e0674881af7391905b14b2f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a5ce794e0674881af7391905b14b2f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a5ce794e0674881af7391905b14b2f4"}}, "title": "Human MAIT cell response profiles biased toward IL-17 or IL-10 are distinct effector states directed by the cytokine milieu.", "authors": [{"family": "Boulouis", "given": "Caroline", "initials": "C", "orcid": "0000-0003-0562-5395", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e56706dacb2488384512533e63fec75.json"}}, {"family": "Mouchtaridi", "given": "Elli", "initials": "E", "orcid": "0009-0005-4154-9010", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b6cef1d4cec4c06b939ed1831f85e4a.json"}}, {"family": "M\u00fcller", "given": "Thomas R", "initials": "TR"}, {"family": "Mak", "given": "Jeffrey Y W", "initials": "JYW", "orcid": "0000-0002-8011-4539", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3b541f7d3b043989ab612d5f2678ee0.json"}}, {"family": "Fairlie", "given": "David P", "initials": "DP", "orcid": "0000-0002-7856-8566", "researcher": {"href": "https://publications.scilifelab.se/researcher/35fe17dcf6bb494f9c95e2dfab5ada19.json"}}, {"family": "Bergman", "given": "Peter", "initials": "P", "orcid": "0000-0003-3306-3713", "researcher": {"href": "https://publications.scilifelab.se/researcher/397d11713c80456bb600b1e4c88ff843.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0122-7234", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c18b8a6cc54dfa8ad14b0c97261bfa.json"}}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Sandberg", "given": "Johan K", "initials": "JK", "orcid": "0000-0002-6275-0750", "researcher": {"href": "https://publications.scilifelab.se/researcher/7468c415a46645a3a4c3d28badcff954.json"}}], "type": "journal article", "published": "2025-02-11", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "6", "pages": "e2414230122", "issn-l": "0027-8424"}, "abstract": "Mucosal-associated invariant T (MAIT) cells are unconventional T cells that mediate rapid antimicrobial immune responses to antigens derived from microbial riboflavin pathway metabolites presented by the evolutionarily conserved MR1 molecules. MAIT cells represent a large pre-expanded T cell subset in humans and are involved in both protective immunity and inflammatory immunopathology. However, what controls the functional heterogeneity of human MAIT cell responses is still largely unclear. Here, combining functional and transcriptomic analyses, we investigate how MAIT cell response programs are influenced by the cytokine milieu at the time of antigen recognition. Activation by MR1-presented antigen together with IL-12 induces intermediate levels of IFN\u03b3 and TNF, as well as a regulatory profile with substantial IL-10 production and elevated expression of TIM-3, LAG-3, and PD-1. Activation by the combination of antigen and IL-12 induces a c-MAF-dependent program required for IL-10 production. The MAIT cell-derived IL-10 mediates both autocrine and paracrine immune regulation. In contrast, coactivation of MAIT cells with IL-18 induces IL-17, GM-CSF, IFN\u03b3, and TNF, without IL-10. Notably, IL-18 dominantly counteracts IL-10 expression. The activation states biased toward IL-10 or IL-17 production are reversible and do not represent stable subsets. Finally, MR1-restricted TCR-mediated activation without cytokine coactivation drives primarily granzyme B cytolytic arming. Altogether, these findings demonstrate that human MAIT cells adapt their functional effector response during antigen recognition to cytokine cues in the microenvironment, and identify programs biased toward either regulatory c-MAF-dependent IL-10 expression, or an inflammatory IL-17 and GM-CSF profile.", "doi": "10.1073/pnas.2414230122", "pmid": "39903121", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11831165"}], "notes": [], "created": "2025-11-21T14:09:08.705Z", "modified": "2025-11-21T14:09:09.031Z"}, {"entity": "publication", "iuid": "84529861f56b4d64a3f4945924b378a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84529861f56b4d64a3f4945924b378a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84529861f56b4d64a3f4945924b378a1"}}, "title": "Epitope Mapping with Sidewinder: An XL-MS and Structural Modeling Approach.", "authors": [{"family": "Str\u00f6baek", "given": "Joel", "initials": "J", "orcid": "0000-0003-1231-0420", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8d9f6cfe0e845d0a4208d442e4b652c.json"}}, {"family": "Tang", "given": "Di", "initials": "D", "orcid": "0000-0001-6323-9375", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2a27467c4094d9f8d8f8402efa333f4.json"}}, {"family": "Gueto-Tettay", "given": "Carlos", "initials": "C", "orcid": "0000-0002-8496-6341", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0e4a5377a88414588686e5630b0be66.json"}}, {"family": "Gomez Toledo", "given": "Alejandro", "initials": "A"}, {"family": "Olofsson", "given": "Berit", "initials": "B", "orcid": "0009-0009-0602-2183", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ad483473b044b7dbc7e6c61ef1c0a73.json"}}, {"family": "Hartman", "given": "Erik", "initials": "E", "orcid": "0000-0001-9997-2405", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cd725d94e9941ea835537ba503fb309.json"}}, {"family": "Heusel", "given": "Moritz", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad3c999da10c41e4a3afda2718815083.json"}}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L", "orcid": "0000-0001-9885-9312", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e99f34fb854beb8d810b05fe941057.json"}}], "type": "journal article", "published": "2025-02-11", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "4", "issn-l": null}, "abstract": "Antibodies are critical to the host's immune defense against bacterial pathogens. Understanding the mechanisms of antibody-antigen interactions is essential for developing new targeted immunotherapies. Building computational workflows that can identify where an antibody binds its cognate antigen and deconvoluting the interaction interface in a high-throughput manner are critical for advancing this field. Cross-linking mass spectrometry (XL-MS) integrated with structural modeling offers a flexible and high-resolution strategy to map protein-protein interactions from low sample amounts. However, cross-linking and in silico modeling have limitations that require robust analytical workflows to make accurate inferences. In this study, we introduce Sidewinder, a modular high-throughput pipeline combining state-of-the-art computational structural prediction and molecular docking with rapid XL-MS analysis, enabling comprehensive interrogation of antibody-antigen systems. We validated this pipeline on antibodies targeting two Streptococcus pyogenes virulence factors. Using recently published data, we identified a well-defined monoclonal antibody epitope on Streptolysin O by generating and querying a large ensemble of interaction models probabilistically. We also showcased the utility of the Sidewinder pipeline by analyzing a more complex system, involving monoclonal antibodies that target the cell wall-anchored M1 protein. The flexibility and robustness of the Sidewinder pipeline provide a powerful framework for future studies of complex antibody-antigen systems, potentially leading to new therapeutic strategies.", "doi": "10.3390/ijms26041488", "pmid": "40003954", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11855800"}, {"db": "pii", "key": "ijms26041488"}], "notes": [], "created": "2025-11-26T16:22:51.051Z", "modified": "2025-11-26T16:26:54.794Z"}, {"entity": "publication", "iuid": "f92276fcc0404b76b42475aafb471f44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f92276fcc0404b76b42475aafb471f44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f92276fcc0404b76b42475aafb471f44"}}, "title": "A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data.", "authors": [{"family": "Abalde", "given": "Samuel", "initials": "S", "orcid": "0000-0001-7790-0603", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ca4ab7834dc493daaa1eb96b5d980c2.json"}}, {"family": "Jondelius", "given": "Ulf", "initials": "U", "orcid": "0000-0003-2847-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/6582e2e560474080a7d89240a3d43edd.json"}}], "type": "journal article", "published": "2025-02-10", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "volume": "74", "issue": "1", "pages": "70-85", "issn-l": "1063-5157"}, "abstract": "Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs-which include three main groups, namely Acoela, Nemertodermatida, and Xenoturbella-have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but other phylogenomic analyses have recovered this clade nested within the deuterostomes, as sister to Ambulacraria. The position of Xenacoelomorpha within the metazoan tree has understandably attracted a lot of attention, overshadowing the study of phylogenetic relationships within this group. Given that Xenoturbella includes only six species whose relationships are well understood, we decided to focus on the most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, we have sequenced 29 transcriptomes, doubling the number of sequenced species, to infer a backbone tree for Acoelomorpha based on genomic data. The recovered topology is mostly congruent with previous studies. The most important difference is the recovery of Paratomella as the first off-shoot within Acoela, dramatically changing the reconstruction of the ancestral acoel. Besides, we have detected incongruence between the gene trees and the species tree, likely linked to incomplete lineage sorting, and some signal of introgression between the families Dakuidae and Mecynostomidae, which hampers inferring the correct placement of this family and, particularly, of the genus Notocelis. We have also used this dataset to infer for the first time diversification times within Acoelomorpha, which coincide with known bilaterian diversification and extinction events. Given the importance of morphological data in acoelomorph phylogenetics, we tested several partitions and models. Although morphological data failed to recover a robust phylogeny, phylogenetic placement has proven to be a suitable alternative when a reference phylogeny is available.", "doi": "10.1093/sysbio/syae057", "pmid": "39451056", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11809588"}, {"db": "pii", "key": "7841810"}], "notes": [], "created": "2024-10-31T12:39:22.128Z", "modified": "2025-11-28T10:50:09.314Z"}, {"entity": "publication", "iuid": "79a9f40ca8e84b22978cef973223751e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79a9f40ca8e84b22978cef973223751e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79a9f40ca8e84b22978cef973223751e"}}, "title": "High-content morphological profiling by Cell Painting in 3D spheroids", "authors": [{"family": "Ringers", "given": "Christa", "initials": "C", "orcid": "0000-0002-0807-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/1870bfae83214898acf048b2ecbd81ba.json"}}, {"family": "Holmberg", "given": "David", "initials": "D", "orcid": "0000-0001-7204-0026", "researcher": {"href": "https://publications.scilifelab.se/researcher/56fa719ef91e45c4bdb4171fa4a40338.json"}}, {"family": "Flobak", "given": "\u00c5smund", "initials": "\u00c5", "orcid": "0000-0002-3357-425X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dbad688aeb44d039f3bc7e51f75b2bf.json"}}, {"family": "Georgieva", "given": "Polina", "initials": "P", "orcid": "0000-0001-8326-4738", "researcher": {"href": "https://publications.scilifelab.se/researcher/394f19ff3cff4b1c94d0a9a92e976b73.json"}}, {"family": "Jarvius", "given": "Malin", "initials": "M", "orcid": "0000-0002-1565-6155", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6b510afc21748adb6b432173c3fdab2.json"}}, {"family": "Johansson", "given": "Martin", "initials": "M", "orcid": "0000-0002-3733-8975", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1fdb7ed5e7047f3963ada15a0f8d48e.json"}}, {"family": "Larsson", "given": "Anders", "initials": "A", "orcid": "0000-0002-2096-8102", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4a4e2ec44f1446e98ee05ff0f45e484.json"}}, {"family": "Ros\u00e9n", "given": "Dan", "initials": "D"}, {"family": "Seashore\u2013Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4645bc97a8024c548111802101b83571.json"}}, {"family": "Visnes", "given": "Torkild", "initials": "T", "orcid": "0000-0003-1047-988X", "researcher": {"href": "https://publications.scilifelab.se/researcher/599a0da924424d098adc248b67fabf05.json"}}, {"family": "Carreras Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications.scilifelab.se/researcher/28ad5f6a1a064e52aca72780adc4bb96.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}], "type": "posted-content", "published": "2025-02-08", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.02.05.636642", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2025-04-15T11:55:48.934Z", "modified": "2025-12-18T19:20:13.620Z"}, {"entity": "publication", "iuid": "e0831ab011e349ca8730591503d89f54", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0831ab011e349ca8730591503d89f54.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0831ab011e349ca8730591503d89f54"}}, "title": "Characterization of the genomic landscape of canine diffuse large B-cell lymphoma reveals recurrent H3K27M mutations linked to progression-free survival.", "authors": [{"family": "van der Heiden", "given": "Anna Darlene", "initials": "AD"}, {"family": "Pensch", "given": "Raphaela", "initials": "R"}, {"family": "Agger", "given": "Sophie", "initials": "S"}, {"family": "Gardner", "given": "Heather L", "initials": "HL"}, {"family": "Hendricks", "given": "William", "initials": "W"}, {"family": "Zismann", "given": "Victoria", "initials": "V"}, {"family": "Wong", "given": "Shukmei", "initials": "S"}, {"family": "Briones", "given": "Natalia", "initials": "N"}, {"family": "Turner", "given": "Bryce", "initials": "B"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K"}, {"family": "London", "given": "Cheryl", "initials": "C"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Arendt", "given": "Maja Louise", "initials": "ML"}], "type": "journal article", "published": "2025-02-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4724", "issn-l": "2045-2322"}, "abstract": "Diffuse large B-cell lymphoma (DLBCL) is an aggressive hematopoietic neoplasm that affects humans as well as dogs. While previous studies on canine DLBCL (cDLBCL) have significantly advanced our understanding of the disease, the majority of this research has relied on whole-exome sequencing, which is limited in its ability to detect copy number aberrations and other genomic changes beyond coding regions. Furthermore, many of these studies lack sufficient clinical follow-up data, making it difficult to draw meaningful associations between genetic variants and patient outcomes. Our study aimed to characterize the mutational landscape of cDLBCL using whole-genome sequencing of matched tumor-normal samples obtained from a cohort of 43 dogs previously enrolled in a clinical trial for which longitudinal follow-up was available. We focused on identifying genes that were significantly or recurrently mutated with coding point mutations, copy number aberrations, and their associations with patient outcomes. We identified 26 recurrently mutated genes, 18 copy number gains, and 8 copy number losses. Consistent with prior studies, the most commonly mutated genes included TRAF3, FBXW7, POT1, TP53, SETD2, DDX3X and TBL1XR1. The most prominent copy number gain occurred on chromosome 13, overlapping key oncogenes such as MYC and KIT, while the most frequent deletion was a focal loss on chromosome 26, encompassing IGL, PRAME, GNAZ, RAB36, RSPH14, and ZNF280B. Notably, our set of recurrently mutated genes was significantly enriched with genes involved in epigenetic regulation. In particular, we identified hotspot mutations in two histone genes, H3C8, and LOC119877878, resulting in H3K27M alterations predicted to dysregulate gene expression. Finally, a survival analysis revealed that H3K27M mutations in H3C8 were associated with increased hazard ratios for progression-free survival. No copy number aberrations were associated with survival. These findings underscore the critical role of epigenetic dysregulation in cDLBCL and affirm the dog as a relevant large animal model for interrogating the biological activity of novel histone-modifying treatment strategies.", "doi": "10.1038/s41598-025-89245-0", "pmid": "39922874", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11807134"}, {"db": "pii", "key": "10.1038/s41598-025-89245-0"}], "notes": [], "created": "2025-11-28T10:47:15.103Z", "modified": "2025-11-28T10:47:15.106Z"}, {"entity": "publication", "iuid": "ae26270a2c64410591f4cbb23c632b69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae26270a2c64410591f4cbb23c632b69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae26270a2c64410591f4cbb23c632b69"}}, "title": "In vivo regulation of the monocyte phenotype by Mycobacterium marinum and the ESX-1 type VII secretion system.", "authors": [{"family": "Munke", "given": "Kristina", "initials": "K"}, {"family": "Wulff", "given": "Line", "initials": "L"}, {"family": "Lienard", "given": "Julia", "initials": "J"}, {"family": "Carlsson", "given": "Fredric", "initials": "F"}, {"family": "Agace", "given": "William W", "initials": "WW"}], "type": "journal article", "published": "2025-02-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4545", "issn-l": "2045-2322"}, "abstract": "Pathogenic mycobacteria require the conserved ESX-1 type VII secretion system to cause disease. In a murine Mycobacterium marinum infection model we previously demonstrated that infiltrating monocytes and neutrophils represent the major bacteria-harbouring cell populations in infected tissue. In the current study we use this model, in combination with scRNA sequencing, to assess the impact of M. marinum infection on the transcriptional profile of infiltrating Ly6C\u207aMHCII\u207a monocytes in vivo. Our findings demonstrate that infection of infiltrating monocytes with M. marinum alters their cytokine expression profile, induces glycolytic metabolism, hypoxia-mediated signaling, nitric oxide synthesis, tissue remodeling, and suppresses responsiveness to IFN\u03b3. We further show that the transcriptional response of bystander monocytes is influenced by ESX-1-dependent mechanisms, including a reduced responsiveness to IFN\u03b3. These findings suggest that mycobacterial infection has pleiotropic effects on monocyte phenotype, with potential implications in bacterial growth restriction and granuloma formation.", "doi": "10.1038/s41598-025-88212-z", "pmid": "39915532", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11802795"}, {"db": "pii", "key": "10.1038/s41598-025-88212-z"}], "notes": [], "created": "2025-09-08T11:29:57.395Z", "modified": "2025-09-08T11:29:57.400Z"}, {"entity": "publication", "iuid": "0aeeb82ee89f48e699ba813ddc764177", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0aeeb82ee89f48e699ba813ddc764177.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0aeeb82ee89f48e699ba813ddc764177"}}, "title": "TGF-\u03b2 induces cholesterol accumulation to regulate the secretion of tumor-derived extracellular vesicles.", "authors": [{"family": "Rodrigues-Junior", "given": "Dorival Mendes", "initials": "DM"}, {"family": "Tsirigoti", "given": "Chrysoula", "initials": "C"}, {"family": "Psatha", "given": "Konstantina", "initials": "K"}, {"family": "Kletsas", "given": "Dimitris", "initials": "D"}, {"family": "Aivaliotis", "given": "Michalis", "initials": "M"}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A"}], "type": "journal article", "published": "2025-02-06", "journal": {"title": "J. Exp. Clin. Cancer Res.", "issn": "1756-9966", "volume": "44", "issue": "1", "pages": "42", "issn-l": "1756-9966"}, "abstract": "Cancer cells are avid extracellular vesicle (EV) producers. EVs transport transforming growth factor-\u03b2 (TGF-\u03b2), which is commonly activated under late stages of cancer progression. Nevertheless, whether TGF-\u03b2 signaling coordinates EV biogenesis is a relevant topic that remains minimally explored.\n\nWe sought after specific TGF-\u03b2 pathway mediators that could regulate EV release. To this end, we used a large number of cancer cell models, coupled to EV cell biological assays, unbiased proteomic and transcriptomic screens, followed by signaling and cancer biology analyses, including drug resistance assays.\n\nWe report that TGF-\u03b2, by activating its type I receptor and MEK-ERK1/2 signaling, increased the numbers of EVs released by human cancer cells. Upon examining cholesterol as a mediator of EV biogenesis, we delineated a pathway whereby ERK1/2 acted by phosphorylating sterol regulatory element-binding protein-2 that transcriptionally induced 7-dehydrocholesterol reductase expression, thus raising cholesterol abundance at both cellular and EV levels. Notably, inhibition of MEK or cholesterol synthesis, which impaired TGF-\u03b2-induced EV secretion, sensitized cancer cells to chemotherapeutic drugs. Furthermore, proteomic profiling of two distinct EV populations revealed that EVs secreted by TGF-\u03b2-stimulated cells were either depleted or enriched for different sets of cargo proteins. Among these, latent-TGF-\u03b21 present in the EVs was not affected by TGF-\u03b2 signaling, while TGF-\u03b2 pathway-related molecules (e.g., matrix metalloproteinases, including MMP9) were either uniquely enriched on EVs or strongly enhanced after TGF-\u03b2 stimulation. EV-associated latent-TGF-\u03b21 activated SMAD signaling, even when EV uptake was blocked by heparin, indicating competent signaling capacity from target cell surface receptors. MMP inhibitor or proteinase treatment blocked EV-mediated SMAD signaling, suggesting that EVs require MMP activity to release the active TGF-\u03b2 from its latent complex, a function also linked to the EV-mediated transfer of pro-migratory potential and ability of cancer cells to survive in the presence of cytotoxic drugs.\n\nHence, we delineated a novel signaling cascade that leads to high rates of EV generation by cancer cells in response to TGF-\u03b2, with cholesterol being a key intermediate step in this mechanism.", "doi": "10.1186/s13046-025-03291-0", "pmid": "39910665", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11800471"}, {"db": "pii", "key": "10.1186/s13046-025-03291-0"}], "notes": [], "created": "2025-11-27T13:03:18.196Z", "modified": "2025-11-27T13:03:18.246Z"}, {"entity": "publication", "iuid": "cb2dbb24ca8e445283868bfaa092da83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb2dbb24ca8e445283868bfaa092da83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb2dbb24ca8e445283868bfaa092da83"}}, "title": "Population history and admixture of the Fulani people from the Sahel.", "authors": [{"family": "Fortes-Lima", "given": "Cesar A", "initials": "CA"}, {"family": "Diallo", "given": "Mame Y", "initials": "MY"}, {"family": "Janou\u0161ek", "given": "V\u00e1clav", "initials": "V"}, {"family": "\u010cern\u00fd", "given": "Viktor", "initials": "V"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}], "type": "journal article", "published": "2025-02-06", "journal": {"title": "Am. J. Hum. Genet.", "issn": "1537-6605", "volume": "112", "issue": "2", "pages": "261-275", "issn-l": "0002-9297"}, "abstract": "The Fulani people, one of the most important pastoralist groups in sub-Saharan Africa, are still largely underrepresented in population genomic research. They speak a Niger-Congo language called Fulfulde or Pulaar and live in scattered locations across the Sahel/Savannah belt, from the Atlantic Ocean to Lake Chad. According to historical records, their ancestors spread from Futa Toro in the Middle Senegal Valley to Futa-Jallon in Guinea and then eastward into the Sahel belt over the past 1,500 years. However, the earlier history of this traditionally pastoral population has not been well studied. To uncover the genetic structure and ancestry of this widespread population, we gathered genome-wide genotype data from 460 individuals across 18 local Fulani populations, along with comparative data from both modern and ancient worldwide populations. This represents a comprehensive geographically wide-scaled genome-wide study of the Fulani. We revealed a genetic component closely associated with all local Fulani populations, suggesting a shared ancestral component possibly linked to the beginning of African pastoralism in the Green Sahara. Comparison to ancient DNA results also identified the presence of an ancient Iberomaurusian-associated component across all Fulani groups, providing additional insights into their deep genetic history. Additionally, our genetic data indicate a later Fulani expansion from the western to the eastern Sahel, characterized by a clinal pattern and admixture with several other African populations north of the equator.", "doi": "10.1016/j.ajhg.2024.12.015", "pmid": "39919708", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11866953"}, {"db": "pii", "key": "S0002-9297(24)00457-9"}], "notes": [], "created": "2025-11-28T10:41:50.237Z", "modified": "2025-11-28T10:41:50.264Z"}, {"entity": "publication", "iuid": "05dfc96807f64f37a3917f85f1198b7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05dfc96807f64f37a3917f85f1198b7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05dfc96807f64f37a3917f85f1198b7e"}}, "title": "Whole genome sequencing in early onset advanced heart failure.", "authors": [{"family": "Linn\u00e9r", "given": "Erik", "initials": "E", "orcid": "0009-0004-6961-8957", "researcher": {"href": "https://publications.scilifelab.se/researcher/666959db0ed3435ab374dcbd50cb9925.json"}}, {"family": "Czuba", "given": "Tomasz", "initials": "T"}, {"family": "Gidl\u00f6f", "given": "Olof", "initials": "O", "orcid": "0000-0002-7402-3139", "researcher": {"href": "https://publications.scilifelab.se/researcher/83f5453e507041b995e0d69a74540c24.json"}}, {"family": "Lundgren", "given": "Jakob", "initials": "J", "orcid": "0000-0001-9338-2906", "researcher": {"href": "https://publications.scilifelab.se/researcher/c929a6ea1c6f4975ad0ec84da3a32f5e.json"}}, {"family": "Bollano", "given": "Entela", "initials": "E", "orcid": "0000-0003-3341-2434", "researcher": {"href": "https://publications.scilifelab.se/researcher/f486393025c0406bbf6c397b7d1b6f05.json"}}, {"family": "Hellberg", "given": "Maria", "initials": "M"}, {"family": "Celik", "given": "Selvi", "initials": "S", "orcid": "0000-0001-7032-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da057ac725d4fb0bdbaddbc06a8ea64.json"}}, {"family": "Pimpalwar", "given": "Neha", "initials": "N"}, {"family": "Rentzsch", "given": "Philipp", "initials": "P", "orcid": "0000-0002-0413-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/372fb956b5634de493dd639dae9e8158.json"}}, {"family": "Martorella", "given": "Molly", "initials": "M", "orcid": "0000-0002-3306-6650", "researcher": {"href": "https://publications.scilifelab.se/researcher/64e0f833822b463b9736178d9a25c861.json"}}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Melander", "given": "Olle", "initials": "O", "orcid": "0000-0002-2581-484X", "researcher": {"href": "https://publications.scilifelab.se/researcher/868a7e41aa054097a85575aa1d9658cc.json"}}, {"family": "Albinsson", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-6936-3967", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac577769c2d44ac7bd8ccc28f69045de.json"}}, {"family": "Dellgren", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4961-9704", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d5ee559ab58458197bab1d119a50824.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Jeppsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-2356-2295", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec361c8c3f84b25a44213af77f4ac31.json"}}, {"family": "Lumbers", "given": "R Thomas", "initials": "RT", "orcid": "0000-0002-9077-4741", "researcher": {"href": "https://publications.scilifelab.se/researcher/a53e4d6591db481f881ec6046d54535b.json"}}, {"family": "Shah", "given": "Sonia", "initials": "S", "orcid": "0000-0001-5860-4526", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6a8568b3cae476199b27818eeb19e4d.json"}}, {"family": "Nilsson", "given": "Johan", "initials": "J", "orcid": "0000-0001-6860-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/c07e3381e15b4806b77d1b575e4ddca2.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications.scilifelab.se/researcher/85de5f6926c94fbd96bbc9428b6a384f.json"}}, {"family": "Lappalainen", "given": "Tuuli", "initials": "T", "orcid": "0000-0002-7746-8109", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f81f8a2e6f4f11ad4504746492fc41.json"}}, {"family": "Levin", "given": "Malin", "initials": "M", "orcid": "0000-0003-1069-5275", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d251e6a73fb49bcbd930f7ec8bd274c.json"}}, {"family": "Ehrencrona", "given": "Hans", "initials": "H", "orcid": "0000-0002-5589-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b89608a8ce941c3b9911630b4ff9720.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG", "orcid": "0000-0001-6285-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e50df6bb7f4194a52546dbd5652e84.json"}}], "type": "journal article", "published": "2025-02-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4306", "issn-l": "2045-2322"}, "abstract": "The genetic contributions to early onset heart failure (HF) are incompletely understood. Genetic testing in advanced HF patients undergoing heart transplantation (HTx) may yield clinical benefits, but data is limited. We performed deep-coverage whole genome sequencing (WGS) in 102 Swedish HTx recipients. Gene lists were compiled through a systematic literature review. Variants were prioritized for pathogenicity and classified manually. We also compared polygenic HF risk scores to a population-based cohort. We found a pathogenic (LP/P) variant in 34 individuals (34%). Testing yield was highest in hypertrophic (63% LP/P carriers), dilated (40%) and arrhythmogenic right ventricular (33%) cardiomyopathy and lower in ischemic cardiomyopathy (10%). A family history was more common in LP/P variant carriers than in non-carriers but was present in less than half of carriers (44% vs 13%, P < 0.001), whereas age was similar. Polygenic risk scores were similar in HTx recipients and the population cohort. In conclusion, we observed a high prevalence of pathogenic cardiomyopathy gene variants in individuals with early-onset advanced HF, which could not accurately be ruled out by family history and age. In contrast, we did not observe higher polygenic risk scores in early onset advanced HF cases than in the general population.", "doi": "10.1038/s41598-025-88465-8", "pmid": "39910139", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11799378"}, {"db": "pii", "key": "10.1038/s41598-025-88465-8"}], "notes": [], "created": "2025-02-11T07:01:17.258Z", "modified": "2025-02-11T07:01:20.425Z"}, {"entity": "publication", "iuid": "85067a3ac4764a808733b9d4d4adc266", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85067a3ac4764a808733b9d4d4adc266.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85067a3ac4764a808733b9d4d4adc266"}}, "title": "Testosterone exacerbates neutrophilia and cardiac injury in myocardial infarction via actions in bone marrow.", "authors": [{"family": "Svedlund Eriksson", "given": "Elin", "initials": "E", "orcid": "0009-0006-0169-6929", "researcher": {"href": "https://publications.scilifelab.se/researcher/afb8b198881944a28e575e8ca8a2cc1d.json"}}, {"family": "Lantero Rodriguez", "given": "Marta", "initials": "M", "orcid": "0000-0002-9912-6716", "researcher": {"href": "https://publications.scilifelab.se/researcher/bee7c52fd83149fbbb01ced1cf5fa79d.json"}}, {"family": "Halvorsen", "given": "Bente", "initials": "B", "orcid": "0000-0002-6529-6485", "researcher": {"href": "https://publications.scilifelab.se/researcher/83218278a90c41609ea44fcd6315d395.json"}}, {"family": "Johansson", "given": "Inger", "initials": "I", "orcid": "0009-0008-3579-9031", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbc07dcc5a824676a0f788ebe060ca02.json"}}, {"family": "M\u00e5rtensson", "given": "Anna K F", "initials": "AKF", "orcid": "0000-0002-8786-4965", "researcher": {"href": "https://publications.scilifelab.se/researcher/13ca4b04916d4318b8e00f1f5f4ca6d3.json"}}, {"family": "Wilhelmson", "given": "Anna S", "initials": "AS", "orcid": "0000-0003-0640-0251", "researcher": {"href": "https://publications.scilifelab.se/researcher/73ed1ad8dfa2406081cef9eb005b3ad6.json"}}, {"family": "Huse", "given": "Camilla", "initials": "C", "orcid": "0000-0002-7694-5196", "researcher": {"href": "https://publications.scilifelab.se/researcher/1025010995224e44bae6f9c15813de38.json"}}, {"family": "Ueland", "given": "Thor", "initials": "T"}, {"family": "Aukrust", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-0919-836X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52ec6832f0742b4be1f6dd2e455a1ed.json"}}, {"family": "Broch", "given": "Kaspar", "initials": "K", "orcid": "0000-0003-4316-805X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c4d9562e7294f849d3ff4508d353bf9.json"}}, {"family": "Gullestad", "given": "Lars", "initials": "L"}, {"family": "Amundsen", "given": "Brage H\u00f8yem", "initials": "BH", "orcid": "0000-0001-7914-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7ee62e8f93047258965bcf42bb4a475.json"}}, {"family": "Andersen", "given": "Geir \u00d8ystein", "initials": "G\u00d8", "orcid": "0000-0003-1578-6440", "researcher": {"href": "https://publications.scilifelab.se/researcher/a498990cfa894f74bd3a273a1bbaee58.json"}}, {"family": "Karlsson", "given": "Mikael C I", "initials": "MCI", "orcid": "0000-0001-5582-614X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b7a0612c55f4ab8865b6e5f59347271.json"}}, {"family": "Hagberg Thulin", "given": "Malin", "initials": "M", "orcid": "0000-0002-8673-1247", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbf6e0d2d6f748e39f32a70e1e4d597f.json"}}, {"family": "Camponeschi", "given": "Alessandro", "initials": "A", "orcid": "0000-0002-6472-2438", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccbaffafd6a24f4abed1e402219fa472.json"}}, {"family": "Trompet", "given": "Dana", "initials": "D", "orcid": "0000-0001-9472-6184", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ef4d02ec2e1427088522df2a759bf3a.json"}}, {"family": "Hammarsten", "given": "Ola", "initials": "O"}, {"family": "Redfors", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Omerovic", "given": "Elmir", "initials": "E"}, {"family": "Levin", "given": "Malin C", "initials": "MC"}, {"family": "Chagin", "given": "Andrei S", "initials": "AS", "orcid": "0000-0002-2696-5850", "researcher": {"href": "https://publications.scilifelab.se/researcher/909bca2fc68645e980a93b99dc150e4c.json"}}, {"family": "Dahl", "given": "Tuva B", "initials": "TB", "orcid": "0000-0001-7818-9411", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff93848d0aac4a9fbf8ec2bbedebadea.json"}}, {"family": "Tivesten", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-8318-0486", "researcher": {"href": "https://publications.scilifelab.se/researcher/55ade4099dfd4859970a6fe21af50870.json"}}], "type": "journal article", "published": "2025-02-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "1142", "issn-l": "2041-1723"}, "abstract": "Men develop larger infarct sizes than women after a myocardial infarction (MI), but the mechanism underlying this sex difference is unknown. Here, we demonstrated that blood neutrophil counts post-MI were higher in male than female mice. Castration-induced testosterone deficiency reduced blood neutrophil counts to the level in females and increased survival post-MI. These effects were mimicked by Osterix-directed ablation of the androgen receptor in bone marrow (BM). Mechanistically, androgens downregulated the leukocyte retention factor CXCL12 in BM stromal cells. Post-hoc analysis of clinical trial data showed that neutrophilia was greater in men than women after reperfusion of first-time ST-elevation MI, and tocilizumab, an interleukin-6 receptor inhibitor, reduced blood neutrophil counts and infarct size to a greater extent in men than women. Our work reveals a previously unknown mechanism connecting testosterone with neutrophilia and MI injury via BM and identifies the importance of considering sex when developing anti-inflammatory strategies to treat MI.", "doi": "10.1038/s41467-025-56217-x", "pmid": "39910039", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11799197"}, {"db": "pii", "key": "10.1038/s41467-025-56217-x"}], "notes": [], "created": "2025-07-08T13:56:49.778Z", "modified": "2025-11-04T11:38:37.313Z"}, {"entity": "publication", "iuid": "58a0c3b2653b49d8b28daf5a2aa1c889", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58a0c3b2653b49d8b28daf5a2aa1c889.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58a0c3b2653b49d8b28daf5a2aa1c889"}}, "title": "Intranasal Delivery of a Ghrelin Mimetic Engages the Brain Ghrelin Signaling System in Mice.", "authors": [{"family": "Poelman", "given": "Ren\u00e9e", "initials": "R", "orcid": "0009-0004-8655-0026", "researcher": {"href": "https://publications.scilifelab.se/researcher/d826c2eaa44a4b859c1f48faa2e07621.json"}}, {"family": "Le May", "given": "Marie V", "initials": "MV", "orcid": "0000-0001-5563-9512", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dad2e705cff43a4a7a1e3954f4452d7.json"}}, {"family": "Sch\u00e9le", "given": "Erik", "initials": "E", "orcid": "0000-0003-2693-7312", "researcher": {"href": "https://publications.scilifelab.se/researcher/4349f37c25c44b419ea6e27f17a1a9a1.json"}}, {"family": "Stoltenborg", "given": "Iris", "initials": "I", "orcid": "0000-0001-5134-8769", "researcher": {"href": "https://publications.scilifelab.se/researcher/50e7803a10d34b4284cd5ee8a3390413.json"}}, {"family": "Dickson", "given": "Suzanne L", "initials": "SL", "orcid": "0000-0002-3822-5294", "researcher": {"href": "https://publications.scilifelab.se/researcher/eabf6c037c6640cf95d64eebfb3f62e9.json"}}], "type": "journal article", "published": "2025-02-05", "journal": {"title": "Endocrinology", "issn": "1945-7170", "volume": "166", "issue": "3", "issn-l": "0013-7227"}, "abstract": "Ghrelin, the endogenous ligand of the growth hormone secretagogue receptor (GHSR), promotes food intake and other feeding behaviors, and stimulates growth hormone (GH) release from the pituitary. Growth hormone secretagogues (GHS), such as GHRP-6 and MK-0677, are synthetic GHSR ligands that activate orexigenic neuropeptide Y neurons that coexpress agouti-related peptide (AgRP) in the arcuate nucleus of the hypothalamus when administered systemically. Systemic GHRP-6 also stimulates GH release in humans and rats. Thus, GHS and ghrelin have therapeutic relevance in patients who could benefit from its orexigenic and/or GH-releasing effects. This study examined whether intranasal delivery of ghrelin, GHRP-6, or MK-0677 engages the brain ghrelin signaling system. Effective compounds and doses were selected based on increased food intake after intranasal application in mice. Only GHRP-6 (5 mg/kg) increased food intake without adverse effects, prompting detailed analysis of meal patterns, neuronal activation in the arcuate nucleus (via Fos mapping) and neurochemical identification of c-fos messenger RNA (mRNA)-expressing neurons using RNAscope. We also assessed the effect of intranasal GHRP-6 on serum GH levels. Intranasal GHRP-6 increased food intake by increasing meal frequency and size. Fos expression in the arcuate nucleus was higher in GHRP-6-treated mice than in saline controls. When examining the neurochemical identity of c-fos-mRNA-expressing neurons, we found coexpression with 63.5 \u00b1 1.9% Ghsr mRNA, 79 \u00b1 6.8% Agrp mRNA, and 11.4 \u00b1 2.5% Ghrh mRNA, demonstrating GHRP-6's ability to engage arcuate nucleus neurons involved in food intake and GH release. Additionally, intranasal GHRP-6 elevated GH serum levels. These findings suggest that intranasal GHRP-6, but not ghrelin or MK-0677, can engage the brain ghrelin signaling system.", "doi": "10.1210/endocr/bqae166", "pmid": "39813130", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11795113"}, {"db": "pii", "key": "7954553"}], "notes": [], "created": "2025-11-05T13:58:56.979Z", "modified": "2025-11-05T13:58:57.267Z"}, {"entity": "publication", "iuid": "c7b79374d64443dd9096f46459dc4a86", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7b79374d64443dd9096f46459dc4a86.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7b79374d64443dd9096f46459dc4a86"}}, "title": "In silico classification and identification co-purified protein complexes yield new structures and multiple MSP assembly states", "authors": [{"family": "Zhang", "given": "Qingyang", "initials": "Q"}, {"family": "Murthy", "given": "Abhinandan Venkatesha", "initials": "AV"}, {"family": "Mim", "given": "Carsten", "initials": "C", "orcid": "0000-0001-6402-8270", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5919b7026fd4229b2593106ee0a727d.json"}}], "type": "posted-content", "published": "2025-02-04", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.02.04.636456", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-13T13:56:05.434Z", "modified": "2025-12-18T19:20:34.390Z"}, {"entity": "publication", "iuid": "d43559cecdac491cb9a1cdb46cb5e27d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d43559cecdac491cb9a1cdb46cb5e27d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d43559cecdac491cb9a1cdb46cb5e27d"}}, "title": "The auxin phenylacetic acid induces NIN expression in the actinorhizal plant Datisca glomerata, whereas cytokinin acts antagonistically.", "authors": [{"family": "Salgado", "given": "Marco Guedes", "initials": "MG", "orcid": "0000-0002-3490-1742", "researcher": {"href": "https://publications.scilifelab.se/researcher/51fc3c1c92834630a9055de1051cf969.json"}}, {"family": "Maity", "given": "Pooja Jha", "initials": "PJ"}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Pawlowski", "given": "Katharina", "initials": "K", "orcid": "0000-0003-2693-885X", "researcher": {"href": "https://publications.scilifelab.se/researcher/19951f24f09646fcab1fd083416665bc.json"}}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "2", "pages": "e0315798", "issn-l": "1932-6203"}, "abstract": "All nitrogen-fixing root nodule symbioses of angiosperms-legume and actinorhizal symbioses-possess a common ancestor. Molecular processes for the induction of root nodules are modulated by phytohormones, as is the case of the first nodulation-related transcription factor NODULE INCEPTION (NIN), whose expression can be induced by exogenous cytokinin in legumes. The process of actinorhizal nodule organogenesis is less well understood. To study the changes exerted by phytohormones on the expression of the orthologs of CYCLOPS, NIN, and NF-YA1 in the actinorhizal host Datisca glomerata, an axenic hydroponic system was established and used to examine the transcriptional responses (RT-qPCR) in roots treated with the synthetic cytokinin 6-Benzylaminopurine (BAP), the natural auxin Phenylacetic acid (PAA), and the synthetic auxin 1-Naphthaleneacetic acid (NAA). The model legume Lotus japonicus was used as positive control. Molecular readouts for auxins and cytokinin were established: DgSAUR1 for PAA, DgGH3.1. for NAA, and DgARR9 for BAP. L. japonicus NIN was induced by BAP, PAA, and NAA in a dosage- and time-dependent manner. While expression of D. glomerata NIN2 could not be induced in roots, D. glomerata NIN1 was induced by PAA; this induction was abolished in the presence of exogenous BAP. Furthermore, the induction of DgNIN1 expression by PAA required ethylene and gibberellic acid. This study suggests that while cytokinin signaling is central for cortex-induced nodules of L. japonicus, it acts antagonistically to the induction of nodule primordia of D. glomerata by PAA in the root pericycle.", "doi": "10.1371/journal.pone.0315798", "pmid": "39899489", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11790169"}, {"db": "pii", "key": "PONE-D-24-19931"}], "notes": [], "created": "2025-11-28T10:53:58.376Z", "modified": "2025-11-28T10:53:58.464Z"}, {"entity": "publication", "iuid": "874f1c17b7aa431f977a1f680546f059", "links": {"self": {"href": "https://publications.scilifelab.se/publication/874f1c17b7aa431f977a1f680546f059.json"}, "display": {"href": "https://publications.scilifelab.se/publication/874f1c17b7aa431f977a1f680546f059"}}, "title": "Reducing methane emissions by developing low-fumarate high-ethanol eco-friendly rice.", "authors": [{"family": "Jin", "given": "Yunkai", "initials": "Y"}, {"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Hu", "given": "Jia", "initials": "J"}, {"family": "Sun", "given": "Kai", "initials": "K"}, {"family": "Xue", "given": "Lihong", "initials": "L"}, {"family": "Bettembourg", "given": "Mathilde", "initials": "M"}, {"family": "Bedada", "given": "Girma", "initials": "G"}, {"family": "Hou", "given": "Pengfu", "initials": "P"}, {"family": "Hao", "given": "Peiying", "initials": "P"}, {"family": "Tang", "given": "Jintian", "initials": "J"}, {"family": "Ye", "given": "Zihong", "initials": "Z"}, {"family": "Liu", "given": "Chunlin", "initials": "C"}, {"family": "Li", "given": "Peng", "initials": "P"}, {"family": "Pan", "given": "Aihu", "initials": "A"}, {"family": "Weng", "given": "Lushui", "initials": "L"}, {"family": "Xiao", "given": "Guoying", "initials": "G"}, {"family": "Moazzami", "given": "Ali A", "initials": "AA"}, {"family": "Yu", "given": "Xiaoping", "initials": "X"}, {"family": "Wu", "given": "Jun", "initials": "J"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Sun", "given": "Chuanxin", "initials": "C"}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Mol Plant", "issn": "1752-9867", "issn-l": "1674-2052", "volume": "18", "issue": "2", "pages": "333-349"}, "abstract": "Methane in rice paddies is mainly produced by methanogenic communities feeding on carbon from root exudates and debris. However, the dominant root secretion governing methane emissions is not yet identified after decades of studies, even though secreted carbohydrates and organic acids have been shown to contribute to methane emissions. In this study, we discovered that fumarate and ethanol are two major rice-orchestrated secretions and play a key role in regulating methane emissions. Fumarate released in the rhizosphere is metabolized by microorganisms, supporting the growth of methanogenic archaea that produce methane as an end carbon product, while ethanol mitigates methane emissions through inhibition of methanogenic activity and growth as well as reducing fumarate synthesis in the rice root. Furthermore, we elucidated the route of fumarate metabolism in the anoxic rhizospheric zone. We found that fumarate in the rice root is produced from acetate via propionate and succinate, and when released into soil directly is oxidized to propionate before conversion via acetate into methane as the end product. The knowledge on fumarate and ethanol metabolism in rice was then used for hybrid breeding of new rice varieties with the property of low methane emission. Cultivation of these novel rice lines or employing our findings for rice cultivation managements showed up to 70% reductions in methane production from seven paddy field sites during 3 years of cultivation trials. Taken together, these findings offer great possibilities for effective mitigation of the global climatic impact of rice cultivation.", "doi": "10.1016/j.molp.2025.01.008", "pmid": "39904305", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S1674-2052(25)00029-2"}], "notes": [], "created": "2025-09-08T11:37:21.068Z", "modified": "2025-11-21T12:24:20.380Z"}, {"entity": "publication", "iuid": "5e435d0ba83e41edb4806fba16d0da8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e435d0ba83e41edb4806fba16d0da8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e435d0ba83e41edb4806fba16d0da8c"}}, "title": "Evolution of Hybrid Inviability Associated With Chromosome Fusions.