{"entity": "journal", "iuid": "a574eb04884e4c0aaf82a210844daf7c", "timestamp": "2026-06-17T07:24:26.203Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Nat%20Commun.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Nat%20Commun"}}, "title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "publications_count": 422, "publications": [{"entity": "publication", "iuid": "69e64360fa0d42d4a7da65ad33e6a6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69e64360fa0d42d4a7da65ad33e6a6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69e64360fa0d42d4a7da65ad33e6a6c4"}}, "title": "Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases.", "authors": [{"family": "Konstantinou", "given": "Aimiliani", "initials": "A", "orcid": "0009-0009-6955-9906", "researcher": {"href": "https://publications.scilifelab.se/researcher/adbee78c31e648518a914fd366c29be5.json"}}, {"family": "C\u00f3rdova-P\u00e9rez", "given": "Alicia", "initials": "A"}, {"family": "Varga", "given": "Julia K", "initials": "JK", "orcid": "0000-0002-5318-2798", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cce1545060342798144f3c8144d4d64.json"}}, {"family": "Madhu", "given": "Priyanka", "initials": "P"}, {"family": "Simonetti", "given": "Leandro", "initials": "L", "orcid": "0000-0003-1283-9770", "researcher": {"href": "https://publications.scilifelab.se/researcher/23530c1a3cef4f499a460ac59c674261.json"}}, {"family": "Vieler", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-3617-1018", "researcher": {"href": "https://publications.scilifelab.se/researcher/d02f57d8ee554f1895fb5cf5d93541ef.json"}}, {"family": "Ishimura", "given": "Ryosuke", "initials": "R"}, {"family": "Lamoliatte", "given": "Frederic", "initials": "F"}, {"family": "Schueler-Furman", "given": "Ora", "initials": "O", "orcid": "0000-0002-1624-0362", "researcher": {"href": "https://publications.scilifelab.se/researcher/5332c64faf114b16bf4a5b5e789d5aa3.json"}}, {"family": "Davey", "given": "Norman E", "initials": "NE", "orcid": "0000-0001-6988-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/c239a7f1b8a344948d80b9104a5fcc96.json"}}, {"family": "Kulathu", "given": "Yogesh", "initials": "Y", "orcid": "0000-0002-3274-1642", "researcher": {"href": "https://publications.scilifelab.se/researcher/1646c4f2949a4a7ea47be413a9a770db.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2026-05-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity is thought to be mediated by the recognition of the ubiquitnated protein itself. In addition to their catalytic domain, USPs have one or more auxiliary domains (ADs) with key functions in regulating DUB activity and localization. We hypothesize that some ADs bind short linear motifs (SLiMs) typically found in intrinsically disordered regions of proteins to achieve targeting to substrates and multiprotein complexes. To test this, we systematically assess the potential of 29 USP-ADs and two full-length USPs for SLiM binding using a combination of proteomic-peptide phage display, peptide SPOT arrays and affinity measurements. We discover SLiM-based interactions for 14 ADs from 9 USP-DUBs, including CYLD, USP11, USP19, USP20, USP22 and USP33, and define the consensus motif and properties of the SLiM-AD binding. Interestingly, we establish that the zf-UBP and DUSP2 domains of USP20 and USP33 are SLiM binding ADs with similar binding profiles, explaining the functional redundancy between the two DUBs. Our work reveals unique motifs recognized by the auxiliary domains CAP-Gly, UBL, zf-UBP and DUSP, with potential functional implications for substrate recognition and complex assemblies.", "doi": "10.1038/s41467-026-73047-7", "pmid": "42151178", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-73047-7"}], "notes": [], "created": "2026-06-08T17:42:03.867Z", "modified": "2026-06-08T17:42:04.152Z"}, {"entity": "publication", "iuid": "b09b02fc5fff4122883cede0ca76ddbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b09b02fc5fff4122883cede0ca76ddbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b09b02fc5fff4122883cede0ca76ddbf"}}, "title": "Mitochondria serve as a holdout compartment for aggregation-prone proteins hindering efficient degradation.", "authors": [{"family": "Gierisch", "given": "Maria E", "initials": "ME", "orcid": "0000-0002-8053-4402", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe10e1b3af59418a8edbd1fea8c37faf.json"}}, {"family": "Barchi", "given": "Enrica", "initials": "E", "orcid": "0009-0007-3209-0003", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a02a6f87294bbd96c11b502f5fba1c.json"}}, {"family": "Marogna", "given": "Mirco", "initials": "M", "orcid": "0009-0000-9866-470X", "researcher": {"href": "https://publications.scilifelab.se/researcher/61ea01f03c4b4995af9e91481cedc783.json"}}, {"family": "Walln\u00f6fer", "given": "Moritz H", "initials": "MH", "orcid": "0000-0002-7688-2359", "researcher": {"href": "https://publications.scilifelab.se/researcher/26832fc473694946b8cd60b280b2a78d.json"}}, {"family": "Ankarcrona", "given": "Maria", "initials": "M", "orcid": "0000-0002-7022-3694", "researcher": {"href": "https://publications.scilifelab.se/researcher/5deb5cb7c18647b5b37d80221b67086c.json"}}, {"family": "Naia", "given": "Luana", "initials": "L", "orcid": "0000-0002-0886-4634", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ae78f608af4f3f8524d5ab4a3c6cdd.json"}}, {"family": "Salomons", "given": "Florian A", "initials": "FA"}, {"family": "Dantuma", "given": "Nico P", "initials": "NP", "orcid": "0000-0002-6090-4170", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ccdd02c787d4a699efd24d297040aa0.json"}}], "type": "journal article", "published": "2026-05-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "17", "issue": "1", "pages": null}, "abstract": "The accumulation of protein aggregates has been causatively linked to the pathogenesis of neurodegenerative diseases. Here, we conduct a genome-wide CRISPR-Cas9 screen to identify cellular factors that regulate the degradation of an aggregation-prone reporter. Genes encoding proteins involved in mitochondrial homeostasis, including the translation factor eIF5A, are enriched among suppressors of the degradation of the reporter. Genetic or chemical inhibition of eIF5A leads to dissociation of the aggregation-prone substrate from mitochondria, which is accompanied by enhanced ubiquitin-dependent proteasomal degradation. The presence of an aggregation-prone, amphipathic helix that localizes the reporter to mitochondria is crucial for the stimulatory effect of eIF5A inhibition on proteasomal degradation. Additionally, inhibition of eIF5A also enhances degradation of mutant huntingtin and \u03b1-synuclein, two disease-associated proteins that contain amphipathic helices and mislocalize to mitochondria. We propose that mitochondria serve as a holdout compartment for aggregation-prone proteins. Therefore, preventing mitochondrial localization of aggregation-prone proteins may offer a viable therapeutic strategy for reducing disease-associated proteins in neurodegenerative disorders.", "doi": "10.1038/s41467-026-72783-0", "pmid": "42098118", "labels": {"CRISPR Functional Genomics": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13153185"}, {"db": "pii", "key": "10.1038/s41467-026-72783-0"}], "notes": [], "created": "2026-05-11T12:46:18.151Z", "modified": "2026-06-08T19:20:13.544Z"}, {"entity": "publication", "iuid": "01a6b1a78bb54a8f8e4c51b7ca9f3d9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/01a6b1a78bb54a8f8e4c51b7ca9f3d9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/01a6b1a78bb54a8f8e4c51b7ca9f3d9b"}}, "title": "Longitudinal protein profiling of blood during childhood into early adulthood.", "authors": [{"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/648c9ed3483a4eb8a1d228cf7e59f6a7.json"}}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Bueno \u00c1lvez", "given": "Mar\u00eda", "initials": "M", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Kebede Merid", "given": "Simon", "initials": "S"}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Kull", "given": "Inger", "initials": "I", "orcid": "0000-0001-6096-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f248045358c4711b1d10d7b9fe9649c.json"}}, {"family": "Merritt", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Klevebro", "given": "Susanna", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.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": "2026-04-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Proteomic research enhances our understanding of health- and disease-related biological processes. Protein profiling during healthy childhood provides important insights into normal physiological development. We longitudinally measured 5416 plasma proteins at four follow-ups during childhood (4-, 8-, 16 years) and early adulthood (24 years) in 100 randomly selected subjects participating in a population-based Swedish cohort, using Olink Explore HT. In total, 3509 proteins were included in the analysis. 54% of the proteins were found to be associated with age, and we observed several protein trajectories from childhood to adulthood based on clustering. In addition to proteins involved in bone, teeth and cartilage formation, we identified differences in proteins involved in neural function, drug metabolism, and hormonal control. There were pronounced sex-related differences in protein levels, particularly at follow-ups 16 and 24, characterized by, for example, growth, response to stimuli and regulation of catabolic processes. We demonstrate dynamic age- and sex-related changes in protein levels during the first two decades of life. Our study results may serve as an important resource in understanding human physiological development, disease etiology, and for future protein biomarker research.", "doi": "10.1038/s41467-026-72095-3", "pmid": "42020385", "labels": {"NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13102979"}, {"db": "pii", "key": "10.1038/s41467-026-72095-3"}], "notes": [], "created": "2026-04-28T06:03:05.109Z", "modified": "2026-04-28T06:03:05.659Z"}, {"entity": "publication", "iuid": "87bf60ec792f4e9caf54376f46b3ad5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87bf60ec792f4e9caf54376f46b3ad5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87bf60ec792f4e9caf54376f46b3ad5f"}}, "title": "Rare regulatory mutations disrupt mesenchymal molecular programs driving endocardial cushion formation in bicuspid aortic valve.", "authors": [{"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Buyan", "given": "Andrey", "initials": "A", "orcid": "0000-0001-9105-4028", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79c4583ae342a5ae931e39f7e282a7.json"}}, {"family": "L\u00e1z\u00e1r", "given": "Enik\u0151", "initials": "E", "orcid": "0000-0001-8664-7531", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd94abaf66dd407da5056c04174fc62d.json"}}, {"family": "Gryzunov", "given": "Nikita", "initials": "N", "orcid": "0009-0000-0782-8650", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bb53aa525ff4269936724c077b2d387.json"}}, {"family": "L\u00e5ng", "given": "Karin", "initials": "K"}, {"family": "Mauron", "given": "Rapha\u00ebl", "initials": "R", "orcid": "0009-0004-0909-3554", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0b2662f1bc40b682ff6923c797877e.json"}}, {"family": "Nozdrin", "given": "Vladimir", "initials": "V", "orcid": "0009-0004-3053-1387", "researcher": {"href": "https://publications.scilifelab.se/researcher/456249fbb9ef48cebc32cc15fe39a35b.json"}}, {"family": "Spalinskas", "given": "Rapolas", "initials": "R", "orcid": "0000-0002-1648-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/18ca0b7337b849a49861aedf2971067e.json"}}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S"}, {"family": "Petersson Sj\u00f6gren", "given": "Madeleine", "initials": "M"}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A", "orcid": "0000-0002-3427-9455", "researcher": {"href": "https://publications.scilifelab.se/researcher/9096109f1be94b7197fd249c4193c9d7.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Kulakovskiy", "given": "Ivan V", "initials": "IV", "orcid": "0000-0002-6554-8128", "researcher": {"href": "https://publications.scilifelab.se/researcher/41163cb5ec5d44668f9c6f06edb379ab.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-9155-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d162f3de0f941e0a91387357892d656.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}], "type": "journal article", "published": "2026-04-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Bicuspid aortic valve, a prevalent congenital malformation, predisposes individuals to severe complications. Although the condition exhibits substantial heritability, known protein-coding and common regulatory mutations explain a minority of cases. To assess the contribution of rare regulatory variants, here we integrate high-resolution three-dimensional genome organization profiling with matched whole-genome sequencing from eight individuals with bicuspid aortic valves and eight with standard tricuspid aortic valves. In bicuspid aortic valve patients, mutation-driven chromatin rewiring affected 1.8-fold more valve development genes than in healthy individuals. Genome-wide in silico analyses show that rare regulatory mutations disrupt the transcriptomes of mesenchymal cell populations necessary for endocardial cushion formation. We identify 198 candidate genes associated with bicuspid aortic valve, revealing pronounced heterogeneity and complex interplay between coding and regulatory mutations. Collectively, our findings establish rare regulatory mutations as contributors to the heritability of bicuspid aortic valve and underscore the need to elucidate their mechanistic roles in disease pathogenesis.", "doi": "10.1038/s41467-026-71758-5", "pmid": "41997951", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13090386"}, {"db": "pii", "key": "10.1038/s41467-026-71758-5"}], "notes": [], "created": "2026-05-11T11:41:45.495Z", "modified": "2026-05-11T11:41:46.015Z"}, {"entity": "publication", "iuid": "b05f9a8302e1405588f93dc3cb79e0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b05f9a8302e1405588f93dc3cb79e0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b05f9a8302e1405588f93dc3cb79e0e5"}}, "title": "Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection.", "authors": [{"family": "Peters", "given": "Marie B A", "initials": "MBA", "orcid": "0000-0001-8994-0864", "researcher": {"href": "https://publications.scilifelab.se/researcher/df4733590d054742b732c2028a8f5e8a.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Kassa", "given": "Eszter", "initials": "E"}, {"family": "Yau", "given": "Wai-Lok", "initials": "WL"}, {"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Niedermoser", "given": "Isabell", "initials": "I", "orcid": "0000-0002-5301-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a2b5c11f4f945a5a273c9fd040bee6f.json"}}, {"family": "Gerold", "given": "Gisa", "initials": "G", "orcid": "0000-0002-1326-5038", "researcher": {"href": "https://publications.scilifelab.se/researcher/6353493de47c4ec58831f79ed94045f4.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}, {"family": "Lundmark", "given": "Richard", "initials": "R", "orcid": "0000-0001-9104-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e1b756caa79468dab0f960e43cd61d3.json"}}, {"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": "2026-04-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "Orthoflaviviruses are RNA viruses that cause serious diseases in humans, with currently no antivirals available. Targeting host factors is emerging as an attractive antiviral approach. However, as a first step, there is a need to understand which host proteins are hijacked and for what purpose. Here, using a combination of fluorescence microscopy, knock-down, crosslinking immunoprecipitation sequencing, mass spectrometry, and in vitro and biophysical assays, we identify nucleoporin-153 (NUP153) as a proviral factor during orthoflavivirus infection. We show that NUP153 is recruited to the virus amplification site on the endoplasmic reticulum to impact the structural to nonstructural viral protein ratios. We find that NUP153 interacts with both the viral proteins NS3 and NS5, and a highly conserved G-rich motif on the viral RNA. These interactions specifically promote the production of viral structural proteins, leading to an efficient virion assembly, virus release and spread to new cells. We propose that NUP153 acts as a key regulator in viral protein ratios, a mechanism that appears conserved among orthoflaviviruses.", "doi": "10.1038/s41467-026-71449-1", "pmid": "41951628", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-71449-1"}], "notes": [], "created": "2026-04-10T12:13:07.525Z", "modified": "2026-04-10T12:13:08.280Z"}, {"entity": "publication", "iuid": "d28a4f21a24a4775aecb9fff4b468e8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d28a4f21a24a4775aecb9fff4b468e8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d28a4f21a24a4775aecb9fff4b468e8a"}}, "title": "Neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER + /HER2- breast cancer: a randomized phase II trial.", "authors": [{"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af6483a77d746c2b838414692f1f4ed.json"}}, {"family": "Tzoras", "given": "Evangelos", "initials": "E"}, {"family": "Sarafidis", "given": "Michail", "initials": "M"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG", "orcid": "0000-0001-9919-4471", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8506000a14a4a5286aa557ab67ef690.json"}}, {"family": "Bj\u00f6hle", "given": "Judith", "initials": "J"}, {"family": "Barnekow", "given": "Elin", "initials": "E"}, {"family": "Margolin", "given": "Sara", "initials": "S"}, {"family": "Isaksson-Friman", "given": "Erika", "initials": "E"}, {"family": "Kessler", "given": "Luisa Edman", "initials": "LE"}, {"family": "Zouzos", "given": "Athanasios", "initials": "A", "orcid": "0000-0003-2654-827X", "researcher": {"href": "https://publications.scilifelab.se/researcher/776e7ba8993b4465a27451629b509490.json"}}, {"family": "Johansson", "given": "Hemming", "initials": "H"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Agartz", "given": "Susanne", "initials": "S"}, {"family": "Gryb\u00e4ck", "given": "Per", "initials": "P", "orcid": "0000-0002-1141-6234", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b5986c379cd4d23a0b48ac328faab63.json"}}, {"family": "Salgkamis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-3020-0359", "researcher": {"href": "https://publications.scilifelab.se/researcher/826836fefcf5440ebef1c404e046a0ca.json"}}, {"family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "researcher": {"href": "https://publications.scilifelab.se/researcher/f786763a4a0e4b5bb865ebb199eb6ca2.json"}}, {"family": "Wang", "given": "Kang", "initials": "K", "orcid": "0000-0001-5401-1803", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bdb074014224910b0f34e893b15e660.