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "N\u00e4svall", "given": "Karin", "initials": "K"}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17672", "issn-l": "0962-1083"}, "abstract": "Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. Less is known about how other rearrangements, such as chromosome fissions and fusions, can affect the evolution of reproductive isolation. Here, we use crosses between populations of the wood white butterfly (Leptidea sinapis) with different karyotypes to identify genomic regions associated with hybrid inviability. We map hybrid inviability candidate loci by contrasting allele frequencies between F2 hybrids that survived until the adult stage with individuals of the same cohort that succumbed to hybrid incompatibilities. Hybrid inviability candidate regions have high genetic differentiation between parental populations, reduced recombination rates, and are enriched near chromosome fusions. By analysing sequencing coverage, we exclude aneuploidies as a direct link between hybrid inviability and chromosome fusions. Instead, our results point to an indirect relationship between hybrid inviability and chromosome fusions, possibly related to reduced recombination in fused chromosomes. Thus, we map postzygotic isolation to chromosomal rearrangements, providing crucial empirical evidence for the idea that chromosome number differences between taxa can contribute to speciation.", "doi": "10.1111/mec.17672", "pmid": "39895489", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-21T13:45:03.334Z", "modified": "2025-11-21T13:45:03.397Z"}, {"entity": "publication", "iuid": "ce8b106b6f714fb9af54bf212eb1a45f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce8b106b6f714fb9af54bf212eb1a45f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce8b106b6f714fb9af54bf212eb1a45f"}}, "title": "Dissociable genetic influences on eye movements during abstract versus naturalistic social scene viewing in infancy.", "authors": [{"family": "Portugal", "given": "Ana Maria", "initials": "AM"}, {"family": "Taylor", "given": "Mark J", "initials": "MJ"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K"}, {"family": "Ronald", "given": "Angelica", "initials": "A"}, {"family": "Falck-Ytter", "given": "Terje", "initials": "T"}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4100", "issn-l": "2045-2322"}, "abstract": "Eye-movement metrics like fixation location and duration are increasingly being used in infancy research. We tested whether fixation durations during meaningful social stimulus viewing involve common or different familial influences than fixation durations during viewing of abstract stimulus. We analysed the duration of fixations, and the allocation of fixations to face and motion, from 536 dizygotic and monozygotic 5-month-old twins in: naturalistic scenes including low- and high-level social features, and abstract scenes only having low-level features. We observed significant genetic influences in both conditions (h2naturalistic = 0.30, 95% confidence interval (CI) 0.14 to 0.44; h2abstract = 0.25, 95% CI 0.09 to 0.39), while shared environmental influences were negligible. Although some genetic influences were shared between the two conditions, unique genetic factors were linked to naturalistic scene viewing, indicating that fixation durations index different phenomena dependent on the context. Heritability for face looking was moderate (h2 = 0.19, 95% CI 0.03 to 0.34), and no familial influences were found for motion looking. Exploratory polygenic score analyses revealed no significant associations with fixation measures. This study underscores the dissociable genetic influences on infants' visual exploration of abstract versus naturalistic stimuli and the importance of considering context when interpreting eye-tracking data.", "doi": "10.1038/s41598-024-83557-3", "pmid": "39900629", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11791049"}, {"db": "pii", "key": "10.1038/s41598-024-83557-3"}], "notes": [], "created": "2025-09-08T11:34:00.982Z", "modified": "2025-11-14T11:07:01.444Z"}, {"entity": "publication", "iuid": "97a9599da59641ebb05e5b7a8fe6ad45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45"}}, "title": "The expanded genome of Hexamita inflata, a free-living diplomonad.", "authors": [{"family": "Akdeniz", "given": "Zeynep", "initials": "Z", "orcid": "0000-0002-5279-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b6a7222e2d3487db2b50842f74e173e.json"}}, {"family": "Havelka", "given": "Michal", "initials": "M"}, {"family": "Stoklasa", "given": "Michal", "initials": "M"}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "\u017d\u00e1rsk\u00fd", "given": "Vojt\u011bch", "initials": "V"}, {"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}, {"family": "Kol\u00edsko", "given": "Martin", "initials": "M"}, {"family": "Provazn\u00edk", "given": "Jan", "initials": "J"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Tachezy", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2025-02-01", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "192", "issn-l": "2052-4463"}, "abstract": "Diplomonads are anaerobic, flagellated protists, being part of the Metamonada group of Eukaryotes. Diplomonads either live as endobionts (parasites and commensals) of animals or free-living in low-oxygen environments. Genomic information is available for parasitic diplomonads like Giardia intestinalis and Spironucleus salmonicida, while little is known about the genomic arrangements of free-living diplomonads. We have generated the first reference genome of a free-living diplomonad, Hexamita inflata. The final version of the genome assembly is fragmented (1241 contigs) but substantially larger (142 Mbp) than the parasitic diplomonad genomes (9.8-14.7 Mbp). It encodes 79,341 proteins; 29,874 have functional annotations and 49,467 are hypothetical proteins. Interspersed repeats comprise 34% of the genome (9617 Retroelements, 2676 DNA transposons). The large expansion of protein-encoding capacity and the interspersed repeats are the major reasons for the large genome size. This genome from a free-living diplomonad will be the basis for further studies of the Diplomonadida lineage and the evolution of parasitism-free living style transitions.", "doi": "10.1038/s41597-025-04514-x", "pmid": "39893204", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11787283"}, {"db": "pii", "key": "10.1038/s41597-025-04514-x"}], "notes": [], "created": "2025-03-07T09:59:16.550Z", "modified": "2025-04-03T08:27:54.918Z"}, {"entity": "publication", "iuid": "5c4dd2644ad441528eafb8748534391f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c4dd2644ad441528eafb8748534391f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c4dd2644ad441528eafb8748534391f"}}, "title": "Using the long-term genetic monitoring network ARMS-MBON to detect marine non-indigenous species along the European coasts", "authors": [{"family": "Pagnier", "given": "Justine", "initials": "J", "orcid": "0000-0002-6531-1374", "researcher": {"href": "https://publications.scilifelab.se/researcher/07e63d48a16f4ec385003d3ef4f5b28a.json"}}, {"family": "Daraghmeh", "given": "Nauras", "initials": "N", "orcid": "0000-0001-8261-824X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca8dad98b940460f8263e1537796f483.json"}}, {"family": "Obst", "given": "Matthias", "initials": "M", "orcid": "0000-0003-0264-9631", "researcher": {"href": "https://publications.scilifelab.se/researcher/03489369c77b4208b48f006a0db3bb84.json"}}], "type": "journal-article", "published": "2025-02-00", "journal": {"title": "Biol Invasions", "issn": "1387-3547", "volume": "27", "issue": "2", "issn-l": null}, "abstract": null, "doi": "10.1007/s10530-024-03503-2", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:41:13.367Z", "modified": "2025-11-28T10:41:13.490Z"}, {"entity": "publication", "iuid": "bf9db0aeeb03448faeb36ffffcc747bd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf9db0aeeb03448faeb36ffffcc747bd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf9db0aeeb03448faeb36ffffcc747bd"}}, "title": "Unravelling the dominant role of phosphorylation degree in governing the functionality of reassembled casein micelles: Implications for future dairy production through precision fermentation", "authors": [{"family": "Che", "given": "Jing", "initials": "J", "orcid": "0000-0002-0489-0683", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bdb1771dbaa4f4e987eafb1ac13d4bf.json"}}, {"family": "Fan", "given": "Zekun", "initials": "Z"}, {"family": "Bijl", "given": "Etske", "initials": "E", "orcid": "0000-0002-7363-5387", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c7ccc5ea1184a81a40dff03ceca3191.json"}}, {"family": "Thomsen", "given": "Julia Prangchat Stub", "initials": "JPS", "orcid": "0009-0006-5703-2961", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ad9e7e2c13c403eaba5922610b4f0e5.json"}}, {"family": "Mijakovic", "given": "Ivan", "initials": "I"}, {"family": "Hettinga", "given": "Kasper", "initials": "K", "orcid": "0000-0002-9017-4447", "researcher": {"href": "https://publications.scilifelab.se/researcher/d64330b9c6074a7998685d972c2d5dd1.json"}}, {"family": "Poulsen", "given": "Nina Aagaard", "initials": "NA"}, {"family": "Larsen", "given": "Lotte Bach", "initials": "LB", "orcid": "0000-0001-9674-0107", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1cd42b0d8d43a28ef0656a24e0c8c5.json"}}], "type": "journal-article", "published": "2025-02-00", "journal": {"title": "Food Hydrocolloids", "issn": "0268-005X", "volume": "159", "pages": "110615", "issn-l": null}, "abstract": null, "doi": "10.1016/j.foodhyd.2024.110615", "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-05T13:48:07.147Z", "modified": "2025-11-05T13:48:07.492Z"}, {"entity": "publication", "iuid": "5959d8a1ef54451098a8e6ac640e7442", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5959d8a1ef54451098a8e6ac640e7442.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5959d8a1ef54451098a8e6ac640e7442"}}, "title": "Unraveling the Genetics of Shared Clinical and Serological Manifestations in Patients With Systemic Inflammatory Autoimmune Diseases.", "authors": [{"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6be89ad73a14d66a3b9439efc9c4099.json"}}, {"family": "Notarnicola", "given": "Antonella", "initials": "A", "orcid": "0000-0003-0272-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/42411ecc60cd4357930ff0e978b3fcd8.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Enocsson", "given": "Helena", "initials": "H", "orcid": "0000-0002-2125-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/e34f7f45437c404da069fe0e83bf11f6.json"}}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Bucher", "given": "Sara Magnusson", "initials": "SM"}, {"family": "Norheim", "given": "Katrine B", "initials": "KB"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Andersson", "given": "Helena", "initials": "H"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Diederichsen", "given": "Louise Pyndt", "initials": "LP"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "with the DISSECT consortium and the ImmunoArray consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "volume": "77", "issue": "2", "pages": "212-225", "issn-l": "2326-5191"}, "abstract": "Systemic inflammatory autoimmune diseases (SIADs) such as systemic lupus erythematosus (SLE), primary Sj\u00f6gren disease (pSS), and idiopathic inflammatory myopathies (myositis) are complex conditions characterized by shared circulating autoantibodies and clinical manifestations, including skin rashes, among others. This study was aimed at elucidating the genetics underlying these common features.\n\nWe performed targeted DNA sequencing of coding and regulatory regions from approximately 1,900 immune-related genes in a large cohort of 2,292 well-characterized Scandinavian patients with SIADs with SLE, pSS, and myositis as well as 1,252 controls. A gene-based functionally weighted genetic score for aggregate testing of all genetic variants, including rare variants, was complemented by in silico functional analyses and in vitro reporter experiments.\n\nCase-control association analysis detected known and potentially novel genetic loci in agreement with previous genetic and transcriptomics findings linked to the SIAD autoimmune background. Intriguingly, case-case comparisons between patient subgroups with and without specific autoantibodies revealed that the subgroups defined by antinuclear antibodies and anti-double-stranded DNA antibodies have unique genetic profiles reflecting their heterogeneity. When focusing on clinical features, we overall showed that dual-specificity phosphatase 1 (DUSP1) protective genetic variants lead to increased gene expression and potentially to anti-inflammatory effects on the SIAD-associated skin phenotype. This is consistent with recent genetic findings on eczema and with the previously reported down-regulation of the MAPK signaling-related gene DUSP1 in other skin disorders.\n\nTogether, this suggests common molecular mechanisms potentially underlying overlapping clinical manifestations shared among different disorders and informs clinical heterogeneity, which could be translated to improve disease diagnostic and treatment, also in more generalized disease frameworks.", "doi": "10.1002/art.42988", "pmid": "39284741", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11782108"}], "notes": [], "created": "2024-11-12T11:40:11.189Z", "modified": "2025-09-08T06:50:36.661Z"}, {"entity": "publication", "iuid": "1df8ac6a6a684581b00cdd0e33a02066", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1df8ac6a6a684581b00cdd0e33a02066.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1df8ac6a6a684581b00cdd0e33a02066"}}, "title": "The structure of FCGBP is formed as a disulfide-mediated homodimer between its C-terminal domains.", "authors": [{"family": "Ehrencrona", "given": "Erik", "initials": "E"}, {"family": "Gallego", "given": "Pablo", "initials": "P", "orcid": "0000-0002-9061-2507", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a72e53fab17431db8fb168095a55c52.json"}}, {"family": "Trillo-Muyo", "given": "Sergio", "initials": "S", "orcid": "0000-0002-3135-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e6b6b830e9145a2ae3e6c10895acbee.json"}}, {"family": "Garcia-Bonete", "given": "Maria-Jose", "initials": "MJ", "orcid": "0000-0002-8832-4338", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca1f7997b83b4b2398d08c2b2a927e5e.json"}}, {"family": "Recktenwald", "given": "Christian V", "initials": "CV"}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC", "orcid": "0000-0002-1900-1869", "researcher": {"href": "https://publications.scilifelab.se/researcher/44b3815603154322a6dac16f2fc1c1e9.json"}}, {"family": "Johansson", "given": "Malin E V", "initials": "MEV", "orcid": "0000-0002-4237-6677", "researcher": {"href": "https://publications.scilifelab.se/researcher/520dab35c19049c8b3f1083a92e60d56.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "FEBS J.", "issn": "1742-4658", "volume": "292", "issue": "3", "pages": "582-601", "issn-l": "1742-464X"}, "abstract": "Mucus in the colon is crucial for intestinal homeostasis by forming a barrier that separates microbes from the epithelium. This is achieved by the structural arrangement of the major mucus proteins, such as MUC2 and FCGBP, both of which are comprised of several von Willebrand D domains (vWD) and assemblies. Numerous disulfide bonds stabilise these domains, and intermolecular bonds generate multimers of MUC2. The oligomeric nature of FCGBP is not known. Human hFCGBP contains 13 vWD domains whereas mouse mFCGBP consists of only 7. We found unpaired cysteines in the vWD1 (human and mouse) and vWD5 (mouse)/vWD11 (human) assemblies which were not involved in disulfide bonds. However, the most C-terminal vWD domains, vWD7 (mouse)/vWD13 (human), formed disulfide-linked dimers. The intermolecular bond between C5284 and C5403 of human hFCGBP was observed by using mass spectrometry to generate the dimer. Cryo-EM structure analysis of recombinant mouse mFCGBP revealed a compact dimer with two symmetric intermolecular disulfide bonds between C2462 and C2581, corresponding to the dimerising cysteines in the human hFCGBP. This compact conformation involves interactions between the vWD assemblies, but although the domains involved at the interface are the same, the nature of the interactions differ. Mouse mFCGBP was also found to exist in a semi-extended conformation. These different interactions offer insights into the dynamic nature of the FCGBP homodimer.", "doi": "10.1111/febs.17383", "pmid": "39754272", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2046101"}, {"db": "pmc", "key": "PMC11796319"}], "notes": [], "created": "2025-11-13T12:40:20.877Z", "modified": "2025-11-13T12:40:21.297Z"}, {"entity": "publication", "iuid": "72f3950c5f524c7085d950d0a69ea825", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72f3950c5f524c7085d950d0a69ea825.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72f3950c5f524c7085d950d0a69ea825"}}, "title": "Single cell sequencing reveals shared clonal signatures in non-malignant B- and tumor cells in T-prolymphocytic leukemia", "authors": [{"family": "Hesselager", "given": "Caroline", "initials": "C"}, {"family": "Th\u00f6rn", "given": "Ingrid", "initials": "I"}, {"family": "Marincevic", "given": "Millaray", "initials": "M"}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Alml\u00f6f", "given": "Jonas", "initials": "J", "orcid": "0000-0002-1211-9821", "researcher": {"href": "https://publications.scilifelab.se/researcher/046904cd12eb4764bd2dcadc876f65d7.json"}}, {"family": "L\u00f6fgren", "given": "Sara", "initials": "S", "orcid": "0000-0002-1680-7349", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fdb4e41eab84ead8f399965e24dfea5.json"}}, {"family": "Westr\u00f6m", "given": "Simone", "initials": "S"}, {"family": "Nord", "given": "Helena", "initials": "H", "orcid": "0000-0002-6098-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/22d8cc445c6b41b4a8488d620995d8c3.json"}}, {"family": "Sutton", "given": "Lesley Ann", "initials": "LA"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Amini", "given": "Rose Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}], "type": "journal-article", "published": "2025-02-00", "journal": {"title": "Blood Neoplasia", "issn": "2950-3280", "pages": "100076", "issn-l": null}, "abstract": null, "doi": "10.1016/j.bneo.2025.100076", "pmid": null, "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-03-19T05:00:30.506Z", "modified": "2025-04-03T08:27:33.854Z"}, {"entity": "publication", "iuid": "adf91460a7004b998f82c1bc861fb29e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/adf91460a7004b998f82c1bc861fb29e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/adf91460a7004b998f82c1bc861fb29e"}}, "title": "Robust approach for production of the human oncology target Aurora kinase B in complex with its binding partner INCENP.", "authors": [{"family": "Mattsson", "given": "Jonna", "initials": "J"}, {"family": "Rogne", "given": "Per", "initials": "P"}, {"family": "Landstr\u00f6m", "given": "Mar\u00e9ne", "initials": "M"}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Biochimie", "issn": "1638-6183", "volume": "229", "pages": "129-140", "issn-l": "0300-9084"}, "abstract": "Protein kinases are key players in many eukaryotic signal transduction cascades and are as a result often linked to human disease. In humans, the mitotic protein kinase family of Aurora kinases consist of three members: Aurora A, B and C. All three members are involved in cell division with proposed implications in various human cancers. The human Aurora kinase B has in particular proven challenging to study with structural biology approaches, and this is mainly due to difficulties in producing the large quantities of active enzyme required for such studies. Here, we present a novel and E. coli-based production system that allows for production of milligram quantities of well-folded and active human Aurora B in complex with its binding partner INCENP. The complex is produced as a continuous polypeptide chain and the resulting fusion protein is cleaved with TEV protease to generate a stable and native heterodimer of the Aurora B:INCENP complex. The activity, stability and degree of phosphorylation of the protein complex was quantified by using a coupled ATPase assay, 31P NMR spectroscopy and mass spectrometry. The developed production system enables isotope labeling and we here report the first 1H-15N-HSQC of the human Aurora B:INCENP complex. Our developed production strategy paves the way for future structural and functional studies of Aurora B and can as such assist the development of novel anticancer drugs targeting this important mitotic protein kinase.", "doi": "10.1016/j.biochi.2024.10.011", "pmid": "39424257", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S0300-9084(24)00237-2"}], "notes": [], "created": "2024-11-13T19:36:45.131Z", "modified": "2025-10-17T13:03:52.415Z"}, {"entity": "publication", "iuid": "b4d32af19a9043ee95844d326c8fa800", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4d32af19a9043ee95844d326c8fa800.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4d32af19a9043ee95844d326c8fa800"}}, "title": "Reduced Alcohol Consumption Following Ablation of Cholinergic Interneurons in the Nucleus Accumbens of Wistar Rats.", "authors": [{"family": "Loft\u00e9n", "given": "Anna", "initials": "A"}, {"family": "Cadeddu", "given": "Davide", "initials": "D"}, {"family": "Danielsson", "given": "Klara", "initials": "K"}, {"family": "Stomberg", "given": "Rosita", "initials": "R"}, {"family": "Adermark", "given": "Louise", "initials": "L", "orcid": "0000-0002-7165-9908", "researcher": {"href": "https://publications.scilifelab.se/researcher/6602087739df48208b4ead747f6752ca.json"}}, {"family": "S\u00f6derpalm", "given": "Bo", "initials": "B"}, {"family": "Ericson", "given": "Mia", "initials": "M", "orcid": "0000-0002-7557-7109", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b639bcd6dc44459a8cf95ff214ce74d.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Addict Biol", "issn": "1369-1600", "volume": "30", "issue": "2", "pages": "e70022", "issn-l": "1355-6215"}, "abstract": "Alcohol use disorder is a severe mental health condition causing medical consequences and preterm death. Alcohol activates the mesolimbic dopamine system leading to an increase of extracellular dopamine (DA) in the nucleus accumbens, an event that is associated with the reinforcing effects of alcohol. Cholinergic interneurons (CIN) are important modulators of accumbal DA signalling, and depletion of accumbal CIN attenuates the alcohol-induced increase in extracellular DA. The aim of this study was to explore the functional role of accumbal CIN in alcohol-related behaviour. To this end, ablation of CIN was induced by local administration of anticholine acetyltransferase-saporin bilaterally into the nucleus accumbens of male Wistar rats. Alcohol consumption in ablated and sham-treated rats was studied using a two-bottle-choice intermittent alcohol consumption paradigm. Rats with depleted CIN consumed significantly less alcohol than sham-treated controls. No differences in sucrose preference, motor activity, water intake or weight gain were noted between treatment groups, suggesting that the ablation selectively affected alcohol-related behaviour. In conclusion, this study further supports a role for accumbal CIN in regulating alcohol-consummatory behaviour.", "doi": "10.1111/adb.70022", "pmid": "39936333", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11815332"}], "notes": [], "created": "2025-11-05T13:54:06.250Z", "modified": "2025-11-05T13:54:06.411Z"}, {"entity": "publication", "iuid": "c8f5dbcb52864b11a987807b315f87ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8f5dbcb52864b11a987807b315f87ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8f5dbcb52864b11a987807b315f87ed"}}, "title": "RNA Sequencing Reveals the Long Non-Coding RNA Signature in Psoriasis Keratinocytes and Identifies CYDAER as a Long Non-Coding RNA Regulating Epidermal Differentiation.", "authors": [{"family": "Freisenhausen", "given": "Jan Cedric", "initials": "JC", "orcid": "0000-0002-3078-0365", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f596e44f3d4dd78d499469c9f0b04e.json"}}, {"family": "Luo", "given": "Longlong", "initials": "L", "orcid": "0000-0002-5931-0666", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6310dd902342b4a74bac1efd4090c0.json"}}, {"family": "Kelemen", "given": "Evelyn", "initials": "E", "orcid": "0000-0002-8357-790X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f1c75b553304176b8cafa84815421e8.json"}}, {"family": "Elton", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-4919-8065", "researcher": {"href": "https://publications.scilifelab.se/researcher/22bf1246696541abafd2c2ad902a3b84.json"}}, {"family": "Skoog", "given": "Viktor", "initials": "V", "orcid": "0009-0005-8862-1534", "researcher": {"href": "https://publications.scilifelab.se/researcher/160d22c12c9743e193a47f6ded86b7ad.json"}}, {"family": "Pivarcsi", "given": "Andor", "initials": "A", "orcid": "0000-0003-2196-1102", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ca870317234573a3da5dffb24bb268.json"}}, {"family": "Sonkoly", "given": "Enik\u00f6", "initials": "E", "orcid": "0000-0002-4909-5413", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c1ce318445d4b2bb586ac1f8ed8ed87.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Exp. Dermatol.", "issn": "1600-0625", "volume": "34", "issue": "2", "pages": "e70054", "issn-l": "0906-6705"}, "abstract": "Psoriasis is a common chronic inflammatory skin disease determined by genetic and environmental factors, resulting in the activation of IL-23/IL-17-mediated immune response, epidermal hyperproliferation, and keratinocyte activation. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts > 500 nucleotides with diverse regulatory functions; their role in epidermal dysfunction in psoriasis is poorly understood. To identify epidermal transcripts with potential roles in psoriasis, including lncRNAs, we performed RNA sequencing on keratinocytes from psoriasis and healthy skin. We identified 889 differentially expressed lncRNAs, many of which with yet unknown functions. RP11-295G20.2 was identified as a lncRNA significantly induced in psoriasis keratinocytes, and this was verified by qRT-PCR and by single-molecule in situ hybridisation. Analysis of subcellular fractions of epidermis revealed a cytoplasmic localisation in line with results of single molecule in situ hybridisation. We report that RP11-295G20.2 has a skin-enriched expression, and within skin it is mainly expressed in suprabasal epidermal layers. Moreover, RP11-295G20.2 is induced by the key psoriasis cytokine IL-17A and shows a dynamic regulation during keratinocyte differentiation with upregulation during early differentiation and downregulation in the late stage. Knockdown of RP11-295G20.2 in keratinocytes promotes terminal differentiation. Based on our findings, we named RP11-295G20.2 Cytoplasmic Differentiation-Associated Epidermal RNA, CYDAER. In summary, our study provides a comprehensive characterisation of the non-coding RNA landscape of psoriasis keratinocytes and identifies CYDAER as a skin-enriched lncRNA regulating keratinocyte differentiation. Our data suggest that overexpression of CYDAER may contribute to altered differentiation in psoriatic epidermis.", "doi": "10.1111/exd.70054", "pmid": "39953783", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11829188"}], "notes": [], "created": "2025-09-08T06:52:12.448Z", "modified": "2025-09-08T06:52:13.267Z"}, {"entity": "publication", "iuid": "3a246b8eb30e4b7e888a99892ab360ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a246b8eb30e4b7e888a99892ab360ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a246b8eb30e4b7e888a99892ab360ac"}}, "title": "Pulmonary exposure to renewable diesel exhaust particles alters protein expression and toxicity profiles in bronchoalveolar lavage fluid and plasma of mice.", "authors": [{"family": "McCarrick", "given": "Sarah", "initials": "S"}, {"family": "Malmborg", "given": "Vilhelm", "initials": "V"}, {"family": "Gren", "given": "Louise", "initials": "L"}, {"family": "Danielsen", "given": "Pernille H\u00f8gh", "initials": "PH"}, {"family": "Tun\u00e9r", "given": "Martin", "initials": "M"}, {"family": "Palmberg", "given": "Lena", "initials": "L"}, {"family": "Broberg", "given": "Karin", "initials": "K"}, {"family": "Pagels", "given": "Joakim", "initials": "J"}, {"family": "Vogel", "given": "Ulla", "initials": "U"}, {"family": "Gliga", "given": "Anda R", "initials": "AR", "orcid": "0000-0003-2775-1632", "researcher": {"href": "https://publications.scilifelab.se/researcher/757d212406354647ad124b988ed69410.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Arch. Toxicol.", "issn": "1432-0738", "volume": "99", "issue": "2", "pages": "797-814", "issn-l": "0340-5761"}, "abstract": "Exposure to diesel exhaust is associated with increased risk of cardiovascular and lung disease. Substituting petroleum diesel with renewable diesel can alter emission properties but the potential health effects remain unclear. This study aimed to explore toxicity and underlying mechanisms of diesel exhaust from renewable fuels. Using proximity extension assay (Olink), 92 proteins linked to inflammation, cardiovascular function, and cancer were analyzed in bronchoalveolar lavage fluid (BALF) and plasma in mice 1 day after pulmonary exposure to exhaust particles at doses of 6, 18, and 54 \u00b5g/mouse. Particles were generated from combustion of renewable (rapeseed methyl ester, RME13, hydrogen-treated vegetable oil, HVO13; both at 13% O2 engine intake) and petroleum diesel (MK1 ultra-low-sulfur diesel at 13% and 17% O2 intake; DEP13 and DEP17). We identified positive dose-response relationships between exposure and proteins in BALF using linear models: 33 proteins for HVO13, 24 for DEP17, 22 for DEP13, and 12 for RME13 (p value < 0.05). In BALF, 11 proteins indicating cytokine signaling and inflammation (CCL2, CXCL1, CCL3L3, CSF2, IL1A, CCL20, TPP1, GDNF, LGMN, ITGB6, PDGFB) were common for all exposures. Several proteins in BALF (e.g., CCL2, CXCL1, CCL3L3, CSF2, IL1A) correlated (rs \u2265 0.5) with neutrophil cell count and DNA damage in BAL cells. Interestingly, plasma protein profiles were only affected by RME13 and, to lesser extent, by DEP13. Overall, we identified inflammation-related changes in the BALF as a common toxic mechanism for the combustion particles. Our protein-based approach enables sensitive detection of inflammatory protein changes across different matrices enhancing understanding of exhaust particle toxicity.", "doi": "10.1007/s00204-024-03915-y", "pmid": "39739031", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11775017"}, {"db": "pii", "key": "10.1007/s00204-024-03915-y"}], "notes": [], "created": "2025-11-25T09:13:22.031Z", "modified": "2025-11-25T09:13:22.077Z"}, {"entity": "publication", "iuid": "b6f2c0aa24c44d3a899a4f6703ca28f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6f2c0aa24c44d3a899a4f6703ca28f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6f2c0aa24c44d3a899a4f6703ca28f1"}}, "title": "Plasma brain-derived tau correlates with cerebral infarct volume.", "authors": [{"family": "Gonzalez-Ortiz", "given": "Fernando", "initials": "F", "orcid": "0000-0001-7897-9456", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4bc7b2303004dcc81fe355d7c15bb4c.json"}}, {"family": "Holmegaard", "given": "Lukas", "initials": "L"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Br\u00e4nnmark", "given": "Cecilia", "initials": "C"}, {"family": "Blomstrand", "given": "Christian", "initials": "C"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}, {"family": "Jood", "given": "Katarina", "initials": "K", "orcid": "0000-0001-8746-1771", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d671938a5264a569660e88b00fde93d.json"}}, {"family": "Blennow", "given": "Kaj", "initials": "K", "orcid": "0000-0002-1890-4193", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e646be026ce42ecbfd4d62eca3f9bce.json"}}, {"family": "Jern", "given": "Christina", "initials": "C", "orcid": "0000-0002-7531-2354", "researcher": {"href": "https://publications.scilifelab.se/researcher/13e58d6c4a2e44cd9067f38a2ff2ea32.json"}}, {"family": "Stanne", "given": "Tara M", "initials": "TM", "orcid": "0000-0001-9668-0407", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3c967b386124a3199b2373de1111d03.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "J. Intern. Med.", "issn": "1365-2796", "volume": "297", "issue": "2", "pages": "173-185", "issn-l": "0954-6820"}, "abstract": "A blood-based biomarker that accurately reflects neuronal injury in acute ischemic stroke could be an easily accessible and cost-effective complement to clinical and radiological evaluation. Here, we investigate whether plasma levels of the novel biomarker brain-derived tau (BD-tau) reflect cerebral infarct volumes and whether BD-tau can improve clinical outcome prediction.\n\nThe present study included 713 consecutive cases from two different hospital-based cohorts, the Sahlgrenska Academy Study on Ischemic Stroke (SAHLSIS) and SAHLSIS phase 2 (SAHLSIS2). Acute stroke severity was determined by the Scandinavian Stroke Scale converted to the National Institutes of Health stroke scale (NIHSS) in SAHLSIS and by the NIHSS in SAHLSIS2. All participants were assessed for functional outcome 3 months after stroke by the modified Rankin Scale, and 254 participants in SAHLSIS had quantitative neuroimaging available.\n\nPlasma BD-tau concentrations and cerebral infarct volumes were highly correlated (\u03c1 0.72, p < 0.001). BD-tau improved the prognostic accuracy of suffering an unfavorable outcome over age and stroke severity in the whole cohort. However, the gain in predictive power was dependent on stroke severity and infarct location. The largest improvement was observed for mild ischemic strokes (NIHSS <5; area under the curve [AUC] = 0.73 for age + NIHSS versus AUC = 0.84 with addition of BD-tau; DeLong p 0.02), posterior circulation stroke (AUC = 0.75 vs. AUC = 0.84; DeLong p 0.06) and more specifically for infarcts in the brainstem/cerebellum (AUC = 0.74 vs. 0.87; DeLong p 0.009).\n\nPlasma BD-tau can provide information on the extent of acute neuronal damage in ischemic stroke and adds prognostic value for outcome, especially for mild and posterior circulation strokes.", "doi": "10.1111/joim.20041", "pmid": "39639627", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11771704"}], "notes": [], "created": "2025-07-08T13:54:34.800Z", "modified": "2025-07-08T13:54:35.034Z"}, {"entity": "publication", "iuid": "ce7ad1afa4874fc6bb73127f9cefddc0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce7ad1afa4874fc6bb73127f9cefddc0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce7ad1afa4874fc6bb73127f9cefddc0"}}, "title": "Phospho-tau serine-262 and serine-356 as biomarkers of pre-tangle soluble tau assemblies in Alzheimer's disease.", "authors": [{"family": "Islam", "given": "Tohidul", "initials": "T", "orcid": "0000-0003-1561-944X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0693554436c4017a605281f3d97d373.json"}}, {"family": "Hill", "given": "Emily", "initials": "E"}, {"family": "Abrahamson", "given": "Eric E", "initials": "EE"}, {"family": "Servaes", "given": "Stijn", "initials": "S"}, {"family": "Smirnov", "given": "Denis S", "initials": "DS"}, {"family": "Zeng", "given": "Xuemei", "initials": "X"}, {"family": "Sehrawat", "given": "Anuradha", "initials": "A"}, {"family": "Chen", "given": "Yijun", "initials": "Y", "orcid": "0009-0001-4579-4057", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e7eb6e67f694af8b1dfb26c4dbcf97c.json"}}, {"family": "Kac", "given": "Przemys\u0142aw R", "initials": "PR", "orcid": "0000-0001-5083-0924", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7d23b25a3774bb696abf5522147d249.json"}}, {"family": "Kvartsberg", "given": "Hlin", "initials": "H", "orcid": "0000-0002-4481-508X", "researcher": {"href": "https://publications.scilifelab.se/researcher/be021173500e46a59ec36f4b34ee607f.json"}}, {"family": "Olsson", "given": "Maria", "initials": "M"}, {"family": "Sjons", "given": "Emma", "initials": "E", "orcid": "0009-0008-5030-114X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9154ad214441e3adc4a094c7c73e32.json"}}, {"family": "Gonzalez-Ortiz", "given": "Fernando", "initials": "F", "orcid": "0000-0001-7897-9456", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4bc7b2303004dcc81fe355d7c15bb4c.json"}}, {"family": "Therriault", "given": "Joseph", "initials": "J"}, {"family": "Tissot", "given": "C\u00e9cile", "initials": "C", "orcid": "0000-0003-2711-3833", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbdaa319e358466696ff529d1221591d.json"}}, {"family": "Del Popolo", "given": "Ivana", "initials": "I", "orcid": "0009-0005-6480-4117", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd3286ad15640dcb5358891c82d0c7a.json"}}, {"family": "Rahmouni", "given": "Nesrine", "initials": "N"}, {"family": "Richardson", "given": "Abbie", "initials": "A"}, {"family": "Mitchell", "given": "Victoria", "initials": "V"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}, {"family": "Pascoal", "given": "Tharick A", "initials": "TA", "orcid": "0000-0001-9057-8014", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bfa45d39b324b2ab78c12ec044ebe48.json"}}, {"family": "Lashley", "given": "Tammaryn", "initials": "T", "orcid": "0000-0001-7389-0348", "researcher": {"href": "https://publications.scilifelab.se/researcher/533fe74a716840b2a55fddf0452f2a23.json"}}, {"family": "Wall", "given": "Mark J", "initials": "MJ"}, {"family": "Galasko", "given": "Douglas", "initials": "D"}, {"family": "Rosa-Neto", "given": "Pedro", "initials": "P", "orcid": "0000-0001-9116-1376", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a2e4f85e17f45489cde7f8d8430daa4.json"}}, {"family": "Ikonomovic", "given": "Milos D", "initials": "MD"}, {"family": "Blennow", "given": "Kaj", "initials": "K", "orcid": "0000-0002-1890-4193", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e646be026ce42ecbfd4d62eca3f9bce.json"}}, {"family": "Karikari", "given": "Thomas K", "initials": "TK", "orcid": "0000-0003-1422-4358", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf3831a3e6a341f4b0a728e591de5b42.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "volume": "31", "issue": "2", "pages": "574-588", "issn-l": "1078-8956"}, "abstract": "Patients with Alzheimer's disease (AD) with little or no quantifiable insoluble brain tau neurofibrillary tangle (NFT) pathology demonstrate stronger clinical benefits of therapies than those with advanced NFTs. The formation of NFTs can be prevented by targeting the intermediate soluble tau assemblies (STAs). However, biochemical understanding and biomarkers of STAs are lacking. We show that Tris-buffered saline-soluble tau aggregates from autopsy-verified AD brain tissues include the core sequence ~tau258-368. In neuropathological assessments, antibodies against the phosphorylation sites serine-262 and serine-356 within the STA core almost exclusively stained granular (that is, prefibrillar) tau aggregates in pre-NFTs while antibodies against phosphorylation at serine-202 and threonine-205 and threonine-231, outside the STA core, stained the entire spectrum of tau aggregates in pre-NFTs and mature NFTs, dystrophic neurites and neuropil threads in the hippocampus. Functionally, a recombinantly produced STA core peptide robustly altered neuronal excitability and synaptic transmission in mouse hippocampal brain slices. Furthermore, we developed a cerebrospinal fluid assay that differentiated STAs in AD from non-AD tauopathies, correlated with the severity of NFT burden and cognitive decline independently of amyloid beta deposition, and with tau positron emission tomography uptake across Braak NFT stages. Together, our findings inform about the status of early-stage tau aggregation, reveal aggregation-relevant phosphorylation epitopes in tau and offer a diagnostic biomarker and targeted therapeutic opportunities for AD.", "doi": "10.1038/s41591-024-03400-0", "pmid": "39930142", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11835754"}, {"db": "pii", "key": "10.1038/s41591-024-03400-0"}], "notes": [], "created": "2025-11-05T13:53:57.536Z", "modified": "2025-11-05T13:53:58.203Z"}, {"entity": "publication", "iuid": "dfd9f82be43c4473bdafe52ed31479ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfd9f82be43c4473bdafe52ed31479ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfd9f82be43c4473bdafe52ed31479ca"}}, "title": "Parasite spillover rather than niche expansion explains infection of host brain by diplostomid eye flukes.", "authors": [{"family": "Diaz-Suarez", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-1726-2563", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f3f9866fe543b78c91c9c62c362cdd.json"}}, {"family": "Kisand", "given": "Veljo", "initials": "V", "orcid": "0000-0002-5535-1639", "researcher": {"href": "https://publications.scilifelab.se/researcher/f34359c7f74a409f98dca6688e368332.json"}}, {"family": "Kahar", "given": "Siim", "initials": "S"}, {"family": "Gross", "given": "Riho", "initials": "R"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}, {"family": "Noreikiene", "given": "Kristina", "initials": "K", "orcid": "0000-0001-7529-4902", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ac9138a3a55468e99283202735f7489.