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Acs", "given": "Balazs", "initials": "B", "orcid": "0000-0002-0972-4633", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe428be3caf4deca0a7839d555f6c33.json"}}, {"family": "Sun", "given": "Wenwen", "initials": "W"}, {"family": "Boyaci", "given": "Ceren", "initials": "C"}, {"family": "Villacampa", "given": "Guillermo", "initials": "G"}, {"family": "Pascual", "given": "Tomas", "initials": "T", "orcid": "0000-0001-8431-3183", "researcher": {"href": "https://publications.scilifelab.se/researcher/c10a027f0fa74b6b9a667edcadf8f50e.json"}}, {"family": "Gavila", "given": "Joaquin", "initials": "J"}, {"family": "Prat", "given": "Aleix", "initials": "A", "orcid": "0000-0003-2377-540X", "researcher": {"href": "https://publications.scilifelab.se/researcher/582dfbb079214acbb35af0a0590b2fb3.json"}}, {"family": "Perou", "given": "Charles", "initials": "C"}, {"family": "Brandberg", "given": "Yvonne", "initials": "Y"}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd38f4f7704144ed9e3f869e197175e6.json"}}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications.scilifelab.se/researcher/7683c0280e9b4145aa54305fb08936a7.json"}}], "type": "journal article", "published": "2026-04-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "In PREDIX LumB patients with estrogen receptor positive and human epidermal growth factor receptor negative (ER + /HER2-) breast cancer > 20 mm and/or with lymph node metastasis were randomized 1:1 to receive either paclitaxel weekly for 12 weeks followed by palbociclib and endocrine therapy for 12 weeks (arm A), or the reverse sequence (arm B). Primary endpoint is objective radiologic response at 12 weeks (ORR12), and key secondary endpoints are ORR24, pathologic complete response, event-free survival, safety and correlative studies of tissue and circulating biomarkers. Whole exome sequencing and RNA sequencing were performed on baseline fresh frozen tissue samples. In total, 179 patients comprise the intention-to-treat population. There is no statistically significant difference between the two arms in ORR12 (59% vs 45%, p = 0.058). An exploratory gene expression analysis identified differentially expressed genes and gene sets between responders and non-responders at 12 weeks. A predictive signature, CDKPredX, comprising 31 genes related to proliferation, ER signaling and immune activity was developed to identify patients resistant to chemotherapy but responding to palbociclib plus endocrine therapy (pinteraction=0.03). The predictive signature was independently validated in the CORALLEEN trial (pinteraction=0.048). Clinicaltrials.gov identifier: NCT02603679.", "doi": "10.1038/s41467-026-71452-6", "pmid": "41951647", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-71452-6"}, {"db": "pmc", "key": "PMC13069018"}, {"db": "ClinicalTrials.gov", "key": "NCT02603679"}], "notes": [], "created": "2026-04-13T07:03:30.099Z", "modified": "2026-04-13T07:03:31.324Z"}, {"entity": "publication", "iuid": "853fcd087cf147129106a699a63b80ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/853fcd087cf147129106a699a63b80ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/853fcd087cf147129106a699a63b80ef"}}, "title": "Tumor-infiltrating immature innate lymphoid cells in colorectal cancer are biased toward ILC1/tissue-resident NK cell differentiation.", "authors": [{"family": "Marchalot", "given": "Anne", "initials": "A", "orcid": "0000-0002-3042-8206", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b674db5dc349eaa4438563f2256290.json"}}, {"family": "Ljunggren", "given": "Malin", "initials": "M"}, {"family": "Stamper", "given": "Christopher", "initials": "C"}, {"family": "Weigel", "given": "Whitney", "initials": "W"}, {"family": "Tibbitt", "given": "Christopher Andrew", "initials": "CA"}, {"family": "Meininger", "given": "Isabel", "initials": "I"}, {"family": "Pandey", "given": "Ram Vinay", "initials": "RV"}, {"family": "Franklin", "given": "Miriam", "initials": "M", "orcid": "0000-0002-9402-9976", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64100c086a644b8b1b7dd56f4f09da5.json"}}, {"family": "Bassett", "given": "John Washington", "initials": "JW"}, {"family": "Wirth", "given": "Lorenz", "initials": "L"}, {"family": "Colorectal Study Group", "given": "", "initials": ""}, {"family": "Lindforss", "given": "Ulrik", "initials": "U"}, {"family": "Jansson-Palmer", "given": "Gabriella", "initials": "G"}, {"family": "Nordenvall", "given": "Caroline", "initials": "C"}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J", "orcid": "0000-0002-1119-0976", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcca878a7f314944bf1a4290cfd5d71d.json"}}], "type": "journal article", "published": "2026-03-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Peritoneal metastases (PM) occur in 10% of patients with colorectal cancer (CRC) and are linked to poor outcomes. Although dysregulated innate lymphoid cells (ILC) have been described in CRC, their function in CRC-PM remains unclear. Here, we analyze tumor samples from CRC and CRC-PM patients using single-cell RNA sequencing (11 patients), flow cytometry (8 patients) and differentiation assays (24 patients). Healthy colon, primary CRC and CRC-PM tumors are infiltrated by heterogeneous populations of ILC3, ILC2, ILC1, tissue resident (tr)NK cells and conventional (c)NK cells. Compared to healthy colons, primary CRC and CRC-PM tumors are depleted of ILC3 but enriched for ILC1, trNK cells and cNK cells. CRC and CRC-PM tumors harbor two immature ILC populations, early NK and na\u00efve (n)ILC, with nILCs being transcriptionally skewed toward ILC1 and trNK cells. Indeed, co-culture of isolated nILCs with OP9-DL1 cells induces intratumoral nILC differentiation into ILC1/trNK-like cells. These findings help understand the immune pathogenesis of CRC and CRC-PM and provide insights for future ILC1 and NK cell-based therapies.", "doi": "10.1038/s41467-026-71085-9", "pmid": "41896575", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13035902"}, {"db": "pii", "key": "10.1038/s41467-026-71085-9"}], "notes": [], "created": "2026-04-10T12:22:32.013Z", "modified": "2026-04-10T12:22:32.241Z"}, {"entity": "publication", "iuid": "bccea3aeba8b476eb4902896a66d3d62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bccea3aeba8b476eb4902896a66d3d62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bccea3aeba8b476eb4902896a66d3d62"}}, "title": "Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.", "authors": [{"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R", "orcid": "0000-0002-4173-8648", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cefc4ed580469ba97e32c95477d485.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Mas-Sandoval", "given": "Alex", "initials": "A"}, {"family": "Yaka", "given": "Reyhan", "initials": "R", "orcid": "0000-0002-9359-4391", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f685d3d3cac4dc6bfd4571041786add.json"}}, {"family": "Fortes-Lima", "given": "Cesar A", "initials": "CA", "orcid": "0000-0002-9310-5009", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a1afb9addfa42b4aa92a74ed8a8586b.json"}}, {"family": "Garc\u00eda Rubio", "given": "Almudena", "initials": "A"}, {"family": "M\u00e1rquez-Grant", "given": "Nicholas", "initials": "N"}, {"family": "Mar\u00ed", "given": "Juanjo", "initials": "J"}, {"family": "Graziani", "given": "Glenda", "initials": "G"}, {"family": "Ferrer Ab\u00e1rzuza", "given": "Antoni", "initials": "A"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Lorca-Francisco", "given": "Lander", "initials": "L", "orcid": "0009-0000-5486-1509", "researcher": {"href": "https://publications.scilifelab.se/researcher/306a8399107a4c078493180672a3a1b7.json"}}, {"family": "Linderholm", "given": "Anna", "initials": "A", "orcid": "0000-0002-1613-9926", "researcher": {"href": "https://publications.scilifelab.se/researcher/27c319330d1e4827858b5612dc203c69.json"}}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "Arauna", "given": "Lara R", "initials": "LR", "orcid": "0000-0003-3317-4261", "researcher": {"href": "https://publications.scilifelab.se/researcher/111d8114dc6f448c9516f8f246ef7925.json"}}, {"family": "P\u00e9rez-Ramallo", "given": "Patxi", "initials": "P", "orcid": "0000-0002-1142-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb111a8997c4fc4a3167bbeabcac042.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2026-03-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Ibiza, an island in present-day Spain, was conquered in 902 CE by the Umayyad Emirate of C\u00f3rdoba. The island remained under Islamic rule until 1235. Here, we analyse the genetic and metagenomic profiles of 13 individuals from an Islamic cemetery in Ibiza, dated to 950-1150 CE. Genome-wide analyses reveal heterogeneity, with ancestry components from Europe, North Africa, and Sub-Saharan Africa. Our analyses estimate that North African gene flow occurred two to seven generations before these individuals lived, suggesting admixture following the Islamic conquest of Iberia and potentially on Ibiza itself. Notably, two individuals trace their Sub-Saharan origins to distinct regions, Senegambia and present-day southern Chad, providing direct evidence of trans-Saharan connections via military and slave networks documented in contemporary Arabic sources. Metagenomic analyses detect several pathogens in this community, with one individual carrying Mycobacterium leprae, offering insight into the presence of leprosy in Ibiza. Our findings align with the historically documented two-pulse demographic model, indicating an initial settlement following the early tenth-century conquest and a second influx associated with Almoravid movements in the twelfth century. These securely dated genomes offer insights into medieval population dynamics and health in the Balearics.", "doi": "10.1038/s41467-026-70615-9", "pmid": "41888119", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13021928"}, {"db": "pii", "key": "10.1038/s41467-026-70615-9"}], "notes": [], "created": "2026-04-10T12:08:45.109Z", "modified": "2026-04-10T12:08:45.877Z"}, {"entity": "publication", "iuid": "dcc99177f164437e8a1a681594fa0445", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcc99177f164437e8a1a681594fa0445.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcc99177f164437e8a1a681594fa0445"}}, "title": "Ribonuclease 4 Functions in Nociceptor-Mediated Nerve Homeostasis.", "authors": [{"family": "Feng", "given": "Xiaona", "initials": "X", "orcid": "0000-0001-6186-1160", "researcher": {"href": "https://publications.scilifelab.se/researcher/ade5499e48344e448626eef177bf1b27.json"}}, {"family": "Zhang", "given": "Kaiwen", "initials": "K", "orcid": "0009-0001-0790-1616", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1880c8da747467795a011858ca2c9bf.json"}}, {"family": "Techameena", "given": "Prach", "initials": "P", "orcid": "0009-0005-9380-2428", "researcher": {"href": "https://publications.scilifelab.se/researcher/835cc139cbbd4e08afd433a817f74ac6.json"}}, {"family": "Quadros", "given": "Rolen M", "initials": "RM"}, {"family": "Adori", "given": "Csaba", "initials": "C"}, {"family": "Murtazina", "given": "Aliia", "initials": "A"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Biagini", "given": "Sofia", "initials": "S", "orcid": "0009-0001-8033-1568", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6a1c687a2e945c0a01cd9ea4729fcd0.json"}}, {"family": "Bayramlik", "given": "Ozun Gokce", "initials": "OG", "orcid": "0009-0006-2130-9674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecf0118536354092bddc54ca48594444.json"}}, {"family": "Lallemend", "given": "Francois", "initials": "F", "orcid": "0000-0001-5484-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9494a8ea444facbf3b564670930ab5.json"}}, {"family": "Gurumurthy", "given": "Channabasavaiah B", "initials": "CB"}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}], "type": "journal article", "published": "2026-03-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "The regulation of nociceptor identity and function is essential, as disruptions can significantly influence pain sensation, yet our understanding of the molecular mechanisms involved remains incomplete. In this study, we identified ribonuclease 4 (RNase4) as selectively expressed in the unmyelinated nociceptor lineage. Analysis of RNase4-deficient mice and single-cell transcriptomic data revealed a cell-autonomous role for RNase4 in regulating nociceptor function. Moreover, in a neuropathic pain model, RNase4 expression was upregulated in nociceptors during the pain and recovery phases, and its deletion altered mechanical sensation. Additionally, RNase4 exerted non-cell- autonomous effects on the myelin structural organization of adjacent myelinated axons. Together, these findings implicate RNase4 as a dual regulator of nociceptor biology and myelin integrity, revealing a molecular pathway for pain regulation and nerve repair.", "doi": "10.1038/s41467-026-70365-8", "pmid": "41876491", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13022371"}, {"db": "pii", "key": "10.1038/s41467-026-70365-8"}], "notes": [], "created": "2026-04-10T12:49:18.049Z", "modified": "2026-04-10T12:49:18.431Z"}, {"entity": "publication", "iuid": "8a88693e35b444ce876a3dd11d760a8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a88693e35b444ce876a3dd11d760a8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a88693e35b444ce876a3dd11d760a8e"}}, "title": "FGFR signaling establishes spatial gradients of secretory cell identities along the airway proximal-distal axis.", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A"}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Eliot", "given": "Orane", "initials": "O"}, {"family": "Koepke", "given": "Janine", "initials": "J"}, {"family": "Millar-B\u00fcchner", "given": "Pamela", "initials": "P"}, {"family": "Manner\u00e5s-Holm", "given": "Louise", "initials": "L"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c94301c7ab74979ae2db1c606d9387b.json"}}, {"family": "Kelm", "given": "Antonia", "initials": "A"}, {"family": "Bouloukou", "given": "Eleni", "initials": "E"}, {"family": "Gaengel", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-2682-2833", "researcher": {"href": "https://publications.scilifelab.se/researcher/b405d74174ae47749815a091affb9aea.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Seeger", "given": "Werner", "initials": "W", "orcid": "0000-0003-1946-0894", "researcher": {"href": "https://publications.scilifelab.se/researcher/36385e53dcd7475ab3f100b63179807b.json"}}, {"family": "Bellusci", "given": "Saverio", "initials": "S"}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}], "type": "journal article", "published": "2026-03-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Secretory cells are major structural and functional constituents of the lung airways. Their heterogeneity, spatial organization and specification mechanisms are partially understood. Here, we analyze secretory lung cell-types at single-cell resolution. In the airway epithelium, we find opposing, partially overlapping gene-expression gradients along the proximal-distal airway axis superimposed on a general gene program encoding detoxification. One graded program is elevated proximally and relates to innate immunity, whereas the other is enriched distally, encoding lipid metabolism and antigen presentation. Intermediately positioned cells express moderate levels of both graded programs creating a differentiation continuum towards each end. Lineage tracing analysis during development reveals the sequential establishment of the gradients in common epithelial progenitors postnatally. We show that Fgfr2b regulates the airway patterning by inducing and maintaining high levels of lipid biosynthesis and vesicle trafficking in distal airways and down-regulating innate-immunity genes in vivo and in airway organoids. Our analysis offers a framework for studying epithelial and lung tissue organization to better understand cellular roles in tissue-level pathology.", "doi": "10.1038/s41467-026-70842-0", "pmid": "41851103", "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": "10.1038/s41467-026-70842-0"}, {"db": "pmc", "key": "PMC13004988"}], "notes": [], "created": "2026-03-23T13:53:27.906Z", "modified": "2026-03-23T13:53:28.385Z"}, {"entity": "publication", "iuid": "6dfc892282ff426f998cbc7c26e3828f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dfc892282ff426f998cbc7c26e3828f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dfc892282ff426f998cbc7c26e3828f"}}, "title": "The N-Myc MB0-MBI region interacts specifically and dynamically with the N-lobe of Aurora kinase A.", "authors": [{"family": "Hultman", "given": "Johanna", "initials": "J", "orcid": "0009-0000-8066-228X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd75d9341822427db7b8b8b8510123fd.json"}}, {"family": "Morad", "given": "Vivian", "initials": "V", "orcid": "0000-0001-9665-4532", "researcher": {"href": "https://publications.scilifelab.se/researcher/36505a4d209d4f439785a062205b180c.json"}}, {"family": "Tanner", "given": "Eliane", "initials": "E"}, {"family": "Kenney", "given": "Tristan M G", "initials": "TMG", "orcid": "0000-0001-8242-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/b739b627992645428ea12ed180dab914.json"}}, {"family": "Pietras", "given": "Zuzanna", "initials": "Z", "orcid": "0000-0002-4501-7311", "researcher": {"href": "https://publications.scilifelab.se/researcher/973d7a63037c432db0f7ca9607b8525b.json"}}, {"family": "Khare", "given": "Lalit Pramod", "initials": "LP"}, {"family": "Derbyshire", "given": "Dean", "initials": "D"}, {"family": "Resetca", "given": "Diana", "initials": "D"}, {"family": "Arrowsmith", "given": "Cheryl H", "initials": "CH"}, {"family": "Aili", "given": "Daniel", "initials": "D", "orcid": "0000-0002-7001-9415", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc760610215a4dee9061f28723b97e62.json"}}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S", "orcid": "0000-0002-7694-285X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6416b323664f4126b70067193d7b8347.json"}}, {"family": "Penn", "given": "Linda Z", "initials": "LZ", "orcid": "0000-0001-8133-5459", "researcher": {"href": "https://publications.scilifelab.se/researcher/780529b33355480890244ff1039ea64f.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}, {"family": "Ahlner", "given": "Alexandra", "initials": "A", "orcid": "0000-0001-7004-8251", "researcher": {"href": "https://publications.scilifelab.se/researcher/08cd17a1108045b5be32cd492a082453.json"}}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M", "orcid": "0000-0002-0492-5890", "researcher": {"href": "https://publications.scilifelab.se/researcher/3caade7942f84928b12656cb7e5f8493.json"}}], "type": "journal article", "published": "2026-02-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "The intrinsically disordered MYC proteins are master regulators of cellular growth and function, but when deregulated they become cancer drivers. MYC-protein interactions are key to oncogenesis, and while disrupting such interactions would be of significant therapeutic benefit, the intrinsically disordered properties of MYC have dramatically hampered their characterization. Here, we apply an integrated structural biology approach to describe the structure and dynamics of the N-Myc-Aurora A complex, which is critical in neuroendocrine tumor progression. We reveal a functional interaction where multiple binding sites on N-Myc interact with the Aurora A N-lobe. The interaction is governed by aromatic clusters within the conserved MB0 and MBI motifs in N-Myc that interact with Aurora A in a dynamic binding mode that allosterically promotes kinase activation. We show that N-Myc binding to the Aurora A N-lobe can be inhibited by the small-molecule AurkinA, providing opportunity for therapeutical strategies to disrupt this interaction.", "doi": "10.1038/s41467-026-69725-1", "pmid": "41735282", "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12936163"}, {"db": "pii", "key": "10.1038/s41467-026-69725-1"}], "notes": [], "created": "2026-04-07T14:24:57.298Z", "modified": "2026-04-07T14:24:58.191Z"}, {"entity": "publication", "iuid": "de111bb9df48495abaad3bd9499c980b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de111bb9df48495abaad3bd9499c980b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de111bb9df48495abaad3bd9499c980b"}}, "title": "MYC modulates TOP2A diffusion to promote substrate detection and activity", "authors": [{"family": "Cameron", "given": "Donald P", "initials": "DP", "orcid": "0000-0002-3175-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/5048967b73144d169369da2c50f936fd.json"}}, {"family": "Jackson", "given": "Kathryn", "initials": "K"}, {"family": "Loffreda", "given": "Alessia", "initials": "A", "orcid": "0000-0003-4523-5666", "researcher": {"href": "https://publications.scilifelab.se/researcher/9024990fa139415bb8b95415f853857d.json"}}, {"family": "M\u00f6ller", "given": "Carl", "initials": "C", "orcid": "0000-0001-9463-6402", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c1c0ee010cc4b92b80ea7646843efda.json"}}, {"family": "Kuzin", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7139-1884", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fffd1dd85a049e6bd92b6c68b5f659f.json"}}, {"family": "Mazzocca", "given": "Matteo", "initials": "M", "orcid": "0000-0003-2079-1535", "researcher": {"href": "https://publications.scilifelab.se/researcher/3723fd392c484487a2f3dd6e86e1549e.json"}}, {"family": "Iliopoulou", "given": "Evanthia", "initials": "E"}, {"family": "Kolbeinsdottir", "given": "Hallgerdur", "initials": "H"}, {"family": "Paluda", "given": "Andrej", "initials": "A", "orcid": "0000-0002-0716-0512", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1803d292e10408b9e8ea99349b27e59.json"}}, {"family": "Pavlova", "given": "Evgeniya", "initials": "E"}, {"family": "Jagodic", "given": "Bea", "initials": "B", "orcid": "0009-0005-0997-8130", "researcher": {"href": "https://publications.scilifelab.se/researcher/db2473744b2f45f58531fc7adc0f9bca.json"}}, {"family": "Lopez Duran", "given": "Brian Saidel", "initials": "BS"}, {"family": "Lamour", "given": "Val\u00e9rie", "initials": "V", "orcid": "0000-0001-7793-4029", "researcher": {"href": "https://publications.scilifelab.se/researcher/831fbc98eff844af82760e66cff024ce.json"}}, {"family": "Westerlund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4767-4868", "researcher": {"href": "https://publications.scilifelab.se/researcher/7afbab9c0cc94ff8bda3b2116039ad8d.json"}}, {"family": "Mazza", "given": "Davide", "initials": "D", "orcid": "0000-0003-2776-4142", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf51d8276b05459ba57162f4da86d020.json"}}, {"family": "Baranello", "given": "Laura", "initials": "L", "orcid": "0000-0001-6039-1849", "researcher": {"href": "https://publications.scilifelab.se/researcher/a33e20ca8e284b5db1cca13e5e6d7940.json"}}], "type": "journal-article", "published": "2026-02-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Topoisomerases alleviate DNA supercoiling by cleaving and resealing DNA strands. Previously, we showed that the oncoprotein MYC recruits and stimulates topoisomerases to remove DNA entanglements generated by oncogenic transcription. Understanding this mechanism may suggest methods to inhibit MYC-driven topoisomerase activation, targeting tumor-specific transcription. Here, we demonstrate that the essential topoisomerase TOP2A in human cells exists in a dynamic equilibrium between sequestration in the nucleolus, substrate searching in transcription hubs, and active engagement on chromatin. This equilibrium is highly responsive to changes in DNA topology, allowing cells to regulate TOP2A levels. Using single molecule tracking, here we show that MYC accelerates TOP2A diffusion in cells. We explain this phenotype by demonstrating that MYC limits TOP2A self-interaction in vitro, while decreasing the size of TOP2A complexes in cells. By increasing TOP2A diffusion, MYC promotes substrate binding and increases TOP2A engagement on chromatin genome-wide, revealing the mechanism underlying MYC stimulation of TOP2A activity.", "doi": "10.1038/s41467-026-69232-3", "pmid": "41663397", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996632"}, {"db": "pii", "key": "10.1038/s41467-026-69232-3"}], "notes": [], "created": "2026-02-12T07:56:19.235Z", "modified": "2026-03-24T09:07:07.272Z"}, {"entity": "publication", "iuid": "a537001d14d34f14b3048bdf35e0b950", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a537001d14d34f14b3048bdf35e0b950.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a537001d14d34f14b3048bdf35e0b950"}}, "title": "Mechanistic insights into PCBP1-driven unfolding of selected i-motif DNA at G1/S checkpoint.", "authors": [{"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Gillet", "given": "Natacha", "initials": "N", "orcid": "0000-0002-7657-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce5b43ffd5e44fbe926a3d26064b6760.json"}}, {"family": "Obi", "given": "Ikenna", "initials": "I", "orcid": "0000-0003-0364-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/e46c65e7b0e540b0a7c225d54c1502d7.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": "2026-02-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "pages": "1149", "issn-l": "2041-1723"}, "abstract": "I-motifs are non-canonical, four-stranded DNA structures in cytosine-rich genomic regions, yet their protein-mediated regulation remains underexplored. Here, we identify PCBP1 (Poly(rC)-binding protein 1) as a selective i-motif-binding protein that unfolds specific i-motifs depending on their protonation and hairpin-forming propensities. Systematic truncation reveals that individual K-homology (KH) domains of PCBP1 cannot selectively bind or unfold i-motifs, but their coordinated actions restore wild-type PCBP1 functions. Using biochemical, biophysical, and molecular dynamics studies, we demonstrate that KH1+2 domains remodel i-motifs, recruiting KH3 to facilitate unfolding and efficient DNA replication. Chromatin and cell-based investigations reveal that PCBP1-knockdown increases i-motif formation at specific genomic loci, coinciding with G1/S arrest and elevated \u03b3H2AX, indicative of genomic instability. During G1/S transition, PCBP1 occupancy peaks at these i-motif loci, ensuring i-motif resolution in early S phase. These findings establish PCBP1 as a critical regulator of i-motif dynamics, directly linking its unfolding activity to G1/S transition and genome stability.", "doi": "10.1038/s41467-026-68822-5", "pmid": "41629296", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-68822-5"}, {"db": "pmc", "key": "PMC12865031"}], "notes": [], "created": "2026-02-04T15:32:08.919Z", "modified": "2026-02-04T15:32:09.419Z"}, {"entity": "publication", "iuid": "c586da7cc0cf4911a6d5d9d9ce6be426", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c586da7cc0cf4911a6d5d9d9ce6be426.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c586da7cc0cf4911a6d5d9d9ce6be426"}}, "title": "Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome.", "authors": [{"family": "Nguyen", "given": "Minh Duc", "initials": "MD", "orcid": "0000-0003-2945-9707", "researcher": {"href": "https://publications.scilifelab.se/researcher/c66f3b3aa7c147558c0c1a7a1b079d09.json"}}, {"family": "Sierra-Magro", "given": "Ana", "initials": "A", "orcid": "0000-0002-2810-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/eae822e08d3443fd9d7addb3616553c5.json"}}, {"family": "Singh", "given": "Vivek", "initials": "V", "orcid": "0000-0003-4656-3362", "researcher": {"href": "https://publications.scilifelab.se/researcher/0576b8ffc93d42f6b47d9d0d7d01bbd0.json"}}, {"family": "Khawaja", "given": "Anas", "initials": "A", "orcid": "0000-0002-9721-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/a699763ef41f49d6b558e208fedc3db8.json"}}, {"family": "Tim\u00f3n-G\u00f3mez", "given": "Alba", "initials": "A", "orcid": "0000-0001-9811-8557", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1bd3e28e3214dd58dc5eddc21d469b3.json"}}, {"family": "Barrientos", "given": "Antoni", "initials": "A", "orcid": "0000-0001-9018-3231", "researcher": {"href": "https://publications.scilifelab.se/researcher/07a9331fc2df454c9c6e288f70c8c976.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}], "type": "journal article", "published": "2026-01-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "The mitochondrial respiratory chain comprises four multimeric complexes (CI-CIV) that drive oxidative phosphorylation by transferring electrons to oxygen and generating the proton gradient required for ATP synthesis. These complexes can associate into supercomplexes (SCs), such as the CI + CIII\u2082 + CIV respirasome, but how SCs form, by joining preassembled complexes or by engaging partially assembled intermediates, remains unresolved. Here, we use cryo-electron microscopy to determine high-resolution structures of native human CI + CIII\u2082 + CIV late-assembly intermediates. Together with biochemical analyses, these structures show that respirasome biogenesis concludes with the final maturation of CIV while it is associated with fully assembled CI and CIII\u2082. We identify HIGD2A as a placeholder factor within isolated and supercomplexed CIV that is replaced by subunit NDUFA4 during the last step of CIV and respirasome assembly. This mechanism suggests that placeholders such as HIGD2A act as molecular timers, preventing premature incorporation of NDUFA4 or its isoforms and ensuring the orderly progression of pre-SC particles into functional respirasomes. Since defects in CIV assembly, including NDUFA4 deficiencies, cause severe encephalomyopathies and neurodegenerative disorders, understanding the molecular architecture and assembly pathways of isolated and supercomplexed CIV offers insight into the pathogenic mechanisms underlying these conditions.", "doi": "10.1038/s41467-025-68274-3", "pmid": "41519940", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-68274-3"}], "notes": [], "created": "2026-01-25T10:08:32.804Z", "modified": "2026-01-25T10:08:33.699Z"}, {"entity": "publication", "iuid": "88fd0d987ac54f598427b2b468187b1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88fd0d987ac54f598427b2b468187b1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88fd0d987ac54f598427b2b468187b1e"}}, "title": "Quantitative optical nanoscopy of mitochondrial-derived vesicles in neurons classifies pre-peroxisomal and clearing organelles.", "authors": [{"family": "Coceano", "given": "Giovanna", "initials": "G", "orcid": "0000-0001-6579-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/e35c28e14e134fe3b4c9ab9efa129df0.json"}}, {"family": "Alvelid", "given": "Jonatan", "initials": "J", "orcid": "0000-0002-3554-9322", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf7f3ec8624f4cef96f96b3c28ffc6b8.json"}}, {"family": "Damenti", "given": "Martina", "initials": "M", "orcid": "0000-0002-4209-5381", "researcher": {"href": "https://publications.scilifelab.se/researcher/048f072498914ea9bc5fcc7d8ae0347e.json"}}, {"family": "Ferretti", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-1848-5950", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc2029e30d4d4d6f9771f1e58d6fc929.json"}}, {"family": "Mueller", "given": "Johannes", "initials": "J"}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Testa", "given": "Ilaria", "initials": "I", "orcid": "0000-0003-4005-4997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d8e8420dada49d6a4ef1da7a06e02f1.json"}}], "type": "journal article", "published": "2026-01-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "pages": "419", "issn-l": "2041-1723"}, "abstract": "Healthy mitochondria are crucial for maintaining neuronal homeostasis. Their activity depends on a dynamic lipid and protein exchange through fusion, fission, and vesicular trafficking. Studying vesicles in neurons is challenging with conventional microscopy due to their small size, heterogeneity, and dynamics. We use multicolour stimulated emission depletion nanoscopy to uncover the ultrastructure of mitochondrial-derived vesicles (MDVs) in live neurons, biosensors to define their functional state, and a pulse-chase strategy to identify their turnover in situ. We identified three populations of vesicular structures: one transporting degradation products originating from oxidative stress, one shuttling cargo and newly translated proteins for local organelle biogenesis and one consisting of small, functional mitochondria. Furthermore, we provide evidence supporting that de novo peroxisomes biogenesis occurs via the fusion of endoplasmic reticulum and MDVs at mitochondrial sites. Our data provide mechanistic insight into organelle biogenesis driven by significant diversity in MDV morphology, functional state, and molecular composition.", "doi": "10.1038/s41467-025-68160-y", "pmid": "41507166", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12796351"}, {"db": "pii", "key": "10.1038/s41467-025-68160-y"}], "notes": [], "created": "2026-01-20T18:41:24.213Z", "modified": "2026-01-20T18:41:24.588Z"}, {"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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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.", "authors": [{"family": "Ahlgren", "given": "Louise", "initials": "L"}, {"family": "Pilheden", "given": "Mattias", "initials": "M"}, {"family": "Sturesson", "given": "Helena", "initials": "H"}, {"family": "Song", "given": "Guangchun", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Walsh", "given": "Michael P", "initials": "MP"}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Maillard", "given": "Maud", "initials": "M"}, {"family": "Zhao", "given": "Huanbin", "initials": "H", "orcid": "0009-0001-4418-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/02a78b74f32d4670b628a8e3fb78ea0a.json"}}, {"family": "Cheng", "given": "Zhongshan", "initials": "Z"}, {"family": "Singh", "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": "https://publications.scilifelab.se/researcher/39a9fea74e284217b80716966bca995b.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Pokrovskaja Tamm", "given": "Katja", "initials": "K", "orcid": "0000-0001-6359-1256", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ec3ee706764024bd748c7a77443845.json"}}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9240-3522", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3199957bd147ec91bbdc04413f1dba.json"}}, {"family": "Lohi", "given": "Olli", "initials": "O", "orcid": "0000-0001-9195-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11a59310dfc40e6a111367914fdba9e.json"}}, {"family": "Fogelstrand", "given": "Linda", "initials": "L", "orcid": "0000-0003-3698-8519", "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "c4979500cf274a2b86a8aa71d352dc26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4979500cf274a2b86a8aa71d352dc26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4979500cf274a2b86a8aa71d352dc26"}}, "title": "Parallel single-cell metabolic analysis and extracellular vesicle profiling reveal vulnerabilities with prognostic significance in acute myeloid leukemia.", "authors": [{"family": "Forte", "given": "Dorian", "initials": "D", "orcid": "0000-0002-8443-605X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e756545d7dce426dbff32a3c78f92b78.json"}}, {"family": "Pellegrino", "given": "Roberto Maria", "initials": "RM", "orcid": "0000-0001-5594-383X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b62fc87e9384d6b801e01cfc3c42bf7.json"}}, {"family": "Falvo", "given": "Paolo", "initials": "P", "orcid": "0000-0001-5743-5046", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4503a1a6b7c435f8c4df48067082ee9.json"}}, {"family": "Garcia-Gonzalez", "given": "Paulina", "initials": "P"}, {"family": "Alabed", "given": "Husam B R", "initials": "HBR"}, {"family": "Maltoni", "given": "Filippo", "initials": "F"}, {"family": "Lombardi", "given": "Davide", "initials": "D"}, {"family": "Bruno", "given": "Samantha", "initials": "S", "orcid": "0000-0001-6375-0595", "researcher": {"href": "https://publications.scilifelab.se/researcher/f57164a4088c4848a46005ef412e4e53.json"}}, {"family": "Barone", "given": "Martina", "initials": "M", "orcid": "0000-0003-3356-9861", "researcher": {"href": "https://publications.scilifelab.se/researcher/a022b64322ee42cf9548077241438fbc.json"}}, {"family": "Pasini", "given": "Federico", "initials": "F", "orcid": "0009-0000-1719-1585", "researcher": {"href": "https://publications.scilifelab.se/researcher/229936b55ccc4a7aabd383ed1792e630.json"}}, {"family": "Fabbri", "given": "Francesco", "initials": "F"}, {"family": "Vannini", "given": "Ivan", "initials": "I"}, {"family": "Donati", "given": "Benedetta", "initials": "B"}, {"family": "Cristiano", "given": "Gianluca", "initials": "G"}, {"family": "Sartor", "given": "Chiara", "initials": "C"}, {"family": "Ronzoni", "given": "Simona", "initials": "S"}, {"family": "Ciarrocchi", "given": "Alessia", "initials": "A", "orcid": "0000-0002-5541-2075", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc007ffa73e84d14a51a234c82a3a0b2.json"}}, {"family": "Buratta", "given": "Sandra", "initials": "S"}, {"family": "Urbanelli", "given": "Lorena", "initials": "L", "orcid": "0000-0003-0621-8476", "researcher": {"href": "https://publications.scilifelab.se/researcher/7006a73ec352432c84b034def82cfc74.json"}}, {"family": "Emiliani", "given": "Carla", "initials": "C"}, {"family": "Soverini", "given": "Simona", "initials": "S"}, {"family": "Catani", "given": "Lucia", "initials": "L"}, {"family": "Bertolini", "given": "Francesco", "initials": "F", "orcid": "0000-0001-5660-3255", "researcher": {"href": "https://publications.scilifelab.se/researcher/99ce5fc0a31645adbe7bb9be33c30d66.json"}}, {"family": "Arg\u00fcello", "given": "Rafael Jos\u00e9", "initials": "RJ", "orcid": "0000-0001-9785-3883", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7ac293788d0406cbf4f385bb9b72559.json"}}, {"family": "Cavo", "given": "Michele", "initials": "M"}, {"family": "Curti", "given": "Antonio", "initials": "A", "orcid": "0000-0002-7752-6049", "researcher": {"href": "https://publications.scilifelab.se/researcher/065c5f8e47094ca085586706cea6782a.json"}}], "type": "journal article", "published": "2024-12-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "10878", "issn-l": "2041-1723"}, "abstract": "Acute myeloid leukemia (AML) is an aggressive disease with a high relapse rate. In this study, we map the metabolic profile of CD34+(CD38low/-) AML cells and the extracellular vesicle signatures in circulation from AML patients at diagnosis. CD34+ AML cells display high antioxidant glutathione levels and enhanced mitochondrial functionality, both associated with poor clinical outcomes. Although CD34+ AML cells are highly dependent on glucose oxidation and glycolysis for energy, those from intermediate- and adverse-risk patients reveal increased mitochondrial dependence. Extracellular vesicles from AML are mainly enriched in stem cell markers and express antioxidant GPX3, with their profiles showing potential prognostic value. Extracellular vesicles enhance mitochondrial functionality and dependence on CD34+ AML cells via the glutathione/GPX4 axis. Notably, extracellular vesicles from adverse-risk patients enhance leukemia cell engraftment in vivo. Here, we show a potential noninvasive approach based on liquid 'cell-extracellular vesicle' biopsy toward a redefined metabolic stratification in AML.", "doi": "10.1038/s41467-024-55231-9", "pmid": "39738118", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11685939"}, {"db": "pii", "key": "10.1038/s41467-024-55231-9"}], "notes": [], "created": "2025-11-18T12:06:28.499Z", "modified": "2025-11-18T12:06:29.260Z"}, {"entity": "publication", "iuid": "f09706baf2a74636a49097f82b60b681", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f09706baf2a74636a49097f82b60b681.