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "292", "issue": "2040", "pages": "20242648", "issn-l": "0962-8452"}, "abstract": "Parasites often occupy specific sites within their host, which has important implications for host performance and parasite transmission. Nonetheless, parasitic infections can occur beyond their typical location within a host, significantly altering host-parasite interactions. Yet, the causes behind the atypical tissue tropism are poorly understood. Here, we focus on a ubiquitous group of diplostomid parasites that form diverse communities in fish eyes. We used targeted DNA metabarcoding (cytochrome c oxydase subunit 1, COX1, 250 bp) to evaluate potential mechanisms underlying eye parasite atypical tissue tropism to the brain of two widespread fish species (Eurasian perch and common roach). We found that the most common eye-infecting species (Tylodelphys clavata, Diplostomum baeri) are present in the brains of perch but not in roach. The bipartite network comprising 5 species and 24 mitochondrial haplotypes revealed no brain-specific haplotypes, indicating an apparent lack of genetic divergence between brain- and eye-infecting parasites. Instead, the prevalence, intensity and diversity of eye infections were positively correlated with brain infections. Thus, our results suggest that the most parsimonious mechanism underlying brain infection is density-dependent spillover rather than parasite divergence-driven niche expansion. We anticipate that 'off-target' infections are likely to be severely underestimated in nature with important ecological, evolutionary and medical implications.", "doi": "10.1098/rspb.2024.2648", "pmid": "39904393", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11793966"}], "notes": [], "created": "2025-11-28T10:50:19.633Z", "modified": "2025-11-28T10:50:19.824Z"}, {"entity": "publication", "iuid": "5327a3ebdfe244b481789f7baf594301", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5327a3ebdfe244b481789f7baf594301.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5327a3ebdfe244b481789f7baf594301"}}, "title": "Pain in idiopathic scoliosis not associated with known genetic variants for pain.", "authors": [{"family": "Cheng", "given": "Tian", "initials": "T", "orcid": "0000-0001-5013-6473", "researcher": {"href": "https://publications.scilifelab.se/researcher/b65aa57c2cae41ed8b5d808377eca30d.json"}}, {"family": "Diarbakerli", "given": "Elias", "initials": "E"}, {"family": "Simony", "given": "Ane", "initials": "A"}, {"family": "\u00d8sterheden Andersen", "given": "Mikkel", "initials": "M"}, {"family": "Danielsson", "given": "Aina", "initials": "A"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Pain Rep", "issn": "2471-2531", "issn-l": null, "volume": "10", "issue": "1", "pages": "e1227"}, "abstract": "Back pain is common in idiopathic scoliosis. The aim of this study was to study known genetic variants associated with pain in individuals with idiopathic scoliosis.\r\n\r\nWe included 1442 individuals with juvenile or adolescent idiopathic scoliosis from Sweden and Denmark. Single nucleotide variants (SNV) genotyping was performed on 37 SNVs. Pain was assessed using 2 questionnaires. The mean pain domain score on the Scoliosis Research Society 22 revised questionnaire (SRS-22r) ranging between 1 (worst) and 5 (best) was dichotomized into a \"back pain group\" (score <4) and a \"no back pain group\" (score \u22654). The EuroQol 5-dimensions (EQ-5D) 3 level pain domain was dichotomized into a \"no pain group\" and a \"pain group.\" Odds ratios were used to describe the associations.\r\n\r\nBased on the SRS-22r pain domain scores, 456 individuals (32%) reported back pain. Based on the EQ-5D questionnaire, 813 individuals (56%) reported moderate or extreme pain/discomfort. The odds ratio for the associations between the selected genetic variants and back pain or pain in general as measured with SRS-22r and EQ-5D-3L ranged between 0.88 to 1.17 and 0.86 to 1.16, with P-values ranging between 0.08 to 0.99 and 0.08 to 0.95.\r\n\r\nThis study suggests that known genetic variants associated with pain do not play a significant role in the development of pain in individuals with idiopathic scoliosis.", "doi": "10.1097/PR9.0000000000001227", "pmid": "39713503", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": null, "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11661741"}, {"db": "pii", "key": "PAINREPORTS-D-23-0205"}], "notes": [], "created": "2025-09-08T07:06:06.228Z", "modified": "2025-11-19T08:43:57.611Z"}, {"entity": "publication", "iuid": "f4f3891ff53f491997316aea1751a0cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4f3891ff53f491997316aea1751a0cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4f3891ff53f491997316aea1751a0cd"}}, "title": "Navigating the maze of mass spectra: a machine-learning guide to identifying diagnostic ions in O-glycan analysis.", "authors": [{"family": "Urban", "given": "James", "initials": "J"}, {"family": "Joeres", "given": "Roman", "initials": "R"}, {"family": "Thom\u00e8s", "given": "Luc", "initials": "L"}, {"family": "Thomsson", "given": "Kristina A", "initials": "KA"}, {"family": "Bojar", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Anal Bioanal Chem", "issn": "1618-2650", "volume": "417", "issue": "5", "pages": "931-943", "issn-l": "1618-2642"}, "abstract": "Structural details of oligosaccharides, or glycans, often carry biological relevance, which is why they are typically elucidated using tandem mass spectrometry. Common approaches to distinguish isomers rely on diagnostic glycan fragments for annotating topologies or linkages. Diagnostic fragments are often only known informally among practitioners or stem from individual studies, with unclear validity or generalizability, causing annotation heterogeneity and hampering new analysts. Drawing on a curated set of 237,000 O-glycomics spectra, we here present a rule-based machine learning workflow to uncover quantifiably valid and generalizable diagnostic fragments. This results in fragmentation rules to robustly distinguish common O-glycan isomers for reduced glycans in negative ion mode. We envision this resource to improve glycan annotation accuracy and concomitantly make annotations more transparent and homogeneous across analysts.", "doi": "10.1007/s00216-024-05500-9", "pmid": "39180595", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11782297"}, {"db": "pii", "key": "10.1007/s00216-024-05500-9"}], "notes": [], "created": "2024-11-27T15:30:40.714Z", "modified": "2025-10-23T12:25:51.518Z"}, {"entity": "publication", "iuid": "9ee81994e9304be4a943c473379bdab4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ee81994e9304be4a943c473379bdab4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ee81994e9304be4a943c473379bdab4"}}, "title": "Modelling age at death reveals Nordic Corded Ware paleodemography", "authors": [{"family": "Tornberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-3323-8512", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fdbf302337d475b88ffbdf48065a5b0.json"}}, {"family": "Vandkilde", "given": "Helle", "initials": "H", "orcid": "0000-0001-9326-7633", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffe755bd12534d9899484dd9756cf5d8.json"}}], "type": "journal-article", "published": "2025-02-00", "journal": {"title": "Archaeol Anthropol Sci", "issn": "1866-9557", "issn-l": null, "volume": "17", "issue": "2", "pages": null}, "abstract": null, "doi": "10.1007/s12520-024-02159-2", "pmid": null, "labels": {"Ancient DNA": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2025-01-21T08:24:34.306Z", "modified": "2025-05-27T08:39:33.518Z"}, {"entity": "publication", "iuid": "7b0840d705db49e6bcae86e862093233", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b0840d705db49e6bcae86e862093233.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b0840d705db49e6bcae86e862093233"}}, "title": "Meat intake in relation to composition and function of gut microbiota.", "authors": [{"family": "Larsson", "given": "Susanna C", "initials": "SC"}, {"family": "Ericson", "given": "Ulrika", "initials": "U"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF"}, {"family": "Arage", "given": "Getachew", "initials": "G"}, {"family": "Ra\u0161o", "given": "Luka Marko", "initials": "LM"}, {"family": "Sayols-Baixeras", "given": "Sergi", "initials": "S"}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Baldanzi", "given": "Gabriel", "initials": "G"}, {"family": "Nguyen", "given": "Diem", "initials": "D"}, {"family": "Nielsen", "given": "H Bj\u00f8rn", "initials": "HB"}, {"family": "Holm", "given": "Jacob B", "initials": "JB"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Ahmad", "given": "Shafqat", "initials": "S"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Clin Nutr", "issn": "1532-1983", "volume": "45", "pages": "124-133", "issn-l": null}, "abstract": "Meat intake is suggested to affect gut microbiome composition and the risk of chronic diseases. We aimed to identify meat-associated gut microbiome features and their association with host factors.\n\nGut microbiota species were profiled by deep shotgun metagenomics sequencing in 9669 individuals. Intake of white meat, unprocessed red meat, and processed red meat was assessed using a food frequency questionnaire. The associations of meat intake with alpha-diversity and relative abundance of gut microbiota species were tested using linear regression models with adjustment for dietary fiber intake, body mass index, and other potential confounders. Meat-associated species were further assessed for association with enrichment of microbial gene function, meat-associated plasma metabolites, and clinical biomarkers.\n\nHigher intake of processed red meat was associated with reduced alpha microbial diversity. White meat, unprocessed, and processed red meat intakes were associated with 36, 14, and 322 microbiota species, respectively. Species associated with processed red meat were enriched for bacterial pathways like amino acid degradation, while those negatively linked were enriched for pathways like homoacetogenesis. Furthermore, species positively associated with processed red meat were to a large extent associated with reduced trimethylamine N-oxide and glutamine levels but increased creatine and carnitine metabolites, fasting insulin and glucose, C-reactive protein, apolipoprotein A1, and triglyceride levels and higher blood pressure.\n\nThis largest to date population-based study on meat and gut microbiota suggests that meat intake, particularly processed red meat, may modify the gut microbiota composition, functional capacity, and health-related biomarkers.", "doi": "10.1016/j.clnu.2024.12.034", "pmid": "39798223", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0261-5614(24)00475-8"}], "notes": [], "created": "2025-11-28T10:42:31.467Z", "modified": "2025-11-28T10:42:31.478Z"}, {"entity": "publication", "iuid": "96d10598a8c646709a856908160899d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96d10598a8c646709a856908160899d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96d10598a8c646709a856908160899d8"}}, "title": "Isotope geolocation and population genomics in Vanessa cardui: Short- and long-distance migrants are genetically undifferentiated.", "authors": [{"family": "Reich", "given": "Megan S", "initials": "MS", "orcid": "0000-0002-0597-4854", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe7c3c3a6e8346e4b235a5c6476bc9dc.json"}}, {"family": "Shipilina", "given": "Daria", "initials": "D", "orcid": "0000-0002-1145-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a7bdbc6654826ab7f06cf3938b5c3.json"}}, {"family": "Talla", "given": "Venkat", "initials": "V", "orcid": "0000-0003-2653-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/703518ce5a1f4e5ea04719016173a867.json"}}, {"family": "Bahleman", "given": "Farid", "initials": "F"}, {"family": "K\u00e9b\u00e9", "given": "Khadim", "initials": "K", "orcid": "0000-0003-0041-4919", "researcher": {"href": "https://publications.scilifelab.se/researcher/e46e3cc21b2949eb9611d101fe31b7dc.json"}}, {"family": "Berger", "given": "Johanna L", "initials": "JL", "orcid": "0000-0003-4847-2413", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1d5d0f9e5e4d39ab429f6dc6905550.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Talavera", "given": "Gerard", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}, {"family": "Bataille", "given": "Cl\u00e9ment P", "initials": "CP", "orcid": "0000-0001-8625-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/70612fa6163b42c6b62ec5aca937421d.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "PNAS Nexus", "issn": "2752-6542", "volume": "4", "issue": "2", "pages": "pgae586", "issn-l": null}, "abstract": "The painted lady butterfly Vanessa cardui is renowned for its virtually cosmopolitan distribution and the remarkable long-distance migrations as part of its annual, multigenerational migratory cycle. In winter, V. cardui individuals inhabit breeding grounds north and south of the Sahara, suggesting distinct migratory behaviors within the species as individuals migrate southward from Europe in the autumn. However, the evolutionary and ecological factors shaping these differences in migratory behavior remain largely unexplored. Here, we performed whole-genome resequencing and analyzed the hydrogen and strontium isotopes of 40 V. cardui individuals simultaneously collected in the autumn from regions both north and south of the Sahara. Our investigation revealed two main migratory groups: (i) short-distance migrants, journeying from temperate Europe to the circum-Mediterranean region and (ii) long-distance migrants, originating from Europe, crossing the Mediterranean Sea and Sahara, and reaching West Africa, covering up to over 4,000 km. Despite these stark differences in migration distance, a genome-wide analysis revealed that short- and long-distance migrants belong to a single intercontinental panmictic population extending from northern Europe to sub-Saharan Africa. Contrary to common biogeographic patterns, the Sahara is not a catalyst for population structuring in this species. No significant genetic differentiation or signs of adaptation and selection were observed between the two migratory phenotypes. Nonetheless, two individuals, who were early arrivals to West Africa covering longer migration distances, exhibited some genetic differentiation. The lack of genetic structure between short- and long-distance migrants suggests that migration distance in V. cardui is a plastic response to environmental conditions.", "doi": "10.1093/pnasnexus/pgae586", "pmid": "39906311", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11792081"}, {"db": "pii", "key": "pgae586"}], "notes": [], "created": "2025-11-21T13:43:02.246Z", "modified": "2025-11-21T13:43:02.809Z"}, {"entity": "publication", "iuid": "e4fb5daacf564be8babcde7781049f5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4fb5daacf564be8babcde7781049f5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4fb5daacf564be8babcde7781049f5f"}}, "title": "Impact of plant diversity in potato-ley strip-cropping systems on soil microbial communities", "authors": [{"family": "Riggi", "given": "L G A", "initials": "LGA"}, {"family": "Ranheim Sveen", "given": "T", "initials": "T"}, {"family": "Casta\u00f1o", "given": "C", "initials": "C", "orcid": "0000-0002-2403-7006", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7bfa857714f425886c4484c15eb59a5.json"}}, {"family": "Onorati", "given": "P", "initials": "P"}, {"family": "van Apeldoorn", "given": "D F", "initials": "DF"}, {"family": "Berri", "given": "M", "initials": "M"}, {"family": "Mommer", "given": "L", "initials": "L"}, {"family": "Clemmensen", "given": "K E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Bahram", "given": "M", "initials": "M", "orcid": "0000-0002-9539-3307", "researcher": {"href": "https://publications.scilifelab.se/researcher/26b5310cd872405aa2716c09a3f9d4bf.json"}}], "type": "journal-article", "published": "2025-02-00", "journal": {"title": "Applied Soil Ecology", "issn": "0929-1393", "volume": "206", "pages": "105777", "issn-l": null}, "abstract": null, "doi": "10.1016/j.apsoil.2024.105777", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-02-28T14:11:35.546Z", "modified": "2025-11-28T10:41:55.541Z"}, {"entity": "publication", "iuid": "9458971190ee41e099e40121d1866819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9458971190ee41e099e40121d1866819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9458971190ee41e099e40121d1866819"}}, "title": "Impact of excess sugar on the whole genome DNA methylation pattern in human sperm.", "authors": [{"family": "J\u00f6nsson", "given": "Josefine", "initials": "J", "orcid": "0000-0003-0709-2828", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4b2eb9eef5496eb27e76fc9fca120a.json"}}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Kugelberg", "given": "Unn", "initials": "U"}, {"family": "Skog", "given": "Signe", "initials": "S"}, {"family": "Lindstr\u00f6m", "given": "Axel", "initials": "A"}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Ofori", "given": "Jones K", "initials": "JK"}, {"family": "Bacos", "given": "Karl", "initials": "K"}, {"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "\u00d6st", "given": "Anita", "initials": "A"}, {"family": "Ling", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-0587-7154", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7c1ea934034c4db99f31a5a9b04691.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Epigenomics", "issn": "1750-192X", "volume": "17", "issue": "2", "pages": "89-104", "issn-l": null}, "abstract": "Dietary factors may regulate the epigenome. We aimed to explore whether a diet intervention, including excess sugar, affects the methylome in human sperm, and to describe the sperm methylome. We used Whole Genome Bisulfite Sequencing (WGBS) to analyze DNA methylation in sperm taken at three time points from 15 males during a diet intervention; i) at baseline, ii) after one week on a standardized diet, and iii) after an additional week on a high-sugar diet providing 150% of their estimated total energy expenditure.\n\nWe identified seven nominal diet-associated differentially methylated regions in sperm (p < 0.05). The diet was nominally associated with methylation of 143 sites linked to fertility (e.g. AHRR, GNAS, and HDAC4), 313 sites in imprinted genes (e.g. GLIS3, PEG10, PEG3, and SNURF), and 42 sites in top 1%-expressed genes (e.g. CHD2) (p < 0.05). In sperm, 3'UTRs and introns had the highest levels of methylation, while 5'UTRs and CpG islands had the lowest levels. Non-expressed genes in human sperm were hypomethylated in exons compared with transcribed genes.\n\nIn human sperm, DNA methylation levels were linked to gene expression, and excess sugar had modest effects on methylation on imprinted and highly expressed genes, and genes affecting fertility.", "doi": "10.1080/17501911.2024.2439782", "pmid": "39707713", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-02-03T07:41:54.349Z", "modified": "2025-02-03T07:41:54.880Z"}, {"entity": "publication", "iuid": "e7a16aa6730e4fb0bd55b3d830ab77b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7a16aa6730e4fb0bd55b3d830ab77b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7a16aa6730e4fb0bd55b3d830ab77b6"}}, "title": "Genetic insights into psychotic major depressive disorder: bridging the mood-psychotic disorder spectrum.", "authors": [{"family": "Nguyen", "given": "Thuy-Dung", "initials": "TD"}, {"family": "Meijsen", "given": "Joeri J", "initials": "JJ"}, {"family": "Sigstr\u00f6m", "given": "Robert", "initials": "R"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Xiong", "given": "Ying", "initials": "Y"}, {"family": "Harder", "given": "Arvid", "initials": "A"}, {"family": "Kowalec", "given": "Kaarina", "initials": "K"}, {"family": "Pasman", "given": "Jo\u00eblle A", "initials": "JA"}, {"family": "Scarpa", "given": "Carolina", "initials": "C"}, {"family": "H\u00f6rbeck", "given": "Elin", "initials": "E"}, {"family": "Jonsson", "given": "Lina", "initials": "L"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Mullins", "given": "Niamh", "initials": "N"}, {"family": "O'Connell", "given": "Kevin S", "initials": "KS"}, {"family": "Dalman", "given": "Christina", "initials": "C"}, {"family": "Helenius", "given": "Dorte", "initials": "D"}, {"family": "Zetterberg", "given": "Richard", "initials": "R"}, {"family": "Larsson", "given": "Henrik", "initials": "H"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Buil", "given": "Alfonso", "initials": "A"}, {"family": "Land\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Lu", "given": "Yi", "initials": "Y"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "112", "pages": "105576", "issn-l": "2352-3964"}, "abstract": "Psychotic major depressive disorder (MDD), a subtype of MDD characterised by psychotic symptoms that occur exclusively during mood episode, is clinically significant yet underexplored genetically due to its rarity. This study comprehensively examines the genetic basis of psychotic MDD and elucidates its position within the mood-psychotic spectrum.\n\nThis population-based cohort study used Swedish and Danish registry data for over 5.1 M individuals born between 1958 and 1993/1996. Specialist-diagnosed psychotic MDD was defined using ICD-10 sub-codes of MDD, F32.2/F32.3. We estimated familial aggregation/coaggregation using generalised estimating equations, heritability and genetic correlations using structural equation modelling. We also analysed \u223c30,000 genotyped MDD cases from the UK Biobank and a Swedish cohort to explore which polygenic risk score (PRS) may predispose individuals to psychotic MDD.\n\nWith over 10,000 psychotic MDD identified from the two nationwide patient registers, this study highlights the familial aggregation of psychotic MDD, co-aggregation with mood and psychotic disorders, and its stronger genetic correlation with schizophrenia compared to non-psychotic MDD. The familial risks increased with closer biological relatedness, suggesting genetic influence. Pedigree-heritability of psychotic MDD was 30.17% (95% CI 23.53-36.80%). While the genetic correlation between psychotic and non-psychotic MDD was high (0.82, 95% CI 0.73-0.92), the psychotic subgroup showed a higher genetic correlation with schizophrenia than non-psychotic MDD (0.67 vs 0.46, p-value 7.55\u221710-4). Within 30,000 genotyped MDD cases, individuals with psychotic MDD had higher mean PRS for schizophrenia and BD but a lower MDD PRS than non-psychotic MDD. PRS for BD type-I was associated with increased odds of psychotic MDD, while BD type-II PRS showed no significant association with psychotic MDD.\n\nThis study provides evidence for the genetic basis of psychotic MDD, underscoring its unique position bridging the spectrum of mood and psychotic disorders. These findings advance our understanding of the aetiology of psychotic MDD and contribute to the limited body of evidence on this phenotype by utilising large-scale population-based data.\n\nEuropean Research Council; US National Institutes of Mental Health; European Union Horizon 2020 Program; Swedish Research Council; Research Council of Norway; Swedish Foundation for Strategic Research; Hj\u00e4rnfonden.", "doi": "10.1016/j.ebiom.2025.105576", "pmid": "39889373", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11830301"}, {"db": "pii", "key": "S2352-3964(25)00020-9"}], "notes": [], "created": "2025-11-28T10:42:43.507Z", "modified": "2025-11-28T10:42:43.568Z"}, {"entity": "publication", "iuid": "718f20f6c2094adcba9c9e51dcdd14ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/718f20f6c2094adcba9c9e51dcdd14ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/718f20f6c2094adcba9c9e51dcdd14ea"}}, "title": "Field-based soil extractions capture more amino acids that are lost during short-term storage", "authors": [{"family": "Buckley", "given": "Scott", "initials": "S"}, {"family": "J\u00e4mtg\u00e5rd", "given": "Sandra", "initials": "S", "orcid": "0000-0002-5222-7878", "researcher": {"href": "https://publications.scilifelab.se/researcher/84162671e5bf4570b9c6b4eec94e96b5.json"}}], "type": "journal-article", "published": "2025-02-00", "journal": {"title": "Geoderma", "issn": "0016-7061", "volume": "454", "pages": "117163", "issn-l": null}, "abstract": null, "doi": "10.1016/j.geoderma.2025.117163", "pmid": null, "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-19T10:49:25.002Z", "modified": "2025-11-19T10:49:25.029Z"}, {"entity": "publication", "iuid": "98c3436054da482d8ed7c2c09222f5c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98c3436054da482d8ed7c2c09222f5c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98c3436054da482d8ed7c2c09222f5c2"}}, "title": "Extracellular Histones as Exosome Membrane Proteins Regulated by Cell Stress.", "authors": [{"family": "Singh", "given": "Birendra", "initials": "B"}, {"family": "Fredriksson Sundbom", "given": "Marcus", "initials": "M", "orcid": "0000-0002-3586-4197", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9fb80c88da9467c9984f169cd3da016.json"}}, {"family": "Muthukrishnan", "given": "Uma", "initials": "U"}, {"family": "Natarajan", "given": "Balasubramanian", "initials": "B"}, {"family": "Stransky", "given": "Stephanie", "initials": "S"}, {"family": "G\u00f6rgens", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-9198-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea5f85e2c23a4515a39a2fa23d665a99.json"}}, {"family": "Nordin", "given": "Joel Z", "initials": "JZ", "orcid": "0000-0002-3653-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/37075c4179534fc8a927c4e1330e92c7.json"}}, {"family": "Wiklander", "given": "Oscar P B", "initials": "OPB"}, {"family": "Sandblad", "given": "Linda", "initials": "L"}, {"family": "Sidoli", "given": "Simone", "initials": "S"}, {"family": "El Andaloussi", "given": "Samir", "initials": "S"}, {"family": "Haney", "given": "Michael", "initials": "M", "orcid": "0000-0002-4049-8910", "researcher": {"href": "https://publications.scilifelab.se/researcher/837c6b12b0ad44f8b1e2a26cb7cd245b.json"}}, {"family": "Gilthorpe", "given": "Jonathan D", "initials": "JD", "orcid": "0000-0002-6884-4774", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eb2a4f38fdc4e0db2516a17d9abdf06.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "J Extracell Vesicles", "issn": "2001-3078", "volume": "14", "issue": "2", "pages": "e70042", "issn-l": "2001-3078"}, "abstract": "Histones are conserved nuclear proteins that function as part of the nucleosome in the regulation of chromatin structure and gene expression. Interestingly, extracellular histones populate biofluids from healthy individuals, and when elevated, may contribute to various acute and chronic diseases. It is generally assumed that most extracellular histones exist as nucleosomes, as components of extracellular chromatin. We analysed cell culture models under normal and stressed conditions to identify pathways of histone secretion. We report that core and linker histones localize to extracellular vesicles (EVs) and are secreted via the multivesicular body/exosome pathway. Upregulation of EV histone secretion occurs in response to cellular stress, with enhanced vesicle secretion and a shift towards a population of smaller EVs. Most histones were membrane associated with the outer surface of EVs. Degradation of EV-DNA did not impact significantly on EV-histone association. Individual histones and histone octamers bound strongly to liposomes and EVs, but nucleosomes did not, showing histones do not require DNA for EV binding. Histones colocalized to tetraspanin positive EVs but using genetic or pharmacological intervention, we found that all known pathways of exosome biogenesis acted positively on histone secretion. Inhibition of autophagy and lysosomal degradation had a strong positive effect on EV histone release. Unexpectedly, EV-associated histones lacked the extensive post-translational modification of their nuclear counterparts, suggesting loss of PTMs may be involved in their trafficking or secretion. Our data does not support a significant role for EV-histones existing as nucleosomes. We show for the first time that histones are secreted from cells as membrane proteins via EVs/exosomes. This fundamental discovery provides support for further investigation of the biological activity of exosome associated histones and their role in disease.", "doi": "10.1002/jev2.70042", "pmid": "39976275", "labels": {"Cryo-EM": "Collaborative", "Integrated Microscopy Technologies Ume\u00e5": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11840699"}], "notes": [], "created": "2025-11-03T12:14:46.643Z", "modified": "2025-11-18T13:15:12.096Z"}, {"entity": "publication", "iuid": "d822f5357c6a448b82142e0a1e71bdac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d822f5357c6a448b82142e0a1e71bdac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d822f5357c6a448b82142e0a1e71bdac"}}, "title": "Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche.", "authors": [{"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Ortega Gim\u00e9nez", "given": "Jes\u00fas", "initials": "J", "orcid": "0000-0001-6599-1675", "researcher": {"href": "https://publications.scilifelab.se/researcher/e60538dadc0a4ee9ade7bc0015d67491.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S", "orcid": "0000-0002-6146-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ebad9d4ddf40949a19776df31a00c7.json"}}, {"family": "Moss", "given": "Oliver", "initials": "O"}, {"family": "Su", "given": "Yi", "initials": "Y", "orcid": "0009-0001-4802-5210", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7f56487ba584ac5b08cfa6c06c6f7a6.json"}}, {"family": "Van Aken", "given": "Olivier", "initials": "O", "orcid": "0000-0003-4024-968X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8174aa4d9e4031822ea281b6f0f9dd.json"}}, {"family": "Runemark", "given": "Anna", "initials": "A", "orcid": "0000-0002-8976-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/e914e2d1ccbd4d35ae574187762ae01f.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "4", "pages": "e17653"}, "abstract": "How gene expression evolves to enable divergent ecological adaptation and how changes in gene expression relate to genomic architecture are pressing questions for understanding the mechanisms enabling adaptation and ecological speciation. Furthermore, how plasticity in gene expression can both contribute to and be affected by the process of ecological adaptation is crucial to understanding gene expression evolution, colonisation of novel niches and response to rapid environmental change. Here, we investigate the role of constitutive and plastic gene expression differences between host races, or host-specific ecotypes, of the peacock fly Tephritis conura, a thistle bud specialist. By cross-fostering larvae to new buds of their natal host plant or the alternative, novel host plant, we uncover extensive constitutive differences in gene expression between the host races, especially genes associated with processing of host plant chemicals. However, evidence for expression plasticity was minimal and limited to the ancestral host race. Genes with host race-specific expression are found more often than expected within a large inversion in the T. conura genome, adding to evidence that inversions are important for enabling diversification in the face of gene flow and underscores that altered gene expression may be key to understanding the evolutionary consequences of inversions.", "doi": "10.1111/mec.17653", "pmid": "39783891", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11789552"}], "notes": [], "created": "2025-01-30T10:48:38.552Z", "modified": "2025-11-28T10:51:21.794Z"}, {"entity": "publication", "iuid": "faee937ae25845dc8d0e74e783341329", "links": {"self": {"href": "https://publications.scilifelab.se/publication/faee937ae25845dc8d0e74e783341329.json"}, "display": {"href": "https://publications.scilifelab.se/publication/faee937ae25845dc8d0e74e783341329"}}, "title": "Epigenetic suppression of creatine kinase B in adipocytes links endoplasmic reticulum stress to obesity-associated inflammation.", "authors": [{"family": "Renzi", "given": "Gianluca", "initials": "G"}, {"family": "Vlassakev", "given": "Ivan", "initials": "I"}, {"family": "Hansen", "given": "Mattias", "initials": "M"}, {"family": "Higos", "given": "Romane", "initials": "R"}, {"family": "Lecoutre", "given": "Simon", "initials": "S"}, {"family": "Elmastas", "given": "Merve", "initials": "M"}, {"family": "Hodek", "given": "Ondrej", "initials": "O"}, {"family": "Moritz", "given": "Thomas", "initials": "T"}, {"family": "Alaeddine", "given": "Lynn M", "initials": "LM"}, {"family": "Frendo-Cumbo", "given": "Scott", "initials": "S"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Kerr", "given": "Alastair", "initials": "A"}, {"family": "Maqdasy", "given": "Salwan", "initials": "S"}, {"family": "Mejhert", "given": "Niklas", "initials": "N"}, {"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Mol Metab", "issn": "2212-8778", "volume": "92", "pages": "102082", "issn-l": "2212-8778"}, "abstract": "In white adipose tissue, disturbed creatine metabolism through reduced creatine kinase B (CKB) transcription contributes to obesity-related inflammation. However, the mechanisms regulating CKB expression in human white adipocytes remain unclear. By screening conditions perturbed in obesity, we identified endoplasmic reticulum (ER) stress as a key suppressor of CKB transcription across multiple cell types. Through follow-up studies, we found that ER stress through the IRE1-XBP1s pathway, promotes CKB promoter methylation via the methyltransferase DNMT3A. This epigenetic change represses CKB transcription, shifting metabolism towards glycolysis and increasing the production of the pro-inflammatory chemokine CCL2. We validated our findings in vivo, demonstrating that individuals living with obesity show an inverse relationship between CKB expression and promoter methylation in white adipocytes, along with elevated CCL2 secretion. Overall, our study uncovers a regulatory axis where ER stress drives inflammation in obesity by reducing CKB abundance, and consequently altering the bioenergetic state of the cell.", "doi": "10.1016/j.molmet.2024.102082", "pmid": "39675471", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11731883"}, {"db": "pii", "key": "S2212-8778(24)00213-8"}], "notes": [], "created": "2025-11-18T12:03:44.169Z", "modified": "2025-11-18T12:03:44.192Z"}, {"entity": "publication", "iuid": "58bd3a84e43d45578c5613d806758ac1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58bd3a84e43d45578c5613d806758ac1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58bd3a84e43d45578c5613d806758ac1"}}, "title": "Earliest modern human genomes constrain timing of Neanderthal admixture.", "authors": [{"family": "S\u00fcmer", "given": "Arev P", "initials": "AP", "orcid": "0009-0001-4834-4414", "researcher": {"href": "https://publications.scilifelab.se/researcher/862f71c337ad4775bb2cdb7cec947e39.json"}}, {"family": "Rougier", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0003-0358-0285", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f83f613a0f4d9fba2f1b9f9d6db45c.json"}}, {"family": "Villalba-Mouco", "given": "Vanessa", "initials": "V", "orcid": "0000-0002-9357-5238", "researcher": {"href": "https://publications.scilifelab.se/researcher/23941efc34474847bc42265d30fd9e58.json"}}, {"family": "Huang", "given": "Yilei", "initials": "Y"}, {"family": "Iasi", "given": "Leonardo N M", "initials": "LNM"}, {"family": "Essel", "given": "Elena", "initials": "E", "orcid": "0000-0002-2642-8043", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c289ad6c2c443dab3e8ac7f9e85979e.json"}}, {"family": "Bossoms Mesa", "given": "Alba", "initials": "A", "orcid": "0009-0008-7556-1722", "researcher": {"href": "https://publications.scilifelab.se/researcher/b11dd9c4aea34fb8bde542f5e983b723.json"}}, {"family": "Furtwaengler", "given": "Anja", "initials": "A"}, {"family": "Peyr\u00e9gne", "given": "St\u00e9phane", "initials": "S", "orcid": "0000-0002-9823-9102", "researcher": {"href": "https://publications.scilifelab.se/researcher/1659db1df364436d87f40641f0778251.json"}}, {"family": "de Filippo", "given": "Cesare", "initials": "C"}, {"family": "Rohrlach", "given": "Adam B", "initials": "AB", "orcid": "0000-0002-4204-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/7627382e0fd34de9ae719356e46d720d.json"}}, {"family": "Pierini", "given": "Federica", "initials": "F"}, {"family": "Mafessoni", "given": "Fabrizio", "initials": "F"}, {"family": "Fewlass", "given": "Helen", "initials": "H"}, {"family": "Zavala", "given": "Elena I", "initials": "EI"}, {"family": "Mylopotamitaki", "given": "Dorothea", "initials": "D"}, {"family": "Bianco", "given": "Raffaela A", "initials": "RA", "orcid": "0009-0004-6087-8031", "researcher": {"href": "https://publications.scilifelab.se/researcher/7270ec1ad3be465db60ff387055b4981.json"}}, {"family": "Schmidt", "given": "Anna", "initials": "A"}, {"family": "Zorn", "given": "Julia", "initials": "J"}, {"family": "Nickel", "given": "Birgit", "initials": "B"}, {"family": "Patova", "given": "Anna", "initials": "A"}, {"family": "Posth", "given": "Cosimo", "initials": "C", "orcid": "0000-0002-8206-3907", "researcher": {"href": "https://publications.scilifelab.se/researcher/828edab40ca74c89947aa70526e7e339.json"}}, {"family": "Smith", "given": "Geoff M", "initials": "GM", "orcid": "0000-0001-7155-5140", "researcher": {"href": "https://publications.scilifelab.se/researcher/15e8227c27944ddb88aebf8a5f7c9e74.json"}}, {"family": "Ruebens", "given": "Karen", "initials": "K"}, {"family": "Sinet-Mathiot", "given": "Virginie", "initials": "V", "orcid": "0000-0003-3228-5824", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ddbcd4720eb4256a8442803e40edcf5.json"}}, {"family": "Stoessel", "given": "Alexander", "initials": "A"}, {"family": "Dietl", "given": "Holger", "initials": "H"}, {"family": "Orschiedt", "given": "J\u00f6rg", "initials": "J", "orcid": "0000-0003-3629-8251", "researcher": {"href": "https://publications.scilifelab.se/researcher/877fc9ff7958467d95c83eb661be2631.json"}}, {"family": "Kelso", "given": "Janet", "initials": "J", "orcid": "0000-0002-3618-322X", "researcher": {"href": "https://publications.scilifelab.se/researcher/57db79fef05b4743bff8345f8c3dfc04.json"}}, {"family": "Zeberg", "given": "Hugo", "initials": "H", "orcid": "0000-0001-7118-1249", "researcher": {"href": "https://publications.scilifelab.se/researcher/090e842ed8ff4cf2a3fe5f8e58118e58.json"}}, {"family": "Bos", "given": "Kirsten I", "initials": "KI", "orcid": "0000-0003-2937-3006", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d58da73fd8f409dac1e23a4b9f6b49f.json"}}, {"family": "Welker", "given": "Frido", "initials": "F", "orcid": "0000-0002-4846-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/7652762c05444a1d86c4b12c637b529b.json"}}, {"family": "Weiss", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0778-5520", "researcher": {"href": "https://publications.scilifelab.se/researcher/1688a83f780c44ba937de8577a9e3956.json"}}, {"family": "McPherron", "given": "Shannon P", "initials": "SP", "orcid": "0000-0002-2063-468X", "researcher": {"href": "https://publications.scilifelab.se/researcher/82ef55ca1bf84d1f9f14ddc414c2e1e4.json"}}, {"family": "Sch\u00fcler", "given": "Tim", "initials": "T", "orcid": "0000-0001-9190-8054", "researcher": {"href": "https://publications.scilifelab.se/researcher/433420b892e444b59e0701877ca6c4cb.json"}}, {"family": "Hublin", "given": "Jean-Jacques", "initials": "J"}, {"family": "Velem\u00ednsk\u00fd", "given": "Petr", "initials": "P", "orcid": "0000-0003-3691-7817", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdae571d1fbd442cad2a729beeb536d9.json"}}, {"family": "Br\u016f\u017eek", "given": "Jaroslav", "initials": "J", "orcid": "0000-0002-2478-9662", "researcher": {"href": "https://publications.scilifelab.se/researcher/a50959d29e93439b8d74e45d321f0004.json"}}, {"family": "Peter", "given": "Benjamin M", "initials": "BM", "orcid": "0000-0003-2526-8081", "researcher": {"href": "https://publications.scilifelab.se/researcher/1860ed14a48048fdb14d9d183e1ee869.json"}}, {"family": "Meyer", "given": "Matthias", "initials": "M", "orcid": "0000-0002-4760-558X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4bd87e0225d422ea165ab0670f6cb20.json"}}, {"family": "Meller", "given": "Harald", "initials": "H", "orcid": "0000-0002-7590-0375", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fa5a199c61b47cb9b4fa3c7ea494ba7.json"}}, {"family": "Ringbauer", "given": "Harald", "initials": "H", "orcid": "0000-0002-4884-9682", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8b1cf3531d40fd9d601705da089011.json"}}, {"family": "Hajdinjak", "given": "Mateja", "initials": "M", "orcid": "0000-0002-4064-0331", "researcher": {"href": "https://publications.scilifelab.se/researcher/cec10fd428c64857b2dc7017e390ab9b.json"}}, {"family": "Pr\u00fcfer", "given": "Kay", "initials": "K", "orcid": "0000-0001-6242-3058", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f96f223bf843a0949f1efa2a44513f.json"}}, {"family": "Krause", "given": "Johannes", "initials": "J", "orcid": "0000-0001-9144-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2416e8bd2bfb4aa3988f4a37fca2de2e.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "638", "issue": "8051", "pages": "711-717"}, "abstract": "Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals1-4. Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlat\u00fd k\u016f\u0148, Czechia3 and Bacho Kiro, Bulgaria2. Here we deepen our understanding of early modern humans by analysing one high-coverage genome and five low-coverage genomes from approximately 45,000-year-old remains from Ilsenh\u00f6hle in Ranis, Germany4, and a further high-coverage genome from Zlat\u00fd k\u016f\u0148. We show that distant familial relationships link the Ranis and Zlat\u00fd k\u016f\u0148 individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbour Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to approximately 45,000-49,000 years ago. This implies that ancestors of all non-Africans sequenced so far resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.", "doi": "10.1038/s41586-024-08420-x", "pmid": "39667410", "labels": {"Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11839475"}, {"db": "pii", "key": "10.1038/s41586-024-08420-x"}], "notes": [], "created": "2025-02-28T14:15:29.929Z", "modified": "2025-05-27T08:41:54.814Z"}, {"entity": "publication", "iuid": "12c089c75858413289c4cd1d95bde9b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12c089c75858413289c4cd1d95bde9b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12c089c75858413289c4cd1d95bde9b4"}}, "title": "DMI fungicide resistance in Zymoseptoria tritici is unlinked to geographical origin and genetic background: a case study in Europe.", "authors": [{"family": "Oreiro", "given": "Eula Gems", "initials": "EG", "orcid": "0000-0001-9852-1549", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4cbd2fbecbd461fa92ea04a5d9ab362.json"}}, {"family": "Samils", "given": "Berit", "initials": "B"}, {"family": "Kildea", "given": "Steven", "initials": "S", "orcid": "0000-0001-8240-6343", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6329730a7674817aac8bb3662a658ca.json"}}, {"family": "Heick", "given": "Thies", "initials": "T"}, {"family": "Hellin", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4777-6036", "researcher": {"href": "https://publications.scilifelab.se/researcher/0895796af24c4eca91bf783cc507f03c.json"}}, {"family": "Legr\u00e8ve", "given": "Anne", "initials": "A"}, {"family": "Rodemann", "given": "Bernd", "initials": "B"}, {"family": "Berg", "given": "Gunilla", "initials": "G"}, {"family": "J\u00f8rgensen", "given": "Lise N", "initials": "LN"}, {"family": "Friberg", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3181-1597", "researcher": {"href": "https://publications.scilifelab.se/researcher/64ea9c2f457f46c48339ad375383475b.json"}}, {"family": "Berlin", "given": "Anna", "initials": "A"}, {"family": "Zhan", "given": "Jiasui", "initials": "J"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Pest Manag Sci", "issn": "1526-4998", "volume": "81", "issue": "2", "pages": "1103-1112", "issn-l": null}, "abstract": "The hemibiotrophic fungus Zymoseptoria tritici causing Septoria tritici blotch (STB), is a devastating foliar pathogen of wheat worldwide. A common group of fungicides used to control STB are the demethylation inhibitors (DMIs). DMI fungicides restrict fungal growth by inhibiting the sterol 14-\u03b1-demethylase, a protein encoded by CYP51 gene and essential for maintaining fungal cell permeability. However, the adaptation of Z. tritici populations in response to intensive and prolonged DMI usage has resulted in a gradual shift towards reduced sensitivity to this group of fungicides. In this study, 311 isolates were collected pre-treatment from nine wheat-growing regions in Europe in 2019. These isolates were analysed by high-throughput amplicon-based sequencing of nine housekeeping genes and the CYP51 gene.\n\nAnalyses based on housekeeping genes and the CYP51 gene revealed a lack of population structure in Z. tritici samples irrespective of geographical origin. Minimum spanning network (MSN) analysis showed clustering of multilocus genotypes (MLGs) based on CYP51 haplotypes, indicating an effect of selection due to DMI fungicide use. The majority of the haplotypes identified in this study have been reported previously. The diversity and frequencies of mutations varied across regions.