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f09706baf2a74636a49097f82b60b681"}}, "title": "VLDLR mediates Semliki Forest virus neuroinvasion through the blood-cerebrospinal fluid barrier.", "authors": [{"family": "Martikainen", "given": "Miika", "initials": "M", "orcid": "0000-0001-8202-701X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3477399dd7474fc6a18863b4c239d81c.json"}}, {"family": "Lugano", "given": "Roberta", "initials": "R"}, {"family": "Pietil\u00e4", "given": "Ilkka", "initials": "I"}, {"family": "Brosch", "given": "Sofie", "initials": "S"}, {"family": "Cabrolier", "given": "Camille", "initials": "C"}, {"family": "Sivaramakrishnan", "given": "Aishwarya", "initials": "A"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M", "orcid": "0000-0003-2685-0575", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3fefc78a0b040faa998efb8fde7b920.json"}}, {"family": "Yu", "given": "Di", "initials": "D", "orcid": "0000-0002-8636-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfc1c71920c74292b4392a2ee108998d.json"}}, {"family": "Dimberg", "given": "Anna", "initials": "A", "orcid": "0000-0003-4422-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/c53166298a214331866c8cbf3bb9a3b9.json"}}, {"family": "Essand", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9725-0422", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5afc47ab0814c09909af3c66217a3a6.json"}}], "type": "journal article", "published": "2024-12-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "10718", "issn-l": "2041-1723"}, "abstract": "Semliki Forest virus (SFV) is a neuropathogenic alphavirus which is of interest both as a model neurotropic alphavirus and as an oncolytic virus with proven potency in preclinical cancer models. In laboratory mice, peripherally administered SFV infiltrates the central nervous system (CNS) and causes encephalitis of varying severity. The route of SFV CNS entrance is poorly understood but has been considered to occur through the blood-brain barrier. Here we show that neuroinvasion of intravenously administered SFV is strictly dependent on very-low-density-lipoprotein receptor (VLDLR) which acts as an entry receptor for SFV. Moreover, SFV primarily enters the CNS through the blood-cerebrospinal fluid (B-CSF) barrier via infecting choroid plexus epithelial cells which show distinctly high expression of VLDLR. This is the first indication of neurotropic alphavirus utilizing choroid plexus for CNS entry, and VLDLR playing a specific and crucial role for mediating SFV entry through this pathway.", "doi": "10.1038/s41467-024-55493-3", "pmid": "39715740", "labels": {"Bioinformatics Support for Computational Resources": "Service", "CRISPR Functional Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11666578"}, {"db": "pii", "key": "10.1038/s41467-024-55493-3"}, {"db": "GEO", "key": "GSE283607"}], "notes": [], "created": "2025-02-28T14:14:51.638Z", "modified": "2025-09-15T09:21:34.660Z"}, {"entity": "publication", "iuid": "fa7febd25a2943dfb4e4ac6af99ee6cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa7febd25a2943dfb4e4ac6af99ee6cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa7febd25a2943dfb4e4ac6af99ee6cb"}}, "title": "Evolution of fast-growing piscivorous herring in the young Baltic Sea.", "authors": [{"family": "Goodall", "given": "Jake", "initials": "J", "orcid": "0000-0003-0960-4241", "researcher": {"href": "https://publications.scilifelab.se/researcher/457d1a2733cc4a569ffeb70750999199.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Bergstr\u00f6m", "given": "Ulf", "initials": "U", "orcid": "0000-0002-5478-0634", "researcher": {"href": "https://publications.scilifelab.se/researcher/d83f775f03154adfabf0a48a00cb1896.json"}}, {"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": "Heimbrand", "given": "Yvette", "initials": "Y", "orcid": "0000-0002-5120-4797", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d473cd11754b15a743173ff7a23502.json"}}, {"family": "Karlsson", "given": "O Magnus", "initials": "OM", "orcid": "0000-0002-2032-6126", "researcher": {"href": "https://publications.scilifelab.se/researcher/b23affc0739a418c972c3723868c0a41.json"}}, {"family": "Larsson", "given": "Josefine", "initials": "J"}, {"family": "Waldetoft", "given": "Hannes", "initials": "H", "orcid": "0009-0006-7326-6231", "researcher": {"href": "https://publications.scilifelab.se/researcher/319b5b610a84404ba3d3d9cd51c027a3.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}, {"family": "Wennerstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2024-12-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "10707", "issn-l": "2041-1723"}, "abstract": "The circumstances under which species diversify to genetically distinct lineages is a fundamental question in biology. Atlantic herring (Clupea harengus) is an extremely abundant zooplanktivorous species that is subdivided into multiple ecotypes that differ regarding spawning time and genetic adaption to local environmental conditions such as temperature, salinity, and light conditions. Here we show using whole genome analysis that multiple populations of piscivorous (fish-eating) herring have evolved sympatrically after the colonization of the brackish Baltic Sea within the last 8000 years postglaciation. The piscivorous ecotype grows faster, and is much larger and less abundant than the zooplanktivorous Baltic herring. Lesions of the gill rakers in the piscivorous ecotype indicated incomplete adaptation to a fish diet. This niche expansion of herring in the young Baltic Sea, with its paucity of piscivorous species, suggests that empty niche space is more important than geographic isolation for the evolution of biodiversity.", "doi": "10.1038/s41467-024-55216-8", "pmid": "39715744", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11666761"}, {"db": "pii", "key": "10.1038/s41467-024-55216-8"}], "notes": [], "created": "2025-02-28T14:14:46.130Z", "modified": "2025-02-28T14:14:46.502Z"}, {"entity": "publication", "iuid": "f26f0c3b05174ceebc02a8fca7a9c62b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f26f0c3b05174ceebc02a8fca7a9c62b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f26f0c3b05174ceebc02a8fca7a9c62b"}}, "title": "Dysregulation of MMP2-dependent TGF-\u00df2 activation impairs fibrous cap formation in type 2 diabetes-associated atherosclerosis.", "authors": [{"family": "Singh", "given": "Pratibha", "initials": "P"}, {"family": "Sun", "given": "Jiangming", "initials": "J", "orcid": "0000-0001-6814-1297", "researcher": {"href": "https://publications.scilifelab.se/researcher/358e5b727c9c40ff94848a9d7a8d5945.json"}}, {"family": "Cavalera", "given": "Michele", "initials": "M"}, {"family": "Al-Sharify", "given": "Dania", "initials": "D"}, {"family": "Matthes", "given": "Frank", "initials": "F", "orcid": "0000-0002-5115-8831", "researcher": {"href": "https://publications.scilifelab.se/researcher/00f734f5167a4de48f38bcdf5e5765ab.json"}}, {"family": "Barghouth", "given": "Mohammad", "initials": "M"}, {"family": "Tengryd", "given": "Christoffer", "initials": "C"}, {"family": "Dun\u00e9r", "given": "Pontus", "initials": "P"}, {"family": "Persson", "given": "Ana", "initials": "A"}, {"family": "Sundius", "given": "Lena", "initials": "L"}, {"family": "Nitulescu", "given": "Mihaela", "initials": "M"}, {"family": "Bengtsson", "given": "Eva", "initials": "E"}, {"family": "Rattik", "given": "Sara", "initials": "S"}, {"family": "Engelbertsen", "given": "Daniel", "initials": "D"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "Nilsson", "given": "Jan", "initials": "J", "orcid": "0000-0002-9752-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8777140448bc47f0a7984db3c15c0e23.json"}}, {"family": "Monaco", "given": "Claudia", "initials": "C", "orcid": "0000-0003-1985-4914", "researcher": {"href": "https://publications.scilifelab.se/researcher/4597888d83b145719b897bf26dc05e4a.json"}}, {"family": "Goncalves", "given": "Isabel", "initials": "I"}, {"family": "Edsfeldt", "given": "Andreas", "initials": "A", "orcid": "0000-0002-2691-9192", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4d8310d9d834bd791b791424774b989.json"}}], "type": "journal article", "published": "2024-12-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "10464", "issn-l": "2041-1723"}, "abstract": "Type 2 diabetes is associated with cardiovascular disease, possibly due to impaired vascular fibrous repair. Yet, the mechanisms are elusive. Here, we investigate alterations in the fibrous repair processes in type 2 diabetes atherosclerotic plaque extracellular matrix by combining multi-omics from the human Carotid Plaque Imaging Project cohort and functional studies. Plaques from type 2 diabetes patients have less collagen. Interestingly, lower levels of transforming growth factor-\u00df distinguish type 2 diabetes plaques and, in these patients, lower levels of fibrous repair markers are associated with cardiovascular events. Transforming growth factor-\u00df2 originates mostly from contractile vascular smooth muscle cells that interact with synthetic vascular smooth muscle cells in the cap, leading to collagen formation and vascular smooth muscle cell differentiation. This is regulated by free transforming growth factor-\u00df2 which is affected by hyperglycemia. Our findings underscore the importance of transforming growth factor-\u00df2-driven fibrous repair in type 2 diabetes as an area for future therapeutic strategies.", "doi": "10.1038/s41467-024-50753-8", "pmid": "39653743", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11628557"}, {"db": "pii", "key": "10.1038/s41467-024-50753-8"}, {"db": "GEO", "key": "GSE159677"}], "notes": [], "created": "2025-11-25T19:20:16.367Z", "modified": "2025-11-25T19:20:16.548Z"}, {"entity": "publication", "iuid": "6befcd3ead5a4b38aa1ed2b2a3efb705", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6befcd3ead5a4b38aa1ed2b2a3efb705.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6befcd3ead5a4b38aa1ed2b2a3efb705"}}, "title": "Coupling cellular drug-target engagement to downstream pharmacology with CeTEAM.", "authors": [{"family": "Valerie", "given": "Nicholas C K", "initials": "NCK", "orcid": "0000-0002-9423-964X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d90c5a1f924c8b97409934dec74b0b.json"}}, {"family": "Sanjiv", "given": "Kumar", "initials": "K"}, {"family": "Mortusewicz", "given": "Oliver", "initials": "O", "orcid": "0000-0002-4290-4994", "researcher": {"href": "https://publications.scilifelab.se/researcher/b62a88fc39a54906a40e28e679c9f624.json"}}, {"family": "Zhang", "given": "Si Min", "initials": "SM", "orcid": "0000-0001-7763-603X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1eac01c3a53d4940ade49b24f13dd214.json"}}, {"family": "Alam", "given": "Seher", "initials": "S"}, {"family": "Pires", "given": "Maria J", "initials": "MJ"}, {"family": "Stigsdotter", "given": "Hannah", "initials": "H"}, {"family": "Rasti", "given": "Azita", "initials": "A"}, {"family": "Langelier", "given": "Marie-France", "initials": "MF", "orcid": "0000-0001-9815-1840", "researcher": {"href": "https://publications.scilifelab.se/researcher/caac2647bbde41dbbd7d5fd31fb2da70.json"}}, {"family": "Rehling", "given": "Daniel", "initials": "D"}, {"family": "Throup", "given": "Adam", "initials": "A", "orcid": "0000-0001-6512-8679", "researcher": {"href": "https://publications.scilifelab.se/researcher/dea6b870fafa471499bd71f1b2693be4.json"}}, {"family": "Purewal-Sidhu", "given": "Oryn", "initials": "O"}, {"family": "Desroses", "given": "Matthieu", "initials": "M"}, {"family": "Onireti", "given": "Jacob", "initials": "J", "orcid": "0009-0003-9745-4446", "researcher": {"href": "https://publications.scilifelab.se/researcher/989eece269e544728082d7764d924d52.json"}}, {"family": "Wakchaure", "given": "Prasad", "initials": "P"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Bostr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Bevc", "given": "Luka", "initials": "L"}, {"family": "Benzi", "given": "Giorgia", "initials": "G"}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Pascal", "given": "John M", "initials": "JM", "orcid": "0000-0002-2714-4317", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee603b6cd7984898bd6cdbb601e4b3e7.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Page", "given": "Brent D G", "initials": "BDG"}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}], "type": "journal article", "published": "2024-12-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "10347", "issn-l": "2041-1723"}, "abstract": "Cellular target engagement technologies enable quantification of intracellular drug binding; however, simultaneous assessment of drug-associated phenotypes has proven challenging. Here, we present cellular target engagement by accumulation of mutant as a platform that can concomitantly evaluate drug-target interactions and phenotypic responses using conditionally stabilized drug biosensors. We observe that drug-responsive proteotypes are prevalent among reported mutants of known drug targets. Compatible mutants appear to follow structural and biophysical logic that permits intra-protein and paralogous expansion of the biosensor pool. We then apply our method to uncouple target engagement from divergent cellular activities of MutT homolog 1 (MTH1) inhibitors, dissect Nudix hydrolase 15 (NUDT15)-associated thiopurine metabolism with the R139C pharmacogenetic variant, and profile the dynamics of poly(ADP-ribose) polymerase 1/2 (PARP1/2) binding and DNA trapping by PARP inhibitors (PARPi). Further, PARP1-derived biosensors facilitated high-throughput screening for PARP1 binders, as well as multimodal ex vivo analysis and non-invasive tracking of PARPi binding in live animals. This approach can facilitate holistic assessment of drug-target engagement by bridging drug binding events and their biological consequences.", "doi": "10.1038/s41467-024-54415-7", "pmid": "39643609", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11624193"}, {"db": "pii", "key": "10.1038/s41467-024-54415-7"}], "notes": [], "created": "2024-12-16T08:43:06.953Z", "modified": "2025-10-17T13:04:27.012Z"}, {"entity": "publication", "iuid": "ce818c732d8b401fa281fcaac2bb2a92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce818c732d8b401fa281fcaac2bb2a92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce818c732d8b401fa281fcaac2bb2a92"}}, "title": "Dynamics of the blood plasma proteome during hyperacute HIV-1 infection.", "authors": [{"family": "Nazziwa", "given": "Jamirah", "initials": "J", "orcid": "0000-0001-9029-7976", "researcher": {"href": "https://publications.scilifelab.se/researcher/f04c46d93e824effa0e312429b63046c.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d66c199ece143a6ab15222d8b55e3ea.json"}}, {"family": "Johansson", "given": "Emil", "initials": "E", "orcid": "0000-0002-4712-3687", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19eeefa1494862861f096865122f81.json"}}, {"family": "\u00c5rman", "given": "Filip", "initials": "F"}, {"family": "Hare", "given": "Jonathan", "initials": "J"}, {"family": "Gounder", "given": "Kamini", "initials": "K"}, {"family": "Rezeli", "given": "Melinda", "initials": "M"}, {"family": "Mohanty", "given": "Tirthankar", "initials": "T", "orcid": "0000-0003-4593-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a9c51697d33414f8197c7833d9dcc04.json"}}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S", "orcid": "0000-0003-4646-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfae5f64ec9d45e282cdfd038539fe25.json"}}, {"family": "Kamali", "given": "Anatoli", "initials": "A"}, {"family": "Karita", "given": "Etienne", "initials": "E"}, {"family": "Kilembe", "given": "William", "initials": "W"}, {"family": "Price", "given": "Matt A", "initials": "MA"}, {"family": "Kaleebu", "given": "Pontiano", "initials": "P"}, {"family": "Allen", "given": "Susan", "initials": "S"}, {"family": "Hunter", "given": "Eric", "initials": "E", "orcid": "0000-0002-4273-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/b302023db3c444bcb63000e675136336.json"}}, {"family": "Ndung'u", "given": "Thumbi", "initials": "T"}, {"family": "Gilmour", "given": "Jill", "initials": "J"}, {"family": "Rowland-Jones", "given": "Sarah L", "initials": "SL", "orcid": "0000-0001-5788-6998", "researcher": {"href": "https://publications.scilifelab.se/researcher/4731197ff0a74962b606ac7b2c0ba7d8.json"}}, {"family": "Sanders", "given": "Eduard", "initials": "E", "orcid": "0000-0002-1062-8921", "researcher": {"href": "https://publications.scilifelab.se/researcher/25c23cf817504f69aa6f5f6a7b8804d2.json"}}, {"family": "Hassan", "given": "Amin S", "initials": "AS", "orcid": "0000-0001-5296-4264", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac3c5d36e98c474bba57a214dcd005ff.json"}}, {"family": "Esbj\u00f6rnsson", "given": "Joakim", "initials": "J", "orcid": "0000-0002-3822-4953", "researcher": {"href": "https://publications.scilifelab.se/researcher/c925b57ea92f4496aa3a1619ef2b0b5f.json"}}], "type": "journal article", "published": "2024-12-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "10593", "issn-l": "2041-1723"}, "abstract": "The complex dynamics of protein expression in plasma during hyperacute HIV-1 infection and its relation to acute retroviral syndrome, viral control, and disease progression are largely unknown. Here, we quantify 1293 blood plasma proteins from 157 longitudinally linked plasma samples collected before, during, and after hyperacute HIV-1 infection of 54 participants from four sub-Saharan African countries. Six distinct longitudinal expression profiles are identified, of which four demonstrate a consistent decrease in protein levels following HIV-1 infection. Proteins involved in inflammatory responses, immune regulation, and cell motility are significantly altered during the transition from pre-infection to one month post-infection. Specifically, decreased ZYX and SCGB1A1 levels, and increased LILRA3 levels are associated with increased risk of acute retroviral syndrome; increased NAPA and RAN levels, and decreased ITIH4 levels with viral control; and increased HPN, PRKCB, and ITGB3 levels with increased risk of disease progression. Overall, this study provides insight into early host responses in hyperacute HIV-1 infection, and present potential biomarkers and mechanisms linked to HIV-1 disease progression and viral load.", "doi": "10.1038/s41467-024-54848-0", "pmid": "39632834", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11618498"}, {"db": "pii", "key": "10.1038/s41467-024-54848-0"}], "notes": [], "created": "2025-02-17T09:25:35.865Z", "modified": "2025-02-17T09:25:37.091Z"}, {"entity": "publication", "iuid": "7efe68cb12144989aaa7d3311aa2b137", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7efe68cb12144989aaa7d3311aa2b137.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7efe68cb12144989aaa7d3311aa2b137"}}, "title": "A landscape of X-inactivation during human T cell development.", "authors": [{"family": "Gylemo", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5253-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e62e3eed2144dd0a2584a3cfbe7800a.json"}}, {"family": "Bensberg", "given": "Maike", "initials": "M", "orcid": "0000-0003-2395-6083", "researcher": {"href": "https://publications.scilifelab.se/researcher/afa6aec5136e46fd97981fa37b8c8295.json"}}, {"family": "Hennings", "given": "Viktoria", "initials": "V"}, {"family": "Lundqvist", "given": "Christina", "initials": "C", "orcid": "0000-0002-2256-4072", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b339e6cc1f48f3a5f736201038ee59.json"}}, {"family": "Camponeschi", "given": "Alessandro", "initials": "A", "orcid": "0000-0002-6472-2438", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccbaffafd6a24f4abed1e402219fa472.json"}}, {"family": "Goldmann", "given": "D\u00f3ra", "initials": "D"}, {"family": "Zhang", "given": "Huan", "initials": "H"}, {"family": "Selimovi\u0107-Pa\u0161i\u0107", "given": "Aida", "initials": "A"}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications.scilifelab.se/researcher/e282901d24c64b16a540eff0d57776f4.json"}}, {"family": "Ekwall", "given": "Olov", "initials": "O", "orcid": "0000-0002-4506-9955", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d7af11d7d30410d8fe5f3b5fbd0ba1d.json"}}, {"family": "Nestor", "given": "Colm E", "initials": "CE", "orcid": "0000-0001-5853-1769", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca9fb12cf5754f36baf12f96f563ddb4.json"}}], "type": "journal article", "published": "2024-12-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "10527", "issn-l": "2041-1723"}, "abstract": "Females exhibit a more robust immune response to both self-antigens and non-self-antigens than males, resulting in a higher prevalence of autoimmune diseases but more effective responses against infection. Increased expression of X-linked immune genes in female T cells is thought to underlie this enhanced response. Here we isolate thymocytes from pediatric thymi of healthy males (46, XY), females (46, XX), a female with completely skewed X-chromosome inactivation (46, XX, cXCI) and a female with Turner syndrome (45, X0). Using whole exome sequencing, RNA sequencing and DNA methylation data, we present a sex-aware expression profile of T cell development and generate a high-resolution map of escape from X-chromosome inactivation (XCI). Unexpectedly, XCI is transcriptionally and epigenetically stable throughout T cell development, and is independent of expression of XIST, the lncRNA responsible for XCI initiation during early embryonic development. In thymocytes, several genes known to escape XCI are expressed from only one X-chromosome. Additionally, we further reveal that a second X-chromosome is dispensable for T cell development. Our study thus provides a high-resolution map of XCI during human development and suggests a re-evaluation of XCI in sex differences in T cell function.", "doi": "10.1038/s41467-024-54110-7", "pmid": "39632794", "labels": {"Clinical Genomics Link\u00f6ping": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11618795"}, {"db": "pii", "key": "10.1038/s41467-024-54110-7"}], "notes": [], "created": "2024-12-10T08:39:23.208Z", "modified": "2024-12-10T08:39:23.536Z"}, {"entity": "publication", "iuid": "be1ccad457054a6ca82002c69b0dacdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be1ccad457054a6ca82002c69b0dacdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be1ccad457054a6ca82002c69b0dacdb"}}, "title": "Streptolysin O accelerates the conversion of plasminogen to plasmin", "authors": [{"family": "Tang", "given": "Di", "initials": "D", "orcid": "0000-0001-6323-9375", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2a27467c4094d9f8d8f8402efa333f4.json"}}, {"family": "Khakzad", "given": "Hamed", "initials": "H", "orcid": "0000-0002-8556-0650", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7b030c1452c4dc9b430deffdf493e6f.json"}}, {"family": "Hjortswang", "given": "Elisabeth", "initials": "E"}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L", "orcid": "0000-0001-9885-9312", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e99f34fb854beb8d810b05fe941057.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": "Malmstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad3c999da10c41e4a3afda2718815083.json"}}], "type": "journal-article", "published": "2024-11-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "10212"}, "abstract": "Group A Streptococcus (GAS) is a human-specific bacterial pathogen that can exploit the plasminogen-plasmin fibrinolysis system to dismantle blood clots and facilitate its spread and survival within the human host. In this study, we use affinity-enrichment mass spectrometry to decipher the host-pathogen protein-protein interaction between plasminogen and streptolysin O, a key cytolytic toxin produced by GAS. This interaction accelerates the conversion of plasminogen to plasmin by both the host tissue-type plasminogen activator and streptokinase, a bacterial plasminogen activator secreted by GAS. Integrative structural mass spectrometry analysis shows that the interaction induces local conformational shifts in plasminogen. These changes lead to the formation of a stabilised intermediate plasminogen-streptolysin O complex that becomes significantly more susceptible to proteolytic processing by plasminogen activators. Our findings reveal a conserved and moonlighting pathomechanistic function for streptolysin O that extends beyond its well-characterised cytolytic activity.", "doi": "10.1038/s41467-024-54173-6", "pmid": "39587097", "labels": {"Structural Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-024-54173-6"}, {"db": "pmc", "key": "PMC11589678"}], "notes": [], "created": "2024-11-27T17:20:53.877Z", "modified": "2024-11-28T17:40:23.904Z"}, {"entity": "publication", "iuid": "0dfd25e1d8be418aa3d787429435a9c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dfd25e1d8be418aa3d787429435a9c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dfd25e1d8be418aa3d787429435a9c5"}}, "title": "Simultaneous detection of membrane contact dynamics and associated Ca2+ signals by reversible chemogenetic reporters.", "authors": [{"family": "Garc\u00eda Casas", "given": "Paloma", "initials": "P"}, {"family": "Rossini", "given": "Michela", "initials": "M", "orcid": "0009-0008-9482-0371", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ba2d2f526f48c5b8f82280fed52d52.json"}}, {"family": "P\u00e5v\u00e9nius", "given": "Linnea", "initials": "L", "orcid": "0000-0001-6730-2458", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0accb4e8c124537b44b5514c66a65a8.json"}}, {"family": "Saeed", "given": "Mezida", "initials": "M", "orcid": "0000-0003-1921-6015", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ce03165a10a4abf8c75b602b26a9d4b.json"}}, {"family": "Arnst", "given": "Nikita", "initials": "N"}, {"family": "Sonda", "given": "Sonia", "initials": "S"}, {"family": "Fernandes", "given": "T\u00e2nia", "initials": "T"}, {"family": "D'Arsi\u00e8", "given": "Irene", "initials": "I"}, {"family": "Bruzzone", "given": "Matteo", "initials": "M", "orcid": "0000-0001-7683-8107", "researcher": {"href": "https://publications.scilifelab.se/researcher/21da8aa83ac444bc8b5d6dcdcdc44984.json"}}, {"family": "Berno", "given": "Valeria", "initials": "V"}, {"family": "Raimondi", "given": "Andrea", "initials": "A", "orcid": "0000-0002-4563-386X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ad3e10197a24764915469622acd0d2b.json"}}, {"family": "Sassano", "given": "Maria Livia", "initials": "ML", "orcid": "0000-0002-2262-6915", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a881586a4434890ab09a921caf17a7b.json"}}, {"family": "Naia", "given": "Luana", "initials": "L", "orcid": "0000-0002-0886-4634", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ae78f608af4f3f8524d5ab4a3c6cdd.json"}}, {"family": "Barbieri", "given": "Elisa", "initials": "E"}, {"family": "Sigismund", "given": "Sara", "initials": "S", "orcid": "0000-0002-1396-4453", "researcher": {"href": "https://publications.scilifelab.se/researcher/34bbb9fa7a964c869d958fa5eff42f21.json"}}, {"family": "Agostinis", "given": "Patrizia", "initials": "P", "orcid": "0000-0003-1314-2115", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0a95bfa33084ef58debd39050675cc0.json"}}, {"family": "Sturlese", "given": "Mattia", "initials": "M", "orcid": "0000-0003-3944-0313", "researcher": {"href": "https://publications.scilifelab.se/researcher/58284eb419184e72b88c55042b21a03b.json"}}, {"family": "Niemeyer", "given": "Barbara A", "initials": "BA", "orcid": "0000-0002-6963-0575", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5261a56f977404b894cd4a5bad1bbc3.json"}}, {"family": "Brismar", "given": "Hjalmar", "initials": "H"}, {"family": "Ankarcrona", "given": "Maria", "initials": "M", "orcid": "0000-0002-7022-3694", "researcher": {"href": "https://publications.scilifelab.se/researcher/5deb5cb7c18647b5b37d80221b67086c.json"}}, {"family": "Gautier", "given": "Arnaud", "initials": "A", "orcid": "0000-0003-1017-9879", "researcher": {"href": "https://publications.scilifelab.se/researcher/31aa58631e6643b28a42c227c45f1ce5.json"}}, {"family": "Pizzo", "given": "Paola", "initials": "P", "orcid": "0000-0001-6077-3265", "researcher": {"href": "https://publications.scilifelab.se/researcher/3faa4d11f4c2408e84d8388887831dfc.json"}}, {"family": "Filadi", "given": "Riccardo", "initials": "R", "orcid": "0000-0002-5871-2620", "researcher": {"href": "https://publications.scilifelab.se/researcher/9957f7c6fbc74ed5a8c22ef55bb348d2.json"}}], "type": "journal article", "published": "2024-11-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9775", "issn-l": "2041-1723"}, "abstract": "Membrane contact sites (MCSs) are hubs allowing various cell organelles to coordinate their activities. The dynamic nature of these sites and their small size hinder analysis by current imaging techniques. To overcome these limitations, we here design a series of reversible chemogenetic reporters incorporating improved, low-affinity variants of splitFAST, and study the dynamics of different MCSs at high spatiotemporal resolution, both in vitro and in vivo. We demonstrate that these versatile reporters suit different experimental setups well, allowing one to address challenging biological questions. Using these probes, we identify a pathway in which calcium (Ca2+) signalling dynamically regulates endoplasmic reticulum-mitochondria juxtaposition, characterizing the underlying mechanism. Finally, by integrating Ca2+-sensing capabilities into the splitFAST technology, we introduce PRINCESS (PRobe for INterorganelle Ca2+-Exchange Sites based on SplitFAST), a class of reporters to simultaneously detect MCSs and measure the associated Ca2+ dynamics using a single biosensor.", "doi": "10.1038/s41467-024-52985-0", "pmid": "39532847", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-024-52985-0"}, {"db": "pmc", "key": "PMC11557831"}], "notes": [], "created": "2024-11-15T10:33:14.658Z", "modified": "2024-11-15T10:33:15.655Z"}, {"entity": "publication", "iuid": "a39f01f3a62f42d88d88d1a5f418c3b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a39f01f3a62f42d88d88d1a5f418c3b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a39f01f3a62f42d88d88d1a5f418c3b7"}}, "title": "A unique symbiosome in an anaerobic single-celled eukaryote.", "authors": [{"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}, {"family": "Gallot-Lavall\u00e9e", "given": "Lucie", "initials": "L", "orcid": "0000-0001-6763-3388", "researcher": {"href": "https://publications.scilifelab.se/researcher/7790fd356f5c4d29a58c22c708e7d886.json"}}, {"family": "Salas-Leiva", "given": "Dayana E", "initials": "DE", "orcid": "0000-0003-2356-3351", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1a8a3928d494986b64ea03f66df2057.json"}}, {"family": "Curtis", "given": "Bruce A", "initials": "BA"}, {"family": "Z\u00e1honov\u00e1", "given": "Krist\u00edna", "initials": "K", "orcid": "0000-0002-5766-0267", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a88cec1dc4398865f4f840535ec9d.json"}}, {"family": "\u010cepi\u010dka", "given": "Ivan", "initials": "I", "orcid": "0000-0002-4322-0754", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f2c1a48df3e4f3f957907c1e547070c.json"}}, {"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Pipaliya", "given": "Shweta", "initials": "S"}, {"family": "Dacks", "given": "Joel B", "initials": "JB", "orcid": "0000-0003-4520-5694", "researcher": {"href": "https://publications.scilifelab.se/researcher/97c30e7e0487483d894192c2c7c76368.json"}}, {"family": "Archibald", "given": "John M", "initials": "JM", "orcid": "0000-0001-7255-780X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc225404ccd7449b95d00245b7d5df38.json"}}, {"family": "Roger", "given": "Andrew J", "initials": "AJ", "orcid": "0000-0003-1370-9820", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf086d9bf6d45d2941c6ba5e8a0e838.json"}}], "type": "journal article", "published": "2024-11-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9726", "issn-l": "2041-1723"}, "abstract": "Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.", "doi": "10.1038/s41467-024-54102-7", "pmid": "39521804", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11550330"}, {"db": "pii", "key": "10.1038/s41467-024-54102-7"}, {"db": "figshare", "key": "10.6084/m9.figshare.24033777"}, {"db": "figshare", "key": "10.6084/m9.figshare.20375619"}, {"db": "figshare", "key": "10.6084/m9.figshare.20375601"}, {"db": "figshare", "key": "10.6084/m9.figshare.22193497"}, {"db": "figshare", "key": "10.6084/m9.figshare.27108724"}, {"db": "figshare", "key": "10.6084/m9.figshare.27108751"}, {"db": "BioProject", "key": "PRJNA634776"}], "notes": [], "created": "2024-11-19T12:30:44.514Z", "modified": "2025-09-12T09:08:56.147Z"}, {"entity": "publication", "iuid": "60264368eb424544b7cc9bf7716494ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60264368eb424544b7cc9bf7716494ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60264368eb424544b7cc9bf7716494ab"}}, "title": "Cancer-associated fibroblast subtypes modulate the tumor-immune microenvironment and are associated with skin cancer malignancy.", "authors": [{"family": "Forsthuber", "given": "Agnes", "initials": "A", "orcid": "0000-0001-6396-0090", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd76e819ba654fc5b30475456f4bb147.json"}}, {"family": "Aschenbrenner", "given": "Bertram", "initials": "B", "orcid": "0000-0003-1177-7109", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8091adf276f4ca5af2e9c295a93b964.json"}}, {"family": "Korosec", "given": "Ana", "initials": "A"}, {"family": "Jacob", "given": "Tina", "initials": "T"}, {"family": "Annusver", "given": "Karl", "initials": "K", "orcid": "0000-0002-9515-7216", "researcher": {"href": "https://publications.scilifelab.se/researcher/941902f72c214c868d0136cf433442a7.json"}}, {"family": "Krajic", "given": "Natalia", "initials": "N", "orcid": "0000-0002-9255-5251", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec8d05c1d9ae4e0698967d93b23d4dc5.json"}}, {"family": "Kholodniuk", "given": "Daria", "initials": "D"}, {"family": "Frech", "given": "Sophie", "initials": "S", "orcid": "0000-0002-6190-8595", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa8e8d558e7c46f1b27722302e4050bb.json"}}, {"family": "Zhu", "given": "Shaohua", "initials": "S"}, {"family": "Purkhauser", "given": "Kim", "initials": "K", "orcid": "0000-0003-1732-9673", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e2a51d5352b4558a358fddca6eada62.json"}}, {"family": "Lipp", "given": "Katharina", "initials": "K"}, {"family": "Werner", "given": "Franziska", "initials": "F"}, {"family": "Nguyen", "given": "Vy", "initials": "V"}, {"family": "Griss", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2206-9511", "researcher": {"href": "https://publications.scilifelab.se/researcher/db31a8cdd1ea4a7d81a7d6d3a52f1f8b.json"}}, {"family": "Bauer", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-0155-1176", "researcher": {"href": "https://publications.scilifelab.se/researcher/00fbdb6833e342acb2f68abf2d7c41b6.json"}}, {"family": "Soler Cardona", "given": "Ana", "initials": "A"}, {"family": "Weber", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-7217-4590", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5b34f118cbb43cfb16a8b0c3038d83b.json"}}, {"family": "Weninger", "given": "Wolfgang", "initials": "W"}, {"family": "Gesslbauer", "given": "Bernhard", "initials": "B"}, {"family": "Staud", "given": "Clement", "initials": "C"}, {"family": "Nedomansky", "given": "Jakob", "initials": "J"}, {"family": "Radtke", "given": "Christine", "initials": "C"}, {"family": "Wagner", "given": "Stephan N", "initials": "SN", "orcid": "0000-0003-4941-7029", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c147211ed64433282e4feee5240852b.json"}}, {"family": "Petzelbauer", "given": "Peter", "initials": "P", "orcid": "0000-0001-7080-5259", "researcher": {"href": "https://publications.scilifelab.se/researcher/a741b6b9df654451ae52e193c19ce837.json"}}, {"family": "Kasper", "given": "Maria", "initials": "M", "orcid": "0000-0002-6117-2717", "researcher": {"href": "https://publications.scilifelab.se/researcher/b036a8a125ca4f0896f2e832e1248dc0.json"}}, {"family": "Lichtenberger", "given": "Beate M", "initials": "BM", "orcid": "0000-0001-6882-0257", "researcher": {"href": "https://publications.scilifelab.se/researcher/92555bb2628c4b29b72398c9608dc721.json"}}], "type": "journal article", "published": "2024-11-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9678", "issn-l": "2041-1723"}, "abstract": "Cancer-associated fibroblasts (CAFs) play a key role in cancer progression and treatment outcome. This study dissects the intra-tumoral diversity of CAFs in basal cell carcinoma, squamous cell carcinoma, and melanoma using molecular and spatial single-cell analysis. We identify three distinct CAF subtypes: myofibroblast-like RGS5+ CAFs, matrix CAFs (mCAFs), and immunomodulatory CAFs (iCAFs). Large-cohort tissue analysis reveals significant shifts in CAF subtype patterns with increasing malignancy. Two CAF subtypes exhibit immunomodulatory properties via different mechanisms. mCAFs sythesize extracellular matrix and may restrict T cell invasion in low-grade tumors via ensheathing tumor nests, while iCAFs are enriched in late-stage tumors, and express high levels of cytokines and chemokines to aid immune cell recruitment and activation. This is supported by the induction of an iCAF-like phenotype with immunomodulatory functions in primary healthy fibroblasts exposed to skin cancer cell secretomes. Thus, targeting CAF variants holds promise to enhance immunotherapy efficacy in skin cancers.", "doi": "10.1038/s41467-024-53908-9", "pmid": "39516494", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11549091"}, {"db": "pii", "key": "10.1038/s41467-024-53908-9"}], "notes": [], "created": "2024-11-25T10:18:25.172Z", "modified": "2024-11-25T10:18:25.564Z"}, {"entity": "publication", "iuid": "484f789d5f624b5eb2c6700b353fef0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/484f789d5f624b5eb2c6700b353fef0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/484f789d5f624b5eb2c6700b353fef0a"}}, "title": "The structure and function of P5A-ATPases.", "authors": [{"family": "Li", "given": "Ping", "initials": "P", "orcid": "0000-0002-7364-3301", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cc17e1d61cb498b88038a9f5dfa6aff.json"}}, {"family": "B\u00e5genholm", "given": "Viktoria", "initials": "V"}, {"family": "H\u00e4gglund", "given": "Per", "initials": "P", "orcid": "0000-0002-6627-7518", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3f8312cdacb4d48b7c080e5fcc26959.json"}}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}, {"family": "Wang", "given": "Kaituo", "initials": "K", "orcid": "0000-0002-5922-7109", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d8ad9a00c1c47fdbf1cadc149914823.