\n\nUsing a high-throughput amplicon-sequencing approach, we found several mutations in the CYP51 gene combined in different haplotypes that are likely to cause fungicide resistance. These mutations occurred irrespective of genetic background or geographical origin. Overall, these results contribute to the development of effective and sustainable risk monitoring for DMI fungicide resistance. \u00a9 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.", "doi": "10.1002/ps.8514", "pmid": "39503283", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11716363"}], "notes": [], "created": "2024-11-11T07:55:09.530Z", "modified": "2025-08-19T13:18:10.746Z"}, {"entity": "publication", "iuid": "e3f6f45f172f4f77b44d3513d048e62d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3f6f45f172f4f77b44d3513d048e62d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3f6f45f172f4f77b44d3513d048e62d"}}, "title": "Combining observational and experimental data to estimate environmental and species drivers of fungal metacommunity dynamics.", "authors": [{"family": "Nenz\u00e9n", "given": "Hedvig Kristina", "initials": "HK", "orcid": "0000-0002-0189-4283", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfea4734d33f49bbb881e7454488268b.json"}}, {"family": "Moor", "given": "Helen", "initials": "H"}, {"family": "O'Hara", "given": "Robert B", "initials": "RB"}, {"family": "J\u00f6nsson", "given": "Mari", "initials": "M"}, {"family": "Nord\u00e9n", "given": "Jenni", "initials": "J", "orcid": "0000-0001-8894-5815", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcaf0631934b4314a6a1a536e00c66d4.json"}}, {"family": "Ottosson", "given": "Elisabet", "initials": "E"}, {"family": "Sn\u00e4ll", "given": "Tord", "initials": "T"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Ecology", "issn": "1939-9170", "volume": "106", "issue": "2", "pages": "e70014", "issn-l": "0012-9658"}, "abstract": "Understanding the distribution and dynamics of species is central to ecology and important for managing biodiversity. The distributions of species in metacommunities are determined by many factors, including environmental conditions and interactions between species. Yet, it is difficult to quantify the effect of species interactions on metacommunity dynamics from observational data. We present an approach to estimate the importance of species interactions that combines data from two observational presence-absence inventories (providing colonization-extinction data) with data from species interaction experiments (providing informative prior distributions in the Bayesian framework). We further illustrate the approach on wood-decay fungi that interact within a downed log through competition for resources and space, and facilitate the succession of other species by decomposing the wood. Specifically, we estimated the relative importance of species interactions by examining how the presence of a species influenced the colonization and extinction probability of other species. Temporal data on fruit body occurrence of 12 species inventoried twice were jointly analyzed with experimental data from two laboratory experiments that aimed to estimate competitive interactions. Both environmental variables and species interactions affected colonization and extinction dynamics. Late-successional fungi had more colonization interactions with predecessor species than early-successional species. We identified several species interactions, and the presence of certain species changed the probability that later-successional species colonized by -81% to 512%. The presence of certain species increased the probability that other species went extinct from a log by 14%-61%. Including the informative priors from experimental data added two colonization interactions and one extinction interaction for which the observational field data was inconclusive. However, most species had no detectable interactions, either because they did not interact or because of low species occupancy, meaning data limitation. We show how temporal presence-absence data can be combined with experimental data to identify which species influence the colonization-extinction dynamics of others. Accounting for species interactions in metacommunity models, in addition to environmental drivers, is important because interactions can have cascading effects on other species.", "doi": "10.1002/ecy.70014", "pmid": "39918170", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11804162"}], "notes": [], "created": "2025-11-28T10:40:10.659Z", "modified": "2025-11-28T10:40:10.849Z"}, {"entity": "publication", "iuid": "34c5c2bee8b840eb96262212b3a6964d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34c5c2bee8b840eb96262212b3a6964d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34c5c2bee8b840eb96262212b3a6964d"}}, "title": "Acute Vestibular Syndrome Unmasking an RFC1-Spectrum Disorder.", "authors": [{"family": "Verrecchia", "given": "Luca", "initials": "L"}, {"family": "Alm", "given": "Victor", "initials": "V", "orcid": "0009-0004-0429-5237", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b7df01bf278424a87b30de0c6306751.json"}}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0003-4503-4717", "researcher": {"href": "https://publications.scilifelab.se/researcher/481958db26a2433ea8d5cc786c3b2bca.json"}}, {"family": "Lenner", "given": "Felix", "initials": "F", "orcid": "0000-0002-9594-0710", "researcher": {"href": "https://publications.scilifelab.se/researcher/075ac1709d46441ebd03420bf9c080e7.json"}}, {"family": "Paivandy", "given": "Aida", "initials": "A"}, {"family": "Feuk", "given": "Lars", "initials": "L"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Paucar", "given": "Martin", "initials": "M", "orcid": "0000-0003-3735-1480", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbc592904eb5402ea48a624471d4b939.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Neurol Genet", "issn": "2376-7839", "volume": "11", "issue": "1", "pages": "e200238", "issn-l": "2376-7839"}, "abstract": "Since the discovery of biallelic pentanucleotide expansions in RFC1 as the cause of cerebellar ataxia, neuropathy, vestibular areflexia syndrome, a wide and growing clinical spectrum has emerged. In this article, we report a man with acute vestibular syndrome that likely unmasked a RFC1-spectrum disorder.\n\nDetailed clinical evaluation, neuroimaging, nerve conduction studies, evaluation of vestibular function, and short-read whole-genome sequencing and targeted long-read adaptive sequencing were performed.\n\nClinical follow-up after acute vestibular syndrome revealed bilateral vestibular areflexia and a gait abnormality with the Scale for the Assessment and Rating of Ataxia score of 5. Brain MRI was normal while 2 electroneurography tests did not show neuropathy. However, severe cough spells raised the suspicion of a RFC1-spectrum disorder. WGS screening detected a recessive intronic pentanucleotide expansion in RFC1, which was verified and sized using long-read adaptive sequencing.\n\nThis is an unusual presentation; oscillopsia after an acute vestibular syndrome and cough spells should alert clinicians about a RFC1-spectrum disorder, even in the absence of neuropathy and neuroradiologic abnormalities.", "doi": "10.1212/NXG.0000000000200238", "pmid": "39839074", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11748027"}, {"db": "pii", "key": "NXG-2024-100195D"}], "notes": [], "created": "2025-11-18T20:47:50.741Z", "modified": "2025-11-28T10:53:37.894Z"}, {"entity": "publication", "iuid": "8697b5a0a59c4c63a1a7ed8dc2750abf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8697b5a0a59c4c63a1a7ed8dc2750abf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8697b5a0a59c4c63a1a7ed8dc2750abf"}}, "title": "1H-19F cross-polarization magic angle spinning dynamic nuclear polarization NMR investigation of advanced pharmaceutical formulations.", "authors": [{"family": "\u0160olt\u00e9sov\u00e1", "given": "M\u00e1ria", "initials": "M"}, {"family": "Pinon", "given": "Arthur C", "initials": "AC"}, {"family": "Aussenac", "given": "Fabien", "initials": "F"}, {"family": "Schlagnitweit", "given": "Judith", "initials": "J"}, {"family": "Reiter", "given": "Christian", "initials": "C"}, {"family": "Purea", "given": "Armin", "initials": "A"}, {"family": "Melzi", "given": "Roberto", "initials": "R"}, {"family": "Engelke", "given": "Frank", "initials": "F"}, {"family": "Martin", "given": "Dave", "initials": "D"}, {"family": "Krambeck", "given": "Stefanie", "initials": "S"}, {"family": "Biscans", "given": "Annabelle", "initials": "A"}, {"family": "Kay", "given": "Emma", "initials": "E"}, {"family": "Emsley", "given": "Lyndon", "initials": "L"}, {"family": "Schantz", "given": "Staffan", "initials": "S"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "J Magn Reson", "issn": "1096-0856", "volume": "371", "pages": "107827", "issn-l": null}, "abstract": "A new 3.2 mm 1H-19F-X magic angle spinning dynamic nuclear polarization NMR (MAS DNP-NMR) probe was developed with a unique coil design with separate radiofrequency channels for 1H excitation and 13C or 19F detection to enable acquisition of 1H-19F cross-polarization (CP) MAS experiments, direct-detected 19F spectra with proton decoupling, and acquisition on 13C with simultaneous double decoupling on the 1H and 19F channels as well as 1H-19F-13C double-CP experiments under low temperature MAS DNP conditions. We use these sequences to study AZD2811, which is an active pharmaceutical ingredient (API), in its pure dry state as well as in its corresponding drug delivery formulation consisting of drug-loaded polymeric nanoparticles (PNPs). Included in this study are also small interfering RNAs (siRNAs) for therapeutic targeting of peptidyl-prolyl cis-trans isomerase B (Ppib) mRNA. We demonstrate that 1H-19F CP MAS experiments performed on the new HFX probe represent a notable advantage over usually acquired direct-detected 19F experiments. The indirect 19F DNP enhancement \u03b5on/off(19F) = 26 was obtained via 1H-19F CP for the pure API impregnated with DNP solution, with an overall 30-fold sensitivity gain compared to the direct-detected 19F experiment under similar conditions. DNP enhancement value of \u03b5on/off(19F) = 42 was obtained via 1H-19F CP for the polymeric nanoparticle suspension and \u03b5on/off(19F) \u2248 150 were obtained for two different siRNAs in frozen DNP solution.", "doi": "10.1016/j.jmr.2024.107827", "pmid": "39793183", "labels": {"Swedish NMR Centre": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1090-7807(24)00211-8"}], "notes": [], "created": "2025-11-27T08:01:47.447Z", "modified": "2025-11-27T08:22:21.284Z"}, {"entity": "publication", "iuid": "8d4a8412b91143359d590e01636497ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d4a8412b91143359d590e01636497ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d4a8412b91143359d590e01636497ae"}}, "title": "Extracellular vesicle surface engineering with integrins (ITGAL & ITGB2) to specifically target ICAM-1-expressing endothelial cells.", "authors": [{"family": "Bergqvist", "given": "Markus", "initials": "M", "orcid": "0009-0003-5716-3716", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d33e374d0642479a80683a989f095a.json"}}, {"family": "Park", "given": "Kyong-Su", "initials": "KS", "orcid": "0000-0003-0902-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e308b29fe144b49f4db27f4b819c18.json"}}, {"family": "Karimi", "given": "Nasibeh", "initials": "N", "orcid": "0000-0003-1499-6876", "researcher": {"href": "https://publications.scilifelab.se/researcher/14632eec875c42038aa0b6983e0ec107.json"}}, {"family": "Yu", "given": "Lijuan", "initials": "L", "orcid": "0000-0003-3558-3800", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b0b4ca8553144b19c236bc09c1c9b81.json"}}, {"family": "L\u00e4sser", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-1279-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/e14e17d2cdb24a9f93991d83811c78b9.json"}}, {"family": "L\u00f6tvall", "given": "Jan", "initials": "J", "orcid": "0000-0001-9195-9249", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cbcaf6b5698411c92e0de9e8fcf390f.json"}}], "type": "journal article", "published": "2025-01-30", "journal": {"title": "J Nanobiotechnology", "issn": "1477-3155", "volume": "23", "issue": "1", "pages": "64", "issn-l": null}, "abstract": "Extracellular vesicles (EVs) are taken up by most cells, however specific or preferential cell targeting remains a hurdle. This study aims to develop an EV that targets cells involved in inflammation, specifically those expressing intercellular adhesion molecule-1 (ICAM-1). To target these cells, we overexpress the ICAM-1 binding receptor \"lymphocyte function-associated antigen-1\" (LFA-1) in HEK293F cells, by sequential transfection of plasmids of the two LFA-1 subunits, ITGAL and ITGB2 (CD11a and CD18). The LFA-1 receptor was strongly overexpressed on the EVs released by the transfected cells. We further loaded these EVs with a therapeutic peptide, targeting myeloid differentiation primary response 88 (Myd88; EVMyd88), through a developed EV open-and-close procedure. Myd88 is a downstream common intracellular messenger for most TLR-receptors. EV expression of LFA-1 increases EV binding to ICAM-1-expressing cells, an effect that was dose-dependently inhibited by a specific neutralizing ICAM-1 antibody. Further, activated human endothelial cells treated with LFA-1 EVMyd88 had increased uptake of these EVs, resulting in dose-dependent inhibition of induced release of IL-8, presumably by targeting Myd88. We conclude that LFA-1-expressing EVMyd88 may be a candidate suitable for delivering therapeutic peptides in inflammatory diseases associated with TLR-activation.", "doi": "10.1186/s12951-025-03125-3", "pmid": "39885580", "labels": {"Glycoproteomics and MS Proteomics": "Service", "Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11780982"}, {"db": "pii", "key": "10.1186/s12951-025-03125-3"}], "notes": [], "created": "2025-10-23T13:06:45.347Z", "modified": "2025-11-05T13:48:02.553Z"}, {"entity": "publication", "iuid": "f1a9c58aaeef4132b2cdec07c05109a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1a9c58aaeef4132b2cdec07c05109a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1a9c58aaeef4132b2cdec07c05109a4"}}, "title": "Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity.", "authors": [{"family": "Cougnoux", "given": "Antony", "initials": "A"}, {"family": "Mahmoud", "given": "Loay", "initials": "L"}, {"family": "Johnsson", "given": "Per A", "initials": "PA"}, {"family": "Eroglu", "given": "Alper", "initials": "A"}, {"family": "Gsell", "given": "Louise", "initials": "L"}, {"family": "Rosenbauer", "given": "Jakob", "initials": "J"}, {"family": "Sandberg", "given": "Rickard", "initials": "R"}, {"family": "Hausser", "given": "Jean", "initials": "J"}], "type": "journal article", "published": "2025-01-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "3811", "issn-l": "2045-2322"}, "abstract": "Combining 3D cultures such as tumor spheroids and organoids with spatial omics holds great potential for tissue biology and cancer research. Yet, this potential is presently limited by technical and financial challenges of spatial omics methods and 3D cultures. To address this, we combine dye diffusion, the Smart-seq3xpress protocol for deep single-cell gene expression profiling, and dedicated probabilistic inference methods into diffusion Smart-seq3 (Smart-seq3D), to reveal the transcriptome of single cells along with their position along the core-periphery axis of spheroids. Applying Smart-seq3D to triple-negative breast tumor spheroids identifies thousands of spatial genes and reveals continuous, ungated spatial gene expression. Spatial gene and pathway expression patterns suggest biologies specific to spheroid regions, which we validate by immunostainings and pharmacological interventions. We use the Smart-seq3D data to test evolutionary principles of spatial tumor heterogeneity. Finally, we characterize aspects of tumor heterogeneity captured by 3D spheroids that are missing from 2D cultures but found in tumors in vivo. Smart-seq3D can offer a cost-efficient approach to explore how cells adapt their transcriptome to different micro-environments, reveal spatial determinants of drug resistance and could serve to characterize spatial interactions between cancer and stromal/immune cells in 3D co-cultures.", "doi": "10.1038/s41598-024-83989-x", "pmid": "39885179", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11782488"}, {"db": "pii", "key": "10.1038/s41598-024-83989-x"}], "notes": [], "created": "2025-04-07T08:46:18.744Z", "modified": "2025-04-07T08:46:18.749Z"}, {"entity": "publication", "iuid": "fdd85dd6bc6544c9abccb2e0a6b9a4fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdd85dd6bc6544c9abccb2e0a6b9a4fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdd85dd6bc6544c9abccb2e0a6b9a4fa"}}, "title": "Modulation of biological activities in adipose derived stem cells by histone deacetylation.", "authors": [{"family": "Abdallah", "given": "Sallam", "initials": "S"}, {"family": "Tabebi", "given": "Mouna", "initials": "M", "orcid": "0000-0002-2873-161X", "researcher": {"href": "https://publications.scilifelab.se/researcher/285705c043f34b55826e7f33ab36a875.json"}}, {"family": "Qanadilo", "given": "Sawsan", "initials": "S"}, {"family": "Ali", "given": "Neserin", "initials": "N"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "D'Arcy", "given": "P\u00e1draig", "initials": "P"}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Sjoberg", "given": "Folke", "initials": "F"}, {"family": "Elmasry", "given": "Moustafa", "initials": "M"}, {"family": "El-Serafi", "given": "Ahmed", "initials": "A"}], "type": "journal article", "published": "2025-01-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "3629"}, "abstract": "Difficult-to-heal wounds management accounts for about 4% of healthcare costs, highlighting the need for innovative solutions. Extracellular signals drive cell proliferation during tissue regeneration, while epigenetic mechanisms regulate stem cell homeostasis, differentiation, and skin repair. Exploring epigenetic regulation in adipose-derived stem cells (ADSCs) holds promise for improving skin injury treatments. We investigated the effects of histone deacetylase inhibitor (SAHA) on ADSCs to better understand its cellular and molecular impacts. ADSCs were treated with SAHA for 72 h, showing no change in cell viability at the studied concentrations. However, the expression of histone deacetylase decreased at 1000 nM, while the cell proliferation marker Ki-67 increased after SAHA treatment, as confirmed by immunofluorescence. CCND1 gene expression increased, whereas protein expression of the proliferating cell nuclear antigen (PCNA) decreased. Cell cycle analysis showed an increase in G2 phase in SAHA-treated cells. Microarray analysis revealed 74 upregulated and 40 downregulated differentially expressed genes, including upregulation of P53 targets, CDKN1A and MDM2. Proteomic analysis identified 631 upregulated and 823 downregulated proteins compared to the vehicle. Pathway enrichment analysis showed cell cycle, ATP-dependent chromatin remodeling and DNA processes were among the affected pathways. This study suggests SAHA modulates ADSCs' biological processes, highlighting its potential for skin regeneration.", "doi": "10.1038/s41598-024-84652-1", "pmid": "39880862", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-024-84652-1"}, {"db": "pmc", "key": "PMC11779964"}], "notes": [], "created": "2025-01-31T10:37:54.632Z", "modified": "2025-03-24T08:23:01.425Z"}, {"entity": "publication", "iuid": "57fc3379fa7d498cbf6dfb3d1a9a5af0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57fc3379fa7d498cbf6dfb3d1a9a5af0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57fc3379fa7d498cbf6dfb3d1a9a5af0"}}, "title": "The di-leucine motif in the host defense peptide LL-37 is essential for initiation of autophagy in human macrophages.", "authors": [{"family": "Rekha", "given": "Rokeya Sultana", "initials": "RS"}, {"family": "Padhi", "given": "Avinash", "initials": "A"}, {"family": "Frengen", "given": "Nicolai", "initials": "N", "orcid": "0000-0003-1834-7638", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c9b75c9a3ed48dbbd4cc4fae9836623.json"}}, {"family": "Hauenstein", "given": "Julia", "initials": "J", "orcid": "0000-0001-6674-4297", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bda375874844045bd86d62d3b25e071.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Agerberth", "given": "Birgitta", "initials": "B"}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}, {"family": "Gu\u00f0mundsson", "given": "Gu\u00f0mundur H", "initials": "GH"}, {"family": "Bergman", "given": "Peter", "initials": "P", "orcid": "0000-0003-3306-3713", "researcher": {"href": "https://publications.scilifelab.se/researcher/397d11713c80456bb600b1e4c88ff843.json"}}], "type": "journal article", "published": "2025-01-28", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "44", "issue": "1", "pages": "115031", "issn-l": null}, "abstract": "The human cathelicidin peptide LL-37 induces autophagy in human macrophages. Different post-translational modifications (PTMs) such as citrullination, acetylation, and formylation impact LL-37, yet their effect on autophagy remains unknown. Thus, we set out to study how the cellular source could impact PTM of LL-37 and subsequent effects on autophagy initiation. Neutrophil-released LL-37 failed to induce autophagy, unlike macrophage-released LL-37. Mass spectrometry analysis revealed modifications on neutrophil-derived LL-37, especially at the N terminus, while macrophage-derived LL-37 remained mostly native. Native LL-37 initiated autophagy, while formylated and acetylated versions did not. Truncated peptides lacking the N-terminal di-leucine motif or substituted with di-alanine did not initiate autophagy. Native LL-37 failed to initiate autophagy in macrophages with genetic inactivation of dipeptidyl peptidase-1. An intact N-terminal di-leucine motif in LL-37 was crucial for autophagy initiation, and modifications abrogated the effects. This pathway presents a novel way to regulate the effects of LL-37 in infection or inflammation.", "doi": "10.1016/j.celrep.2024.115031", "pmid": "39708316", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(24)01382-2"}], "notes": [], "created": "2025-02-28T14:11:56.119Z", "modified": "2025-11-28T10:42:15.993Z"}, {"entity": "publication", "iuid": "b7086e5f716e435090388237fe0eaeb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7086e5f716e435090388237fe0eaeb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7086e5f716e435090388237fe0eaeb5"}}, "title": "Lack of ST2 aggravates glioma invasiveness, vascular abnormality, and immune suppression.", "authors": [{"family": "Wicher", "given": "Grzegorz", "initials": "G"}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Vaccaro", "given": "Alessandra", "initials": "A"}, {"family": "Vemuri", "given": "Kalyani", "initials": "K"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M"}, {"family": "Olofsson", "given": "Tommie", "initials": "T"}, {"family": "Imbria", "given": "Rebeca-Noemi", "initials": "RN"}, {"family": "Belting", "given": "Mattias", "initials": "M"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}, {"family": "Dimberg", "given": "Anna", "initials": "A"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}], "type": "journal article", "published": "2025-01-27", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "volume": "7", "issue": "1", "pages": "vdaf010", "issn-l": null}, "abstract": "Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, characterized by aggressive growth and a dismal prognosis. Interleukin-33 (IL-33) and its receptor ST2 have emerged as regulators of glioma growth, but their exact function in tumorigenesis has not been deciphered. Indeed, previous studies on IL-33 in cancer have yielded somewhat opposing results as to whether it is pro- or anti-tumorigenic.\n\nIL-33 expression was assessed in a GBM tissue microarray and public databases. As in vivo models we used orthotopic xenografts of patient-derived GBM cells, and syngenic models with grafted mouse glioma cells.\n\nWe analyzed the role of IL-33 and its receptor ST2 in nonmalignant cells of the glioma microenvironment and found that IL-33 levels are increased in cells surrounding the tumor. Protein complexes of IL-33 and ST2 are mainly found outside of the tumor core. The IL-33-producing cells consist primarily of oligodendrocytes. To determine the function of IL-33 in the tumor microenvironment, we used mice lacking the ST2 receptor. When glioma cells were grafted to ST2-deficient mouse brains, the resulting tumors exhibited a more invasive growth pattern, and are associated with poorer survival, compared to wild-type mice. Tumors in ST2-deficient hosts are more invasive, with increased expression of extracellular matrix remodeling enzymes and enhanced tumor angiogenesis. Furthermore, the absence of ST2 leads to a more immunosuppressive environment.\n\nOur findings reveal that glia-derived IL-33 and its receptor ST2 participate in modulating tumor invasiveness, tumor vasculature, and immunosuppression in glioma.", "doi": "10.1093/noajnl/vdaf010", "pmid": "39931535", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11808570"}, {"db": "pii", "key": "vdaf010"}], "notes": [], "created": "2025-09-08T11:37:18.675Z", "modified": "2025-09-08T11:37:18.685Z"}, {"entity": "publication", "iuid": "e6431c56a9a44473a9004b296677bac7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6431c56a9a44473a9004b296677bac7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6431c56a9a44473a9004b296677bac7"}}, "title": "Association between alcohol consumption and peripheral artery disease: two de novo prospective cohorts and a systematic review with meta-analysis.", "authors": [{"family": "Yuan", "given": "Shuai", "initials": "S", "orcid": "0000-0001-5055-5627", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a51e0853b654cdcb2d42ebc5d73b52a.json"}}, {"family": "Wu", "given": "Jing", "initials": "J"}, {"family": "Chen", "given": "Jie", "initials": "J", "orcid": "0000-0002-4029-4192", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dbfd7fc4a2d4fe38a244f78cf48dce2.json"}}, {"family": "Sun", "given": "Yuhao", "initials": "Y", "orcid": "0000-0001-6987-3721", "researcher": {"href": "https://publications.scilifelab.se/researcher/aabdcfb442cd4ac7931e27767753bec3.json"}}, {"family": "Burgess", "given": "Stephen", "initials": "S", "orcid": "0000-0001-5365-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd2dcaf4dbb4e4c91c2af460b8fa98f.json"}}, {"family": "Li", "given": "Xue", "initials": "X"}, {"family": "\u00c5kesson", "given": "Agneta", "initials": "A"}, {"family": "Larsson", "given": "Susanna C", "initials": "SC"}], "type": "systematic review", "published": "2025-01-27", "journal": {"title": "Eur J Prev Cardiol", "issn": "2047-4881", "volume": "32", "issue": "2", "pages": "149-155", "issn-l": "2047-4873"}, "abstract": "The association between alcohol consumption and risk of peripheral artery disease (PAD) is inconclusive. We conducted this study to examine the association between alcohol consumption and PAD risk in two de novo cohort studies and a meta-analysis of observational studies.\n\nA systematic review was conducted to identify studies on alcohol consumption in relation to PAD risk. We further used data from two cohorts of 70 116 Swedish and 405 406 British adults and performed a meta-analysis of results from previously published studies and current cohort studies. There was a U-shaped association between alcohol consumption and incident PAD risk in the Swedish and British cohorts. The meta-analysis of results of these two cohorts and previously published studies found that compared with non- or never-drinkers, the relative risk of PAD was 0.83 [95% confidence interval (CI) 0.77-0.89], 0.81 (95% CI 0.74-0.90), and 0.94 (95% CI 0.83-1.07) for light, moderate, and high-to-heavy alcohol drinkers, respectively. The nonlinear meta-analysis revealed a possibly U-shaped association between alcohol consumption and PAD risk (P nonlinearity <0.001). The risk of PAD was observed to be the lowest for 2 drinks/week and to be pronounced for \u226510 drinks/week. All these associations persisted in a sensitivity meta-analysis including cohort and other types of observational studies.\n\nAlcohol intake \u22642 drinks/week was associated with a reduced risk of PAD, and the risk of PAD became pronounced with intake \u226510 drinkers/week.", "doi": "10.1093/eurjpc/zwae142", "pmid": "38626304", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "EMS197946"}, {"db": "pmc", "key": "PMC7616826"}, {"db": "pii", "key": "7646796"}], "notes": [], "created": "2025-02-28T14:17:20.622Z", "modified": "2025-02-28T14:17:20.701Z"}, {"entity": "publication", "iuid": "694184d0fedc41c3ba78ea06f31e7668", "links": {"self": {"href": "https://publications.scilifelab.se/publication/694184d0fedc41c3ba78ea06f31e7668.json"}, "display": {"href": "https://publications.scilifelab.se/publication/694184d0fedc41c3ba78ea06f31e7668"}}, "title": "Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells.", "authors": [{"family": "Fegraeus", "given": "Kim", "initials": "K"}, {"family": "Riihim\u00e4ki", "given": "Miia", "initials": "M"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Akula", "given": "Srinivas", "initials": "S"}, {"family": "Wernersson", "given": "Sara", "initials": "S", "orcid": "0000-0003-3067-7875", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d03168eb2f54a91897b5b738e2c5137.json"}}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}], "type": "journal article", "published": "2025-01-24", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "1", "pages": "e0317343", "issn-l": "1932-6203"}, "abstract": "Single-cell RNA sequencing (scRNA-seq) is a valuable tool for investigating cellular heterogeneity in diseases such as equine asthma (EA). This study evaluates the HIVE\u2122 scRNA-seq method, a pico-well-based technology, for processing bronchoalveolar lavage (BAL) cells from horses with EA. The HIVE method offers practical advantages, including compatibility with both field and clinical settings, as well as a gentle workflow suited for handling sensitive cells. Our results show that the major cell types in equine BAL were successfully identified; however, the proportions of T cells and macrophages deviated from cytological expectations, with macrophages being overrepresented and T cells underrepresented. Despite these limitations, the HIVE method confirmed previously identified T cell and macrophage subpopulations and defined other BAL cell subsets. However, compared to previous studies T helper subsets were less clearly defined. Additionally, consistent with previous scRNA-seq studies, the HIVE method detected fewer granulocytes and mast cells than anticipated in the total BAL samples. Nevertheless, applying the method to purified mast cells recovered an expected number of cells. A small set of eosinophils were also detected which have not been characterized in earlier studies. In summary these findings suggest that while the HIVE method shows promise for certain applications, further optimization is needed to improve the accuracy of cell type representation, particularly for granulocytes and mast cells, in BAL samples.", "doi": "10.1371/journal.pone.0317343", "pmid": "39854349", "labels": {"NGI Short read": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11760581"}, {"db": "pii", "key": "PONE-D-24-13492"}], "notes": [], "created": "2025-05-12T05:47:24.783Z", "modified": "2025-11-14T11:09:01.384Z"}, {"entity": "publication", "iuid": "125b428021b44c89958afc733cf7ae8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/125b428021b44c89958afc733cf7ae8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/125b428021b44c89958afc733cf7ae8d"}}, "title": "Precise and interpretable neural networks reveal epigenetic signatures of aging across youth in health and disease.", "authors": [{"family": "Mart\u00ednez-Enguita", "given": "David", "initials": "D"}, {"family": "Hillerton", "given": "Thomas", "initials": "T"}, {"family": "\u00c5kesson", "given": "Julia", "initials": "J"}, {"family": "Kling", "given": "Daniel", "initials": "D"}, {"family": "Lerm", "given": "Maria", "initials": "M"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}], "type": "journal article", "published": "2025-01-23", "journal": {"title": "Front Aging", "issn": "2673-6217", "volume": "5", "pages": "1526146", "issn-l": null}, "abstract": "DNA methylation (DNAm) age clocks are powerful tools for measuring biological age, providing insights into aging risks and outcomes beyond chronological age. While traditional models are effective, their interpretability is limited by their dependence on small and potentially stochastic sets of CpG sites. Here, we propose that the reliability of DNAm age clocks should stem from their capacity to detect comprehensive and targeted aging signatures.\n\nWe compiled publicly available DNAm whole-blood samples (n = 17,726) comprising the entire human lifespan (0-112 years). We used a pre-trained network-coherent autoencoder (NCAE) to compress DNAm data into embeddings, with which we trained interpretable neural network epigenetic clocks. We then retrieved their age-specific epigenetic signatures of aging and examined their functional enrichments in age-associated biological processes.\n\nWe introduce NCAE-CombClock, a novel highly precise (R2 = 0.978, mean absolute error = 1.96 years) deep neural network age clock integrating data-driven DNAm embeddings and established CpG age markers. Additionally, we developed a suite of interpretable NCAE-Age neural network classifiers tailored for adolescence and young adulthood. These clocks can accurately classify individuals at critical developmental ages in youth (AUROC = 0.953, 0.972, and 0.927, for 15, 18, and 21 years) and capture fine-grained, single-year DNAm signatures of aging that are enriched in biological processes associated with anatomic and neuronal development, immunoregulation, and metabolism. We showcased the practical applicability of this approach by identifying candidate mechanisms underlying the altered pace of aging observed in pediatric Crohn's disease.\n\nIn this study, we present a deep neural network epigenetic clock, named NCAE-CombClock, that improves age prediction accuracy in large datasets, and a suite of explainable neural network clocks for robust age classification across youth. Our models offer broad applications in personalized medicine and aging research, providing a valuable resource for interpreting aging trajectories in health and disease.", "doi": "10.3389/fragi.2024.1526146", "pmid": "39916723", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11799293"}, {"db": "pii", "key": "1526146"}], "notes": [], "created": "2025-11-28T10:54:34.248Z", "modified": "2025-11-28T10:54:34.265Z"}, {"entity": "publication", "iuid": "e91f3d289b5744af8e560cfea7c0910e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e91f3d289b5744af8e560cfea7c0910e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e91f3d289b5744af8e560cfea7c0910e"}}, "title": "A de novo, mosaic and complex chromosome 21 rearrangement causes APP triplication and familial autosomal dominant early onset Alzheimer disease.", "authors": [{"family": "Ehn", "given": "Emma", "initials": "E"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Laffita-Mesa", "given": "Jose M", "initials": "JM"}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0003-4503-4717", "researcher": {"href": "https://publications.scilifelab.se/researcher/481958db26a2433ea8d5cc786c3b2bca.json"}}, {"family": "Schoumans", "given": "Jacqueline", "initials": "J"}, {"family": "Portaankorva", "given": "Anne M", "initials": "AM"}, {"family": "Viitanen", "given": "Matti", "initials": "M"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Nennesmo", "given": "Inger", "initials": "I"}, {"family": "Graff", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9949-2951", "researcher": {"href": "https://publications.scilifelab.se/researcher/3faadb7b187046b090d947f85d8c4dd1.json"}}], "type": "journal article", "published": "2025-01-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "2912", "issn-l": "2045-2322"}, "abstract": "Copy number variation (CNV) of the amyloid-\u03b2 precursor protein gene (APP) is a known cause of autosomal dominant Alzheimer disease (ADAD), but de novo genetic variants causing ADAD are rare. We report a mother and daughter with neuropathologically confirmed definite Alzheimer disease (AD) and extensive cerebral amyloid angiopathy (CAA). Copy number analysis identified an increased number of APP copies and genome sequencing (GS) revealed the underlying complex genomic rearrangement (CGR) including a triplication of APP with two unique breakpoint junctions (BPJs). The mosaic state in the mother had likely occurred de novo. Digital droplet PCR (ddPCR) on 42 different tissues, including 17 different brain regions, showed the derivative chromosome at varying mosaic levels (20-96%) in the mother who had symptom onset at age 58 years. In contrast, the derivative chromosome was present in all analyzed cells in the daughter whose symptom onset was at 34 years. This study reveals the architecture of a de novo CGR causing APP triplication and ADAD with a striking difference in age at onset between the fully heterozygous daughter compared to the mosaic mother. The GS analysis identified the complexity of the CGR illustrating its usefulness in identifying structural variants (SVs) in neurodegenerative disorders.", "doi": "10.1038/s41598-025-86645-0", "pmid": "39849058", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11759332"}, {"db": "pii", "key": "10.1038/s41598-025-86645-0"}], "notes": [], "created": "2025-01-30T10:52:39.932Z", "modified": "2025-11-18T20:45:12.186Z"}, {"entity": "publication", "iuid": "1c261fe71b2644728865f93158bb34bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c261fe71b2644728865f93158bb34bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c261fe71b2644728865f93158bb34bf"}}, "title": "Comprehensive Approach for Sequential MALDI-MSI Analysis of Lipids, N-Glycans, and Peptides in Fresh-Frozen Rodent Brain Tissues.", "authors": [{"family": "Lee", "given": "Yea-Rin", "initials": "YR"}, {"family": "Kaya", "given": "Ibrahim", "initials": "I"}, {"family": "Wik", "given": "Elin", "initials": "E"}, {"family": "Baijnath", "given": "Sooraj", "initials": "S"}, {"family": "Lod\u00e9n", "given": "Henrik", "initials": "H", "orcid": "0000-0002-2416-5251", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd5349a708e242769091df471639f5b6.json"}}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Zhang", "given": "Xiaoqun", "initials": "X"}, {"family": "Sehlin", "given": "Dag", "initials": "D", "orcid": "0000-0002-9430-3859", "researcher": {"href": "https://publications.scilifelab.se/researcher/d91af72928af4dcb9ead88ba6d33d942.json"}}, {"family": "Syv\u00e4nen", "given": "Stina", "initials": "S", "orcid": "0000-0002-8196-4041", "researcher": {"href": "https://publications.scilifelab.se/researcher/758608b82e734dd8a18b78723f0fc05c.json"}}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}], "type": "journal article", "published": "2025-01-21", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "97", "issue": "2", "pages": "1338-1346", "issn-l": "0003-2700"}, "abstract": "Multiomics analysis of single tissue sections using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) provides comprehensive molecular insights. However, optimizing tissue sample preparation for MALDI-MSI to achieve high sensitivity and reproducibility for various biomolecules, such as lipids, N-glycans, and tryptic peptides, presents a significant challenge. This study introduces a robust and reproducible protocol for the comprehensive sequential analysis of the latter molecules using MALDI-MSI in fresh-frozen rodent brain tissue samples. The optimization process involved testing multiple organic solvents, which identified serial washing in ice-cold methanol, followed by chloroform as optimal for N-glycan analysis. Integrating this optimized protocol into MALDI-MSI workflows enabled comprehensive sequential analysis of lipids (in dual polarity mode), N-glycans, and tryptic peptides within the same tissue sections, enhancing both the efficiency and reliability. Validation across diverse rodent brain tissue samples confirmed the protocol's robustness and versatility. The optimized methodology was subsequently applied to a transgenic Alzheimer's disease (AD) mouse model (tgArcSwe) as a proof of concept. In the AD model, significant molecular alterations were observed in various sphingolipid and glycerophospholipid species, as well as in biantennary and GlcNAc-bisecting N-glycans, particularly in the cerebral cortex. These region-specific alterations are potentially associated with amyloid-beta (A\u03b2) plaque accumulation, which may contribute to cognitive and memory impairments. The proposed standardized methodology represents a significant advancement in neurobiological research, providing valuable insights into disease mechanisms and laying the foundation for potential preclinical applications. It could aid the development of diagnostic biomarkers and targeted therapies for AD and other neurodegenerative diseases, such as Parkinson's disease.", "doi": "10.1021/acs.analchem.4c05665", "pmid": "39781894", "labels": {"Spatial Mass Spectrometry": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11755403"}], "notes": [], "created": "2025-11-21T09:59:56.923Z", "modified": "2025-11-21T09:59:57.060Z"}, {"entity": "publication", "iuid": "e4d664134fa14e3f9777bf6603b31f4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4d664134fa14e3f9777bf6603b31f4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4d664134fa14e3f9777bf6603b31f4a"}}, "title": "Visualization using NIPTviewer support the clinical interpretation of noninvasive prenatal testing results.", "authors": [{"family": "Smeds", "given": "Patrik", "initials": "P"}, {"family": "Baranowska K\u00f6rberg", "given": "Izabella", "initials": "I"}, {"family": "Melin", "given": "Malin", "initials": "M", "orcid": "0000-0002-6589-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/190c3991975c43ec952a81df72292c9a.json"}}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}], "type": "journal article", "published": "2025-01-20", "journal": {"title": "BMC Med Genomics", "issn": "1755-8794", "volume": "18", "issue": "1", "pages": "15", "issn-l": "1755-8794"}, "abstract": "Noninvasive prenatal testing (NIPT) is increasingly used to screen for fetal chromosomal aneuploidy by analyzing cell-free DNA (cfDNA) in peripheral maternal blood. The method provides an opportunity for early detection of large genetic abnormalities without an increased risk of miscarriage due to invasive procedures. Commercial applications for use at clinical laboratories often take advantage of DNA sequencing technologies and include the bioinformatic workup of the sequence data. The interpretation of the test results and the clinical report writing, however, remains the responsibility of the diagnostic laboratory. In order to facilitate this step, we developed NIPTviewer, a web-based application to visualize and guide the interpretation of NIPT data results.\n\nNIPTviewer has a database functionality to store the NIPT results and a web interface for user interaction and visualization. The application has been implemented as part of a novel analysis pipeline for NIPT in a diagnostic laboratory at Uppsala University Hospital. The validation data set included 84 previously analyzed plasma samples with known results regarding chromosomes 13, 18, 21, X and Y. They were sequenced in six different experiments, uploaded to NIPTviewer and assigned to a clinical laboratory geneticist for interpretation. The results of all previously analyzed samples were replicated.