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": "2024-11-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9605", "issn-l": "2041-1723"}, "abstract": "Endoplasmic reticulum (ER) membrane resident P5A-ATPases broadly affect protein biogenesis and quality control, and yet their molecular function remains debated. Here, we report cryo-EM structures of a P5A-ATPase, CtSpf1, covering multiple transport intermediates of the E1 \u2192 E1-ATP \u2192 E1P-ADP \u2192 E1P \u2192 E2P \u2192 E2.Pi \u2192 E2 \u2192 E1 cycle. In the E2P and E2.Pi states a cleft spans the entire membrane, holding a polypeptide cargo molecule. The cargo includes an ER luminal extension, pinpointed as the C-terminus in the E2.Pi state, which reenters the membrane in E2P. The E1 structure harbors a cytosol-facing cavity that is blocked by an insertion we refer to as the Plug-domain. The Plug-domain is nestled to key ATPase features and is displaced in the E1P-ADP and E1P states. Collectively, our findings are compatible with a broad range of proteins as cargo, with the P5A-ATPases serving a role in membrane removal of helices, although insertion/secretion cannot be excluded, as well as with a mechanistic role of the Plug-domain.", "doi": "10.1038/s41467-024-53757-6", "pmid": "39505844", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-024-53757-6"}], "notes": [], "created": "2024-11-07T08:43:16.978Z", "modified": "2024-11-07T08:43:17.628Z"}, {"entity": "publication", "iuid": "192a4d6ad38642009586ef73e08341d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/192a4d6ad38642009586ef73e08341d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/192a4d6ad38642009586ef73e08341d5"}}, "title": "A bispecific CD40 agonistic antibody allowing for antibody-peptide conjugate formation to enable cancer-specific peptide delivery, resulting in improved T proliferation and anti-tumor immunity in mice.", "authors": [{"family": "Mebrahtu", "given": "Aman", "initials": "A"}, {"family": "Laur\u00e9n", "given": "Ida", "initials": "I", "orcid": "0000-0003-0041-6084", "researcher": {"href": "https://publications.scilifelab.se/researcher/37ecae2143cf4534935defaca37e85ca.json"}}, {"family": "Veerman", "given": "Rosanne", "initials": "R"}, {"family": "Akpinar", "given": "G\u00f6zde G\u00fccl\u00fcler", "initials": "GG"}, {"family": "Lord", "given": "Martin", "initials": "M", "orcid": "0000-0002-3238-3187", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e14847c142f4c359f2d531601436897.json"}}, {"family": "Kostakis", "given": "Alexandros", "initials": "A", "orcid": "0009-0006-2252-2645", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd8822cc00c43788aaa88dc17f4b1e4.json"}}, {"family": "Astorga-Wells", "given": "Juan", "initials": "J", "orcid": "0000-0003-1017-8841", "researcher": {"href": "https://publications.scilifelab.se/researcher/14530d9aa03747858976b4889e959fe5.json"}}, {"family": "Dahllund", "given": "Leif", "initials": "L"}, {"family": "Olsson", "given": "Anders", "initials": "A"}, {"family": "Andersson", "given": "Oscar", "initials": "O"}, {"family": "Persson", "given": "Jonathan", "initials": "J"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "D\u00f6nnes", "given": "Pierre", "initials": "P", "orcid": "0000-0002-4613-2952", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d32d60f9b547be8096c448fc013246.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Mangsbo", "given": "Sara", "initials": "S", "orcid": "0000-0002-1355-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/c743bbcad6554f049c8fc5f64a6801bc.json"}}], "type": "journal article", "published": "2024-11-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9542", "issn-l": "2041-1723"}, "abstract": "Current antibody-based immunotherapy depends on tumor antigen shedding for proper T cell priming. Here we select a novel human CD40 agonistic drug candidate and generate a bispecific antibody, herein named BiA9*2_HF, that allows for rapid antibody-peptide conjugate formation. The format is designed to facilitate peptide antigen delivery to CD40 expressing cells combined with simultaneous CD40 agonistic activity. In vivo, the selected bispecific antibody BiA9*2_HF loaded with peptide cargos induces improved antigen-specific proliferation of CD8+ (10-15 fold) and CD4+ T cells (2-7 fold) over control in draining lymph nodes. In both virus-induced and neoantigen-based mouse tumor models, BiA9*2_HF demonstrates therapeutic efficacy and elevated safety profile, with complete tumor clearance, as well as measured abscopal impact on tumor growth. The BiA9*2_HF drug candidate can thus be utilized to tailor immunotherapeutics for cancer patients.", "doi": "10.1038/s41467-024-53839-5", "pmid": "39500897", "labels": {"Affinity Proteomics Uppsala": "Service", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11538452"}, {"db": "pii", "key": "10.1038/s41467-024-53839-5"}], "notes": [], "created": "2024-11-21T12:13:07.375Z", "modified": "2025-10-17T13:05:07.247Z"}, {"entity": "publication", "iuid": "07cd66044bbe4799bb39d2ca83fa2edf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07cd66044bbe4799bb39d2ca83fa2edf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07cd66044bbe4799bb39d2ca83fa2edf"}}, "title": "High-parametric protein maps reveal the spatial organization in early-developing human lung.", "authors": [{"family": "Sariyar", "given": "Sanem", "initials": "S", "orcid": "0000-0003-0735-5595", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a057942e8804bd19530d9faf484c72f.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Hansen", "given": "Jan Niklas", "initials": "JN", "orcid": "0000-0002-0489-7535", "researcher": {"href": "https://publications.scilifelab.se/researcher/272dfc4476064018bc7ed0235b7d3e55.json"}}, {"family": "Marco Salas", "given": "Sergio", "initials": "S", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Mardamshina", "given": "Mariya", "initials": "M", "orcid": "0000-0003-0066-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff68d3499c01447b8a48d99b86bd882b.json"}}, {"family": "Martinez Casals", "given": "Anna", "initials": "A"}, {"family": "Ballllosera Navarro", "given": "Frederic", "initials": "F"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z", "orcid": "0000-0002-4350-2524", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89be535ddfa4c6ab46201fb383f4a2b.json"}}, {"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"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": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a2b9ccd9ae84cdfbcb663591f39a77b.json"}}], "type": "journal article", "published": "2024-10-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "9381"}, "abstract": "The respiratory system, including the lungs, is essential for terrestrial life. While recent research has advanced our understanding of lung development, much still relies on animal models and transcriptome analyses. In this study conducted within the Human Developmental Cell Atlas (HDCA) initiative, we describe the protein-level spatiotemporal organization of the lung during the first trimester of human gestation. Using high-parametric tissue imaging with a 30-plex antibody panel, we analyzed human lung samples from 6 to 13 post-conception weeks, generating data from over 2 million cells across five developmental timepoints. We present a resource detailing spatially resolved cell type composition of the developing human lung, including proliferative states, immune cell patterns, spatial arrangement traits, and their temporal evolution. This represents an extensive single-cell resolved protein-level examination of the developing human lung and provides a valuable resource for further research into the developmental roots of human respiratory health and disease.", "doi": "10.1038/s41467-024-53752-x", "pmid": "39477961", "labels": {"BioImage Informatics": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Spatial Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11525936"}, {"db": "pii", "key": "10.1038/s41467-024-53752-x"}], "notes": [], "created": "2024-11-13T10:04:30.594Z", "modified": "2025-12-19T07:56:09.718Z"}, {"entity": "publication", "iuid": "62515568135543558aea5335722cb034", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62515568135543558aea5335722cb034.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62515568135543558aea5335722cb034"}}, "title": "Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.", "authors": [{"family": "Shafighi", "given": "Shadi", "initials": "S"}, {"family": "Geras", "given": "Agnieszka", "initials": "A"}, {"family": "Jurzysta", "given": "Barbara", "initials": "B"}, {"family": "Sahaf Naeini", "given": "Alireza", "initials": "A"}, {"family": "Filipiuk", "given": "Igor", "initials": "I"}, {"family": "Ra Czkowska", "given": "Alicja", "initials": "A"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Koperski", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Nowis", "given": "Dominika", "initials": "D", "orcid": "0000-0003-2748-9523", "researcher": {"href": "https://publications.scilifelab.se/researcher/7645c7bdbd1b436bbb1c218b8e0ce355.json"}}, {"family": "Carbone", "given": "Alessandra", "initials": "A", "orcid": "0000-0003-2098-5743", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e13fee16a84747a22b438ce26facf7.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications.scilifelab.se/researcher/b956941833b843f6ace483bf4c21e643.json"}}, {"family": "Szczurek", "given": "Ewa", "initials": "E", "orcid": "0000-0002-1320-6695", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca6b8a8caa7494aaec1b0cab3270a31.json"}}], "type": "journal article", "published": "2024-10-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9343", "issn-l": "2041-1723"}, "abstract": "Spatial and genomic heterogeneity of tumors are crucial factors influencing cancer progression, treatment, and survival. However, a technology for direct mapping the clones in the tumor tissue based on somatic point mutations is lacking. Here, we propose Tumoroscope, the first probabilistic model that accurately infers cancer clones and their localization in close to single-cell resolution by integrating pathological images, whole exome sequencing, and spatial transcriptomics data. In contrast to previous methods, Tumoroscope explicitly addresses the problem of deconvoluting the proportions of clones in spatial transcriptomics spots. Applied to a reference prostate cancer dataset and a newly generated breast cancer dataset, Tumoroscope reveals spatial patterns of clone colocalization and mutual exclusion in sub-areas of the tumor tissue. We further infer clone-specific gene expression levels and the most highly expressed genes for each clone. In summary, Tumoroscope enables an integrated study of the spatial, genomic, and phenotypic organization of tumors.", "doi": "10.1038/s41467-024-53374-3", "pmid": "39472583", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Other": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11522407"}, {"db": "pii", "key": "10.1038/s41467-024-53374-3"}], "notes": [], "created": "2024-10-31T12:37:56.764Z", "modified": "2025-02-28T14:14:34.895Z"}, {"entity": "publication", "iuid": "704c6abb74634b1aab41f82f95856143", "links": {"self": {"href": "https://publications.scilifelab.se/publication/704c6abb74634b1aab41f82f95856143.json"}, "display": {"href": "https://publications.scilifelab.se/publication/704c6abb74634b1aab41f82f95856143"}}, "title": "Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors.", "authors": [{"family": "Bian", "given": "Xiaowei", "initials": "X", "orcid": "0000-0001-8999-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0cad0181bff479bb4a04d047bd9bd35.json"}}, {"family": "Piipponen", "given": "Minna", "initials": "M"}, {"family": "Liu", "given": "Zhuang", "initials": "Z"}, {"family": "Luo", "given": "Lihua", "initials": "L", "orcid": "0000-0002-2129-4226", "researcher": {"href": "https://publications.scilifelab.se/researcher/b541fd2e348741ff8dfaad99a0ce453c.json"}}, {"family": "Geara", "given": "Jennifer", "initials": "J"}, {"family": "Chen", "given": "Yongjian", "initials": "Y"}, {"family": "Sangsuwan", "given": "Traimate", "initials": "T"}, {"family": "Maselli", "given": "Monica", "initials": "M"}, {"family": "Diaz", "given": "Candice", "initials": "C"}, {"family": "Bain", "given": "Connor A", "initials": "CA"}, {"family": "Eenjes", "given": "Evelien", "initials": "E"}, {"family": "Genander", "given": "Maria", "initials": "M", "orcid": "0000-0002-2428-8040", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee0b27ddbb154eadbf3293d090720481.json"}}, {"family": "Crichton", "given": "Michael", "initials": "M"}, {"family": "Cash", "given": "Jenna L", "initials": "JL"}, {"family": "Archambault", "given": "Louis", "initials": "L"}, {"family": "Haghdoost", "given": "Siamak", "initials": "S"}, {"family": "Fradette", "given": "Julie", "initials": "J"}, {"family": "Sommar", "given": "Pehr", "initials": "P"}, {"family": "Halle", "given": "Martin", "initials": "M", "orcid": "0000-0002-6222-956X", "researcher": {"href": "https://publications.scilifelab.se/researcher/789d6dc42b2d45fd98574075ee17ee73.json"}}, {"family": "Xu Land\u00e9n", "given": "Ning", "initials": "N", "orcid": "0000-0003-4868-3798", "researcher": {"href": "https://publications.scilifelab.se/researcher/c55a2caeb6cd4858aa3326b6e92d09c6.json"}}], "type": "journal article", "published": "2024-10-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9286", "issn-l": "2041-1723"}, "abstract": "Radiotherapy (RT), a common cancer treatment, unintentionally harms surrounding tissues, including the skin, and hinders wound healing years after treatment. This study aims to understand the mechanisms behind these late-onset adverse effects. We compare skin biopsies from previously irradiated (RT+) and non-irradiated (RT-) sites in breast cancer survivors who underwent RT years ago. Here we show that the RT+ skin has compromised healing capacity and fibroblast functions. Using ATAC-seq, we discover altered chromatin landscapes in RT+ fibroblasts, with THBS1 identified as a crucial epigenetically primed wound repair-related gene. This is further confirmed by single-cell RNA-sequencing and spatial transcriptomic analysis of human wounds. Notably, fibroblasts in both murine and human post-radiation wound models show heightened and sustained THBS1 expression, impairing fibroblast motility and contractility. Treatment with anti-THBS1 antibodies promotes ex vivo wound closure in RT+ skin from breast cancer survivors. Our findings suggest that fibroblasts retain a long-term radiation memory in the form of epigenetic changes. Targeting this maladaptive epigenetic memory could mitigate RT's late-onset adverse effects, improving the quality of life for cancer survivors.", "doi": "10.1038/s41467-024-53295-1", "pmid": "39468077", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11519383"}, {"db": "pii", "key": "10.1038/s41467-024-53295-1"}], "notes": [], "created": "2024-10-31T12:36:31.716Z", "modified": "2024-11-25T10:18:20.060Z"}, {"entity": "publication", "iuid": "af16f7f2a5004801bdd004545bd190b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af16f7f2a5004801bdd004545bd190b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af16f7f2a5004801bdd004545bd190b9"}}, "title": "The DoGA consortium expression atlas of promoters and genes in 100 canine tissues.", "authors": [{"family": "H\u00f6rtenhuber", "given": "Matthias", "initials": "M", "orcid": "0000-0002-5599-5565", "researcher": {"href": "https://publications.scilifelab.se/researcher/a02296c8f90742c6a9de21e12359560c.json"}}, {"family": "Hyt\u00f6nen", "given": "Marjo K", "initials": "MK", "orcid": "0000-0003-1976-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e3788ab09f415f918f0bf9ed441fac.json"}}, {"family": "Mukarram", "given": "Abdul Kadir", "initials": "AK"}, {"family": "Arumilli", "given": "Meharji", "initials": "M"}, {"family": "Araujo", "given": "C\u00e9sar L", "initials": "CL"}, {"family": "Quintero", "given": "Ileana", "initials": "I", "orcid": "0000-0001-7040-1289", "researcher": {"href": "https://publications.scilifelab.se/researcher/208e9727fc004f10acca1e3ed3244366.json"}}, {"family": "Syrj\u00e4", "given": "Pernilla", "initials": "P"}, {"family": "Airas", "given": "Niina", "initials": "N"}, {"family": "Kaukonen", "given": "Maria", "initials": "M", "orcid": "0000-0002-2146-4694", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4e0e0816a714e72976563c625549785.json"}}, {"family": "Ky\u00f6stil\u00e4", "given": "Kaisa", "initials": "K"}, {"family": "Niskanen", "given": "Julia", "initials": "J", "orcid": "0000-0002-2871-6890", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c9070b3a4bb4b9f93f85caf587b2b98.json"}}, {"family": "Jokinen", "given": "Tarja S", "initials": "TS", "orcid": "0000-0001-6389-0109", "researcher": {"href": "https://publications.scilifelab.se/researcher/435d360e63f94f48831777352c2e1d9a.json"}}, {"family": "Mottaghitalab", "given": "Faezeh", "initials": "F", "orcid": "0000-0001-6495-6667", "researcher": {"href": "https://publications.scilifelab.se/researcher/faed0b7f48c144de81c6720b9866b50f.json"}}, {"family": "Takan", "given": "I\u015f\u0131l", "initials": "I", "orcid": "0000-0002-0269-6625", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7c6daf8dc524e21a2d44de764146965.json"}}, {"family": "Salokorpi", "given": "Noora", "initials": "N"}, {"family": "Raman", "given": "Amitha", "initials": "A"}, {"family": "Stevens", "given": "Irene", "initials": "I", "orcid": "0000-0003-3823-1499", "researcher": {"href": "https://publications.scilifelab.se/researcher/90f6fa81197146ae946e2f68630c1238.json"}}, {"family": "Iivanainen", "given": "Antti", "initials": "A", "orcid": "0000-0003-1002-3225", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f39943341f5457986553f672841ae04.json"}}, {"family": "Yoshihara", "given": "Masahito", "initials": "M", "orcid": "0000-0002-8915-9282", "researcher": {"href": "https://publications.scilifelab.se/researcher/4303ab7a18254bb59f8e2386a7f7fb0a.json"}}, {"family": "Gusev", "given": "Oleg", "initials": "O", "orcid": "0000-0002-6203-9758", "researcher": {"href": "https://publications.scilifelab.se/researcher/31d4a1b245d449428a6fe219c91cde24.json"}}, {"family": "Bannasch", "given": "Danika", "initials": "D", "orcid": "0000-0002-7614-7207", "researcher": {"href": "https://publications.scilifelab.se/researcher/828a952f3be54507bedcb950fbafaf12.json"}}, {"family": "Sukura", "given": "Antti", "initials": "A", "orcid": "0000-0002-8992-1695", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea53fec228424344bd642575de25aec3.json"}}, {"family": "Schoenebeck", "given": "Jeffrey J", "initials": "JJ", "orcid": "0000-0003-4964-2138", "researcher": {"href": "https://publications.scilifelab.se/researcher/674777750c7144d783483e2c8f130b8b.json"}}, {"family": "DoGA Consortium", "given": "", "initials": ""}, {"family": "Ezer", "given": "Sini", "initials": "S"}, {"family": "Katayama", "given": "Shintaro", "initials": "S", "orcid": "0000-0001-7581-5157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7765acd351b40c091615258c3d751b4.json"}}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications.scilifelab.se/researcher/eda6a90f9d9046ada163d9843d169393.json"}}, {"family": "Kere", "given": "Juha", "initials": "J", "orcid": "0000-0003-1974-0271", "researcher": {"href": "https://publications.scilifelab.se/researcher/102085fb1c3147ceaf8dcb7651df1303.json"}}, {"family": "Lohi", "given": "Hannes", "initials": "H", "orcid": "0000-0003-1087-5532", "researcher": {"href": "https://publications.scilifelab.se/researcher/903f658d43ea414fb37ef530df3e15e4.json"}}], "type": "journal article", "published": "2024-10-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9082", "issn-l": "2041-1723"}, "abstract": "The dog, Canis lupus familiaris, is an important model for studying human diseases. Unlike many model organisms, the dog genome has a comparatively poor functional annotation, which hampers gene discovery for development, morphology, disease, and behavior. To fill this gap, we established a comprehensive tissue biobank for both the dog and wolf samples. The biobank consists of 5485 samples representing 132 tissues from 13 dogs, 12 dog embryos, and 24 wolves. In a subset of 100 tissues from nine dogs and 12 embryos, we characterized gene expression activity for each promoter, including alternative and novel, i.e., previously not annotated, promoter regions, using the 5' targeting RNA sequencing technology STRT2-seq. We identified over 100,000 promoter region candidates in the recent canine genome assembly, CanFam4, including over 45,000 highly reproducible sites with gene expression and respective tissue enrichment levels. We provide a promoter and gene expression atlas with interactive, open data resources, including a data coordination center and genome browser track hubs. We demonstrated the applicability of Dog Genome Annotation (DoGA) data and resources using multiple examples spanning canine embryonic development, morphology and behavior, and diseases across species.", "doi": "10.1038/s41467-024-52798-1", "pmid": "39433728", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11494170"}, {"db": "pii", "key": "10.1038/s41467-024-52798-1"}], "notes": [], "created": "2025-02-28T14:14:28.582Z", "modified": "2025-02-28T14:14:29.644Z"}, {"entity": "publication", "iuid": "2424a9f7eb5c4b9f85690b0af2c8405e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2424a9f7eb5c4b9f85690b0af2c8405e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2424a9f7eb5c4b9f85690b0af2c8405e"}}, "title": "Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma.", "authors": [{"family": "Karlsson", "given": "Jenny", "initials": "J", "orcid": "0000-0001-7681-0059", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e2ccecaff1d41bfa863dde6616eeadd.json"}}, {"family": "Yasui", "given": "Hiroaki", "initials": "H"}, {"family": "Ma\u00f1as", "given": "Adriana", "initials": "A", "orcid": "0000-0002-6955-1754", "researcher": {"href": "https://publications.scilifelab.se/researcher/7220571c605044f980abf2933374aa1a.json"}}, {"family": "Andersson", "given": "Natalie", "initials": "N", "orcid": "0000-0002-3643-4404", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7ef3a8564354a78a23180c7550a03ff.json"}}, {"family": "Hansson", "given": "Karin", "initials": "K", "orcid": "0000-0002-6993-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c0c991068644f61b10c986deff8fb7f.json"}}, {"family": "Aaltonen", "given": "Kristina", "initials": "K", "orcid": "0000-0001-5104-735X", "researcher": {"href": "https://publications.scilifelab.se/researcher/68a63e2719d246a99fc51e8e3ed05cee.json"}}, {"family": "Jansson", "given": "Caroline", "initials": "C"}, {"family": "Durand", "given": "Geoffroy", "initials": "G"}, {"family": "Ravi", "given": "Naveen", "initials": "N"}, {"family": "Ferro", "given": "Michele", "initials": "M"}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Chattopadhyay", "given": "Subhayan", "initials": "S"}, {"family": "Paulsson", "given": "Kajsa", "initials": "K", "orcid": "0000-0001-7950-222X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2033b23811f1432c90ad860dd993e7a8.json"}}, {"family": "Spierings", "given": "Diana", "initials": "D", "orcid": "0000-0001-8403-474X", "researcher": {"href": "https://publications.scilifelab.se/researcher/62825465dc084c7ebd10b71e274d5eb2.json"}}, {"family": "Foijer", "given": "Floris", "initials": "F", "orcid": "0000-0003-0989-3127", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ef3e70e2b5249029ff65894fd11b851.json"}}, {"family": "Valind", "given": "Anders", "initials": "A", "orcid": "0000-0002-1654-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/08f05da015554b19852439d14cb8e99b.json"}}, {"family": "Bexell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9426-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda650768a264d93a80f40da6cb8d7e1.json"}}, {"family": "Gisselsson", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3653582762b14f9a9ad2fe6aba511115.json"}}], "type": "journal article", "published": "2024-10-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8992", "issn-l": "2041-1723"}, "abstract": "Neuroblastoma (NB) is one of the most lethal childhood cancers due to its propensity to become treatment resistant. By spatial mapping of subclone geographies before and after chemotherapy across 89 tumor regions from 12 NBs, we find that densely packed territories of closely related subclones present at diagnosis are replaced under effective treatment by islands of distantly related survivor subclones, originating from a different most recent ancestor compared to lineages dominating before treatment. Conversely, in tumors that progressed under treatment, ancestors of subclones dominating later in disease are present already at diagnosis. Chemotherapy treated xenografts and cell culture models replicate these two contrasting scenarios and show branching evolution to be a constant feature of proliferating NB cells. Phylogenies based on whole genome sequencing of 505 individual NB cells indicate that a rich repertoire of parallel subclones emerges already with the first oncogenic mutations and lays the foundation for clonal replacement under treatment.", "doi": "10.1038/s41467-024-53334-x", "pmid": "39419962", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11486966"}, {"db": "pii", "key": "10.1038/s41467-024-53334-x"}], "notes": [], "created": "2024-11-14T09:28:32.271Z", "modified": "2024-11-17T16:43:33.354Z"}, {"entity": "publication", "iuid": "2ba158e4da984af6a8835a79e148a316", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ba158e4da984af6a8835a79e148a316.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ba158e4da984af6a8835a79e148a316"}}, "title": "Prevalent and persistent new-onset autoantibodies in mild to severe COVID-19.", "authors": [{"family": "Jernbom", "given": "August F", "initials": "AF", "orcid": "0000-0002-7773-1851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe6400bde68b46899515cef5bea05fca.json"}}, {"family": "Skoglund", "given": "Lovisa", "initials": "L", "orcid": "0009-0002-7863-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6bab6ea5e824b13ad5b77a6fa08523e.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"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": "Rostami", "given": "Elham", "initials": "E", "orcid": "0000-0003-1218-6247", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4e5d32d3023425c9940f1eb1ed876b4.json"}}, {"family": "Rasmusson", "given": "Annica", "initials": "A", "orcid": "0000-0002-7228-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef833f6dd204c189586fba5c33d1d58.json"}}, {"family": "Cunningham", "given": "Janet L", "initials": "JL", "orcid": "0000-0001-7876-7779", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab30dd6c6874bc7a227a8699c4a7085.json"}}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-1345-6491", "researcher": {"href": "https://publications.scilifelab.se/researcher/130fb6ef6b774613a767e98f9f9b2eb4.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d155273b5b54e61b773f263e4f2ce9b.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2024-10-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8941", "issn-l": "2041-1723"}, "abstract": "Autoantibodies have been shown to be implied in COVID-19 but the emerging autoantibody repertoire remains largely unexplored. We investigated the new-onset autoantibody repertoire in 525 healthcare workers and hospitalized COVID-19 patients at five time points over a 16-month period in 2020 and 2021 using proteome-wide and targeted protein and peptide arrays. Our results show that prevalent new-onset autoantibodies against a wide range of antigens emerged following SARS-CoV-2 infection in relation to pre-infectious baseline samples and remained elevated for at least 12 months. We found an increased prevalence of new-onset autoantibodies after severe COVID-19 and demonstrated associations between distinct new-onset autoantibodies and neuropsychiatric symptoms post-COVID-19. Using epitope mapping, we determined the main epitopes of selected new-onset autoantibodies, validated them in independent cohorts of neuro-COVID and pre-pandemic healthy controls, and identified sequence similarities suggestive of molecular mimicry between main epitopes and the conserved fusion peptide of the SARS-CoV-2 Spike glycoprotein. Our work describes the complexity and dynamics of the autoantibody repertoire emerging with COVID-19 and supports the need for continued analysis of the new-onset autoantibody repertoire to elucidate the mechanisms of the post-COVID-19 condition.", "doi": "10.1038/s41467-024-53356-5", "pmid": "39414823", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11484904"}, {"db": "pii", "key": "10.1038/s41467-024-53356-5"}], "notes": [], "created": "2024-10-21T13:07:04.870Z", "modified": "2024-10-21T13:07:05.227Z"}, {"entity": "publication", "iuid": "ff4c4a6fe0524e3bb928418664c5a917", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff4c4a6fe0524e3bb928418664c5a917.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff4c4a6fe0524e3bb928418664c5a917"}}, "title": "Resilience of genetic diversity in forest trees over the Quaternary.", "authors": [{"family": "Milesi", "given": "Pascal", "initials": "P", "orcid": "0000-0001-8580-4291", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59e048cc6a4159a1829885b370d978.json"}}, {"family": "Kastally", "given": "Chedly", "initials": "C", "orcid": "0000-0002-1820-4752", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d98c61ddd95447186180256d00410bd.json"}}, {"family": "Dauphin", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-0982-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/8378e4ef12e34498b4f355a5ebcc0f0e.json"}}, {"family": "Cervantes", "given": "Sandra", "initials": "S", "orcid": "0000-0003-0793-5784", "researcher": {"href": "https://publications.scilifelab.se/researcher/9de980d11e35480e90f301e14b2e69df.json"}}, {"family": "Bagnoli", "given": "Francesca", "initials": "F", "orcid": "0000-0001-6909-0006", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc651aee75cf4447a747f642037e813d.json"}}, {"family": "Budde", "given": "Katharina B", "initials": "KB"}, {"family": "Cavers", "given": "Stephen", "initials": "S", "orcid": "0000-0003-2139-9236", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ab207ecaffd4f528dc5b4376ecc1c14.json"}}, {"family": "Fady", "given": "Bruno", "initials": "B"}, {"family": "Faivre-Rampant", "given": "Patricia", "initials": "P", "orcid": "0000-0003-0777-6621", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1ebde17a7204461b9c65dbb6b0fff56.json"}}, {"family": "Gonz\u00e1lez-Mart\u00ednez", "given": "Santiago C", "initials": "SC", "orcid": "0000-0002-4534-3766", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6337448ae7f457fb17f11dabf6e48be.json"}}, {"family": "Grivet", "given": "Delphine", "initials": "D", "orcid": "0000-0001-8168-4456", "researcher": {"href": "https://publications.scilifelab.se/researcher/655a75d7756f41099d9fcbcb17fdb512.json"}}, {"family": "Gugerli", "given": "Felix", "initials": "F", "orcid": "0000-0003-3878-1845", "researcher": {"href": "https://publications.scilifelab.se/researcher/027bd6add3a340c6aaf002c02f464095.json"}}, {"family": "Jorge", "given": "V\u00e9ronique", "initials": "V", "orcid": "0000-0002-5016-3006", "researcher": {"href": "https://publications.scilifelab.se/researcher/34dd9cdd219940fcaf811cc98730e8e6.json"}}, {"family": "Lesur Kupin", "given": "Isabelle", "initials": "I"}, {"family": "Ojeda", "given": "Dario I", "initials": "DI"}, {"family": "Olsson", "given": "Sanna", "initials": "S", "orcid": "0000-0002-1199-4499", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5a60a1a580d4634a6ca32dd1d4ba101.json"}}, {"family": "Opgenoorth", "given": "Lars", "initials": "L", "orcid": "0000-0003-0737-047X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b5ea2081d1341babd837bcfb8a4fd27.json"}}, {"family": "Pinosio", "given": "Sara", "initials": "S", "orcid": "0000-0002-1820-3637", "researcher": {"href": "https://publications.scilifelab.se/researcher/c691c7bb0181439ca1384d27061b59d9.json"}}, {"family": "Plomion", "given": "Christophe", "initials": "C"}, {"family": "Rellstab", "given": "Christian", "initials": "C", "orcid": "0000-0002-0221-5975", "researcher": {"href": "https://publications.scilifelab.se/researcher/d777277731b146da897676fb82ea4d7f.json"}}, {"family": "Rogier", "given": "Odile", "initials": "O", "orcid": "0000-0001-6879-364X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d3148f27d7f4510a143eaf9eb3ceb1e.json"}}, {"family": "Scalabrin", "given": "Simone", "initials": "S", "orcid": "0000-0001-8686-8385", "researcher": {"href": "https://publications.scilifelab.se/researcher/06cae7b93e7e48c187df2bb95fd3031f.json"}}, {"family": "Scotti", "given": "Ivan", "initials": "I"}, {"family": "Vendramin", "given": "Giovanni G", "initials": "GG", "orcid": "0000-0001-9921-7872", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70f1198e7b4482fabb1a5167eab3c0f.json"}}, {"family": "Westergren", "given": "Marjana", "initials": "M", "orcid": "0000-0002-4204-0161", "researcher": {"href": "https://publications.scilifelab.se/researcher/d082e25234e7480382aa7c068f65ed49.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6958-5172", "researcher": {"href": "https://publications.scilifelab.se/researcher/87ba3d35a88442848f22835c85fadbce.json"}}, {"family": "GenTree Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2024-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8538", "issn-l": "2041-1723"}, "abstract": "The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of Ne over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes.", "doi": "10.1038/s41467-024-52612-y", "pmid": "39402024", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11473659"}, {"db": "pii", "key": "10.1038/s41467-024-52612-y"}], "notes": [], "created": "2024-11-25T10:18:08.923Z", "modified": "2024-11-25T10:18:09.656Z"}, {"entity": "publication", "iuid": "67f7141c96474ec1bb0e2619dd27f05f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67f7141c96474ec1bb0e2619dd27f05f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67f7141c96474ec1bb0e2619dd27f05f"}}, "title": "De novo production of protoberberine and benzophenanthridine alkaloids through metabolic engineering of yeast.", "authors": [{"family": "Jiao", "given": "Xiang", "initials": "X", "orcid": "0000-0001-8043-3719", "researcher": {"href": "https://publications.scilifelab.se/researcher/405364bbdf444b598c5bc13a3c6e4426.json"}}, {"family": "Fu", "given": "Xiaozhi", "initials": "X", "orcid": "0000-0002-4465-7528", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb3c34994ca41afa148487fc571aa8d.json"}}, {"family": "Li", "given": "Qishuang", "initials": "Q", "orcid": "0000-0002-2148-7917", "researcher": {"href": "https://publications.scilifelab.se/researcher/7afb27a365e047039b7134b38461d4bc.json"}}, {"family": "Bu", "given": "Junling", "initials": "J"}, {"family": "Liu", "given": "Xiuyu", "initials": "X"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Huang", "given": "Luqi", "initials": "L"}, {"family": "Guo", "given": "Juan", "initials": "J", "orcid": "0000-0002-1327-4428", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f6b24fad40f4fe480512aa9da62682a.json"}}, {"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": "2024-10-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8759", "issn-l": "2041-1723"}, "abstract": "Protoberberine alkaloids and benzophenanthridine alkaloids (BZDAs) are subgroups of benzylisoquinoline alkaloids (BIAs), which represent a diverse class of plant-specialized natural metabolites with many pharmacological properties. Microbial biosynthesis has been allowed for accessibility and scalable production of high-value BIAs. Here, we engineer Saccharomyces cerevisiae to de novo produce a series of protoberberines and BZDAs, including palmatine, berberine, chelerythrine, sanguinarine and chelirubine. An ER compartmentalization strategy is developed to improve vacuole protein berberine bridge enzyme (BBE) activity, resulting in >200% increase on the production of the key intermediate (S)-scoulerine. Another promiscuous vacuole protein dihydrobenzophenanthridine oxidase (DBOX) has been identified to catalyze two-electron oxidation on various tetrahydroprotoberberines at N7-C8 position and dihydrobenzophenanthridine alkaloids. Furthermore, cytosolically expressed DBOX can alleviate the limitation on BBE. This study highlights the potential of microbial cell factories for the biosynthesis of a diverse group of BIAs through engineering of heterologous plant enzymes.", "doi": "10.1038/s41467-024-53045-3", "pmid": "39384562", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11464499"}, {"db": "pii", "key": "10.1038/s41467-024-53045-3"}], "notes": [], "created": "2024-11-15T12:07:09.645Z", "modified": "2024-11-27T15:29:12.299Z"}, {"entity": "publication", "iuid": "db72b1430ff149429d4ed6274c089a9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db72b1430ff149429d4ed6274c089a9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db72b1430ff149429d4ed6274c089a9b"}}, "title": "Unmasking AlphaFold to integrate experiments and predictions in multimeric complexes.", "authors": [{"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Azinas", "given": "Stavros", "initials": "S", "orcid": "0000-0002-3744-9229", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ec0cb5b5df4b4f89780ce3a08efc89.