\n\nNIPTviewer facilitates NIPT results interpretation and has been implemented as part of a NIPT analysis routine that was accredited by the national accreditation body for Sweden (Swedac).", "doi": "10.1186/s12920-025-02086-8", "pmid": "39833870", "labels": {"Clinical Genomics Uppsala": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11748546"}, {"db": "pii", "key": "10.1186/s12920-025-02086-8"}], "notes": [], "created": "2025-03-19T04:59:24.616Z", "modified": "2025-03-24T08:23:37.812Z"}, {"entity": "publication", "iuid": "1c57a97c200a453f883feb3a6b0e660d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c57a97c200a453f883feb3a6b0e660d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c57a97c200a453f883feb3a6b0e660d"}}, "title": "Numerous rRNA molecules form the apicomplexan mitoribosome via repurposed protein and RNA elements.", "authors": [{"family": "Shikha", "given": "Shikha", "initials": "S", "orcid": "0000-0002-7878-1463", "researcher": {"href": "https://publications.scilifelab.se/researcher/2de6231587194596b907dddf06be1b45.json"}}, {"family": "Tobiasson", "given": "Victor", "initials": "V", "orcid": "0000-0001-8920-017X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5208789057a94d0d9575476bf9c88d5a.json"}}, {"family": "Ferreira Silva", "given": "Mariana", "initials": "M"}, {"family": "Ovciarikova", "given": "Jana", "initials": "J"}, {"family": "Beraldi", "given": "Dario", "initials": "D", "orcid": "0000-0003-1504-5212", "researcher": {"href": "https://publications.scilifelab.se/researcher/2912e8a492a04a1aa8e3dab72e1ed37c.json"}}, {"family": "M\u00fchleip", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1877-2282", "researcher": {"href": "https://publications.scilifelab.se/researcher/921b5acb5b7c402fa06c8c148cbd5340.json"}}, {"family": "Sheiner", "given": "Lilach", "initials": "L", "orcid": "0000-0001-5909-2307", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e426f417f194a75ae9fbc76ea24040e.json"}}], "type": "journal article", "published": "2025-01-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "817", "issn-l": "2041-1723"}, "abstract": "Mitochondrial ribosomes (mitoribosomes) are essential, and their function of synthesising mitochondrial proteins is universal. The core of almost all mitoribosomes is formed from a small number of long and self-folding rRNA molecules. In contrast, the mitoribosome of the apicomplexan parasite Toxoplasma gondii assembles from over 50 extremely short rRNA molecules. Here, we use cryo-EM to discover the features that enable this unusual mitoribosome to perform its function. We reveal that poly-A tails added to rRNA molecules are integrated into the ribosome, and we demonstrate their essentiality for mitoribosome formation and for parasite survival. This is a distinct function for poly-A tails, which are otherwise known primarily as stabilisers of messenger RNAs. Furthermore, while ribosomes typically consist of unique rRNA sequences, here nine sequences are used twice, each copy integrated in a different mitoribosome domain, revealing one of the mechanisms enabling the extreme mitochondrial genome reduction characteristic to Apicomplexa and to a large group of related microbial eukaryotes. Finally, several transcription factor-like proteins are repurposed to compensate for reduced or lost critical ribosomal domains, including members of the ApiAP2 family thus far considered to be DNA-binding transcription factors.", "doi": "10.1038/s41467-025-56057-9", "pmid": "39827269", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11742926"}, {"db": "pii", "key": "10.1038/s41467-025-56057-9"}], "notes": [], "created": "2025-11-13T09:43:13.776Z", "modified": "2025-11-13T09:43:13.956Z"}, {"entity": "publication", "iuid": "0729e1b65266450092168ec789fee122", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0729e1b65266450092168ec789fee122.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0729e1b65266450092168ec789fee122"}}, "title": "Life-history adaptation under climate warming magnifies the agricultural footprint of a cosmopolitan insect pest.", "authors": [{"family": "Burc", "given": "Estelle", "initials": "E"}, {"family": "Girard-Tercieux", "given": "Camille", "initials": "C"}, {"family": "Metz", "given": "Moa", "initials": "M"}, {"family": "Cazaux", "given": "Elise", "initials": "E"}, {"family": "Baur", "given": "Julian", "initials": "J", "orcid": "0000-0002-4739-2756", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e69e394b67145188a77f90365f3fe15.json"}}, {"family": "Koppik", "given": "Mareike", "initials": "M"}, {"family": "R\u00eago", "given": "Alexandre", "initials": "A"}, {"family": "Hart", "given": "Alex F", "initials": "AF"}, {"family": "Berger", "given": "David", "initials": "D", "orcid": "0000-0003-0196-6109", "researcher": {"href": "https://publications.scilifelab.se/researcher/c788f99e9df4435587f7e991eae4311e.json"}}], "type": "journal article", "published": "2025-01-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "827", "issn-l": "2041-1723"}, "abstract": "Climate change is affecting population growth rates of ectothermic pests with potentially dire consequences for agriculture and global food security. However, current projection models of pest impact typically overlook the potential for rapid genetic adaptation, making current forecasts uncertain. Here, we predict how climate change adaptation in life-history traits of insect pests affects their growth rates and impact on agricultural yields by unifying thermodynamics with classic theory on resource acquisition and allocation trade-offs between foraging, reproduction, and maintenance. Our model predicts that warming temperatures will favour resource allocation towards maintenance coupled with increased resource acquisition through larval foraging, and the evolution of this life-history strategy results in both increased population growth rates and per capita host consumption, causing a double-blow on agricultural yields. We find support for these predictions by studying thermal adaptation in life-history traits and gene expression in the wide-spread insect pest, Callosobruchus maculatus; with 5 years of evolution under experimental warming causing an almost two-fold increase in its predicted agricultural footprint. These results show that pest adaptation can offset current projections of agricultural impact and emphasize the need for integrating a mechanistic understanding of life-history evolution into forecasts of pest impact under climate change.", "doi": "10.1038/s41467-025-56177-2", "pmid": "39827176", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11743133"}, {"db": "pii", "key": "10.1038/s41467-025-56177-2"}], "notes": [], "created": "2025-09-08T11:37:34.656Z", "modified": "2025-09-08T11:37:34.821Z"}, {"entity": "publication", "iuid": "a8e768d017534882926ec31cc6be13df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8e768d017534882926ec31cc6be13df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8e768d017534882926ec31cc6be13df"}}, "title": "From library to landscape: integrative annotation workflows for compound libraries in drug repurposing", "authors": [{"family": "Reinshagen", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-8080-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/8414f1d0ee0144c88a72beb83f38e21c.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Gadiya", "given": "Yojana", "initials": "Y", "orcid": "0000-0002-7683-0452", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda537ad863640fbbe1b3e85e05092bb.json"}}, {"family": "Gustavsson", "given": "Anna Lena", "initials": "AL"}, {"family": "Tanoli", "given": "Ziaurrehman", "initials": "Z", "orcid": "0000-0003-2435-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/313c5ea401cf4c178d088e587d9f288f.json"}}, {"family": "Aittokallio", "given": "Tero", "initials": "T", "orcid": "0000-0002-0886-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/47e0db692d16440ea6779948c188713a.json"}}, {"family": "Huchting", "given": "Johanna", "initials": "J"}, {"family": "Jenmalm-Jensen", "given": "Annika", "initials": "A"}, {"family": "Gribbon", "given": "Philip", "initials": "P"}, {"family": "Zaliani", "given": "Andrea", "initials": "A"}, {"family": "Ballante", "given": "Flavio", "initials": "F", "orcid": "0000-0002-4831-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/20429d2a46f4479a9c262875794a3a9d.json"}}], "type": "journal-article", "published": "2025-01-18", "journal": {"title": "Database (Oxford)", "issn": "1758-0463", "issn-l": "1758-0463", "volume": "2025", "issue": null, "pages": null}, "abstract": "In the rapidly advancing landscape of drug discovery and repurposing, efficient access and integration of chemical and bioactivity data from public repositories have become essential. To address this need, we developed two complementary annotation pipelines (KNIME- and Python-based) that automate the extraction and integration of curated chemical and bioactivity data from public repositories. These pipelines support any user-provided compound library, enabling reproducible workflows that integrate data from heterogeneous sources such as ChEMBL and PubChem. As part of the REMEDi4ALL project, with the aim of establishing a European platform for drug repurposing, we validated our framework using a harmonized subset of the Specs repurposing collection, which includes >5000 compounds available at the partner institutes. We also developed two interactive dashboards that support multilayered analyses and visualization by integrating chemical properties, bioactivity profiles, and relational data. Our results demonstrate that this framework streamlines the collection of harmonized data and facilitates analyses that are critical for drug repurposing efforts, while remaining versatile for broader applications in drug discovery. Moreover, the analysis of the annotations reveals that the Specs subset includes chemical scaffolds representative of a significant portion of approved drugs and compounds undergoing clinical evaluation, underscoring its potential as a rich source of drug repurposing candidates. Both pipeline protocols are publicly available online, and the dashboards are open access.", "doi": "10.1093/database/baaf081", "pmid": "41364066", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12687465"}, {"db": "pii", "key": "8374761"}], "notes": [], "created": "2026-03-17T12:54:07.801Z", "modified": "2026-03-17T13:00:51.224Z"}, {"entity": "publication", "iuid": "683be6a6a7cd4499a0b9a0d985a05de7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/683be6a6a7cd4499a0b9a0d985a05de7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/683be6a6a7cd4499a0b9a0d985a05de7"}}, "title": "Anti-correlation of LacI association and dissociation rates observed in living cells.", "authors": [{"family": "Kandavalli", "given": "Vinodh", "initials": "V", "orcid": "0000-0001-9093-156X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9d49615bb4748ebb37f589af26b5489.json"}}, {"family": "Zikrin", "given": "Spartak", "initials": "S", "orcid": "0000-0002-7802-8869", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a82f27ea7bf43deaded33d359270820.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.json"}}, {"family": "Jones", "given": "Daniel", "initials": "D", "orcid": "0000-0002-7902-996X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd395b3f8ea147a38d72f7ae3ad74b06.json"}}], "type": "journal article", "published": "2025-01-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "764", "issn-l": "2041-1723"}, "abstract": "The rate at which transcription factors (TFs) bind their cognate sites has long been assumed to be limited by diffusion, and thus independent of binding site sequence. Here, we systematically test this assumption using cell-to-cell variability in gene expression as a window into the in vivo association and dissociation kinetics of the model transcription factor LacI. Using a stochastic model of the relationship between gene expression variability and binding kinetics, we performed single-cell gene expression measurements to infer association and dissociation rates for a set of 35 different LacI binding sites. We found that both association and dissociation rates differed significantly between binding sites, and moreover observed a clear anticorrelation between these rates across varying binding site strengths. These results contradict the long-standing hypothesis that TF binding site strength is primarily dictated by the dissociation rate, but may confer the evolutionary advantage that TFs do not get stuck in near-operator sequences while searching.", "doi": "10.1038/s41467-025-56053-z", "pmid": "39824877", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11748676"}, {"db": "pii", "key": "10.1038/s41467-025-56053-z"}], "notes": [], "created": "2025-11-28T10:45:13.067Z", "modified": "2025-11-28T10:45:13.291Z"}, {"entity": "publication", "iuid": "443d7ad81eeb46d7a9973684b78752e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/443d7ad81eeb46d7a9973684b78752e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/443d7ad81eeb46d7a9973684b78752e3"}}, "title": "A two-wave survey study examining the impact of different sources of pregnancy information on pregnancy-related anxiety among Swedish women.", "authors": [{"family": "Geusens", "given": "Femke", "initials": "F"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}], "type": "journal article", "published": "2025-01-17", "journal": {"title": "Eur J Midwifery", "issn": "2585-2906", "volume": "9", "issn-l": null}, "abstract": "During pregnancy, women rely on a variety of sources to obtain information. However, not all of these sources are equally reliable, and there is the concern that especially online information-seeking may increase pregnancy-related anxiety. This study examines to what extent different sources of pregnancy information are associated with concurrent pregnancy-related anxiety (RQ1) and changes in pregnancy-related anxiety throughout the pregnancy (RQ2).\n\nThis study was integrated into the ongoing Swedish Mom2B study (sub-study data collection: December 2022-April 2024), where women complete weekly questionnaires via a research app. Each trimester, they received questions about their use of information sources and pregnancy-related anxiety.\n\nOur sample consisted of 751 pregnant women (273 with at least two waves of data). Using the midwife (\u03b2= -0.14, p<0.001; 95% CI: -3.32 - -1.13) or social circle (\u03b2= -0.08, p<0.05; 95% CI: -2.83 - -0.07) as a source of pregnancy-and childbirth-related information was associated with lower levels of pregnancy-related anxiety. In contrast, reliance on online sources for information was associated with higher levels of anxiety (\u03b2=0.14, p<0.001; 95% CI: 1.52-5.03). Except for (e-)books, which lowered the odds of improving anxiety (OR=0.62, p<0.01; 95% CI: 0.45-0.85), none of the information sources predicted changes in pregnancy-related anxiety over time.\n\nNot all information sources play an equal role in relation to pregnancy-related anxiety. Interpersonal sources in particular may help mitigate anxiety. However, future research with more nuanced methodologies and shorter measurement intervals could clarify possible causal relationships and refine our understanding of how various information sources affect pregnancy-related anxiety over time.", "doi": "10.18332/ejm/197169", "pmid": "39830436", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11739933"}, {"db": "pii", "key": "EJM-9-06"}], "notes": [], "created": "2025-11-28T10:54:13.800Z", "modified": "2025-11-28T10:54:13.817Z"}, {"entity": "publication", "iuid": "bdbfa9803d4f4b56abcf611c35836e4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdbfa9803d4f4b56abcf611c35836e4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdbfa9803d4f4b56abcf611c35836e4b"}}, "title": "A spatiotemporal atlas of human spermatogenesis", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Hikmet", "given": "Feria", "initials": "F"}, {"family": "M\u00e9ar", "given": "Loren", "initials": "L"}, {"family": "Gustavsson", "given": "Jonas", "initials": "J"}, {"family": "Miranda", "given": "Gisele", "initials": "G"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Schutten", "given": "Rutger", "initials": "R", "orcid": "0000-0001-8787-8868", "researcher": {"href": "https://publications.scilifelab.se/researcher/83314cf7a93543bf9cd6f68f9657e99e.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Stukenborg", "given": "Jan Bernd", "initials": "JB"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "posted-content", "published": "2025-01-17", "journal": {"title": "res sq", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.21203/rs.3.rs-5594800/v1", "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T12:59:38.185Z", "modified": "2025-12-22T07:55:55.559Z"}, {"entity": "publication", "iuid": "743d28f6b482437cbd6cb3100af43d83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/743d28f6b482437cbd6cb3100af43d83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/743d28f6b482437cbd6cb3100af43d83"}}, "title": "New insights into the N-glycomes of Dictyostelium species.", "authors": [{"family": "Hykollari", "given": "Alba", "initials": "A"}, {"family": "Malzl", "given": "Daniel", "initials": "D"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Eschenbach", "given": "Carina", "initials": "C"}, {"family": "Kiani\u010dkov\u00e1", "given": "Krist\u00edna", "initials": "K"}, {"family": "Wilson", "given": "Iain B H", "initials": "IBH"}, {"family": "Paschinger", "given": "Katharina", "initials": "K"}], "type": "journal article", "published": "2025-01-16", "journal": {"title": "BBA Adv", "issn": "2667-1603", "volume": "7", "pages": "100142", "issn-l": null}, "abstract": "Dictyostelia are cellular slime molds, a group of Amoebozoa, that form multicellular fruiting bodies out of aggregating cells able of differentiating into resistant spore forms. In previous studies on Dictyostelium discoideum, it was demonstrated that their N-glycans, as in most eukaryotes, derive from the Glc3Man9GlcNAc2-PP-Dol precursor; however, unique glyco-epitopes, including intersecting GlcNAc, core \u03b11,3-fucosylation, sulphation and methylphosphorylation, were detected. In the present study, we have examined the N-glycans of two other Dictyostelium species, D. purpureum, whose genome is also sequenced, and D. giganteum. The detailed glycomic analysis of their fruiting bodies was based on isomeric separation of the glycan structures by HPLC, followed by mass spectrometry in combination with enzymatic digests and chemical treatments. Two features absent from the 'model' dictyostelid D. discoideum were found: especially in D. purpureum, a long linear galactose arm \u03b21,4-linked to the \u03b21,4-N-acetylglucosamine on the 'lower' A-branch of its oligo-mannosylated structures could be identified. In contrast, neutral N-glycans with multiple fucose residues attached to terminal mannoses were found in D. giganteum. All three species have common modifications on their anionic N-glycans: while (methyl)phosphorylated residues are always associated with terminal mannose residues, the sulphation position differs. While D. discoideum has 6-sulphation of subterminal mannose residues, D. giganteum and D. purpureum may rather have 2-sulphation of core \u03b11,6-mannose. Overall, we have discovered species-specific glycan variations and our data will contribute to future comparative and functional studies on these three species within the same genus.", "doi": "10.1016/j.bbadva.2025.100142", "pmid": "39911813", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11795075"}, {"db": "pii", "key": "S2667-1603(25)00005-5"}], "notes": [], "created": "2025-11-20T18:09:49.952Z", "modified": "2025-11-20T18:35:22.601Z"}, {"entity": "publication", "iuid": "0fbeef5aada44fa29aa458238f0272a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fbeef5aada44fa29aa458238f0272a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fbeef5aada44fa29aa458238f0272a3"}}, "title": "A thermoplastic chip for 2D and 3D correlative assays combining screening and high-resolution imaging of immune cell responses.", "authors": [{"family": "van Ooijen", "given": "Hanna", "initials": "H"}, {"family": "Verron", "given": "Quentin", "initials": "Q", "orcid": "0000-0001-5800-4379", "researcher": {"href": "https://publications.scilifelab.se/researcher/a961009c75cf42499996cfd89e7c46e5.json"}}, {"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "Sandoz", "given": "Patrick A", "initials": "PA", "orcid": "0000-0002-8379-7267", "researcher": {"href": "https://publications.scilifelab.se/researcher/acd737132e4b4b378257ae8f0316b3a2.json"}}, {"family": "Frisk", "given": "Thomas W", "initials": "TW", "orcid": "0000-0002-3996-9279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8a1aeeab11e4180afd6551faf16ab9f.json"}}, {"family": "Carannante", "given": "Valentina", "initials": "V"}, {"family": "Olofsson", "given": "Karl", "initials": "K"}, {"family": "Wagner", "given": "Arnika K", "initials": "AK", "orcid": "0000-0002-0339-8259", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dd10981a93a490b940ca41d2bde96a3.json"}}, {"family": "Sandstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "\u00d6nfelt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5178-7593", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bcdcf94cab40ff92319869d243f5d8.json"}}], "type": "journal article", "published": "2025-01-16", "journal": {"title": "Cell Reports Methods", "issn": "2667-2375", "pages": "100965", "issn-l": null}, "abstract": "We present an easy-to-use, disposable, thermoplastic microwell chip designed to support screening and high-resolution imaging of single-cell behavior in two- and three-dimensional (2D and 3D) cell cultures. We show that the chip has excellent optical properties and provide simple protocols for efficient long-term cell culture of suspension and adherent cells, the latter grown either as monolayers or as hundreds of single, uniformly sized spheroids. We then demonstrate the applicability of the system for single-cell analysis by correlating the dynamic cytotoxic response of single immune cells grown under different metabolic conditions to their intracellular cytolytic load at the end of the assay. Additionally, we illustrate highly multiplex cytotoxicity screening of tumor spheroids in the chip, comparing the effect of environment cues characteristic of the tumor microenvironment on natural killer (NK)-cell-induced killing. Following the functional screening, we perform high-resolution 3D immunofluorescent imaging of infiltrating NK cells within the spheroid volumes.", "doi": "10.1016/j.crmeth.2025.100965", "pmid": "39826552", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "S2667-2375(25)00001-3"}], "notes": [], "created": "2025-01-23T11:28:33.594Z", "modified": "2025-04-07T07:24:00.541Z"}, {"entity": "publication", "iuid": "4db366ede54745dea666acec483fc00d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4db366ede54745dea666acec483fc00d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4db366ede54745dea666acec483fc00d"}}, "title": "Liquid crystal nanoparticles for oral combination antibiotic therapies: A strategy towards protecting commensal gut bacteria during treatment.", "authors": [{"family": "He", "given": "Xiguo", "initials": "X"}, {"family": "Karlsson", "given": "Philip A", "initials": "PA"}, {"family": "Xiong", "given": "Ruisheng", "initials": "R"}, {"family": "Moodie", "given": "Lindon W K", "initials": "LWK"}, {"family": "Wang", "given": "Helen", "initials": "H"}, {"family": "Bergstr\u00f6m", "given": "Christel A S", "initials": "CAS"}, {"family": "Hubert", "given": "Madlen", "initials": "M"}], "type": "journal article", "published": "2025-01-15", "journal": {"title": "Journal of Colloid and Interface Science", "issn": "1095-7103", "volume": "678", "issue": "Pt B", "pages": "287-300", "issn-l": "0021-9797"}, "abstract": "Antibiotics are essential for treating infections and reducing risks during medical interventions. However, many commonly used antibiotics lack the physiochemical properties for an efficient oral administration when treating systemic infection. Instead, we are reliant on intravenous delivery, which presents complications outside of clinical settings. Developing novel formulations for oral administration is a potential solution to this problem. We engineered hexosome and cubosome liquid crystal nanoparticles (LCNPs) characterized by small-angle X-ray scattering and cryogenic transmission electron microscopy, and could encapsulate the antibiotics vancomycin (VAN) and clarithromycin (CLA) with high loading efficiencies. By rationally choosing stable lipid building blocks, the loaded LCNPs demonstrated excellent resilience against enzymatic degradation in an in vitro gut model LCNP stability is crucial as premature antibiotic leakage can negatively impact the gut microbiota. In screens against the representative gut bacteria Enterococcus faecalis and Escherichia coli, our LCNPs provided a protective effect. Furthermore, we explored co-administration and dual loading strategies of VAN and CLA, and demonstrated effective loading, stability and protection for E. faecalis and E. coli. This work represents a proof of concept for the early-stage development of antibiotic-loaded LCNPs to treat systemic infection via oral administration, opening opportunities for combination antibiotic therapies.", "doi": "10.1016/j.jcis.2024.08.230", "pmid": "39245019", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9797(24)02013-7"}], "notes": [], "created": "2025-10-29T14:11:39.986Z", "modified": "2025-11-03T12:18:11.010Z"}, {"entity": "publication", "iuid": "4a3f70d7e71249f296fedd39d16f9a47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a3f70d7e71249f296fedd39d16f9a47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a3f70d7e71249f296fedd39d16f9a47"}}, "title": "Influence of TEMPO on preparation of softwood nanofibrils and their hydrogel network properties.", "authors": [{"family": "Ba\u015f", "given": "Ya\u011fmur", "initials": "Y"}, {"family": "Berglund", "given": "Linn", "initials": "L"}, {"family": "Stevanic", "given": "Jasna S", "initials": "JS"}, {"family": "Scheepers", "given": "Gerhard", "initials": "G"}, {"family": "Niittyl\u00e4", "given": "Totte", "initials": "T"}, {"family": "Oksman", "given": "Kristiina", "initials": "K"}], "type": "journal article", "published": "2025-01-15", "journal": {"title": "Carbohydr Polym", "issn": "1879-1344", "volume": "348", "issue": "Pt A", "pages": "122812", "issn-l": "0144-8617"}, "abstract": "From an economic and environmental perspective, the use of less chemicals in the production of cellulose nanofibrils (CNFs) is advantageous. In this study, we investigated the oxidation (TEMPO/NaClO2/NaClO, pH 6.8) of softwood (SW) particles with varying amounts of TEMPO (16, 8 or 0 mg g-1 of wood). Following, TEMPO-oxidized SW nanofibrils (TO-SWNFs) were obtained by nanofibrillation and their size, morphology, and crystallite size were assessed. Hydrogel networks of TO-SWNFs were prepared and mechanical properties were measured in dH2O and phosphate buffered saline (PBS) to compare their performance for possible biomedical applications such as wound dressings. The results reveal that the presence of TEMPO is of importance for TO-SWNF network properties, presenting higher eq. H2O absorption (\u22482500 %) and elongation at break (\u224810 %) with good wet strength (\u2248180 kPa). In addition, a decrease in use of TEMPO catalyst from 16 to 8 mg g-1 of wood is possible, without detrimental effects on hydrogel network properties (dH2O absorption \u2248 2000 %, elongation at break \u2248 13 %, wet strength \u2248 190 kPa) related to applications as wound dressings.", "doi": "10.1016/j.carbpol.2024.122812", "pmid": "39562087", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S0144-8617(24)01038-5"}], "notes": [], "created": "2025-11-18T12:06:42.065Z", "modified": "2025-11-18T12:06:42.111Z"}, {"entity": "publication", "iuid": "c0a170cb5ae3408e91a64005c2b3d9d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0a170cb5ae3408e91a64005c2b3d9d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0a170cb5ae3408e91a64005c2b3d9d8"}}, "title": "The Progression of Mycosis Fungoides During Treatment with Mogamulizumab: A BIO-MUSE Case Study of the Tumor and Immune Response in Peripheral Blood and Tissue.", "authors": [{"family": "Johansson", "given": "Angelica", "initials": "A"}, {"family": "Kalliara", "given": "Eirini", "initials": "E", "orcid": "0000-0001-8772-0729", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3f612ec081c41ddac4197c048de1174.json"}}, {"family": "Belfrage", "given": "Emma", "initials": "E", "orcid": "0000-0003-1717-0842", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0653ff766f14999a063d7e22699dbcb.json"}}, {"family": "Alling", "given": "Teodor", "initials": "T", "orcid": "0000-0003-1680-5666", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc40366f546d4f338859e606b4c81525.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69051a0275c442c8c0d5621b4000929.json"}}, {"family": "Gerdtsson", "given": "Anna Sandstr\u00f6m", "initials": "AS", "orcid": "0000-0003-1932-0365", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2092b7829e2419f97169f5201219c47.json"}}, {"family": "Gullberg", "given": "Urban", "initials": "U"}, {"family": "Porwit", "given": "Anna", "initials": "A"}, {"family": "Drott", "given": "Kristina", "initials": "K", "orcid": "0000-0002-9350-7016", "researcher": {"href": "https://publications.scilifelab.se/researcher/b05dfcaa99634010ac68cd37e1067a45.json"}}, {"family": "Ek", "given": "Sara", "initials": "S", "orcid": "0000-0002-1388-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/56861b5f5cac4b23ab86b19b4650aa3d.json"}}], "type": "journal article", "published": "2025-01-14", "journal": {"title": "Biomedicines", "issn": "2227-9059", "issn-l": null, "volume": "13", "issue": "1", "pages": null}, "abstract": "Background/objectives: Mycosis fungoides (MF) is a rare malignancy, with an indolent course in the early stages of the disease. However, due to major molecular and clinical heterogeneity, patients at an advanced stage of the disease have variable responses to treatment and considerably reduced life expectancy. Today, there is a lack of specific markers for the progression from early to advanced stages of the disease. To address these challenges, the non-interventional BIO-MUSE trial was initiated. Here, we report on a case study involving one patient, where combined omics analysis of tissue and blood was used to reveal the unique molecular features associated with the progression of the disease. Methods: We applied 10\u00d7 genomics-based single-cell RNA sequencing to CD3+ peripheral T-cells, combined with T-cell receptor sequencing, to samples collected at multiple timepoints during the progression of the disease. In addition, GeoMx-based digital spatial profiling of T-helper (CD3+/CD8-), T-cytotoxic (CD3+/CD8+), and CD163+ cells was performed on skin biopsies. Results. The results pinpoint targets, such as transforming growth factor \u03b21, as some of the mechanisms underlying disease progression, which may have the potential to improve patient prognostication and the development of precision medicine efforts. Conclusions: We propose that in patients with MF, the evolution of the malignant clone and the associated immune response need to be studied jointly to define relevant strategies for intervention.", "doi": "10.3390/biomedicines13010186", "pmid": "39857770", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11761615"}, {"db": "pii", "key": "biomedicines13010186"}], "notes": [], "created": "2025-02-17T09:14:22.991Z", "modified": "2025-11-10T14:09:46.472Z"}, {"entity": "publication", "iuid": "ed287063ad0847889af6e47af4f02168", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed287063ad0847889af6e47af4f02168.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed287063ad0847889af6e47af4f02168"}}, "title": "An activin receptor-like kinase 1-governed monocytic lineage shapes an immunosuppressive landscape in breast cancer metastases.", "authors": [{"family": "Safaee Talkhoncheh", "given": "Mehrnaz", "initials": "M"}, {"family": "Sj\u00f6lund", "given": "Jonas", "initials": "J"}, {"family": "Bolivar", "given": "Paulina", "initials": "P"}, {"family": "Kurzejamska", "given": "Ewa", "initials": "E"}, {"family": "Cordero", "given": "Eugenia", "initials": "E"}, {"family": "Vall\u00e8s Pag\u00e8s", "given": "Teia", "initials": "T"}, {"family": "Larsson", "given": "Sara", "initials": "S"}, {"family": "Lehn", "given": "Sophie", "initials": "S"}, {"family": "Frimannsson", "given": "Gustav", "initials": "G"}, {"family": "Ingesson", "given": "Viktor", "initials": "V"}, {"family": "Braun", "given": "Sebastian", "initials": "S"}, {"family": "Pantaleo", "given": "Jessica", "initials": "J"}, {"family": "Oudenaarden", "given": "Clara", "initials": "C"}, {"family": "Lauss", "given": "Martin", "initials": "M"}, {"family": "Pearsall", "given": "R Scott", "initials": "RS"}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Rolny", "given": "Charlotte", "initials": "C"}, {"family": "Bocci", "given": "Matteo", "initials": "M"}, {"family": "Pietras", "given": "Kristian", "initials": "K"}], "type": "journal article", "published": "2025-01-14", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "135", "issue": "5", "issn-l": "0021-9738"}, "abstract": "The biology centered around the TGF-\u03b2 type I receptor activin receptor-like kinase (ALK) 1 (encoded by ACVRL1) has been almost exclusively based on its reported endothelial expression pattern since its first functional characterization more than 2 decades ago. Here, in efforts to better define the therapeutic context in which to use ALK1 inhibitors, we uncover a population of tumor-associated macrophages (TAMs) that, by virtue of their unanticipated Acvrl1 expression, are effector targets for adjuvant antiangiogenic immunotherapy in mouse models of metastatic breast cancer. The combinatorial benefit depended on ALK1-mediated modulation of the differentiation potential of bone marrow-derived granulocyte-macrophage progenitors, the release of CD14+ monocytes into circulation, and their eventual extravasation. Notably, ACVRL1+ TAMs coincided with an immunosuppressive phenotype and were overrepresented in human cancers progressing on therapy. Accordingly, breast cancer patients with a prominent ACVRL1hi TAM signature exhibited a significantly shorter survival. In conclusion, we shed light on an unexpected multimodal regulation of tumorigenic phenotypes by ALK1 and demonstrate its utility as a target for antiangiogenic immunotherapy.", "doi": "10.1172/JCI183086", "pmid": "39808498", "labels": {"Clinical Genomics Lund": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11870737"}, {"db": "pii", "key": "183086"}], "notes": [], "created": "2025-11-10T14:22:12.628Z", "modified": "2025-11-28T10:52:14.448Z"}, {"entity": "publication", "iuid": "2d986718e5874eb7957b646b4e881227", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d986718e5874eb7957b646b4e881227.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d986718e5874eb7957b646b4e881227"}}, "title": "Low impact of Zostera marina meadows on sediment and water microbiota under brackish conditions.", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Delgado", "given": "Luis F", "initials": "LF"}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fern\u00e1ndez-Ju\u00e1rez", "given": "V\u00edctor", "initials": "V"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Pansch", "given": "Christian", "initials": "C"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}, {"family": "Bengtsson", "given": "Mia M", "initials": "MM"}, {"family": "Gyrait\u0117", "given": "Greta", "initials": "G"}, {"family": "Katar\u017eyt\u0117", "given": "Marija", "initials": "M"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Martin", "given": "Georg", "initials": "G"}, {"family": "Piwosz", "given": "Kasia", "initials": "K"}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}], "type": "journal article", "published": "2025-01-11", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "20", "issue": "1", "pages": "2", "issn-l": null}, "abstract": "Zostera marina is an important ecosystem engineer influencing shallow water environments and possibly shaping the microbiota in surrounding sediments and water. Z. marina is typically found in marine systems, but it can also proliferate under brackish conditions. Changes in salinity generally have a strong impact on the biota, especially at the salty divide between salinity 6 and 9. To better understand the impact of the salty divide on the interaction between Z. marina and the surrounding sediment and water microbiota, we investigated the effects of Z. marina meadows on the surrounding microbiota across a salinity range of 6-15 in the Baltic Sea during the summer using 16S and 18S rRNA gene amplicon sequencing.\n\nSalinity was the most important factor for structuring the microbiota within both water and sediment. The presence of Z. marina affected the composition of the bacterial and eukaryotic community and bacterial alpha diversity in the sediment. However, this effect was confined to alpha-mesohaline conditions (salinity 9-15). The impact of Z. marina below salinity 9 on water and sediment microbiota was insignificant.\n\nIncreasing salinity was associated with a longer leaf length of Z. marina, causing an increased canopy height, which affects the sediment microbiota through reduced water velocity. Hence, we propose that the canopy effect may be the major predictor explaining Z. marina's interactions with the surrounding microbiota at salinity 9-15. These findings emphasize the importance of the physical effects of Z. marina meadow ecosystem services and have important implications for Z. marina management under brackish conditions in a changing climate.", "doi": "10.1186/s40793-024-00662-6", "pmid": "39799374", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11724437"}, {"db": "pii", "key": "10.1186/s40793-024-00662-6"}], "notes": [], "created": "2025-11-21T13:50:12.826Z", "modified": "2025-11-21T13:50:12.830Z"}, {"entity": "publication", "iuid": "ff3859bb07664273873b0c450fa280cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff3859bb07664273873b0c450fa280cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff3859bb07664273873b0c450fa280cc"}}, "title": "A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei.", "authors": [{"family": "Jonsdottir", "given": "Thorey K", "initials": "TK", "orcid": "0000-0002-0618-4731", "researcher": {"href": "https://publications.scilifelab.se/researcher/43607032b6e9486889f0c34a4e0437f6.json"}}, {"family": "Paoletta", "given": "Martina S", "initials": "MS", "orcid": "0000-0001-7318-489X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f221d2972a8945b4b0d49bfa602c64a0.json"}}, {"family": "Ishizaki", "given": "Takahiro", "initials": "T", "orcid": "0000-0002-4677-5608", "researcher": {"href": "https://publications.scilifelab.se/researcher/adcbcb52e9ba4744a10527038143d759.json"}}, {"family": "Hernandez", "given": "Sophia", "initials": "S", "orcid": "0000-0002-7851-5501", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae5365af3a2f43548e1a2c72bf341e79.json"}}, {"family": "Ivanova", "given": "Maria", "initials": "M", "orcid": "0000-0003-1063-3576", "researcher": {"href": "https://publications.scilifelab.se/researcher/f179f259deb24b3a9dc6d8329cc42ee5.json"}}, {"family": "Herrera Curbelo", "given": "Alicia", "initials": "A"}, {"family": "Saiki", "given": "Paulina A", "initials": "PA"}, {"family": "Selinger", "given": "Martin", "initials": "M", "orcid": "0000-0002-5420-9702", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc68cdd8b8d748499e552a6e700d7e55.json"}}, {"family": "Das", "given": "Debojyoti", "initials": "D", "orcid": "0000-0001-6811-3333", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c763bab024a492d8e534a1e541c21dc.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Bushell", "given": "Ellen S C", "initials": "ESC", "orcid": "0000-0003-2863-4112", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6d25e8481034aaaafb7453ab00af664.json"}}], "type": "journal article", "published": "2025-01-11", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "53", "issue": "2", "pages": null}, "abstract": "Many Plasmodium genes remain uncharacterized due to low genetic tractability. Previous large-scale knockout screens have only been able to target about half of the genome in the more genetically tractable rodent malaria parasite Plasmodium berghei. To overcome this limitation, we have developed a scalable CRISPR system called P. berghei high-throughput (PbHiT), which uses a single cloning step to generate targeting vectors with 100-bp homology arms physically linked to a guide RNA (gRNA) that effectively integrate into the target locus. We show that PbHiT coupled with gRNA sequencing robustly recapitulates known knockout mutant phenotypes in pooled transfections. Furthermore, we provide an online resource of knockout and tagging designs to target the entire P. berghei genome and scale-up vector production using a pooled ligation approach. This work presents for the first time a tool for high-throughput CRISPR screens in Plasmodium for studying the parasite's biology at scale.", "doi": "10.1093/nar/gkaf005", "pmid": "39844455", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11754126"}, {"db": "pii", "key": "7973899"}], "notes": [], "created": "2025-11-19T10:27:39.428Z", "modified": "2025-11-24T10:10:45.104Z"}, {"entity": "publication", "iuid": "50660d74b49b4131a8622208135d9542", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50660d74b49b4131a8622208135d9542.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50660d74b49b4131a8622208135d9542"}}, "title": "Effects of compost amendments and experimental drought on grassland soil microbial communities.", "authors": [{"family": "Guasconi", "given": "Daniela", "initials": "D", "orcid": "0000-0003-3739-0877", "researcher": {"href": "https://publications.scilifelab.se/researcher/1393c3be58a14d8b89434d38994fbef4.json"}}, {"family": "Hugelius", "given": "Gustaf", "initials": "G"}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE"}, {"family": "Cousins", "given": "Sara A O", "initials": "SAO"}, {"family": "Juhanson", "given": "Jaanis", "initials": "J"}, {"family": "Manzoni", "given": "Stefano", "initials": "S"}, {"family": "Roth", "given": "Nina", "initials": "N"}, {"family": "Fransson", "given": "Petra", "initials": "P"}], "type": "journal article", "published": "2025-01-10", "journal": {"title": "FEMS Microbiol. Lett.", "issn": "1574-6968", "volume": "372", "issn-l": "0378-1097"}, "abstract": "Prolonged drought is a major stressor for grassland ecosystems. In addition to decreasing plant productivity, it can affect soil microbial activities and thus destabilize nutrient cycling and carbon (C) sequestration. Soil organic amendments (OAs), such as compost, can be used to enhance soil fertility and mitigate drought effects. In this study, we evaluated the responses of fungal and bacterial communities to a 3-year-long experimental drought and compost treatment across four soil depths in two Swedish grasslands and at an upper and a lower topographic position. Results showed that while drought reduced soil moisture and compost amendment increased C content in the topsoil, the effects on microbial abundance and community composition within this time frame were weak, and detectable only in the topsoil. Fungal abundance increased with compost addition, which also affected community composition, while fungal communities were resistant to drought. Bacterial communities were not significantly affected by any of the treatments. This suggests that microbial ecosystem functions were resistant to the experimentally reduced precipitation. Overall, variation between sampling sites was more important for microbial community composition than treatments, highlighting the need for a better understanding of small-spatial-scale environmental controls on soil microbial and plant communities and their ecosystem functions.", "doi": "10.1093/femsle/fnaf108", "pmid": "41051250", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12527337"}, {"db": "pii", "key": "8275753"}], "notes": [], "created": "2025-11-04T10:54:01.939Z", "modified": "2025-11-28T10:49:00.649Z"}, {"entity": "publication", "iuid": "bc0935a69afd4244a818a5f794c2d7e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc0935a69afd4244a818a5f794c2d7e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc0935a69afd4244a818a5f794c2d7e7"}}, "title": "Bacteroidales T6SS minor Hcp subunits form heteromers recognising effectors", "authors": [{"family": "San-Miguel", "given": "Sergio G", "initials": "SG"}, {"family": "Al-Ammari", "given": "Manal Kamal Saleh", "initials": "MKS"}, {"family": "Johansson", "given": "Emma", "initials": "E"}, {"family": "Kowalska", "given": "Anna", "initials": "A"}, {"family": "Sauer", "given": "Uwe", "initials": "U", "orcid": "0000-0002-3420-439X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d011e944ae54d47aed374d548007812.json"}}, {"family": "Batista", "given": "Paulo Ricardo", "initials": "PR"}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Uhlin", "given": "Bernt Eric", "initials": "BE", "orcid": "0000-0002-2991-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/9faa19d33fd84728bb6df987ba16475f.json"}}, {"family": "Cisneros", "given": "David A", "initials": "DA", "orcid": "0000-0001-9919-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/19f7a4aba7af436899b5d63f95f0dcda.json"}}], "type": "posted-content", "published": "2025-01-10", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.01.09.632221", "pmid": null, "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-17T11:25:11.604Z", "modified": "2025-12-18T19:23:20.382Z"}, {"entity": "publication", "iuid": "c575b869292647788dd14aecde31fc5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c575b869292647788dd14aecde31fc5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c575b869292647788dd14aecde31fc5f"}}, "title": "Bacterial community responses to micropollutants in chemically stressed small rivers in Kenya using environmental DNA.", "authors": [{"family": "Verb\u00fccheln", "given": "Nicolai", "initials": "N", "orcid": "0009-0003-7017-9413", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd94f69e78414b1697902ed955a458d9.json"}}, {"family": "Schaufelberger", "given": "Sonja", "initials": "S"}, {"family": "Cardis", "given": "Tibaud", "initials": "T"}, {"family": "Tanui", "given": "Isaac C", "initials": "IC"}, {"family": "Kandie", "given": "Faith", "initials": "F"}, {"family": "Brack", "given": "Werner", "initials": "W"}, {"family": "Backhaus", "given": "Thomas", "initials": "T"}, {"family": "Inostroza", "given": "Pedro A", "initials": "PA", "orcid": "0000-0001-7399-8308", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cea8a42ffc2454d86f5f829b5dd7eff.json"}}], "type": "journal article", "published": "2025-01-10", "journal": {"title": "FEMS Microbiol. Lett.", "issn": "1574-6968", "volume": "372", "issn-l": "0378-1097"}, "abstract": "The responses of bacterial communities to changing environmental conditions are manifold but can include structural as well as functional alterations depending on the environmental stressors and toxic chemicals they are exposed to (e.g. pharmaceuticals, personal care products, pesticides, and industrial chemicals). In this study, environmental DNA was extracted from surface water samples collected from four small rivers in the Lake Victoria South Basin (Western Kenya) to (i) evaluate whether alpha- and beta-diversity change in dependency of land-use types, (ii) identify the environmental variables that explain alterations in community structure, (iii) qualitatively and quantitatively assess the consequences of antimicrobial stress on bacterial communities, and (iv) evaluate bacterial functional changes related to the degradation of organic chemicals. Our findings suggest that bacterial community composition is a more sensitive indicator to reflect the impact of chemical pollution derived from different types of land use compared to alpha-diversity. Nutrients and stress from chemical pollution were the variables explaining the dissimilarities between bacterial communities in small, forested, urbanised, and agricultural rivers. Furthermore, an assessment of potential ecological functions associated with the biodegradation of toxic chemicals unveiled a season-specific decline in bacterial degradation potential in all four rivers.", "doi": "10.1093/femsle/fnaf113", "pmid": "41100179", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12598650"}, {"db": "pii", "key": "8287733"}], "notes": [], "created": "2025-11-28T10:49:05.709Z", "modified": "2025-11-28T10:49:05.762Z"}, {"entity": "publication", "iuid": "6c276021592e42bf829461a46e283293", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c276021592e42bf829461a46e283293.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c276021592e42bf829461a46e283293"}}, "title": "Airway MMP-12 and DNA methylation in COPD: an integrative approach.", "authors": [{"family": "Eriksson Str\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Kebede Merid", "given": "Simon", "initials": "S"}, {"family": "Linder", "given": "Robert", "initials": "R"}, {"family": "Pourazar", "given": "Jamshid", "initials": "J"}, {"family": "Lindberg", "given": "Anne", "initials": "A"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Behndig", "given": "Annelie F", "initials": "AF"}], "type": "journal article", "published": "2025-01-10", "journal": {"title": "Respir. Res.", "issn": "1465-993X", "volume": "26", "issue": "1", "pages": "10", "issn-l": "1465-9921"}, "abstract": "In COPD, the balance between matrix metalloproteinases (MMPs) and their natural inhibitors [tissue inhibitors of metalloproteinases (TIMPs)] is shifted towards excessive degradation, reflected in bronchoalveolar lavage (BAL) as increased MMP concentrations. Because of their critical role in lung homeostasis, MMP activity is tightly regulated, but to what extent this regulation occurs through epigenetic mechanisms remains unknown.\n\nTo explore the interplay between MMPs, TIMPs, and DNA methylation (DNAm) we (1) analysed MMP-9, -12, and TIMP-1 concentrations in BAL fluid, and profiled DNAm in BAL cells from 18 COPD and 30 control subjects, (2) estimated protein-COPD relationships using multivariable regression, (3) identified protein quantitative trait methylation loci (pQTMs) with COPD as a potential modifier in a separate interaction model, and (4) integrated significant interactions with a previous COPD GWAS meta-analysis.\n\nCOPD was associated with higher levels of BAL MMP-12 (p = 0.016) but not with MMP-9 or TIMP-1. Further examination of MMP-12 identified association with DNAm at 34 loci (pQTMs), with TGFBR2 (p = 2.25 \u00d7 10-10) and THBS4 (p = 1.11 \u00d7 10-9) among the top ten pQTM genes. The interaction model identified 66 sites where the DNAm-MMP-12 association was significantly different in COPD compared to controls. Of these, one was colocalized with SNPs previously associated with COPD.\n\nOur findings indicate that airway MMP-12 may partially be regulated by epigenetic mechanisms and that this regulation is disrupted in COPD. Furthermore, integration with COPD GWAS data suggests that this dysregulation is influenced by a combination of environmental factors, disease processes, and genetics, with the latter potentially playing a lesser role.", "doi": "10.1186/s12931-024-03088-3", "pmid": "39794761", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11724436"}, {"db": "pii", "key": "10.1186/s12931-024-03088-3"}], "notes": [], "created": "2025-09-08T11:34:14.781Z", "modified": "2025-09-08T11:34:14.809Z"}, {"entity": "publication", "iuid": "d88276ac569d4cd0bd561502c908ae43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d88276ac569d4cd0bd561502c908ae43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d88276ac569d4cd0bd561502c908ae43"}}, "title": "Impact of Linker Composition on VHL PROTAC Cell Permeability.", "authors": [{"family": "Abeje", "given": "Yordanos Esubalew", "initials": "YE"}, {"family": "Wieske", "given": "Lianne H E", "initials": "LHE", "orcid": "0000-0003-4617-7605", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ee9a8547a194235a4d32170996b53e9.json"}}, {"family": "Poongavanam", "given": "Vasanthanathan", "initials": "V", "orcid": "0000-0002-8880-9247", "researcher": {"href": "https://publications.scilifelab.se/researcher/d037f230665c490dada0a50ecc8c106f.json"}}, {"family": "Maassen", "given": "Stefanie", "initials": "S"}, {"family": "Atilaw", "given": "Yoseph", "initials": "Y"}, {"family": "Cromm", "given": "Philipp", "initials": "P"}, {"family": "Lehmann", "given": "Lutz", "initials": "L"}, {"family": "Erdelyi", "given": "Mate", "initials": "M", "orcid": "0000-0003-0359-5970", "researcher": {"href": "https://publications.scilifelab.se/researcher/f772b571449e417ca6fda2eee361a0c3.json"}}, {"family": "Meibom", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4978-9842", "researcher": {"href": "https://publications.scilifelab.se/researcher/3034131b5fc94a24b8ab1a350205d960.json"}}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9805d4f39cc48f79a6e6ba076917021.json"}}], "type": "journal article", "published": "2025-01-09", "journal": {"title": "J. Med. Chem.", "issn": "1520-4804", "volume": "68", "issue": "1", "pages": "638-657", "issn-l": "0022-2623"}, "abstract": "The discovery of cell permeable and orally bioavailable von Hippel-Lindau (VHL) proteolysis targeting chimeras (PROTACs) is challenging as their structures locates them at, or beyond, the outer limits of oral druggable space. We have designed a set of nine VHL PROTACs and found that the linker had a profound impact on passive cell permeability. Determination of the solution ensembles in a nonpolar solvent revealed that high permeability was correlated to the ability of the PROTACs to adopt folded conformations that have a low solvent accessible 3D polar surface area. Our results suggest that the design of cell permeable VHL PROTACs could focus on linkers that facilitate shielding of polar surface area in the VHL ligand in a nonpolar but not in a polar environment. In addition, we found that not only intramolecular hydrogen bonds, but also NH-\u03c0 and \u03c0-\u03c0 interactions contribute to the stabilization of low-polarity conformations, and thereby to high cell permeability.", "doi": "10.1021/acs.jmedchem.4c02492", "pmid": "39693386", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11726670"}], "notes": [], "created": "2025-11-27T08:14:24.112Z", "modified": "2025-11-27T08:14:24.481Z"}, {"entity": "publication", "iuid": "fd23b37917bf4c6f8b0bb095abb3235d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd23b37917bf4c6f8b0bb095abb3235d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd23b37917bf4c6f8b0bb095abb3235d"}}, "title": "The type of environment has a greater impact on the larval microbiota of Anopheles arabiensis than on the microbiota of their breeding water.", "authors": [{"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Nilsson", "given": "Louise K J", "initials": "LKJ"}, {"family": "Brunius", "given": "Carl", "initials": "C", "orcid": "0000-0003-3957-870X", "researcher": {"href": "https://publications.scilifelab.se/researcher/560a5d14ee83421680058b00df2ac9e2.json"}}, {"family": "Feltelius", "given": "Vilhelm", "initials": "V"}, {"family": "Elleby", "given": "Rasmus", "initials": "R"}, {"family": "Hopkins", "given": "Richard J", "initials": "RJ"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2025-01-07", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "101", "issue": "1", "issn-l": "0168-6496"}, "abstract": "Mosquito larvae of the genus Anopheles develop entirely in water, frequently visiting the surface for air. The aquatic environment plays a key role in shaping their microbiota, but the connection between environmental characteristics of breeding sites and larval microbiota remains underexplored. This study focuses on Anopheles arabiensis, which inhabits the surface microlayer (SML) of breeding sites, a zone with high particle density. We hypothesized that the SML could allow us to capture the diversity of the surrounding environment, and in turn its influence on the larval microbial communities. To test this, we collected A. arabiensis larvae and SML samples from various breeding sites categorized by environmental features. Our results confirm that breeding site characteristics are significant drivers of the bacterial species present in mosquito larvae. Additionally, we found that the larval micro-environment selectively shapes its microbiota, highlighting a dynamic interplay between environmental and internal factors. Interestingly, specific bacterial families were associated with the presence or absence of larvae in breeding sites, suggesting potential ecological roles. These findings expand our understanding of vector-mosquito microbiota, emphasizing the importance of breeding site features in shaping larval microbial communities and providing a foundation for future research on mosquito ecology and control strategies.", "doi": "10.1093/femsec/fiae161", "pmid": "39694819", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11737318"}, {"db": "pii", "key": "7928135"}], "notes": [], "created": "2025-09-08T11:37:32.415Z", "modified": "2025-09-08T11:37:32.533Z"}, {"entity": "publication", "iuid": "c00a60f65c6949b7ae95fbd1ea808a22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c00a60f65c6949b7ae95fbd1ea808a22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c00a60f65c6949b7ae95fbd1ea808a22"}}, "title": "Pervasive horizontal transmission of Wolbachia in natural populations of closely related and widespread tropical skipper butterflies.", "authors": [{"family": "Ribeiro", "given": "Pedro", "initials": "P"}, {"family": "Butenko", "given": "Anzhelika", "initials": "A"}, {"family": "Linke", "given": "Daniel", "initials": "D"}, {"family": "Ghanavi", "given": "Hamid Reza", "initials": "HR"}, {"family": "Meier", "given": "Joana Isabel", "initials": "JI"}, {"family": "Wahlberg", "given": "Niklas", "initials": "N"}, {"family": "Matos-Marav\u00ed", "given": "P\u00e1vel", "initials": "P"}], "type": "journal article", "published": "2025-01-07", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "25", "issue": "1", "pages": "5", "issn-l": "1471-2180"}, "abstract": "The endosymbiotic relationship between Wolbachia bacteria and insects has been of interest for many years due to their diverse types of host reproductive phenotypic manipulation and potential role in the host's evolutionary history and population dynamics. Even though infection rates are high in Lepidoptera and specifically in butterflies, and reproductive manipulation is present in these taxa, less attention has been given to understanding how Wolbachia is acquired and maintained in their natural populations, across and within species having continental geographical distributions.\n\nWe used whole genome sequencing data to investigate the phylogenetics, demographic history, and infection rate dynamics of Wolbachia in four species of the Spicauda genus of skipper butterflies (Lepidoptera: Hesperiidae), a taxon that presents sympatric and often syntopic distribution, with drastic variability in species abundance in the Neotropical region. We show that infection is maintained by high turnover rates driven mainly by pervasive horizontal transmissions, while also presenting novel cases of double infection by distantly related supergroups of Wolbachia in S. simplicius.\n\nOur results suggest that Wolbachia population dynamics is host species-specific, with genetic cohesiveness across wide geographical distributions. We demonstrate that low coverage whole genome sequencing data can be used for an exhaustive assessment of Wolbachia infection in natural populations of butterflies, as well as its dynamics in closely related host species. This ultimately leads to a better understanding of the endosymbiotic population dynamics of Wolbachia and its effects on the host's biology and evolution.", "doi": "10.1186/s12866-024-03719-1", "pmid": "39773184", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11706079"}, {"db": "pii", "key": "10.1186/s12866-024-03719-1"}], "notes": [], "created": "2025-11-21T13:17:30.064Z", "modified": "2025-11-21T13:17:30.067Z"}, {"entity": "publication", "iuid": "d4b4f0a80cd14ee693ded92c677e97f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4b4f0a80cd14ee693ded92c677e97f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4b4f0a80cd14ee693ded92c677e97f8"}}, "title": "Dynamic binding of the bacterial chaperone Trigger factor to translating ribosomes in Escherichia coli.", "authors": [{"family": "H\u00e4vermark", "given": "Tora", "initials": "T", "orcid": "0000-0002-3794-3243", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8aca0712dea4996a8ba3f51b0a5d126.json"}}, {"family": "Metelev", "given": "Mikhail", "initials": "M", "orcid": "0000-0003-2829-6395", "researcher": {"href": "https://publications.scilifelab.se/researcher/39cdcb1c403140be9798d220fcf6e535.json"}}, {"family": "Lundin", "given": "Erik", "initials": "E", "orcid": "0000-0001-7490-1715", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c91e90244bd49d196b4ceee714d43dc.json"}}, {"family": "Volkov", "given": "Ivan L", "initials": "IL", "orcid": "0000-0001-7288-6363", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ee4772a638c4efb8c3a2cae1d6de400.json"}}, {"family": "Johansson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8811-2629", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7c7f4a540fa4bc2b5176c48bde2b0d7.json"}}], "type": "journal article", "published": "2025-01-07", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "1", "pages": "e2409536121", "issn-l": "0027-8424"}, "abstract": "The bacterial chaperone Trigger factor (TF) binds to ribosome-nascent chain complexes (RNCs) and cotranslationally aids the folding of proteins in bacteria. Decades of studies have given a broad, but often conflicting, description of the substrate specificity of TF, its RNC-binding dynamics, and competition with other RNC-binding factors, such as the Signal Recognition Particle (SRP). Previous RNC-binding kinetics experiments were commonly conducted on stalled RNCs in reconstituted systems, and consequently, may not be representative of the interaction of TF with ribosomes translating mRNA in the cytoplasm of the cell. Here, we used single-particle tracking (SPT) to measure TF binding to actively translating ribosomes inside living Escherichia coli. In cells, TF displays distinct binding modes-longer (ca 1 s) and shorter (ca 50 ms) RNC bindings. Consequently, we conclude that TF, on average, stays bound to the RNC for only a fraction of the translation cycle. Further, binding events are interrupted only by transient excursions to a freely diffusing state (ca 40 ms), suggesting a highly dynamic binding and unbinding cycle of TF in vivo. We also show that TF competes with SRP for RNC binding, and in doing so, tunes the binding selectivity of SRP.", "doi": "10.1073/pnas.2409536121", "pmid": "39739798", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11725819"}], "notes": [], "created": "2025-11-28T10:48:13.448Z", "modified": "2025-11-28T10:48:13.523Z"}, {"entity": "publication", "iuid": "8dabe8b76a1242a79844e89147083cc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8dabe8b76a1242a79844e89147083cc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8dabe8b76a1242a79844e89147083cc1"}}, "title": "Stress granule formation is regulated by signaling machinery involving Sch9/Ypk1, sphingolipids, and Ubi4.", "authors": [{"family": "Chen", "given": "Lihua", "initials": "L"}, {"family": "Gao", "given": "Yuan", "initials": "Y"}, {"family": "Hao", "given": "Xinxin", "initials": "X"}, {"family": "Yang", "given": "Xiaoxue", "initials": "X"}, {"family": "Lindstr\u00f6m", "given": "Michelle", "initials": "M"}, {"family": "Jiang", "given": "Shan", "initials": "S"}, {"family": "Cao", "given": "Xiuling", "initials": "X"}, {"family": "Liu", "given": "Huisheng", "initials": "H"}, {"family": "Nystr\u00f6m", "given": "Thomas", "initials": "T"}, {"family": "Sunnerhagen", "given": "Per", "initials": "P"}, {"family": "Liu", "given": "Beidong", "initials": "B"}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Theranostics", "issn": "1838-7640", "volume": "15", "issue": "5", "pages": "1987-2005", "issn-l": null}, "abstract": "Rationale: Stress granules (SGs) are membraneless organelles that are formed in response to various stresses. Multiple cellular processes have been reported to be involved in SG formation. However, the signaling cascades that coordinate SG formation remain to be elucidated. Methods: By performing two high-content imaging-based phenomic screens, we identified multiple signaling components that form a possible signal transduction pathway that regulates SG formation. Results: We found that Sch9 and Ypk1 function in an early step of SG formation, leading to a decrease in intermediate long-chain base sphingolipids (LCBs). This further downregulates the polyubiquitin precursor protein Ubi4 through upregulating the deubiquitinase Ubp3. Decreased levels of cellular free ubiquitin may subsequently facilitate Lsm7 phase separation and thus trigger SG formation. Conclusion: The signaling pathway identified in this work, together with its conserved components, provides valuable clues for understanding the mechanisms underlying SG formation and SG-associated human diseases.", "doi": "10.7150/thno.98199", "pmid": "39897563", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11780528"}, {"db": "pii", "key": "thnov15p1987"}], "notes": [], "created": "2025-11-05T13:48:10.339Z", "modified": "2025-11-05T13:48:10.423Z"}, {"entity": "publication", "iuid": "626dde82bebd4d8bb7880ecc0a2237e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0"}}, "title": "Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users.", "authors": [{"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Boger", "given": "Mathias Franzen", "initials": "MF"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Burgener", "given": "Adam D", "initials": "AD"}, {"family": "Bradley", "given": "Frideborg", "initials": "F", "orcid": "0000-0003-3006-7284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d51eaeb949e94bd39ab3605d495dc647.json"}}, {"family": "Lajoie", "given": "Julie", "initials": "J"}, {"family": "Omollo", "given": "Kenneth", "initials": "K"}, {"family": "Kimani", "given": "Joshua", "initials": "J"}, {"family": "Fowke", "given": "Keith", "initials": "K"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Broliden", "given": "Kristina", "initials": "K", "orcid": "0000-0003-2224-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/95346da4e5984d48bbb50032797155e5.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "1014"}, "abstract": "The injectable contraceptive, depot medroxyprogesterone acetate (DMPA), is associated with compromised cervical mucosal barriers. High-resolution spatial transcriptomics is applied here to reveal the spatial localization of these altered molecular markers. Ectocervical tissue samples from Kenyan sex workers using DMPA, or non-hormonal contraceptives, underwent spatial transcriptomics and gene set enrichment analyses. Integrated systemic estradiol levels and bulk tissue gene expression data from a larger cohort enhanced the study's scope. Unsupervised clustering unveiled four epithelial and seven submucosal layers, showcasing spatially restricted and diverse functional epithelial responses, and a less structured submucosal spatial ordering. DMPA associated with mucosal-wide immunoglobulin gene upregulation, verified by CD20+ B-cell immunostaining, and upregulated immune markers adjacent to the basal membrane. Downregulated genes represented spatially restricted disrupted epithelial barrier integrity and submucosal extracellular matrix dysfunction. The transcriptional profile was associated with markers of estrogen regulation. Collectively, our findings reveal estrogen-modulated distinct ectocervical transcriptional profiles associated with DMPA usage. While upregulation of immunoglobulin genes occurs throughout the mucosa, activation of innate immune responses and dysregulation of barrier integrity markers are spatially restricted. These results extend previous analyses using bulk transcriptomics and provide insights into the molecular landscape influenced by DMPA, shedding light on contraceptive effects and health implications.", "doi": "10.1038/s41598-024-83775-9", "pmid": "39762272", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11704007"}, {"db": "pii", "key": "10.1038/s41598-024-83775-9"}], "notes": [], "created": "2025-01-23T12:51:23.407Z", "modified": "2025-11-19T08:36:34.197Z"}, {"entity": "publication", "iuid": "be2943c4178e4522a7aec07e5c5f5cc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be2943c4178e4522a7aec07e5c5f5cc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be2943c4178e4522a7aec07e5c5f5cc6"}}, "title": "Positive Selection on Mammalian Immune Genes-Effects of Gene Function and Selective Constraint.", "authors": [{"family": "Nandakumar", "given": "Mridula", "initials": "M", "orcid": "0000-0003-4133-7200", "researcher": {"href": "https://publications.scilifelab.se/researcher/62b3ae7920a94445baa9c525a56c0973.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Carlsson", "given": "Fredric", "initials": "F", "orcid": "0000-0003-0875-4395", "researcher": {"href": "https://publications.scilifelab.se/researcher/d970f49b801a41eaafe818b724c03cda.json"}}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L", "orcid": "0000-0001-5219-7448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a732076e5acc4ede94cc864cd90c99f3.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "42", "issue": "1", "issn-l": "0737-4038"}, "abstract": "Genome-wide analyses of various taxa have repeatedly shown that immune genes are important targets of positive selection. However, little is known about what factors determine which immune genes are under positive selection. To address this question, we here focus on the mammalian immune system and investigate the importance of gene function and other factors such as gene expression, protein-protein interactions, and overall selective constraint as determinants of positive selection. We compiled a list of >1,100 immune genes that were divided into six functional categories and analyzed using data from rodents. Genes encoding proteins that are in direct interactions with pathogens, such as pattern recognition receptors (PRRs), are often expected to be key targets of positive selection. We found that categories containing cytokines, cytokine receptors, and other cell surface proteins involved in, for example, cell-cell interactions were at least as important targets as PRRs, with three times higher rate of positive selection than nonimmune genes. The higher rate of positive selection on cytokines and cell surface proteins was partly an effect of these categories having lower selective constraint. Nonetheless, cytokines had a higher rate of positive selection than nonimmune genes even at a given level of selective constraint, indicating that gene function per se can also be a determinant of positive selection. These results have broad implications for understanding the causes of positive selection on immune genes, specifically the relative importance of host-pathogen coevolution versus other processes.", "doi": "10.1093/molbev/msaf016", "pmid": "39834162", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11783303"}, {"db": "pii", "key": "7965092"}], "notes": [], "created": "2025-11-21T09:29:18.915Z", "modified": "2025-11-21T09:29:19.178Z"}, {"entity": "publication", "iuid": "a2b04350713c4675a839e6c03573f3d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b04350713c4675a839e6c03573f3d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b04350713c4675a839e6c03573f3d5"}}, "title": "Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.", "authors": [{"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Clinton", "given": "Samantha L\u00f3pez", "initials": "SL", "orcid": "0000-0003-1364-9135", "researcher": {"href": "https://publications.scilifelab.se/researcher/46b97ad0ac8541dc807e570724e58c69.json"}}, {"family": "Guinet", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-9922-2118", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca893ff5227f41a699fa68cca126600e.json"}}, {"family": "Wijnands", "given": "Flore", "initials": "F", "orcid": "0009-0009-6254-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/06418b4f9e90443d94452c87fb0b0588.json"}}, {"family": "Johnson", "given": "Ernst", "initials": "E", "orcid": "0009-0004-0745-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/891a915ffd054c57b7c0d107c4e1b7e1.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kinsella", "given": "Cormac M", "initials": "CM", "orcid": "0000-0001-9865-4608", "researcher": {"href": "https://publications.scilifelab.se/researcher/33c6e2a784b14b768416842ab8b0cbfd.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Gigascience", "issn": "2047-217X", "volume": "14", "issn-l": "2047-217X"}, "abstract": "Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.", "doi": "10.1093/gigascience/giaf108", "pmid": "41041810", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12491943"}, {"db": "pii", "key": "8271467"}], "notes": [], "created": "2025-10-30T13:19:17.629Z", "modified": "2025-11-28T10:49:20.910Z"}, {"entity": "publication", "iuid": "e5a9e55a7e644b75843cb3c89288987a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5a9e55a7e644b75843cb3c89288987a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5a9e55a7e644b75843cb3c89288987a"}}, "title": "Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.", "authors": [{"family": "Lawniczak", "given": "Mara K N", "initials": "MKN", "orcid": "0000-0002-3006-2080", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfedca8b315044e38532128233e793df.json"}}, {"family": "Kocot", "given": "Kevin M", "initials": "KM", "orcid": "0000-0002-8673-2688", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d7d30e573044edfa4fa84c31a990a06.json"}}, {"family": "Astrin", "given": "Jonas J", "initials": "JJ", "orcid": "0000-0003-1961-1162", "researcher": {"href": "https://publications.scilifelab.se/researcher/196b7bc855154263a30e7dc2d5f1fae8.json"}}, {"family": "Blaxter", "given": "Mark", "initials": "M", "orcid": "0000-0003-2861-949X", "researcher": {"href": "https://publications.scilifelab.se/researcher/57825ba0f3a9418c95818206f6506a8c.json"}}, {"family": "Sotero-Caio", "given": "Cibele G", "initials": "CG", "orcid": "0000-0002-3112-0000", "researcher": {"href": "https://publications.scilifelab.se/researcher/01c8c109887d446391c6a1da2b160ae5.json"}}, {"family": "Barker", "given": "Katharine B", "initials": "KB", "orcid": "0000-0002-4788-0223", "researcher": {"href": "https://publications.scilifelab.se/researcher/54bef131a9ee4d01a673be303c4e6095.json"}}, {"family": "Childers", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-0747-8539", "researcher": {"href": "https://publications.scilifelab.se/researcher/23f9cda134ba47d8930eb56178a8978a.json"}}, {"family": "Coddington", "given": "Jonathan", "initials": "J", "orcid": "0000-0001-6004-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1b5d867f8df4d15912371407adea6e0.json"}}, {"family": "Davis", "given": "Paul", "initials": "P", "orcid": "0000-0001-5545-0824", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d83aa44e7ea4b859a5f2a187f00bd20.json"}}, {"family": "Howe", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-2237-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee1dac1c74d3497aa987c5a615f2d6c4.json"}}, {"family": "Johnson", "given": "Warren E", "initials": "WE", "orcid": "0000-0002-5954-186X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8835881e3e9f477c88d2ebdd8f56911b.json"}}, {"family": "McKenna", "given": "Duane D", "initials": "DD", "orcid": "0000-0002-7823-8727", "researcher": {"href": "https://publications.scilifelab.se/researcher/d04401d6d43d4a26bcf2aa2a3cef0c0e.json"}}, {"family": "Wideman", "given": "Jeremy G", "initials": "JG", "orcid": "0000-0002-4426-9533", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3403a41c09c480d982a8c1ec018aede.json"}}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Ras", "given": "Verena", "initials": "V", "orcid": "0000-0003-3938-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/11ed1c583ca6441a8fb63aeeba09c332.json"}}, {"family": "Santos", "given": "Bernardo F", "initials": "BF", "orcid": "0000-0002-2634-3066", "researcher": {"href": "https://publications.scilifelab.se/researcher/00fcf7b94bbc48718c8788e81344ced3.json"}}, {"family": "Earth BioGenome Project Samples and Processing Subcommittee\n", "given": "", "initials": ""}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Gigascience", "issn": "2047-217X", "issn-l": "2047-217X", "volume": "14", "issue": null, "pages": null}, "abstract": "The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Life. Currently in its first phase, the project is targeting family-level representatives and is progressing rapidly. Here we outline recommended standards and considerations in sample acquisition and processing for those involved in biodiverse reference genome creation. These standards and recommendations will evolve with advances in related processes. Additionally, we discuss the challenges raised by the ambitions for later phases of the project, highlighting topics related to sample collection and processing that require further development.", "doi": "10.1093/gigascience/giaf041", "pmid": "40440092", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Long read": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12121479"}, {"db": "pii", "key": "8152780"}], "notes": [], "created": "2025-11-11T12:48:04.150Z", "modified": "2025-11-16T15:03:51.155Z"}, {"entity": "publication", "iuid": "f03fa87b287c4a4dbe0102b0c98c9205", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f03fa87b287c4a4dbe0102b0c98c9205.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f03fa87b287c4a4dbe0102b0c98c9205"}}, "title": "Analysis-ready VCF at Biobank scale using Zarr.", "authors": [{"family": "Czech", "given": "Eric", "initials": "E", "orcid": "0000-0002-4254-4255", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0e21d447a9449239d9b86d7c914def4.json"}}, {"family": "Tyler", "given": "Will", "initials": "W"}, {"family": "White", "given": "Tom", "initials": "T"}, {"family": "Jeffery", "given": "Ben", "initials": "B", "orcid": "0000-0002-1982-6801", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78f19bbd831415888401c9da9f21afb.json"}}, {"family": "Millar", "given": "Timothy R", "initials": "TR", "orcid": "0000-0002-5142-8811", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cf1756a518a4c0ea81f84fbe7601fdf.json"}}, {"family": "Elsworth", "given": "Benjamin", "initials": "B", "orcid": "0000-0001-7328-4233", "researcher": {"href": "https://publications.scilifelab.se/researcher/79e783b811504d93bd5f9f62d367b6c8.json"}}, {"family": "Guez", "given": "J\u00e9r\u00e9my", "initials": "J", "orcid": "0009-0007-6406-5187", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc75ff112f094d18af6fe11837c0a785.json"}}, {"family": "Hancox", "given": "Jonny", "initials": "J", "orcid": "0009-0003-5799-5299", "researcher": {"href": "https://publications.scilifelab.se/researcher/c30408b6f07a484faf4548e2c1cfd924.json"}}, {"family": "Karczewski", "given": "Konrad J", "initials": "KJ", "orcid": "0000-0003-2878-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/096bfb156b54478e9a3f9c9d7730bc43.json"}}, {"family": "Miles", "given": "Alistair", "initials": "A", "orcid": "0000-0001-9018-4680", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a1ed566e4094bfbbd02125004b3b5ad.json"}}, {"family": "Tallman", "given": "Sam", "initials": "S", "orcid": "0000-0001-7183-6276", "researcher": {"href": "https://publications.scilifelab.se/researcher/1583d2c9f189432182094fff666f8dc5.json"}}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1cd4d11f8d443e8ff305f923b8fbb0.json"}}, {"family": "Wojdyla", "given": "Rafal", "initials": "R", "orcid": "0009-0005-0735-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/bba48e71bad248e7a13b11cac0ac1af7.json"}}, {"family": "Zabad", "given": "Shadi", "initials": "S", "orcid": "0000-0002-8003-9284", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f9abcfa26374c50977b281e85609ba6.json"}}, {"family": "Hammerbacher", "given": "Jeff", "initials": "J", "orcid": "0000-0001-6596-8563", "researcher": {"href": "https://publications.scilifelab.se/researcher/321413798f474d36adcb402eafd20d22.json"}}, {"family": "Kelleher", "given": "Jerome", "initials": "J", "orcid": "0000-0002-7894-5253", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd5258b200943949537f9b6c0dd24f5.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Gigascience", "issn": "2047-217X", "volume": "14", "issn-l": "2047-217X"}, "abstract": "Variant Call Format (VCF) is the standard file format for interchanging genetic variation data and associated quality control metrics. The usual row-wise encoding of the VCF data model (either as text or packed binary) emphasizes efficient retrieval of all data for a given variant, but accessing data on a field or sample basis is inefficient. The Biobank-scale datasets currently available consist of hundreds of thousands of whole genomes and hundreds of terabytes of compressed VCF. Row-wise data storage is fundamentally unsuitable and a more scalable approach is needed.\n\nZarr is a format for storing multidimensional data that is widely used across the sciences, and is ideally suited to massively parallel processing. We present the VCF Zarr specification, an encoding of the VCF data model using Zarr, along with fundamental software infrastructure for efficient and reliable conversion at scale. We show how this format is far more efficient than standard VCF-based approaches, and competitive with specialized methods for storing genotype data in terms of compression ratios and single-threaded calculation performance. We present case studies on subsets of 3 large human datasets (Genomics England: $n$=78,195; Our Future Health: $n$=651,050; All of Us: $n$=245,394) along with whole genome datasets for Norway Spruce ($n$=1,063) and SARS-CoV-2 ($n$=4,484,157). We demonstrate the potential for VCF Zarr to enable a new generation of high-performance and cost-effective applications via illustrative examples using cloud computing and GPUs.\n\nLarge row-encoded VCF files are a major bottleneck for current research, and storing and processing these files incurs a substantial cost. The VCF Zarr specification, building on widely used, open-source technologies, has the potential to greatly reduce these costs, and may enable a diverse ecosystem of next-generation tools for analysing genetic variation data directly from cloud-based object stores, while maintaining compatibility with existing file-oriented workflows.", "doi": "10.1093/gigascience/giaf049", "pmid": "40451243", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12127038"}, {"db": "pii", "key": "8154315"}], "notes": [], "created": "2025-11-03T11:31:25.593Z", "modified": "2025-11-03T11:31:27.796Z"}, {"entity": "publication", "iuid": "86f41b0106b74ed29f7b2805f52d8e60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86f41b0106b74ed29f7b2805f52d8e60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86f41b0106b74ed29f7b2805f52d8e60"}}, "title": "Model-informed drug development for antimicrobials: translational pharmacokinetic-pharmacodynamic modelling of apramycin to facilitate prediction of efficacious dose in complicated urinary tract infections.", "authors": [{"family": "Hern\u00e1ndez-Lozano", "given": "Irene", "initials": "I", "orcid": "0000-0002-3700-7690", "researcher": {"href": "https://publications.scilifelab.se/researcher/673e5e401f4644be92c4c7335fcc3c32.json"}}, {"family": "Aranzana-Climent", "given": "Vincent", "initials": "V"}, {"family": "Cao", "given": "Sha", "initials": "S", "orcid": "0000-0003-3033-9219", "researcher": {"href": "https://publications.scilifelab.se/researcher/d978ff3633ce4286b1aa7fb0f8df2b74.json"}}, {"family": "Matias", "given": "Carina", "initials": "C"}, {"family": "Ulf Hansen", "given": "Jon", "initials": "J"}, {"family": "Liepinsh", "given": "Edgars", "initials": "E"}, {"family": "Hughes", "given": "Diarmaid", "initials": "D", "orcid": "0000-0002-7456-9182", "researcher": {"href": "https://publications.scilifelab.se/researcher/19a78e8c5738475ab04ce3922a10e7e1.json"}}, {"family": "Hobbie", "given": "Sven N", "initials": "SN"}, {"family": "Vingsbo Lundberg", "given": "Carina", "initials": "C"}, {"family": "Friberg", "given": "Lena E", "initials": "LE", "orcid": "0000-0002-2979-679X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23b6e6225d15433f8eccc444c450adfc.json"}}], "type": "journal article", "published": "2025-01-03", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "volume": "80", "issue": "1", "pages": "301-310", "issn-l": "0305-7453"}, "abstract": "The use of mouse models of complicated urinary tract infection (cUTI) has usually been limited to a single timepoint assessment of bacterial burden. Based on longitudinal in vitro and in vivo data, we developed a pharmacokinetic-pharmacodynamic (PKPD) model to assess the efficacy of apramycin, a broad-spectrum aminoglycoside antibiotic, in mouse models of cUTI.\n\nTwo Escherichia coli strains were studied (EN591 and ATCC 700336). Apramycin exposure-effect relationships were established with in vitro time-kill data at pH 6 and pH 7.4 and in mice with cUTI. Immunocompetent mice were treated with apramycin (1.5-30 mg/kg) starting 24 h post-infection. Kidney and bladder tissue were collected 6-96 h post-infection for cfu determination. A PKPD model integrating all data was developed and simulations were performed to predict bacterial burden in humans.\n\nTreatment with apramycin reduced the bacterial load in kidneys and bladder tissue up to 4.3-log compared with vehicle control. In vitro and in vivo tissue time-course efficacy data were integrated into the PKPD model, showing 76%-98% reduction of bacterial net growth and 3- to 145-fold increase in apramycin potency in vivo compared with in vitro. Simulations suggested that an 11 mg/kg daily dose would be sufficient to achieve bacterial stasis in kidneys and bladder in humans.\n\nPKPD modelling with in vitro and in vivo PK and PD data enabled simultaneous evaluation of the different components that influence drug effect, an approach that had not yet been evaluated for antibiotics in the cUTI model and that has potential to enhance model-informed drug development of antibiotics.", "doi": "10.1093/jac/dkae409", "pmid": "39548844", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11695905"}, {"db": "pii", "key": "7901715"}], "notes": [], "created": "2025-02-28T14:18:55.109Z", "modified": "2025-02-28T14:18:55.278Z"}, {"entity": "publication", "iuid": "f37aef8025654f5c8f8278810568a147", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f37aef8025654f5c8f8278810568a147.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f37aef8025654f5c8f8278810568a147"}}, "title": "Microbial methanogenesis fueled by freshwater infiltration and oil biodegradation in the Siljan impact structure, Sweden", "authors": [{"family": "van Dam", "given": "Femke", "initials": "F"}, {"family": "Kiet\u00e4v\u00e4inen", "given": "Riikka", "initials": "R"}, {"family": "Westmeijer", "given": "George", "initials": "G"}, {"family": "Reinhardt", "given": "Manuel", "initials": "M"}, {"family": "Ono", "given": "Shuhei", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Ketzer", "given": "Marcelo", "initials": "M"}, {"family": "McIntosh", "given": "Jennifer C", "initials": "JC"}, {"family": "Drake", "given": "Henrik", "initials": "H"}], "type": "journal-article", "published": "2025-01-03", "journal": {"title": "Discov Appl Sci", "issn": "3004-9261", "volume": "7", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1007/s42452-024-06418-8", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:41:45.046Z", "modified": "2025-11-28T10:41:45.067Z"}, {"entity": "publication", "iuid": "0c93730d9dd14ab48b73ff3ca9878f55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c93730d9dd14ab48b73ff3ca9878f55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c93730d9dd14ab48b73ff3ca9878f55"}}, "title": "Pantothenate kinase 4 controls skeletal muscle substrate metabolism.", "authors": [{"family": "Miranda-Cervantes", "given": "Adriana", "initials": "A", "orcid": "0009-0009-8170-5101", "researcher": {"href": "https://publications.scilifelab.se/researcher/92c3d51b0d5547c2967137ba46c0bc20.json"}}, {"family": "Fritzen", "given": "Andreas M", "initials": "AM", "orcid": "0000-0001-8793-9739", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfe40934c44241ae9c9775e5966e2944.json"}}, {"family": "Raun", "given": "Steffen H", "initials": "SH"}, {"family": "Hodek", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0001-8307-9575", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e3bcef870804d4f9ec3d3e257cbc323.json"}}, {"family": "M\u00f8ller", "given": "Lisbeth L V", "initials": "LLV", "orcid": "0000-0003-1885-0102", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5031e341c004fdbb3c48f8159455033.json"}}, {"family": "Johann", "given": "Kornelia", "initials": "K"}, {"family": "Deisen", "given": "Luisa", "initials": "L"}, {"family": "Gregorevic", "given": "Paul", "initials": "P", "orcid": "0000-0002-7418-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0db9536f286420a8cb58c97704ff408.json"}}, {"family": "Gudiksen", "given": "Anders", "initials": "A"}, {"family": "Artati", "given": "Anna", "initials": "A"}, {"family": "Adamski", "given": "Jerzy", "initials": "J", "orcid": "0000-0001-9259-0199", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4906c15dbbf4968aa09d398302578f1.json"}}, {"family": "Andersen", "given": "Nicoline R", "initials": "NR"}, {"family": "Sigvardsen", "given": "Casper M", "initials": "CM", "orcid": "0000-0002-9891-5721", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c01caeb8b5c48fa8b9ef06dd6c2384f.json"}}, {"family": "Carl", "given": "Christian S", "initials": "CS", "orcid": "0000-0002-9551-5837", "researcher": {"href": "https://publications.scilifelab.se/researcher/a831e2cb7b9c465d84407afe5f2f5e02.json"}}, {"family": "Voldstedlund", "given": "Christian T", "initials": "CT", "orcid": "0000-0002-6368-8995", "researcher": {"href": "https://publications.scilifelab.se/researcher/777bfb6f108f4e66a8f04eabbb9c1e1d.json"}}, {"family": "Kj\u00f8bsted", "given": "Rasmus", "initials": "R", "orcid": "0000-0002-0628-4994", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd0c686a41344b249192643a23e9ce69.json"}}, {"family": "Hauck", "given": "Stefanie M", "initials": "SM", "orcid": "0000-0002-1630-6827", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcc26d030c9548598e85094fe036d190.json"}}, {"family": "Schjerling", "given": "Peter", "initials": "P"}, {"family": "Jensen", "given": "Thomas E", "initials": "TE", "orcid": "0000-0001-6139-8268", "researcher": {"href": "https://publications.scilifelab.se/researcher/a36948f538fc4858a69d706e52a3f111.json"}}, {"family": "Cebrian-Serrano", "given": "Alberto", "initials": "A", "orcid": "0000-0002-4737-0215", "researcher": {"href": "https://publications.scilifelab.se/researcher/595cbf9bffd044f1843755c5cf9e4218.json"}}, {"family": "J\u00e4hnert", "given": "Markus", "initials": "M", "orcid": "0000-0001-6459-7318", "researcher": {"href": "https://publications.scilifelab.se/researcher/11a089cfba4d48268b2cf792e01c23ba.json"}}, {"family": "Gottmann", "given": "Pascal", "initials": "P", "orcid": "0000-0002-9791-783X", "researcher": {"href": "https://publications.scilifelab.se/researcher/847d1ef723c74aa58beba753ef3c085c.json"}}, {"family": "Burtscher", "given": "Ingo", "initials": "I"}, {"family": "Lickert", "given": "Heiko", "initials": "H", "orcid": "0000-0002-4597-8825", "researcher": {"href": "https://publications.scilifelab.se/researcher/a96d6282848146d0a627a3b36f79bb42.json"}}, {"family": "Pilegaard", "given": "Henriette", "initials": "H", "orcid": "0000-0002-1071-0327", "researcher": {"href": "https://publications.scilifelab.se/researcher/2592a05febba4a44819b20b5dcac5ce8.json"}}, {"family": "Sch\u00fcrmann", "given": "Annette", "initials": "A", "orcid": "0000-0002-4113-4377", "researcher": {"href": "https://publications.scilifelab.se/researcher/9145876644c8417f829f440cc5a31087.json"}}, {"family": "Tsch\u00f6p", "given": "Matthias H", "initials": "MH", "orcid": "0000-0002-4744-371X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a16535fb02146598846443de90f925b.json"}}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "M\u00fcller", "given": "Timo D", "initials": "TD", "orcid": "0000-0002-0624-9339", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f16d48a131042c1908b1f9394714fa1.json"}}, {"family": "Sylow", "given": "Lykke", "initials": "L", "orcid": "0000-0003-0905-5932", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8f76299a7e642008b90f4bdee53e6af.json"}}, {"family": "Kiens", "given": "Bente", "initials": "B", "orcid": "0000-0001-5705-5625", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ff3bc60ee9d4402bebf3a96d79a9eed.json"}}, {"family": "Richter", "given": "Erik A", "initials": "EA", "orcid": "0000-0002-6850-3056", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b8efad73a8b45ccab3c9379fc0e5d3e.json"}}, {"family": "Kleinert", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8069-9055", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ba2dbbe059a44a2b0ad9dcf82a13bf3.json"}}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "345", "issn-l": "2041-1723"}, "abstract": "Metabolic flexibility in skeletal muscle is essential for maintaining healthy glucose and lipid metabolism, and its dysfunction is closely linked to metabolic diseases. Exercise enhances metabolic flexibility, making it an important tool for discovering mechanisms that promote metabolic health. Here we show that pantothenate kinase 4 (PanK4) is a new conserved exercise target with high abundance in muscle. Muscle-specific deletion of PanK4 impairs fatty acid oxidation which is related to higher intramuscular acetyl-CoA and malonyl-CoA levels. Elevated acetyl-CoA levels persist regardless of feeding state and are associated with whole-body glucose intolerance, reduced insulin-stimulated glucose uptake in glycolytic muscle, and impaired glucose uptake during exercise. Conversely, increasing PanK4 levels in glycolytic muscle lowers acetyl-CoA and enhances glucose uptake. Our findings highlight PanK4 as an important regulator of acetyl-CoA levels, playing a key role in both muscle lipid and glucose metabolism.", "doi": "10.1038/s41467-024-55036-w", "pmid": "39746949", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11695632"}, {"db": "pii", "key": "10.1038/s41467-024-55036-w"}], "notes": [], "created": "2025-11-18T12:03:37.103Z", "modified": "2025-11-18T12:03:38.520Z"}, {"entity": "publication", "iuid": "36465c1e65bd499d940371185242fb06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36465c1e65bd499d940371185242fb06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36465c1e65bd499d940371185242fb06"}}, "title": "Hydrological regime of a continental river system predicts bacterial macroecological patterns.", "authors": [{"family": "Demeter", "given": "Katalin", "initials": "K", "orcid": "0000-0002-4260-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/5df5f47af9c9454bbf13ea30dfef4df3.json"}}, {"family": "Savio", "given": "Domenico", "initials": "D", "orcid": "0000-0001-5322-9536", "researcher": {"href": "https://publications.scilifelab.se/researcher/66c6378c7ebf41cca7c709a88fcf27c2.json"}}, {"family": "Kirschner", "given": "Alexander K T", "initials": "AKT", "orcid": "0000-0002-9797-3073", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fb459d6e22e4c39983578abae121f74.json"}}, {"family": "Reischer", "given": "Georg H", "initials": "GH", "orcid": "0000-0002-3962-8685", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1d9145cd724db1803aae7a6ff3319a.json"}}, {"family": "Kolarevic", "given": "Stoimir", "initials": "S"}, {"family": "Parajka", "given": "Juraj", "initials": "J", "orcid": "0000-0002-1177-5181", "researcher": {"href": "https://publications.scilifelab.se/researcher/2698181b5e734debaeb74650004ed055.json"}}, {"family": "Derx", "given": "Julia", "initials": "J", "orcid": "0000-0002-9931-088X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6845bf4cbe784c41b4efe52b87b887c1.json"}}, {"family": "Jakwerth", "given": "Stefan", "initials": "S"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C", "orcid": "0000-0001-7418-0831", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fed784d185749498b07f7458c9ccfb6.json"}}, {"family": "Blaschke", "given": "Alfred P", "initials": "AP", "orcid": "0000-0001-8617-5802", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa8d81f7cfcc4a82acce9690a4d6cffc.json"}}, {"family": "Mach", "given": "Robert L", "initials": "RL", "orcid": "0000-0003-2375-7244", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a53d6c16f2f4e978764b982ba485e97.json"}}, {"family": "Bl\u00f6schl", "given": "G\u00fcnter", "initials": "G", "orcid": "0000-0003-2227-8225", "researcher": {"href": "https://publications.scilifelab.se/researcher/8791191bfcb041d28768a3cda7206d16.json"}}, {"family": "Farnleitner", "given": "Andreas H", "initials": "AH", "orcid": "0000-0002-0542-5425", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f1019fab4eb42a8896e3aa2c2cced44.json"}}, {"family": "Eiler", "given": "Alexander", "initials": "A", "orcid": "0000-0001-9916-9567", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7286785c9334dcba90273b69f81c018.json"}}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "19", "issue": "1", "issn-l": "1751-7362"}, "abstract": "Modeling bacterial dynamics in large river systems is crucial for predicting continental-scale ecosystem functioning under anthropogenic pressures. Although the River Continuum and Metacommunity concepts have provided theoretical frameworks, quantitative parameters necessary for microbial macroecological models remain scarce. Here, we present results from two whole-river surveys, conducted six years apart along 2600 km of the Danube River. Using bacterial secondary production, cell counts, and 16S ribosomal RNA (rRNA) gene amplicon sequencing, we quantified carbon, cell, phylotype, and diversity turnover along the river. Carbon incorporation per cell declined with water travel time by 6000-21 000 atoms per hour. Bacterial cells multiplied every eight days, resulting in four to six doublings during downstream transport. Growth responses at the level of individual phylotypes differed up to a hundredfold from these bulk community estimates. Bacterial diversity dynamics were dominated by phylotype turnover rather than phylotype loss. Turnover ranged from 0.92 to 0.96 along the river, indicating an almost complete replacement of phylotypes with 2%-11% of headwater-associated amplicon sequence variants (ASVs) persisting under base-flow conditions. Richness declined gradually downstream at a rate of ~0.13 ASVs per hour. Variations in bacterial secondary production, cell abundance, and observed ASVs were best explained by models combining hydrological and water quality parameters, whereas beta diversity followed a gradual development primarily structured by water travel time. Together, these results identify water travel time as the key integrative parameter governing microbial macroecological dynamics along large rivers, with environmental conditions fine-tuning local responses. These models can help predict changes in microbial diversity and functioning under anthropogenic alterations.", "doi": "10.1093/ismejo/wrag013", "pmid": "41626752", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "8454621"}, {"db": "pmc", "key": "PMC12927878"}], "notes": [], "created": "2026-02-24T19:07:12.652Z", "modified": "2026-02-24T19:07:14.084Z"}, {"entity": "publication", "iuid": "630c6b879a394e56a6da4a3e9e6b4e3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/630c6b879a394e56a6da4a3e9e6b4e3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/630c6b879a394e56a6da4a3e9e6b4e3a"}}, "title": "Evolutionary convergence of sensory circuits in the pallium of amniotes.", "authors": [{"family": "Rueda-Ala\u00f1a", "given": "Eneritz", "initials": "E", "orcid": "0000-0003-3045-4970", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bb18f180ec34c8db47e1c2c426e8b75.json"}}, {"family": "Senovilla-Ganzo", "given": "Rodrigo", "initials": "R", "orcid": "0000-0001-6615-0923", "researcher": {"href": "https://publications.scilifelab.se/researcher/a219f65014ad4d4ca0490065268f9f72.json"}}, {"family": "Grillo", "given": "Marco", "initials": "M", "orcid": "0000-0003-2155-0645", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd8bec6567444558acbcbd1b3d28f7a.json"}}, {"family": "V\u00e1zquez", "given": "Enrique", "initials": "E", "orcid": "0000-0003-1157-2592", "researcher": {"href": "https://publications.scilifelab.se/researcher/94f6012fb4884610aee7a53a83d05b2c.json"}}, {"family": "Marco-Salas", "given": "Sergio", "initials": "S"}, {"family": "Gallego-Flores", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-0773-0578", "researcher": {"href": "https://publications.scilifelab.se/researcher/73718d9c9e4746d2873846e656bfaea1.json"}}, {"family": "Orde\u00f1ana-Manso", "given": "Aitor", "initials": "A", "orcid": "0009-0004-3059-7693", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d077ff29c2942b496a5db4528d11e9d.json"}}, {"family": "Ftara", "given": "Artemis", "initials": "A", "orcid": "0009-0002-9538-2330", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c642890eb02433c9bf6b80ac8381ec1.json"}}, {"family": "Escobar", "given": "Laura", "initials": "L", "orcid": "0000-0003-0955-2015", "researcher": {"href": "https://publications.scilifelab.se/researcher/a50ee5fb3c0f489bbe3fcdf6f21c38c6.json"}}, {"family": "Bengur\u00eda", "given": "Alberto", "initials": "A", "orcid": "0000-0002-5536-566X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7973b74670604884bfb79720113c136f.json"}}, {"family": "Quintas", "given": "Ana", "initials": "A", "orcid": "0000-0003-3721-7580", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1a34002b0f04842a0e3d27ee54b6a81.json"}}, {"family": "Dopazo", "given": "Ana", "initials": "A", "orcid": "0000-0002-4910-1684", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dc6607087b646a59c93cd60bd63a5d6.json"}}, {"family": "R\u00e1bano", "given": "Miriam", "initials": "M"}, {"family": "Vivanco", "given": "Mar\u00eda dM", "initials": "MD", "orcid": "0000-0002-9540-247X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2e1a2ef64d14abc9c1c70cc27813d05.json"}}, {"family": "Aransay", "given": "Ana Mar\u00eda", "initials": "AM", "orcid": "0000-0002-8271-612X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5d69b81c2124684ac1b1b083cb12af7.json"}}, {"family": "Garrigos", "given": "Daniel", "initials": "D", "orcid": "0000-0003-1337-1321", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6ac980bcaa240d68b4fb56396efe10a.json"}}, {"family": "Toval", "given": "\u00c1ngel", "initials": "\u00c1", "orcid": "0000-0003-4798-1216", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8cbbde730264df2a83233006353ff57.json"}}, {"family": "Ferr\u00e1n", "given": "Jos\u00e9 Luis", "initials": "JL", "orcid": "0000-0002-3413-9452", "researcher": {"href": "https://publications.scilifelab.se/researcher/be12e65f57474382a7f8d270768858dc.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Encinas-P\u00e9rez", "given": "Juan Manuel", "initials": "JM", "orcid": "0000-0002-0402-972X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1166eb648864bbb9db379a7dfb60557.json"}}, {"family": "De Pitt\u00e0", "given": "Maurizio", "initials": "M", "orcid": "0000-0001-5799-5182", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8f95eb7ffc44c8faa4793fe1a03ac41.json"}}, {"family": "Garc\u00eda-Moreno", "given": "Fernando", "initials": "F", "orcid": "0000-0001-9048-4237", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e744494aab348dfb0f084dcef8338c2.json"}}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "Science", "issn": "1095-9203", "volume": "387", "issue": "6735", "pages": "eadp3411", "issn-l": "0036-8075"}, "abstract": "The amniote pallium contains sensory circuits that are structurally and functionally equivalent, yet their evolutionary relationship remains unresolved. We used birthdating analysis, single-cell RNA and spatial transcriptomics, and mathematical modeling to compare the development and evolution of known pallial circuits across birds (chick), lizards (gecko), and mammals (mouse). We reveal that neurons within these circuits' stations are generated at varying developmental times and brain regions across species and found an early developmental divergence in the transcriptomic progression of glutamatergic neurons. Our research highlights developmental distinctions and functional similarities in the sensory circuit between birds and mammals, suggesting the convergence of high-order sensory processing across amniote lineages.", "doi": "10.1126/science.adp3411", "pmid": "39946453", "labels": {"In Situ Sequencing": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T06:51:47.033Z", "modified": "2025-11-28T06:51:48.304Z"}, {"entity": "publication", "iuid": "c42cf07b07844cabbe0ad109571234eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c42cf07b07844cabbe0ad109571234eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c42cf07b07844cabbe0ad109571234eb"}}, "title": "Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.", "authors": [{"family": "Jeevannavar", "given": "Aditya", "initials": "A"}, {"family": "Florenza", "given": "Javier", "initials": "J"}, {"family": "Divne", "given": "Anna-Maria", "initials": "A"}, {"family": "Tamminen", "given": "Manu", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362", "volume": "19", "issue": "1", "pages": null}, "abstract": "Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as downregulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free, and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.", "doi": "10.1093/ismejo/wraf046", "pmid": "40057978", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Single cell": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11973420"}, {"db": "pii", "key": "8064733"}], "notes": [], "created": "2025-09-08T06:54:54.550Z", "modified": "2025-11-21T14:35:21.491Z"}, {"entity": "publication", "iuid": "72f3a3d242e74c4099a9732a095b6219", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72f3a3d242e74c4099a9732a095b6219.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72f3a3d242e74c4099a9732a095b6219"}}, "title": "Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.", "authors": [{"family": "Aguilera-Campos", "given": "Karla Iveth", "initials": "KI", "orcid": "0000-0003-1299-341X", "researcher": {"href": "https://publications.scilifelab.se/researcher/331e2dcabae64ae281c9c354bb4a259d.json"}}, {"family": "Boisard", "given": "Julie", "initials": "J", "orcid": "0000-0002-6191-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3ceb5d8238e4855a09ea93d10f74f1c.json"}}, {"family": "T\u00f6rnblom", "given": "Viktor", "initials": "V", "orcid": "0009-0008-8017-8402", "researcher": {"href": "https://publications.scilifelab.se/researcher/295329ac66314e54882a8feaa4528309.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}, {"family": "Behnck\u00e9-Serra", "given": "Ada", "initials": "A", "orcid": "0009-0007-8632-8494", "researcher": {"href": "https://publications.scilifelab.se/researcher/31ba0c2817d14321bfb4a3e3d83f1fe7.json"}}, {"family": "Cotillas", "given": "Elena Aramendia", "initials": "EA"}, {"family": "Stairs", "given": "Courtney Weir", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "19", "issue": "1", "issn-l": "1751-7362"}, "abstract": "Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.", "doi": "10.1093/ismejo/wraf171", "pmid": "40795332", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12453579"}, {"db": "pii", "key": "8228259"}], "notes": [], "created": "2025-11-28T10:49:37.264Z", "modified": "2025-11-28T10:49:37.595Z"}, {"entity": "publication", "iuid": "2b73ca54c3084fd0a10807dd653a2ee9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b73ca54c3084fd0a10807dd653a2ee9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b73ca54c3084fd0a10807dd653a2ee9"}}, "title": "A Rationally Designed Azobenzene Photoswitch for DNA G-Quadruplex Regulation in Live Cells.", "authors": [{"family": "Dudek", "given": "Marta", "initials": "M", "orcid": "0000-0001-6749-0903", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfd0b47759f64c6284a7cc1b6cea407d.json"}}, {"family": "L\u00f3pez-Pacios", "given": "Luc\u00eda", "initials": "L", "orcid": "0009-0007-6892-3652", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d7130d8c2449eba6a0bb4cc393db9e.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}, {"family": "Nogueira", "given": "Juan J", "initials": "JJ", "orcid": "0000-0001-7419-5670", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d6768a2a4754dd8bc73ca8da7fbcc26.json"}}, {"family": "Martinez-Fernandez", "given": "Lara", "initials": "L", "orcid": "0000-0001-5361-9390", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f2a252e469b4a2487e10962010d6ee0.json"}}, {"family": "Deiana", "given": "Marco", "initials": "M", "orcid": "0000-0002-7815-4494", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9efbe74ca3940029d782d3ba645fa34.json"}}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "Angew. Chem. Int. Ed. Engl.", "issn": "1521-3773", "volume": "64", "issue": "1", "pages": "e202413000", "issn-l": "1433-7851"}, "abstract": "G-quadruplex (G4) DNA structures are increasingly acknowledged as promising targets in cancer research, and the development of G4-specific stabilizing compounds may lay a fundamental foundation in precision medicine for cancer treatment. Here, we propose a light-responsive G4-binder for precise modulation of drug activation, providing dynamic and spatiotemporal control over G4-associated biological processes contributing to cancer cell death. We developed a specialized fluorinated azobenzene (AB) switch equipped with a quinoline unit and a positively charged carboxamide side chain, Q-Azo4F-C, designed for targeted binding to G4 structures within cells. Biophysical studies, combined with molecular dynamics simulations, provide insights into the unique coordination modes of the photoswitchable ligand in its trans and cis configurations when interacting with G4s. The observed variations in complexation processes between the two isomeric states in different cancer cell lines manifest in more than 25-fold reversible cytotoxic activity. Immunostaining conducted with the structure-specific G4 antibody (BG4), establishes a direct correlation between cytotoxicity and the varying extent of G4 induction regulated by the two isoforms. Finally, we demonstrate the photo-driven reversible regulation of G4 structures in lung cancer cells by Q-Azo4F-C. Our findings highlight the potential of light-responsive G4-binders in advancing precision cancer therapy through dynamic control of G4-mediated pathways.", "doi": "10.1002/anie.202413000", "pmid": "39268751", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2025-04-23T10:01:09.406Z", "modified": "2025-10-17T13:04:26.954Z"}, {"entity": "publication", "iuid": "56f2be4738414a2bb34f30ee5eda8d1c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56f2be4738414a2bb34f30ee5eda8d1c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56f2be4738414a2bb34f30ee5eda8d1c"}}, "title": "Single-cell proteo-transcriptomic profiling reveals altered characteristics of stem and progenitor cells in patients receiving cytoreductive hydroxyurea in early-phase chronic myeloid leukemia.", "authors": [{"family": "Komic", "given": "Hana", "initials": "H"}, {"family": "Nilsson", "given": "Malin S", "initials": "MS"}, {"family": "Wennstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Bandaru", "given": "Tagore Sanketh", "initials": "TS"}, {"family": "Jaako", "given": "Pekka", "initials": "P"}, {"family": "Hellstrand", "given": "Kristoffer", "initials": "K"}, {"family": "Thor\u00e9n", "given": "Fredrik B", "initials": "FB"}, {"family": "Martner", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-01-01", "journal": {"title": "Haematologica", "issn": "1592-8721", "issn-l": "0390-6078", "volume": "110", "issue": "1", "pages": "117-128"}, "abstract": "Hydroxyurea (HU) is frequently used in the early phase of chronic myeloid leukemia (CML) to achieve cytoreduction prior to tyrosine kinase inhibitor therapy. However, its impact on CML stem and progenitor cells (SPC) remains largely unknown. This study utilized targeted proteo-transcriptomic expression data on 596 genes and 51 surface proteins in 60,000 CD14-CD34+ cells from chronic phase CML patients to determine effects of short-term HU treatment (4-19 days) on CML SPC. Peripheral blood and bone marrow samples were obtained from 17 CML patients eligible for short-term HU treatment (3 patients before and after HU, 7 patients before HU and 7 patients after HU) and subjected to single-cell CITE-sequencing and/or flow cytometry analysis. The analysis revealed enhanced frequencies of hemoglobin-expressing (HBA1, HBA2, HBB) erythroid progenitor cells in blood and bone marrow following HU treatment. In addition, there was an accumulation of cell subsets with S/G2/M phase-related gene and protein expression, likely representing cells arrested in, or progressing slowly through, the cell cycle. The increased frequency of cells in S/G2/M phase after HU was observed already among the most immature leukemic stem cells (LSC), and patients with a large fraction of LSC in the S/G2/M phase showed poor responsiveness to tyrosine kinase inhibitor treatment. We conclude that short-term HU treatment entails differentiation of erythroid progenitor cells and alters the characteristics of LSC in CML. The results imply that studies of LSC and progenitor populations in CML should take effects of initial HU therapy into account.", "doi": "10.3324/haematol.2024.285071", "pmid": "39157872", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC11694111"}], "notes": [], "created": "2025-02-03T07:42:24.770Z", "modified": "2025-02-28T08:05:18.309Z"}, {"entity": "publication", "iuid": "ff4fe70fec054722bb6c07825a0a005c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff4fe70fec054722bb6c07825a0a005c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff4fe70fec054722bb6c07825a0a005c"}}, "title": "Non-nucleosomal (CENP-A/H4)2 - DNA complexes as a possible platform for centromere organization.", "authors": [{"family": "Ali-Ahmad", "given": "Ahmad", "initials": "A"}, {"family": "Mors", "given": "Mira", "initials": "M"}, {"family": "Carrer", "given": "Manuel", "initials": "M"}, {"family": "Li", "given": "Xinmeng", "initials": "X"}, {"family": "Bilokapi\u0107", "given": "Silvija", "initials": "S"}, {"family": "Hali\u0107", "given": "Mario", "initials": "M"}, {"family": "Cascella", "given": "Michele", "initials": "M"}, {"family": "Sekuli\u0107", "given": "Nikolina", "initials": "N", "orcid": "0000-0001-7555-3222", "researcher": {"href": "https://publications.scilifelab.se/researcher/8001cf16e3564c6f92230d00a03c9081.json"}}], "type": "journal article", "published": "2025-01-01", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The centromere is a part of the chromosome that is essential for the even segregation of duplicated chromosomes during cell division. It is epigenetically defined by the presence of the histone H3 variant CENP-A. CENP-A associates specifically with a group of 16 proteins that form the centromere-associated network of proteins (CCAN). In mitosis, the kinetochore forms on the CCAN to connect the duplicated chromosomes to the microtubules protruding from the cell poles. Previous studies have shown that CENP-A replaces H3 in nucleosomes, and recently the structures of CENP-A-containing nucleosomes in complex with CCANs have been revealed, but they show only a limited interaction between CCANs and CENP-A. Here, we report the cryoEM structure of 2x(CENP-A/H4)2-di-tetramers assembled on DNA in the absence of H2A/H2B histone dimer and speculate how (CENP-A/H4)2-tetramers and -di-tetramers might serve as a platform for CCAN organization.", "doi": "10.1101/2024.12.31.630874", "pmid": "39803555", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11722257"}, {"db": "pii", "key": "2024.12.31.630874"}], "notes": [], "created": "2025-11-03T14:02:25.613Z", "modified": "2025-11-03T14:02:25.745Z"}, {"entity": "publication", "iuid": "a748b4d74c7342cc95cfa6d89417bef1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a748b4d74c7342cc95cfa6d89417bef1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a748b4d74c7342cc95cfa6d89417bef1"}}, "title": "Dark carbon fixation is a common process in the water column of stratified boreal lakes.", "authors": [{"family": "Martin", "given": "Ga\u00ebtan", "initials": "G"}, {"family": "Rissanen", "given": "Antti J", "initials": "AJ"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Peura", "given": "Sari", "initials": "S"}], "type": "journal article", "published": "2025-01-01", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "958", "pages": "177433", "issn-l": "0048-9697"}, "abstract": "CO2 fixation (i.e. primary production) is a key function of all ecosystems, providing the carbon and energy that fuel the entire food web. It also plays an important role in mitigating climate change as CO2 is the most important greenhouse gas. While photosynthesis is regarded as the most important carbon fixation pathway, prokaryotes able to fix carbon in the absence of light (chemolithoautotrophs) can also be a significant source of energy in a light-limited ecosystem. Boreal lakes, notoriously colored and stratified with respect to oxygen and nutrients, present ideal conditions for this so-called dark carbon fixation by the chemolithoautotrophs. However, the prevalence of dark carbon fixation in boreal lakes remains unknown. Here, we measured dark carbon fixation in Swedish lakes from the boreal and boreo-nemoral zones, during summer stratification. We detected dark carbon fixation in 16 out of the 17 lakes studied, and concluded that dark fixation is a widespread phenomenon in boreal lakes. Moreover, the average dark primary production ranged from 18.5 % in the epilimnion to 81.4 % in the hypolimnion of all tested lakes. Our data further suggests that chemolithoautotrophic activity is mostly driven by iron-oxidizing bacteria. The chemolithoautotrophic guild is diverse and seems to be composed of both ubiquitous bacteria, like Gallionellaceae or Chromatiaceae, and endemic taxa, such as Ferrovaceae, which appears to be favored by a low pH. These results are particularly exciting as they suggest that dark carbon fixation could partly compensate for the low photosynthetic capacity in lakes with dark-colored water.", "doi": "10.1016/j.scitotenv.2024.177433", "pmid": "39522777", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(24)07590-9"}], "notes": [], "created": "2025-01-02T10:28:48.083Z", "modified": "2025-11-28T10:44:31.434Z"}, {"entity": "publication", "iuid": "cfad17f87f184fd5835abd8daa9d8ef3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cfad17f87f184fd5835abd8daa9d8ef3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cfad17f87f184fd5835abd8daa9d8ef3"}}, "title": "Vitamin B12 release through bacteriophage-mediated cell lysis of the marine bacterium Sulfitobacter sp. M39.", "authors": [{"family": "Sultana", "given": "Sabiha", "initials": "S", "orcid": "0000-0002-5243-8712", "researcher": {"href": "https://publications.scilifelab.se/researcher/20328a220fee49ce8c1d310446b21771.json"}}, {"family": "Bruns", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4267-7832", "researcher": {"href": "https://publications.scilifelab.se/researcher/7647be1e5f7244adac5972d8ff1afc44.json"}}, {"family": "Pacheco-Valenciana", "given": "Armando", "initials": "A", "orcid": "0009-0009-2801-0917", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4ac80e812df42d29f6b1138b20a834e.json"}}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Wilkes", "given": "Heinz", "initials": "H", "orcid": "0000-0002-0421-0107", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0cda4730d9e4f22906dca5cde7abcdf.json"}}, {"family": "Simon", "given": "Meinhard", "initials": "M", "orcid": "0000-0002-6151-6989", "researcher": {"href": "https://publications.scilifelab.se/researcher/9eb2e53a290f4762885d7796af9b48ad.json"}}, {"family": "Garcia", "given": "Sarahi", "initials": "S", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Wienhausen", "given": "Gerrit", "initials": "G", "orcid": "0000-0002-3562-5997", "researcher": {"href": "https://publications.scilifelab.se/researcher/d663d8ca36b545028fe4383709ccd0a3.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "5", "issue": "1", "pages": "ycaf136", "issn-l": null}, "abstract": "Vitamin B12 (B12) is an essential cofactor for vital metabolic processes in both prokaryotes and eukaryotes. De novo B12 biosynthesis is exclusively carried out by a modicum of prokaryotes, although being required by most organisms. Recently, it has been demonstrated that not all B12-prototrophic bacteria voluntarily share this vital cofactor and, therefore, are termed B12-retainers. Consequently, low biosynthesis potential and limited voluntary release lead to a large discrepancy between availability and demand for B12 in the ocean, indicating that release of B12 may be an important control. Hence, in this study, we examined a specific release process, cell lysis after phage infection. We isolated bacteriophages specific for the B12-prototrophic, yet B12-retainer bacterium Sulfitobacter sp. M39. The addition of the bacteriophages to a Sulfitobacter sp. M39 mono-culture led to a significant increase in virus-like particles, reduced bacterial growth, and quantifiable extracellular dissolved B12. When introducing bacteriophages to a co-culture comprising the host bacterium and the B12-auxotrophic diatom Thalassiosira pseudonana, we observed rapid response in the form of microalgal growth. Our results indicate that B12 is released as a result of bacteriophage-mediated cell lysis of Sulfitobacter sp. M39, enabling the growth of T. pseudonana in co-culture and possibly other microbes in nature. Therefore, we propose that bacteriophage-mediated cell lysis is a key mechanism for the release of essential metabolites, including vitamins, and given the estimated bacteriophage infection rates in the ocean, it plays a crucial role in the B-vitamin cycle in the marine environment.", "doi": "10.1093/ismeco/ycaf136", "pmid": "40994829", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12456174"}, {"db": "pii", "key": "ycaf136"}], "notes": [], "created": "2025-11-28T10:49:31.823Z", "modified": "2025-11-28T10:49:32.173Z"}, {"entity": "publication", "iuid": "f05fd6c1911a466280e1a2ff55f943e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f05fd6c1911a466280e1a2ff55f943e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f05fd6c1911a466280e1a2ff55f943e3"}}, "title": "Trees First Inhibit Then Promote Litter Decomposition in the Subarctic.", "authors": [{"family": "Jonsson", "given": "Micael", "initials": "M", "orcid": "0000-0002-1618-2617", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea45358bb3a146ffac63c13cba7f56c9.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Casta\u00f1o", "given": "Carles", "initials": "C"}, {"family": "Parker", "given": "Thomas C", "initials": "TC"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Ecol. Lett.", "issn": "1461-0248", "volume": "28", "issue": "1", "pages": "e70063", "issn-l": "1461-023X"}, "abstract": "Trees affect organic matter decomposition through allocation of recently fixed carbon belowground, but the magnitude and direction of this effect may depend on substrate type and decomposition stage. Here, we followed mass loss, chemical composition and fungal colonisation of leaf and root litters incubated in mountain birch forests over 4 years, in plots where belowground carbon allocation was severed by tree girdling or in control plots. Initially, girdling stimulated leaf and root litter mass loss by 12% and 22%, respectively, suggesting competitive release of saprotrophic decomposition when tree-mediated competition by ectomycorrhizal fungi was eliminated (Gadgil effect). After 4 years, girdling instead hampered mass loss of root litter by 30%, suggesting late-stage priming of decomposition in the presence of trees, in parallel with increased growth of shrubs and associated fungi following tree elimination. Hence, different mechanisms driving early- and late-stage litter decomposition should be considered in climate-feedback evaluations of plant-soil interactions.", "doi": "10.1111/ele.70063", "pmid": "39829292", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11744340"}], "notes": [], "created": "2025-03-07T09:47:53.171Z", "modified": "2025-10-17T13:03:52.434Z"}, {"entity": "publication", "iuid": "da8fa3d842b64984abe7d1407e8504e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da8fa3d842b64984abe7d1407e8504e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da8fa3d842b64984abe7d1407e8504e8"}}, "title": "The Transcriptomic and Gene Fusion Landscape of Pleomorphic Salivary Gland Adenomas.", "authors": [{"family": "Afshari", "given": "Maryam Kakay", "initials": "MK"}, {"family": "Tejera Nevado", "given": "Paloma", "initials": "P"}, {"family": "Fehr", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0002-2657-1392", "researcher": {"href": "https://publications.scilifelab.se/researcher/c833fc4136e34aa29e70836e5206875e.json"}}, {"family": "Huang", "given": "Junchi", "initials": "J"}, {"family": "J\u00e4wert", "given": "Fredrik", "initials": "F"}, {"family": "Nilsson", "given": "Jonas A", "initials": "JA"}, {"family": "Stenman", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-1017-7363", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ccb9761a5d6409095e090cf9a1edd9c.json"}}, {"family": "Andersson", "given": "Mattias K", "initials": "MK", "orcid": "0000-0001-6391-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c9dacff6854c5e968b9b615ef34956.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Genes Chromosomes Cancer", "issn": "1098-2264", "volume": "64", "issue": "1", "pages": "e70023", "issn-l": "1045-2257"}, "abstract": "Pleomorphic adenoma (PA) is the most common salivary gland tumor. PAs are characterized by chromosomal rearrangements of 8q12 and 12q14-15, leading to gene fusions involving the PLAG1 and HMGA2 oncogenes. Here, we performed the first comprehensive study of the transcriptomic and gene fusion landscape of 38 cytogenetically characterized PAs. RNA-seq identified PLAG1 or HMGA2 fusions in 33/38 cases (87%), of which 15 were novel fusions. Fusions were found also in tumors with normal karyotype, demonstrating that they are generated by cryptic rearrangements. PLAG1 was mainly activated by promoter swapping and HMGA2 by truncation of its 3'-part. RNA-seq revealed upregulation of genes involved in extracellular matrix production, WNT-signaling, and epithelial-mesenchymal transition in PA compared to normal salivary tissue. Principal component analysis identified two PA subclusters characterized by PLAG1- and HMGA2-activation, respectively, that differed in expression of genes involved in the immune system, cell adhesion, and microenvironment remodeling. Moreover, comparative analyses of PA and salivary carcinomas revealed that PA resembles myoepithelial carcinoma. Our study reveals new oncogenic gene fusions and expands our knowledge about the molecular underpinnings of PA.", "doi": "10.1002/gcc.70023", "pmid": "39812386", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11734380"}], "notes": [], "created": "2025-11-28T10:40:15.903Z", "modified": "2025-11-28T10:40:16.003Z"}, {"entity": "publication", "iuid": "408854eb0c68488e8f43d442b1150e6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/408854eb0c68488e8f43d442b1150e6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/408854eb0c68488e8f43d442b1150e6c"}}, "title": "Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.", "authors": [{"family": "Siljanen", "given": "Henri M P", "initials": "HMP", "orcid": "0000-0002-3197-1438", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a1fb0f39c4547438d0cdb35457a312c.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Hilts", "given": "Angus S", "initials": "AS"}, {"family": "Bagnoud", "given": "Alexandre", "initials": "A"}, {"family": "Alves", "given": "Ricardo J E", "initials": "RJE"}, {"family": "Jones", "given": "Christopher M", "initials": "CM"}, {"family": "Kerou", "given": "Melina", "initials": "M"}, {"family": "Sousa", "given": "Felipa L", "initials": "FL"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}, {"family": "Biasi", "given": "Christina", "initials": "C"}, {"family": "Schleper", "given": "Christa", "initials": "C", "orcid": "0000-0002-1918-2735", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ef5a3f76ba14a498f4eb6f0a7eeb465.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "5", "issue": "1", "pages": "ycaf183", "issn-l": null}, "abstract": "Microorganisms are key players in the global cycling of nitrogen and carbon, controlling their availability and fluxes, including the emissions of the powerful greenhouse gases nitrous oxide and methane. Standard sequencing methods often reveal only a limited fraction of their diversity, because of their low relative abundance, the insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage of DNA amplification-based assays. Here, we developed and tested a targeted metagenomics approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic nitrogen and methane cycling. We designed comprehensive probe libraries for each of the 14 target marker genes comprising 264 111 unique probes. In validation experiments with mock communities, targeted metagenomics yielded gene profiles similar to the original communities. Only GC content had a small effect on probe efficiency, as low GC targets were less efficiently detected than those with high GC, within the mock communities. Furthermore, the relative abundances of the marker genes obtained using targeted or traditional shotgun metagenomics were significantly correlated. In addition, using archaeal amoA genes as a case-study, targeted metagenomics identified a substantially higher taxonomic diversity and a larger number of sequence reads per sample, yielding diversity estimates 28 or 1.24 times higher than shotgun metagenomics or amplicon sequencing, respectively. Our results show that targeted metagenomics complements current approaches to characterize key microbial populations and functional guilds in biogeochemical cycles in different ecosystems, enabling more detailed, simultaneous characterization of multiple functional genes.", "doi": "10.1093/ismeco/ycaf183", "pmid": "41221508", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12598625"}, {"db": "pii", "key": "ycaf183"}], "notes": [], "created": "2025-11-21T12:38:28.515Z", "modified": "2025-11-21T12:38:28.801Z"}, {"entity": "publication", "iuid": "fb964a37469d46c3b8bea7ec226da10b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb964a37469d46c3b8bea7ec226da10b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb964a37469d46c3b8bea7ec226da10b"}}, "title": "Structural basis for lipid transfer by the ATG2A-ATG9A complex.", "authors": [{"family": "Wang", "given": "Yang", "initials": "Y", "orcid": "0000-0002-3839-0003", "researcher": {"href": "https://publications.scilifelab.se/researcher/9892fd666eaf4519bae74ec10977512e.json"}}, {"family": "Dahmane", "given": "Selma", "initials": "S"}, {"family": "Ti", "given": "Rujuan", "initials": "R", "orcid": "0000-0002-5169-8491", "researcher": {"href": "https://publications.scilifelab.se/researcher/b530a2ed7e1246b1842cfa8611ffc75d.json"}}, {"family": "Mai", "given": "Xinyi", "initials": "X", "orcid": "0009-0004-7828-061X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa46a9e3371a409c804847b14923f4a6.json"}}, {"family": "Zhu", "given": "Lizhe", "initials": "L", "orcid": "0000-0001-8252-7807", "researcher": {"href": "https://publications.scilifelab.se/researcher/8275c054d43b45b79f49c1a95b10a806.json"}}, {"family": "Carlson", "given": "Lars-Anders", "initials": "LA", "orcid": "0000-0003-2342-6488", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba0e366ce21e49b48212bbed5a0a7bd1.json"}}, {"family": "Stjepanovic", "given": "Goran", "initials": "G", "orcid": "0000-0002-4841-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/a25e20f893d94f8d963403da7eb2a5e1.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "32", "issue": "1", "pages": "35-47", "issn-l": "1545-9985"}, "abstract": "Autophagy is characterized by the formation of double-membrane vesicles called autophagosomes. Autophagy-related proteins (ATGs) 2A and 9A have an essential role in autophagy by mediating lipid transfer and re-equilibration between membranes for autophagosome formation. Here we report the cryo-electron microscopy structures of human ATG2A in complex with WD-repeat protein interacting with phosphoinositides 4 (WIPI4) at 3.2 \u00c5 and the ATG2A-WIPI4-ATG9A complex at 7 \u00c5 global resolution. On the basis of molecular dynamics simulations, we propose a mechanism of lipid extraction from the donor membranes. Our analysis revealed 3:1 stoichiometry of the ATG9A-ATG2A complex, directly aligning the ATG9A lateral pore with ATG2A lipid transfer cavity, and an interaction of the ATG9A trimer with both the N-terminal and the C-terminal tip of rod-shaped ATG2A. Cryo-electron tomography of ATG2A liposome-binding states showed that ATG2A tethers lipid vesicles at different orientations. In summary, this study provides a molecular basis for the growth of the phagophore membrane and lends structural insights into spatially coupled lipid transport and re-equilibration during autophagosome formation.", "doi": "10.1038/s41594-024-01376-6", "pmid": "39174844", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41594-024-01376-6"}], "notes": [], "created": "2024-11-27T11:37:36.821Z", "modified": "2025-10-29T14:46:12.392Z"}, {"entity": "publication", "iuid": "cb9abacb425b499abdf2ca6a8bf4b41a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb9abacb425b499abdf2ca6a8bf4b41a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb9abacb425b499abdf2ca6a8bf4b41a"}}, "title": "Plasma proteomics in epilepsy: Network-based identification of proteins associated with seizures.", "authors": [{"family": "Ashtiani", "given": "Saman Hosseini", "initials": "SH"}, {"family": "Akel", "given": "Sarah", "initials": "S"}, {"family": "Berger", "given": "Evelin", "initials": "E"}, {"family": "Zelano", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Epilepsy Res", "issn": "1872-6844", "volume": "209", "pages": "107480", "issn-l": null}, "abstract": "Identification of potential biomarkers of seizures.\n\nIn this exploratory study, we quantified plasma protein intensities in 15 patients with recent seizures compared to 15 patients with long-standing seizure freedom. Using TMT-based proteomics we found fifty-one differentially expressed proteins.\n\nNetwork analyses including co-expression networks and protein-protein interaction networks, using the STRING database, followed by network centrality and modularity analyses revealed 22 protein modules, with one module showing a significant association with seizures. The protein-protein interaction network centered around this module identified a subnetwork of 125 proteins, grouped into four clusters. Notably, one cluster (mainly enriching inflammatory pathways and Gene Ontology terms) demonstrated the highest enrichment of known epilepsy-related genes.\n\nOverall, our network-based approach identified a protein module linked with seizures. The module contained known markers of epilepsy and inflammation. The results also demonstrate the potential of network analysis in discovering new biomarkers for improved epilepsy management.", "doi": "10.1016/j.eplepsyres.2024.107480", "pmid": "39626528", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0920-1211(24)00195-5"}], "notes": [], "created": "2025-10-23T12:18:27.646Z", "modified": "2025-10-23T12:18:27.652Z"}, {"entity": "publication", "iuid": "4e7a9e7c4d2c4b9f97fe7db41cc35680", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e7a9e7c4d2c4b9f97fe7db41cc35680.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e7a9e7c4d2c4b9f97fe7db41cc35680"}}, "title": "Modification of xylan in secondary walls alters cell wall biosynthesis and wood formation programs and improves saccharification.", "authors": [{"family": "Sivan", "given": "Pramod", "initials": "P", "orcid": "0000-0001-5297-2221", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bed5958298d4ca08df06860c94a3878.json"}}, {"family": "Urbancsok", "given": "J\u00e1nos", "initials": "J", "orcid": "0000-0003-3237-6806", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6f0e25417543f49060959d3af92967.json"}}, {"family": "Donev", "given": "Evgeniy N", "initials": "EN", "orcid": "0000-0002-7279-0481", "researcher": {"href": "https://publications.scilifelab.se/researcher/26467c84e2664b4980a4ed04335860ad.json"}}, {"family": "Derba-Maceluch", "given": "Marta", "initials": "M", "orcid": "0000-0002-8034-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5be452cef9048e19a08fa8043b74329.json"}}, {"family": "Barbut", "given": "F\u00e9lix R", "initials": "FR", "orcid": "0000-0001-5395-6776", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df5c17bbf0440fd8be22761c2df9a6f.json"}}, {"family": "Yassin", "given": "Zakiya", "initials": "Z", "orcid": "0000-0001-6878-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cd7ddc17274c0c9eabb07ae4e6c8e0.json"}}, {"family": "Gandla", "given": "Madhavi L", "initials": "ML", "orcid": "0000-0003-2798-6298", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1e32323239243999cbb5f1dcc06279a.json"}}, {"family": "Mitra", "given": "Madhusree", "initials": "M", "orcid": "0000-0002-8653-8770", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1827f45c7f4853888f15d857b7e414.json"}}, {"family": "Heinonen", "given": "Saara E", "initials": "SE", "orcid": "0000-0002-5069-2370", "researcher": {"href": "https://publications.scilifelab.se/researcher/3756b55888f745e6b7af3783e80b6037.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Cermanov\u00e1", "given": "Kate\u0159ina", "initials": "K", "orcid": "0009-0006-5809-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/16ca192806d6450fb69225e175eef629.json"}}, {"family": "Karady", "given": "Michal", "initials": "M", "orcid": "0000-0002-5603-706X", "researcher": {"href": "https://publications.scilifelab.se/researcher/114911ccd31849e1a7584b5a52e9eb14.json"}}, {"family": "Scheepers", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-5630-1377", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a566216ee146d1bba50d7f8779a6f8.json"}}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ", "orcid": "0000-0003-3866-0111", "researcher": {"href": "https://publications.scilifelab.se/researcher/1769e674df8649ce82a0d058f0a309dc.json"}}, {"family": "Master", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-6837-9817", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b15165d3c44d74a533948db1aa2d9a.json"}}, {"family": "Vilaplana", "given": "Francisco", "initials": "F", "orcid": "0000-0003-3572-7798", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ee4f3eaece8487fb5cb34ce6cfbbcbf.json"}}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Plant Biotechnol. J.", "issn": "1467-7652", "volume": "23", "issue": "1", "pages": "174-197", "issn-l": "1467-7644"}, "abstract": "Wood of broad-leaf tree species is a valued source of renewable biomass for biorefinery and a target for genetic improvement efforts to reduce its recalcitrance. Glucuronoxylan (GX) plays a key role in recalcitrance through its interactions with cellulose and lignin. To reduce recalcitrance, we modified wood GX by expressing GH10 and GH11 endoxylanases from Aspergillus nidulans in hybrid aspen (Populus tremula L. \u00d7 tremuloides Michx.) and targeting the enzymes to cell wall. The xylanases reduced tree height, modified cambial activity by increasing phloem and reducing xylem production, and reduced secondary wall deposition. Xylan molecular weight was decreased, and the spacing between acetyl and MeGlcA side chains was reduced in transgenic lines. The transgenic trees produced hypolignified xylem having thin secondary walls and deformed vessels. Glucose yields of enzymatic saccharification without pretreatment almost doubled indicating decreased recalcitrance. The transcriptomics, hormonomics and metabolomics data provided evidence for activation of cytokinin and ethylene signalling pathways, decrease in ABA levels, transcriptional suppression of lignification and a subset of secondary wall biosynthetic program, including xylan glucuronidation and acetylation machinery. Several candidate genes for perception of impairment in xylan integrity were detected. These candidates could provide a new target for uncoupling negative growth effects from reduced recalcitrance. In conclusion, our study supports the hypothesis that xylan modification generates intrinsic signals and evokes novel pathways regulating tree growth and secondary wall biosynthesis.", "doi": "10.1111/pbi.14487", "pmid": "39436777", "labels": {"Cryo-EM": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11672743"}], "notes": [], "created": "2024-11-26T10:43:47.363Z", "modified": "2025-11-18T12:14:05.231Z"}, {"entity": "publication", "iuid": "290689bdb98b41e3a73b4db0e3880ab2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/290689bdb98b41e3a73b4db0e3880ab2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/290689bdb98b41e3a73b4db0e3880ab2"}}, "title": "Influence of gas composition on carbonation of quicklime granules derived from different limestone types", "authors": [{"family": "Olovsson", "given": "Katarzyna", "initials": "K", "orcid": "0000-0003-0264-0119", "researcher": {"href": "https://publications.scilifelab.se/researcher/35ec465dffc94fa99f81a50743663025.json"}}, {"family": "Ma", "given": "Charlie", "initials": "C", "orcid": "0000-0002-0555-5924", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfe1a7690d74481f8f301a43e338a923.json"}}, {"family": "Niinipuu", "given": "Mirva", "initials": "M", "orcid": "0000-0002-8890-835X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2560d090c446d3a9d077962995e03e.json"}}, {"family": "Eriksson", "given": "Matias", "initials": "M", "orcid": "0000-0002-8230-8847", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c55106cf10249b99b89441637f69785.json"}}, {"family": "Brostr\u00f6m", "given": "Markus", "initials": "M", "orcid": "0000-0003-1095-9154", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dfb704d36cc4a56b4af4feba403366b.json"}}], "type": "journal-article", "published": "2025-01-00", "journal": {"title": "Chemical Engineering Journal", "issn": "1385-8947", "volume": "506", "pages": "159543", "issn-l": null}, "abstract": null, "doi": "10.1016/j.cej.2025.159543", "pmid": null, "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [], "notes": [], "created": "2025-06-23T08:15:59.332Z", "modified": "2025-06-23T08:15:59.651Z"}, {"entity": "publication", "iuid": "193d0e547a784b80b269e0e08086d427", "links": {"self": {"href": "https://publications.scilifelab.se/publication/193d0e547a784b80b269e0e08086d427.json"}, "display": {"href": "https://publications.scilifelab.se/publication/193d0e547a784b80b269e0e08086d427"}}, "title": "High temperature exposure of MgO-based refractory material to biomass and coal ash with/without quicklime", "authors": [{"family": "Wagri", "given": "Naresh Kumar", "initials": "NK", "orcid": "0000-0002-3342-6257", "researcher": {"href": "https://publications.scilifelab.se/researcher/0837fb6c09c24a40969724ae3775e30e.json"}}, {"family": "Carlborg", "given": "Markus", "initials": "M", "orcid": "0000-0003-1170-2203", "researcher": {"href": "https://publications.scilifelab.se/researcher/26fe5bc8719f49819b89db2ffb27b86a.json"}}, {"family": "Eriksson", "given": "Matias", "initials": "M", "orcid": "0000-0002-8230-8847", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c55106cf10249b99b89441637f69785.json"}}, {"family": "Ma", "given": "Charlie", "initials": "C", "orcid": "0000-0002-0555-5924", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfe1a7690d74481f8f301a43e338a923.json"}}, {"family": "Brostr\u00f6m", "given": "Markus", "initials": "M"}, {"family": "Andersson", "given": "Britt M", "initials": "BM"}], "type": "journal-article", "published": "2025-01-00", "journal": {"title": "Ceramics International", "issn": "0272-8842", "volume": "51", "issue": "3", "pages": "3665-3674", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ceramint.2024.11.342", "pmid": null, "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-03T14:31:12.497Z", "modified": "2025-11-03T14:31:13.028Z"}, {"entity": "publication", "iuid": "fba0d7b6a97747c09f80ef78ddda9b8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fba0d7b6a97747c09f80ef78ddda9b8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fba0d7b6a97747c09f80ef78ddda9b8a"}}, "title": "Genomic prediction for yield and malting traits in barley using metabolomic and near-infrared spectra", "authors": [{"family": "Raffo", "given": "Miguel A", "initials": "MA", "orcid": "0000-0002-5330-0117", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4f26266129c4358a4145db198d39ef1.json"}}, {"family": "Sarup", "given": "Pernille", "initials": "P"}, {"family": "Jensen", "given": "Just", "initials": "J"}, {"family": "Guo", "given": "Xiangyu", "initials": "X"}, {"family": "Jensen", "given": "Jens D", "initials": "JD"}, {"family": "Orabi", "given": "Jihad", "initials": "J"}, {"family": "Jahoor", "given": "Ahmed", "initials": "A"}, {"family": "Christensen", "given": "Ole F", "initials": "OF"}], "type": "journal-article", "published": "2025-01-00", "journal": {"title": "Theor. Appl. Genet.", "issn": "0040-5752", "volume": "138", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1007/s00122-024-04806-7", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:05:20.932Z", "modified": "2025-11-27T08:05:20.992Z"}, {"entity": "publication", "iuid": "5349c9c87a5f4d3ca6bfb3ddc7dd6e9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5349c9c87a5f4d3ca6bfb3ddc7dd6e9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5349c9c87a5f4d3ca6bfb3ddc7dd6e9e"}}, "title": "Genomic analyses of Streptococcus uberis reveal high diversity but few antibiotic resistance genes.", "authors": [{"family": "Myren\u00e5s", "given": "Mattias", "initials": "M"}, {"family": "Fasth", "given": "Charlotta", "initials": "C"}, {"family": "Waller", "given": "Karin Persson", "initials": "KP"}, {"family": "Pedersen", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Vet. Microbiol.", "issn": "1873-2542", "pages": "110319", "volume": "300", "issn-l": "0378-1135"}, "abstract": "This study aimed to investigate the diversity of milk isolates of Streptococcus uberis from Swedish dairy cows with mastitis, focusing on antibiotic resistance and virulence genes. We analyzed 115 S. uberis isolates using whole genome sequencing revealing a high level of diversity. Within the same farms, we identified both indistinguishable strains with identical sequence types (ST), and distinct isolates belonging to different ST types. This suggests both clonal and non-clonal spread of the bacterium, although primarily non-clonal. We found small clusters of two to eight closely related isolates both within and between farms. Differences in penicillin susceptibility were observed, probably linked to specific variants of penicillin-binding proteins. Few isolates were resistant to antibiotics, and few resistance genes were detected. In most cases, only one or two resistance genes were present, and only one isolate was multi-drug resistant. Two isolates had resistance genes against tetracyclines, a tet(M) and a tet(O) gene, two had a resistance gene against lincosamides, an lnu(C) and an lnu(D) gene, while a single isolate had an erm(B) gene conferring resistance to both macrolides and lincosamides. A single isolate carried a mef(A) gene, which confers resistance to macrolides via an efflux pump mechanism. However, we found aminoglycoside genes in 10 isolates, all 10 had the ant(6)-Ia gene, and one in addition aph(3')-IIIa, and a spectinomycin resistance gene, spw, in eight isolates. Finally, one isolate carried a streptothricin resistance gene, sat4. The genes sat4 and spw have apparently not previously been reported in S. uberis. Interestingly, isolates with elevated MIC to penicillin also significantly more often carried other resistance factors. Most isolates carried several virulence genes, including genes for capsule formation, adhesion to host cells or extracellular matrix proteins, and acquisition of essential nutritional factors, such as amino acids, iron and manganese.", "doi": "10.1016/j.vetmic.2024.110319", "pmid": "39637769", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0378-1135(24)00341-9"}], "notes": [], "created": "2024-12-02T10:18:20.717Z", "modified": "2025-12-04T19:40:02.674Z"}, {"entity": "publication", "iuid": "ee11bee97a924e04a5bba733daee0f30", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee11bee97a924e04a5bba733daee0f30.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee11bee97a924e04a5bba733daee0f30"}}, "title": "GBA1 T369M and Parkinson's disease - Further evidence of a lack of association in the Swedish population.", "authors": [{"family": "Brolin", "given": "Kajsa Atterling", "initials": "KA"}, {"family": "B\u00e4ckstr\u00f6m", "given": "David", "initials": "D"}, {"family": "Wallenius", "given": "Joel", "initials": "J"}, {"family": "Gan-Or", "given": "Ziv", "initials": "Z"}, {"family": "Puschmann", "given": "Andreas", "initials": "A"}, {"family": "Hansson", "given": "Oskar", "initials": "O"}, {"family": "Swanberg", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Parkinsonism Relat Disord", "issn": "1873-5126", "volume": "130", "pages": "107191", "issn-l": null}, "abstract": "Variants in GBA1 are important genetic risk factors in Parkinson's disease (PD). GBA1 T369M has been linked to an \u223c80 % increased PD risk but the reports are conflicting and the relevance of GBA1 variants in different populations varies. A lack of association between T369M and PD in the Swedish population was recently reported but needs further validation. We therefore investigated T369M in 1,808 PD patients and 2,183 controls and our results support that T369M is not a risk factor for PD in the Swedish population.", "doi": "10.1016/j.parkreldis.2024.107191", "pmid": "39514913", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pii", "key": "S1353-8020(24)01203-3"}], "notes": [], "created": "2025-11-13T07:38:17.747Z", "modified": "2025-11-13T07:38:17.752Z"}, {"entity": "publication", "iuid": "7d89d814d9874e31955b377449ab58ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d89d814d9874e31955b377449ab58ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d89d814d9874e31955b377449ab58ee"}}, "title": "Fear extinction retention in children, adolescents, and adults.", "authors": [{"family": "Widegren", "given": "Ebba", "initials": "E"}, {"family": "Vegelius", "given": "Johan", "initials": "J"}, {"family": "Frick", "given": "Matilda A", "initials": "MA"}, {"family": "Roy", "given": "Ashika A", "initials": "AA"}, {"family": "M\u00f6ller", "given": "Stefan", "initials": "S"}, {"family": "Kleberg", "given": "Johan Lundin", "initials": "JL"}, {"family": "Hoppe", "given": "Johanna Motilla", "initials": "JM"}, {"family": "Hjorth", "given": "Olof", "initials": "O"}, {"family": "F\u00e4llmar", "given": "David", "initials": "D"}, {"family": "Pine", "given": "Daniel S", "initials": "DS"}, {"family": "Brocki", "given": "Karin", "initials": "K"}, {"family": "Gingnell", "given": "Malin", "initials": "M"}, {"family": "Frick", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Dev Cogn Neurosci", "issn": "1878-9307", "volume": "71", "pages": "101509", "issn-l": null}, "abstract": "Past results suggest that fear extinction and the return of extinguished fear are compromised in adolescents. However, findings have been inconclusive as there is a lack of fear extinction and extinction retention studies including children, adolescents and adults. In the present study, 36 children (6-9 years), 40 adolescents (13-17 years) and 44 adults (30-40 years), underwent a two-day fear conditioning task. Habituation, acquisition, and extinction were performed on the first day and an extinction retention test > 24 h later. Skin conductance responses were recorded during all phases of fear conditioning and functional magnetic resonance imaging (fMRI) was conducted during the fear retention test. All groups acquired and extinguished fear as measured with SCR, with no group differences in SCR during extinction retention. The groups had largely similar neural fear responses during the retention test, apart from adolescents displaying stronger amygdala fear response than children, with no differences between adolescents and adults. The findings do not support an adolescent extinction dip, and there was only marginal evidence of progressive changes in fear conditioning across development. In contrast to findings in rodents, fear conditioning in humans may elicit similar physiological responses and recruit similar neural networks from childhood to adulthood.", "doi": "10.1016/j.dcn.2025.101509", "pmid": "39799854", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11773086"}, {"db": "pii", "key": "S1878-9293(25)00004-0"}], "notes": [], "created": "2025-11-28T10:42:36.595Z", "modified": "2025-11-28T10:42:36.614Z"}, {"entity": "publication", "iuid": "bdd145617e0c401ea708379b0493f458", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdd145617e0c401ea708379b0493f458.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdd145617e0c401ea708379b0493f458"}}, "title": "Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden.", "authors": [{"family": "T\u00e5ng Hallb\u00e4ck", "given": "Erika", "initials": "E"}, {"family": "Bj\u00f6rkman", "given": "Jonas T", "initials": "JT"}, {"family": "Dyrkell", "given": "Fredrik", "initials": "F"}, {"family": "Welander", "given": "Jenny", "initials": "J"}, {"family": "Fang", "given": "Hong", "initials": "H"}, {"family": "Sylvin", "given": "Isak", "initials": "I"}, {"family": "Kaden", "given": "Ren", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications.scilifelab.se/researcher/018870b1d0034ee09552a3ae451d5504.json"}}, {"family": "Eilers", "given": "Hinnerk", "initials": "H"}, {"family": "S\u00f6derlund Strand", "given": "Anna", "initials": "A"}, {"family": "Mernelius", "given": "Sara", "initials": "S"}, {"family": "Berglind", "given": "Linda", "initials": "L"}, {"family": "Campillay Lagos", "given": "Amaya", "initials": "A"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}, {"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "11", "issue": "1", "issn-l": null}, "abstract": "Background. National epidemiological investigations of microbial infections greatly benefit from the increased information gained by whole-genome sequencing (WGS) in combination with standardized approaches for data sharing and analysis.Aim. To evaluate the quality and accuracy of WGS data generated by different laboratories but analysed by joint pipelines to reach a national surveillance approach.Methods. A national methicillin-resistant Staphylococcus aureus (MRSA) collection of 20 strains was distributed to nine participating laboratories that performed in-house procedures for WGS. Raw data were shared and analysed by three pipelines: 1928 Diagnostics, JASEN (GMS pipeline) and CLC-Genomics Workbench. The outcomes were compared according to quality, correct strain identification and genetic distances.Results. One isolate contained intraspecies contamination and was excluded from further analysis. The mean sequencing depth varied between sites and technologies. However, all analysis methods identified 12 strains that belonged to one of five outbreak clusters. The cut-off definition was set to <10 allele differences for core genome multilocus sequence typing (cgMLST) and <20 genetic differences for SNP analysis in a pairwise comparison.Conclusions. MRSA isolates, which are whole genome sequenced by different laboratories and analysed using the same bioinformatic pipelines, yielded comparable results for outbreak clustering for both cgMLST and SNP, using the 1928 analysis pipeline. In this study, JASEN was best suited to analyse Illumina data and CLC to analyse within respective technology. In the future, real-time sharing of data and harmonized analysis within the Genomic Medicine Sweden consortium will further facilitate investigations of outbreaks and transmission routes.", "doi": "10.1099/mgen.0.001331", "pmid": "39869391", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11893271"}], "notes": [], "created": "2025-03-19T04:58:38.247Z", "modified": "2025-11-19T15:18:20.002Z"}, {"entity": "publication", "iuid": "b1486cd2f8e04ed5a94771fa99efe1eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1486cd2f8e04ed5a94771fa99efe1eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1486cd2f8e04ed5a94771fa99efe1eb"}}, "title": "DNA methylation in cord blood partially mediates the effects of prepregnancy BMI on early childhood offspring BMI.", "authors": [{"family": "Maguolo", "given": "Alice", "initials": "A", "orcid": "0000-0002-8921-2012", "researcher": {"href": "https://publications.scilifelab.se/researcher/cac232a66c6745f7b74d2b52ec0d007a.json"}}, {"family": "J\u00f6nsson", "given": "Josefine", "initials": "J"}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Maziarz", "given": "Marlena", "initials": "M"}, {"family": "Vaag", "given": "Allan", "initials": "A"}, {"family": "Malchau Carlsen", "given": "Emma", "initials": "E"}, {"family": "N\u00f8rgaard", "given": "Kirsten", "initials": "K"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Renault", "given": "Kristina M", "initials": "KM"}, {"family": "Ling", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-0587-7154", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7c1ea934034c4db99f31a5a9b04691.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Obesity (Silver Spring)", "issn": "1930-739X", "volume": "33", "issue": "1", "pages": "177-189", "issn-l": "1930-7381"}, "abstract": "We investigated whether prepregnancy BMI (prePregBMI) in women with obesity was associated with differential DNA methylation (DNAm) in cord blood (CB) and whether DNAm may mediate the association of prePregBMI and early childhood BMI z score (BMIz).\n\nFrom the Treatment of Obese Pregnant Women (TOP) study, 232 mother-child pairs were included. We conducted an epigenome-wide association study on prePregBMI and CB DNAm (450k array), followed by causal mediation analyses to test whether DNAm may mediate effects of prePregBMI on BMIz at age 36 months (BMIz36).\n\nDNAm at 5345 CpG sites annotated to 2842 genes, which were overrepresented in biological processes linked to carbohydrate metabolism and plasma lipoprotein particle clearance, was associated with prePregBMI (false discovery rate < 10%). Causal mediation analyses of 168 methylation sites associated with BMIz36 (p < 0.05) and overlapping with the 5345 prePregBMI-associated sites identified two sites on SYT7 and DEAF1, partially mediating the effect of prePregBMI on BMIz36 (p \u2264 0.01). After cross-validation, a methylation risk score including these two sites could predict the highest quartile of BMIz36 and fat mass (in grams) with area under the curve = 0.72 (95% CI: 0.58-0.85) and area under the curve = 0.71 (95% CI: 0.58-0.85), respectively.\n\nCB DNAm at birth may partially mediate effects of prePregBMI on early childhood BMIz36, supporting its plausible role in influencing individual future obesity risk.", "doi": "10.1002/oby.24174", "pmid": "39663190", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11664306"}], "notes": [], "created": "2025-10-30T13:55:22.871Z", "modified": "2025-10-30T13:55:22.979Z"}, {"entity": "publication", "iuid": "55cc172df86e4099b106c060fad2288c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55cc172df86e4099b106c060fad2288c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55cc172df86e4099b106c060fad2288c"}}, "title": "Compound heterozygosity for two variants in BMP5 in human skeletal dysostosis with atrioventricular septal defect.", "authors": [{"family": "Gregersen", "given": "Pernille Ax\u00e9l", "initials": "PA", "orcid": "0000-0003-3424-0590", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2dcac90613841b7bb9301807a321e1e.json"}}, {"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A"}, {"family": "Graversen", "given": "Lise", "initials": "L", "orcid": "0000-0003-2395-8281", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed33e53a027c4074b6a42b576e644b2a.json"}}, {"family": "Brix", "given": "Nis", "initials": "N"}, {"family": "Lindel\u00f6f", "given": "Hillevi", "initials": "H"}, {"family": "Jensen", "given": "Uffe Birk", "initials": "UB"}, {"family": "Farholt", "given": "Stense", "initials": "S"}, {"family": "Rubak", "given": "Sune", "initials": "S"}, {"family": "Bjerre", "given": "Jesper", "initials": "J"}, {"family": "Piticchio", "given": "Serena G", "initials": "SG"}, {"family": "Terkelsen", "given": "Thorkild", "initials": "T"}, {"family": "Nishimura", "given": "Gen", "initials": "G"}, {"family": "Hellfritzsch", "given": "Michel Bach", "initials": "MB"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G"}], "type": "case reports", "published": "2025-01-00", "journal": {"title": "Clin. Genet.", "issn": "1399-0004", "volume": "107", "issue": "1", "pages": "78-82", "issn-l": "0009-9163"}, "abstract": "The growth and development of the skeleton is regulated by bone morphogenetic proteins of which several are linked to genetic skeletal disorders. So far, no human skeletal malformations have been associated with variants in BMP5. Here, we report a patient with biallelic loss of function variants in BMP5 and a syndromic phenotype including skeletal dysostosis, dysmorphic features, hypermobility, laryngo-tracheo-bronchomalacia and atrioventricular septal defect. We discuss the phenotype in relation to the known tissue-specific expression of Bmp5 and similar morphological abnormalities previously reported in experimental animal models. Our findings suggest a new association between BMP5 variants and a range of developmental anomalies, involving ears, heart and skeleton, thereby increasing understanding of BMP5's role in human development.", "doi": "10.1111/cge.14616", "pmid": "39239663", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11608849"}], "notes": [], "created": "2024-11-27T15:01:51.628Z", "modified": "2025-11-18T20:44:04.808Z"}, {"entity": "publication", "iuid": "656ad6d489a54917a2c05b8bc7e803cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/656ad6d489a54917a2c05b8bc7e803cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/656ad6d489a54917a2c05b8bc7e803cc"}}, "title": "Comparative Analysis of Traditional and Pharmacometric-Based Pharmacoeconomic Modeling in the Cost-Utility Evaluation of Sunitinib Therapy.", "authors": [{"family": "Centanni", "given": "Maddalena", "initials": "M", "orcid": "0000-0001-6594-9813", "researcher": {"href": "https://publications.scilifelab.se/researcher/4305500882954dad917066dff43f3df8.json"}}, {"family": "Nijhuis", "given": "Janine", "initials": "J"}, {"family": "Karlsson", "given": "Mats O", "initials": "MO", "orcid": "0000-0003-1258-8297", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b7ca3868f0b431799ea51c4641d1e5a.json"}}, {"family": "Friberg", "given": "Lena E", "initials": "LE", "orcid": "0000-0002-2979-679X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23b6e6225d15433f8eccc444c450adfc.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Pharmacoeconomics", "issn": "1179-2027", "volume": "43", "issue": "1", "pages": "31-43", "issn-l": null}, "abstract": "Cost-utility analyses (CUAs) increasingly use models to predict long-term outcomes and translate trial data to real-world settings. Model structure uncertainty affects these predictions. This study compares pharmacometric against traditional pharmacoeconomic model evaluations for CUAs of sunitinib in gastrointestinal stromal tumors (GIST).\n\nA two-arm trial comparing sunitinib 37.5 mg daily with no treatment was simulated using a pharmacometric-based pharmacoeconomic model framework. Overall, four existing models [time-to-event (TTE) and Markov models] were re-estimated to the survival data and linked to logistic regression models describing the toxicity data [neutropenia, thrombocytopenia, hypertension, fatigue, and hand-foot syndrome (HFS)] to create traditional pharmacoeconomic model frameworks. All five frameworks were used to simulate clinical outcomes and sunitinib treatment costs, including a therapeutic drug monitoring (TDM) scenario.\n\nThe pharmacometric model framework predicted that sunitinib treatment costs an additional 142,756 euros per quality adjusted life year (QALY) compared with no treatment, with deviations - 21.2% (discrete Markov), - 15.1% (continuous Markov), + 7.2% (TTE Weibull), and + 39.6% (TTE exponential) from the traditional model frameworks. The pharmacometric framework captured the change in toxicity over treatment cycles (e.g., increased HFS incidence until cycle 4 with a decrease thereafter), a pattern not observed in the pharmacoeconomic frameworks (e.g., stable HFS incidence over all treatment cycles). Furthermore, the pharmacoeconomic frameworks excessively forecasted the percentage of patients encountering subtherapeutic concentrations of sunitinib over the course of time (pharmacoeconomic: 24.6% at cycle 2 to 98.7% at cycle 16, versus pharmacometric: 13.7% at cycle 2 to 34.1% at cycle 16).\n\nModel structure significantly influences CUA predictions. The pharmacometric-based model framework more closely represented real-world toxicity trends and drug exposure changes. The relevance of these findings depends on the specific question a CUA seeks to address.", "doi": "10.1007/s40273-024-01438-z", "pmid": "39327347", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11724784"}, {"db": "pii", "key": "10.1007/s40273-024-01438-z"}], "notes": [], "created": "2025-11-28T10:41:39.516Z", "modified": "2025-11-28T10:41:39.635Z"}, {"entity": "publication", "iuid": "29a0dbb0cdc140658fd8f1844edd0aad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29a0dbb0cdc140658fd8f1844edd0aad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29a0dbb0cdc140658fd8f1844edd0aad"}}, "title": "Chemogenomic Screening in a Patient\u2010Derived 3D Fatty Liver Disease Model Reveals the CHRM1\u2010TRPM8 Axis as a Novel Module for Targeted Intervention", "authors": [{"family": "Youhanna", "given": "Sonia", "initials": "S"}, {"family": "Kemas", "given": "Aurino M", "initials": "AM"}, {"family": "Wright", "given": "Shane C", "initials": "SC"}, {"family": "Zhong", "given": "Yi", "initials": "Y"}, {"family": "Klumpp", "given": "Britta", "initials": "B"}, {"family": "Klein", "given": "Kathrin", "initials": "K"}, {"family": "Motso", "given": "Aikaterini", "initials": "A"}, {"family": "Michel", "given": "Maurice", "initials": "M"}, {"family": "Ziegler", "given": "Nicole", "initials": "N"}, {"family": "Shang", "given": "Mingmei", "initials": "M"}, {"family": "Sabatier", "given": "Pierre", "initials": "P"}, {"family": "Kannt", "given": "Aimo", "initials": "A"}, {"family": "Sheng", "given": "Hongda", "initials": "H"}, {"family": "Oliva\u2010Vilarnau", "given": "Nuria", "initials": "N"}, {"family": "B\u00fcttner", "given": "Florian A", "initials": "FA"}, {"family": "Seashore\u2010Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Schreiner", "given": "Jonas", "initials": "J"}, {"family": "Windbergs", "given": "Maike", "initials": "M"}, {"family": "Cornillet", "given": "Martin", "initials": "M"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK"}, {"family": "H\u00fclsmeier", "given": "Andreas J", "initials": "AJ"}, {"family": "Hornemann", "given": "Thorsten", "initials": "T"}, {"family": "Olsen", "given": "Jesper V", "initials": "JV"}, {"family": "Wang", "given": "Yi", "initials": "Y"}, {"family": "Gramignoli", "given": "Roberto", "initials": "R"}, {"family": "Sundstr\u00f6m", "given": "Michael", "initials": "M"}, {"family": "Lauschke", "given": "Volker M", "initials": "VM", "orcid": "0000-0002-1140-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/29c123916fbf4948a911560c1a259496.json"}}], "type": "journal-article", "published": "2025-01-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "12", "issue": "3", "issn-l": null}, "abstract": null, "doi": "10.1002/advs.202407572", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2025-04-23T09:39:57.949Z", "modified": "2025-10-17T13:04:26.969Z"}, {"entity": "publication", "iuid": "14530d7aa2004964a747e0dc46f3c5aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14530d7aa2004964a747e0dc46f3c5aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14530d7aa2004964a747e0dc46f3c5aa"}}, "title": "Can genetic diversity in microalgae species be explained by climate: an overview of metabarcoding with diatoms.", "authors": [{"family": "Kula\u0161", "given": "Antonija", "initials": "A", "orcid": "0000-0003-0619-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/08acba03d1b445a7b4d0571c287b723b.json"}}, {"family": "Lemonnier", "given": "Clarisse", "initials": "C"}, {"family": "Alric", "given": "Benjamin", "initials": "B"}, {"family": "Kahlert", "given": "Maria", "initials": "M"}, {"family": "Trobajo", "given": "Rosa", "initials": "R"}, {"family": "Udovi\u010d", "given": "Marija Gligora", "initials": "MG"}, {"family": "Rimet", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "5", "issue": "1", "pages": "ycaf171", "issn-l": null}, "abstract": "Diatoms, a diverse and abundant group of microalgae, play a crucial role in the functioning of rivers, and are widely used as indicators of ecological quality. This microalgae group has an intraspecific genetic diversity that is poorly understood on a global scale. We examined their genetic diversity using metabarcoding data from Nordic to Equatorial rivers (n = 1103 samples). Notably, 61% of genetic variants were endemic to a single climate zone, including 33% from the Equatorial zone. Looking at the genetic diversity within species, one third of the species showed geographic pattern between climate zones and the phylogenetic structure of their communities indicated that they were shaped by environmental filtering. Another third showed no geographic pattern, and their communities were in majority shaped by neutral processes. A final group was between these two situations. Interestingly, no geographic pattern was observed within the same climate zones, even in regions over 10 000 km apart. We conclude that the numerous species showing allopatric diversification between climate zones, would deserve to be separated into new species to improve diatom-based biomonitoring tools. For future studies, expanding geographical sampling coverage, together with using multi-markers or metagenomes approaches would enable to go beyond these results.", "doi": "10.1093/ismeco/ycaf171", "pmid": "41104113", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12527276"}, {"db": "pii", "key": "ycaf171"}], "notes": [], "created": "2025-11-18T15:39:43.663Z", "modified": "2025-11-18T15:39:43.810Z"}, {"entity": "publication", "iuid": "9baaf85a6b744b00baac397292f47517", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9baaf85a6b744b00baac397292f47517.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9baaf85a6b744b00baac397292f47517"}}, "title": "A comprehensive human embryo reference tool using single-cell RNA-sequencing data", "authors": [{"family": "Zhao", "given": "Cheng", "initials": "C", "orcid": "0000-0003-0518-5924", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cd6a95b29e44b3fa8fed63033d26393.json"}}, {"family": "Plaza Reyes", "given": "Alvaro", "initials": "A", "orcid": "0000-0003-1167-6316", "researcher": {"href": "https://publications.scilifelab.se/researcher/36f7ddaf16ac45bfad26c96f292f2072.json"}}, {"family": "Schell", "given": "John Paul", "initials": "JP"}, {"family": "Weltner", "given": "Jere", "initials": "J"}, {"family": "Ortega", "given": "Nicol\u00e1s M", "initials": "NM"}, {"family": "Zheng", "given": "Yi", "initials": "Y", "orcid": "0000-0002-2685-3680", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5ae32c43903498dab060a3a31695705.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Baqu\u00e9-Vidal", "given": "Laura", "initials": "L", "orcid": "0009-0008-8128-6069", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cbb3bfdf71e4002acffa6b14ef58c60.json"}}, {"family": "Sokka", "given": "Joonas", "initials": "J", "orcid": "0000-0002-0377-8841", "researcher": {"href": "https://publications.scilifelab.se/researcher/f834bc634e2049539fb66b3286020ed4.json"}}, {"family": "Trokovic", "given": "Ras", "initials": "R", "orcid": "0000-0002-3065-6663", "researcher": {"href": "https://publications.scilifelab.se/researcher/510f22386f8744e2a50d7f803b3da831.json"}}, {"family": "Cox", "given": "Brian", "initials": "B"}, {"family": "Rossant", "given": "Janet", "initials": "J", "orcid": "0000-0002-3731-5466", "researcher": {"href": "https://publications.scilifelab.se/researcher/be15218445df4636ab47e1a1dcf8d69c.json"}}, {"family": "Fu", "given": "Jianping", "initials": "J", "orcid": "0000-0001-9629-6739", "researcher": {"href": "https://publications.scilifelab.se/researcher/127bba88c5534146ae9ba1b10929bb4b.json"}}, {"family": "Petropoulos", "given": "Sophie", "initials": "S", "orcid": "0000-0003-2293-8238", "researcher": {"href": "https://publications.scilifelab.se/researcher/0766fd90df1f4199a000eb84b06e2d31.json"}}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}], "type": "journal-article", "published": "2025-01-00", "journal": {"title": "Nat Methods", "issn": "1548-7091", "issn-l": "1548-7091", "volume": "22", "issue": "1", "pages": "193-206"}, "abstract": "Stem cell-based embryo models offer unprecedented experimental tools for studying early human development. The usefulness of embryo models hinges on their molecular, cellular and structural fidelities to their in vivo counterparts. To authenticate human embryo models, single-cell RNA sequencing has been utilized for unbiased transcriptional profiling. However, an organized and integrated human single-cell RNA-sequencing dataset, serving as a universal reference for benchmarking human embryo models, remains unavailable. Here we developed such a reference through the integration of six published human datasets covering development from the zygote to the gastrula. Lineage annotations are contrasted and validated with available human and nonhuman primate datasets. Using stabilized Uniform Manifold Approximation and Projection, we constructed an early embryogenesis prediction tool, where query datasets can be projected on the reference and annotated with predicted cell identities. Using this reference tool, we examined published human embryo models, highlighting the risk of misannotation when relevant references are not utilized for benchmarking and authentication.", "doi": "10.1038/s41592-024-02493-2", "pmid": "39543283", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11725501"}, {"db": "pii", "key": "10.1038/s41592-024-02493-2"}], "notes": [], "created": "2024-11-14T12:28:22.114Z", "modified": "2025-12-04T19:32:09.248Z"}, {"entity": "publication", "iuid": "b017843641ad4057b8fde4e7fc40569e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b017843641ad4057b8fde4e7fc40569e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b017843641ad4057b8fde4e7fc40569e"}}, "title": "A Non-Centrifugation Method to Concentrate and Purify Extracellular Vesicles Using Superabsorbent Polymer Followed by Size Exclusion Chromatography.", "authors": [{"family": "Bergqvist", "given": "Markus", "initials": "M", "orcid": "0009-0003-5716-3716", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d33e374d0642479a80683a989f095a.json"}}, {"family": "L\u00e4sser", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-1279-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/e14e17d2cdb24a9f93991d83811c78b9.json"}}, {"family": "Crescitelli", "given": "Rossella", "initials": "R", "orcid": "0000-0002-1714-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d4b955f26ca4a679deb090e30d0ccf1.json"}}, {"family": "Park", "given": "Kyong-Su", "initials": "KS", "orcid": "0000-0003-0902-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e308b29fe144b49f4db27f4b819c18.json"}}, {"family": "L\u00f6tvall", "given": "Jan", "initials": "J", "orcid": "0000-0001-9195-9249", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cbcaf6b5698411c92e0de9e8fcf390f.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "J Extracell Vesicles", "issn": "2001-3078", "volume": "14", "issue": "1", "pages": "e70037", "issn-l": "2001-3078"}, "abstract": "Extracellular vesicles (EVs) can be isolated and purified from cell cultures and biofluids using different methodologies. Here, we explored a novel EV isolation approach by combining superabsorbent polymers (SAP) in a dialysis membrane with size exclusion chromatography (SEC) to achieve high concentration and purity of EVs without the use of ultracentrifugation (UC). Suspension HEK293 cells transfected with CD63 coupled with Thermo Luciferase were used to quantify the EV yield and purity. The 500 mL conditioned medium volume was initially reduced by pressure ultrafiltration, followed by UC, SAP or a centrifugal filter unit (CFU). Using either of these methods, the EVs were concentrated to a final volume of approximately 1 mL, with retained functionality. The yield, quantified by luciferase activity, was highest with UC (70%-80%), followed by SAP (60%-70%) and CFU (50%-60%). Further purification of the EVs was performed by iodixanol density cushion (IDC) or SEC (Sepharose CL-2B or 6B, in either 10 or 20 mL columns). Although the IDC and Sepharose CL-2B (10 mL) achieved the highest yields, the purity was slightly higher (30%) with IDC. In conclusion, combining SAP concentration with CL-2B SEC is an alternative and efficient way to isolate EVs without using UC.", "doi": "10.1002/jev2.70037", "pmid": "39840900", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11752139"}], "notes": [], "created": "2025-11-05T13:48:00.099Z", "modified": "2025-11-05T13:48:00.169Z"}, {"entity": "publication", "iuid": "33b75bf975e94c45bf5d4b231d05391f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33b75bf975e94c45bf5d4b231d05391f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33b75bf975e94c45bf5d4b231d05391f"}}, "title": "Producing dissolving pulp from agricultural waste", "authors": [{"family": "Wojtasz", "given": "Joanna", "initials": "J"}, {"family": "Sj\u00f6stedt", "given": "Niclas", "initials": "N"}, {"family": "Storm", "given": "Benjamin", "initials": "B"}, {"family": "Parayil", "given": "Manuel Mammen", "initials": "MM"}, {"family": "Ulefors", "given": "Amanda", "initials": "A"}, {"family": "Nilsson", "given": "Linnea", "initials": "L"}, {"family": "Hern\u00e1ndez Leal", "given": "Maria Alejandra", "initials": "MA"}, {"family": "Michud", "given": "Anne", "initials": "A"}, {"family": "\u00d6stlund", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Rydberg", "given": "Tomas", "initials": "T"}, {"family": "Bernin", "given": "Diana", "initials": "D", "orcid": "0000-0002-9611-2263", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad134b1d8ab41b8a8a3318801d92e10.json"}}], "type": "journal-article", "published": "2025-00-00", "journal": {"title": "RSC Sustain.", "issn": "2753-8125", "volume": "3", "issue": "5", "pages": "2210-2220", "issn-l": null}, "abstract": null, "doi": "10.1039/d4su00534a", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-06-11T13:34:14.026Z", "modified": "2025-10-17T13:03:52.467Z"}, {"entity": "publication", "iuid": "af0d181b15e0476d8f4d1f701ba25a03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af0d181b15e0476d8f4d1f701ba25a03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af0d181b15e0476d8f4d1f701ba25a03"}}, "title": "Cord Blood Biomarkers Predict Psoriasis Many Years Before Diagnosis: A Prospective Birth Cohort Study", "authors": [{"family": "Das", "given": "Debojyoti", "initials": "D"}, {"family": "Ludvigsson", "given": "Johnny", "initials": "J"}], "type": "journal-article", "published": "2025-00-00", "journal": {"title": "Arch Clin Biomed Res 2025", "issn": "2572-5017", "issn-l": null, "volume": "9", "issue": "3", "pages": null}, "abstract": null, "doi": "10.26502/acbr.50170452", "pmid": null, "labels": {"Affinity Proteomics Uppsala": "Service", "National Genomics Infrastructure": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-25T19:19:11.236Z", "modified": "2025-11-26T11:08:19.953Z"}]}