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": "2024-10-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8724", "issn-l": "2041-1723"}, "abstract": "Since the release of AlphaFold, researchers have actively refined its predictions and attempted to integrate it into existing pipelines for determining protein structures. These efforts have introduced a number of functionalities and optimisations at the latest Critical Assessment of protein Structure Prediction edition (CASP15), resulting in a marked improvement in the prediction of multimeric protein structures. However, AlphaFold's capability of predicting large protein complexes is still limited and integrating experimental data in the prediction pipeline is not straightforward. In this study, we introduce AF_unmasked to overcome these limitations. Our results demonstrate that AF_unmasked can integrate experimental information to build larger or hard to predict protein assemblies with high confidence. The resulting predictions can help interpret and augment experimental data. This approach generates high quality (DockQ score > 0.8) structures even when little to no evolutionary information is available and imperfect experimental structures are used as a starting point. AF_unmasked is developed and optimised to fill incomplete experimental structures (structural inpainting), which may provide insights into protein dynamics. In summary, AF_unmasked provides an easy-to-use method that efficiently integrates experiments to predict large protein complexes more confidently.", "doi": "10.1038/s41467-024-52951-w", "pmid": "39379372", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Cryo-EM": "Service", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11461844"}, {"db": "pii", "key": "10.1038/s41467-024-52951-w"}], "notes": [], "created": "2024-11-08T10:09:12.989Z", "modified": "2024-11-15T15:09:44.609Z"}, {"entity": "publication", "iuid": "990a4c0efe6a494e853fd554e4896362", "links": {"self": {"href": "https://publications.scilifelab.se/publication/990a4c0efe6a494e853fd554e4896362.json"}, "display": {"href": "https://publications.scilifelab.se/publication/990a4c0efe6a494e853fd554e4896362"}}, "title": "Lowering of the singlet-triplet energy gap via intramolecular exciton-exciton coupling", "authors": [{"family": "Sch\u00e4fer", "given": "Clara", "initials": "C", "orcid": "0000-0001-7634-3980", "researcher": {"href": "https://publications.scilifelab.se/researcher/58fcf0b78e574d5f9a52fcab14632117.json"}}, {"family": "Ringstr\u00f6m", "given": "Rasmus", "initials": "R", "orcid": "0000-0002-3340-957X", "researcher": {"href": "https://publications.scilifelab.se/researcher/196bf7aecdf44f5bbb1797a248cfbca9.json"}}, {"family": "Hanrieder", "given": "J\u00f6rg", "initials": "J", "orcid": "0000-0001-6059-198X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e65454100674f98bf8f2575093f2441.json"}}, {"family": "Rahm", "given": "Martin", "initials": "M", "orcid": "0000-0001-7645-5923", "researcher": {"href": "https://publications.scilifelab.se/researcher/28b5174b9b294c99862216b7d8ebe91b.json"}}, {"family": "Albinsson", "given": "Bo", "initials": "B", "orcid": "0000-0002-5991-7863", "researcher": {"href": "https://publications.scilifelab.se/researcher/373f9b13c3cf4e05978f223218a388fa.json"}}, {"family": "B\u00f6rjesson", "given": "Karl", "initials": "K", "orcid": "0000-0001-8533-201X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc22ad4eb905493e9ae51616b197edd4.json"}}], "type": "journal-article", "published": "2024-10-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-024-53122-7", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:07:10.905Z", "modified": "2025-11-27T08:07:11.329Z"}, {"entity": "publication", "iuid": "88fdebe09a364acd8a3d8b6f9e56465e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88fdebe09a364acd8a3d8b6f9e56465e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88fdebe09a364acd8a3d8b6f9e56465e"}}, "title": "The lncRNA SNHG26 drives the inflammatory-to-proliferative state transition of keratinocyte progenitor cells during wound healing.", "authors": [{"family": "Li", "given": "Dongqing", "initials": "D", "orcid": "0000-0003-0588-9390", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d51ff81e8ec4cc5a429dd095a0c315f.json"}}, {"family": "Liu", "given": "Zhuang", "initials": "Z"}, {"family": "Zhang", "given": "Letian", "initials": "L"}, {"family": "Bian", "given": "Xiaowei", "initials": "X", "orcid": "0000-0001-8999-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0cad0181bff479bb4a04d047bd9bd35.json"}}, {"family": "Wu", "given": "Jianmin", "initials": "J", "orcid": "0000-0002-8223-1667", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8b209cc41384aefa1fb3d70e564e3f3.json"}}, {"family": "Li", "given": "Li", "initials": "L"}, {"family": "Chen", "given": "Yongjian", "initials": "Y"}, {"family": "Luo", "given": "Lihua", "initials": "L", "orcid": "0000-0002-2129-4226", "researcher": {"href": "https://publications.scilifelab.se/researcher/b541fd2e348741ff8dfaad99a0ce453c.json"}}, {"family": "Pan", "given": "Ling", "initials": "L"}, {"family": "Kong", "given": "Lingzhuo", "initials": "L"}, {"family": "Xiao", "given": "Yunting", "initials": "Y"}, {"family": "Wang", "given": "Jiating", "initials": "J"}, {"family": "Zhang", "given": "Xiya", "initials": "X"}, {"family": "Wang", "given": "Wang", "initials": "W"}, {"family": "Toma", "given": "Maria", "initials": "M", "orcid": "0000-0002-4766-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/80f80639a3774c5bb5007d1f9af63a0e.json"}}, {"family": "Piipponen", "given": "Minna", "initials": "M"}, {"family": "Sommar", "given": "Pehr", "initials": "P"}, {"family": "Xu Land\u00e9n", "given": "Ning", "initials": "N", "orcid": "0000-0003-4868-3798", "researcher": {"href": "https://publications.scilifelab.se/researcher/c55a2caeb6cd4858aa3326b6e92d09c6.json"}}], "type": "journal article", "published": "2024-10-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8637", "issn-l": "2041-1723"}, "abstract": "The cell transition from an inflammatory phase to a subsequent proliferative phase is crucial for wound healing, yet the driving mechanism remains unclear. By profiling lncRNA expression changes during human skin wound healing and screening lncRNA functions, we identify SNHG26 as a pivotal regulator in keratinocyte progenitors underpinning this phase transition. Snhg26-deficient mice exhibit impaired wound repair characterized by delayed re-epithelization accompanied by exacerbated inflammation. Single-cell transcriptome analysis combined with gain-of-function and loss-of-function of SNHG26 in vitro and ex vivo reveals its specific role in facilitating inflammatory-to-proliferative state transition of keratinocyte progenitors. A mechanistic study unravels that SNHG26 interacts with and relocates the transcription factor ILF2 from inflammatory genomic loci, such as JUN, IL6, IL8, and CCL20, to the genomic locus of LAMB3. Collectively, our findings suggest that lncRNAs play cardinal roles in expediting tissue repair and regeneration and may constitute an invaluable reservoir of therapeutic targets in reparative medicine.", "doi": "10.1038/s41467-024-52783-8", "pmid": "39366968", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Spatial omics": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11452505"}, {"db": "pii", "key": "10.1038/s41467-024-52783-8"}], "notes": [], "created": "2024-10-18T07:13:08.010Z", "modified": "2025-02-28T14:14:23.292Z"}, {"entity": "publication", "iuid": "9b81114066764b15946e9e8731fac1e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b81114066764b15946e9e8731fac1e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b81114066764b15946e9e8731fac1e5"}}, "title": "The single-cell transcriptomic atlas iPain identifies senescence of nociceptors as a therapeutical target for chronic pain treatment.", "authors": [{"family": "Techameena", "given": "Prach", "initials": "P", "orcid": "0009-0005-9380-2428", "researcher": {"href": "https://publications.scilifelab.se/researcher/835cc139cbbd4e08afd433a817f74ac6.json"}}, {"family": "Feng", "given": "Xiaona", "initials": "X"}, {"family": "Zhang", "given": "Kaiwen", "initials": "K", "orcid": "0009-0001-0790-1616", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1880c8da747467795a011858ca2c9bf.json"}}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}], "type": "journal article", "published": "2024-10-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8585", "issn-l": "2041-1723"}, "abstract": "Chronic pain remains a significant medical challenge with complex underlying mechanisms, and an urgent need for new treatments. Our research built and utilized the iPain single-cell atlas to study chronic pain progression in dorsal root and trigeminal ganglia. We discovered that senescence of a small subset of pain-sensing neurons may be a driver of chronic pain. This mechanism was observed in animal models after nerve injury and in human patients diagnosed with chronic pain or diabetic painful neuropathy. Notably, treatment with senolytics, drugs that remove senescent cells, reversed pain symptoms in mice post-injury. These findings highlight the role of cellular senescence in chronic pain development, demonstrate the therapeutic potential of senolytic treatments, and underscore the value of the iPain atlas for future pain research.", "doi": "10.1038/s41467-024-52052-8", "pmid": "39362841", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11450014"}, {"db": "pii", "key": "10.1038/s41467-024-52052-8"}], "notes": [], "created": "2024-10-16T12:42:25.382Z", "modified": "2024-11-25T10:17:57.934Z"}, {"entity": "publication", "iuid": "d82774b91b3543f98a71d6c065a62093", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d82774b91b3543f98a71d6c065a62093.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d82774b91b3543f98a71d6c065a62093"}}, "title": "Claustrum and dorsal endopiriform cortex complex cell-identity is determined by Nurr1 and regulates hallucinogenic-like states in mice.", "authors": [{"family": "Mantas", "given": "Ioannis", "initials": "I", "orcid": "0000-0001-6288-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/025776ae147144dab1e2f10a5761b9ed.json"}}, {"family": "Flais", "given": "Ivana", "initials": "I"}, {"family": "Masarapu", "given": "Yuvarani", "initials": "Y", "orcid": "0000-0002-3267-2085", "researcher": {"href": "https://publications.scilifelab.se/researcher/055fa17f6cdd490e87182c94c847c440.json"}}, {"family": "Ionescu", "given": "Tudor", "initials": "T"}, {"family": "Frapard", "given": "Sol\u00e8ne", "initials": "S", "orcid": "0000-0002-2649-7225", "researcher": {"href": "https://publications.scilifelab.se/researcher/a336a6a31fae4766afbb5e376a4a12a3.json"}}, {"family": "Jung", "given": "Felix", "initials": "F"}, {"family": "Le Merre", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4205-7411", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba592e9aa93b433cb85ff11a786b0a71.json"}}, {"family": "Saarinen", "given": "Marcus", "initials": "M"}, {"family": "Tiklova", "given": "Katarina", "initials": "K"}, {"family": "Salmani", "given": "Behzad Yaghmaeian", "initials": "BY", "orcid": "0000-0002-4221-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb9b5976d0b34622aff0e9a564b3ae54.json"}}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Zhang", "given": "Xiaoqun", "initials": "X", "orcid": "0000-0002-9461-8682", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f307c88103d43b1b0b893fa59a8e828.json"}}, {"family": "Chergui", "given": "Karima", "initials": "K"}, {"family": "Carl\u00e9n", "given": "Marie", "initials": "M", "orcid": "0000-0003-1658-1631", "researcher": {"href": "https://publications.scilifelab.se/researcher/88931dd9e39c48e2820b89080c3945ad.json"}}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Hengerer", "given": "Bastian", "initials": "B", "orcid": "0000-0002-7811-9795", "researcher": {"href": "https://publications.scilifelab.se/researcher/2adf2c1fe0954f018f91ebce7d06d945.json"}}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}], "type": "journal article", "published": "2024-09-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8176", "issn-l": "2041-1723"}, "abstract": "The Claustrum/dorsal endopiriform cortex complex (CLA) is an enigmatic brain region with extensive glutamatergic projections to multiple cortical areas. The transcription factor Nurr1 is highly expressed in the CLA, but its role in this region is not understood. By using conditional gene-targeted mice, we show that Nurr1 is a crucial regulator of CLA neuron identity. Although CLA neurons remain intact in the absence of Nurr1, the distinctive gene expression pattern in the CLA is abolished. CLA has been hypothesized to control hallucinations, but little is known of how the CLA responds to hallucinogens. After the deletion of Nurr1 in the CLA, both hallucinogen receptor expression and signaling are lost. Furthermore, functional ultrasound and Neuropixel electrophysiological recordings revealed that the hallucinogenic-receptor agonists' effects on functional connectivity between prefrontal and sensorimotor cortices are altered in Nurr1-ablated mice. Our findings suggest that Nurr1-targeted strategies provide additional avenues for functional studies of the CLA.", "doi": "10.1038/s41467-024-52429-9", "pmid": "39289358", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Other": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11408527"}, {"db": "pii", "key": "10.1038/s41467-024-52429-9"}], "notes": [], "created": "2024-10-31T12:38:39.729Z", "modified": "2024-10-31T12:38:39.977Z"}, {"entity": "publication", "iuid": "7b6e38c48c924d3eabf203bb4f233e86", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b6e38c48c924d3eabf203bb4f233e86.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b6e38c48c924d3eabf203bb4f233e86"}}, "title": "Aging is associated with functional and molecular changes in distinct hematopoietic stem cell subsets.", "authors": [{"family": "Su", "given": "Tsu-Yi", "initials": "TY", "orcid": "0000-0001-5242-1788", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2f68b50420b4a30bca04f6bd918f9ae.json"}}, {"family": "Hauenstein", "given": "Julia", "initials": "J", "orcid": "0000-0001-6674-4297", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bda375874844045bd86d62d3b25e071.json"}}, {"family": "Somuncular", "given": "Ece", "initials": "E"}, {"family": "Dumral", "given": "\u00d6zge", "initials": "\u00d6", "orcid": "0000-0002-9980-2702", "researcher": {"href": "https://publications.scilifelab.se/researcher/8288edd47f70479e93e1fc441d486997.json"}}, {"family": "Leonard", "given": "Elory", "initials": "E"}, {"family": "Gustafsson", "given": "Charlotte", "initials": "C"}, {"family": "Tzortzis", "given": "Efthymios", "initials": "E", "orcid": "0009-0003-6026-7938", "researcher": {"href": "https://publications.scilifelab.se/researcher/93161f233bfd4f9caa1248405b7d44e2.json"}}, {"family": "Forlani", "given": "Aurora", "initials": "A"}, {"family": "Johansson", "given": "Anne-Sofie", "initials": "AS", "orcid": "0000-0003-4999-2058", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdd394f77602494e8459dca3a688d306.json"}}, {"family": "Qian", "given": "Hong", "initials": "H", "orcid": "0000-0002-2512-9199", "researcher": {"href": "https://publications.scilifelab.se/researcher/37ab658477844e98bbfa587344e4d7c7.json"}}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R"}, {"family": "Luc", "given": "Sidinh", "initials": "S", "orcid": "0000-0001-7006-6169", "researcher": {"href": "https://publications.scilifelab.se/researcher/f327bb15ee1648d49ffad8c644192df4.json"}}], "type": "journal article", "published": "2024-09-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7966", "issn-l": "2041-1723"}, "abstract": "Age is a risk factor for hematologic malignancies. Attributes of the aging hematopoietic system include increased myelopoiesis, impaired adaptive immunity, and a functional decline of the hematopoietic stem cells (HSCs) that maintain hematopoiesis. Changes in the composition of diverse HSC subsets have been suggested to be responsible for age-related alterations, however, the underlying regulatory mechanisms are incompletely understood in the context of HSC heterogeneity. In this study, we investigated how distinct HSC subsets, separated by CD49b, functionally and molecularly change their behavior with age. We demonstrate that the lineage differentiation of both lymphoid-biased and myeloid-biased HSC subsets progressively shifts to a higher myeloid cellular output during aging. In parallel, we show that HSCs selectively undergo age-dependent gene expression and gene regulatory changes in a progressive manner, which is initiated already in the juvenile stage. Overall, our studies suggest that aging intrinsically alters both cellular and molecular properties of HSCs.", "doi": "10.1038/s41467-024-52318-1", "pmid": "39261515", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11391069"}, {"db": "pii", "key": "10.1038/s41467-024-52318-1"}], "notes": [], "created": "2024-11-25T10:18:03.590Z", "modified": "2024-11-25T10:18:03.797Z"}, {"entity": "publication", "iuid": "c7ecb17ccdff4efda58f939fa358a220", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7ecb17ccdff4efda58f939fa358a220.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7ecb17ccdff4efda58f939fa358a220"}}, "title": "DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor.", "authors": [{"family": "Pandiloski", "given": "Ninoslav", "initials": "N"}, {"family": "Horv\u00e1th", "given": "Vivien", "initials": "V"}, {"family": "Karlsson", "given": "Ofelia", "initials": "O"}, {"family": "Koutounidou", "given": "Symela", "initials": "S"}, {"family": "Dorazehi", "given": "Fereshteh", "initials": "F"}, {"family": "Christoforidou", "given": "Georgia", "initials": "G"}, {"family": "Matas-Fuentes", "given": "Jon", "initials": "J", "orcid": "0009-0000-9253-1172", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a4d7313057548238c742aefc9c07ca8.json"}}, {"family": "Gerdes", "given": "Patricia", "initials": "P", "orcid": "0000-0002-1148-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8571bfad113498c8fdb09fb74d7b2bd.json"}}, {"family": "Garza", "given": "Raquel", "initials": "R", "orcid": "0000-0002-2524-3055", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d53399af304283ba62e0646acdc612.json"}}, {"family": "J\u00f6nsson", "given": "Marie E", "initials": "ME"}, {"family": "Adami", "given": "Anita", "initials": "A", "orcid": "0000-0002-9421-7942", "researcher": {"href": "https://publications.scilifelab.se/researcher/174398a7905b490ba8a41108d65bfe1d.json"}}, {"family": "Atacho", "given": "Diahann A M", "initials": "DAM"}, {"family": "Johansson", "given": "Jenny G", "initials": "JG"}, {"family": "Englund", "given": "Elisabet", "initials": "E", "orcid": "0000-0002-2708-2443", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c98fa2b2e7e4e318cd00eb1e8e3ac7a.json"}}, {"family": "Kokaia", "given": "Zaal", "initials": "Z", "orcid": "0000-0003-2296-2449", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ebc09333cc34bc3a614697c418e54d1.json"}}, {"family": "Jakobsson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0669-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b08f33ec79b4a36a5f62223d7174201.json"}}, {"family": "Douse", "given": "Christopher H", "initials": "CH", "orcid": "0000-0002-1604-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645238072a64ecdae736e3194b536c2.json"}}], "type": "journal article", "published": "2024-08-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7534", "issn-l": "2041-1723"}, "abstract": "The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. How HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains largely unknown. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding, and simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric \u03b1-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.", "doi": "10.1038/s41467-024-50765-4", "pmid": "39214989", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Lund": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11364546"}, {"db": "pii", "key": "10.1038/s41467-024-50765-4"}], "notes": [], "created": "2024-09-03T12:21:18.337Z", "modified": "2025-02-28T14:14:17.953Z"}, {"entity": "publication", "iuid": "a3c5e0204138422aa03a305231f99f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3c5e0204138422aa03a305231f99f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3c5e0204138422aa03a305231f99f89"}}, "title": "An intronic copy number variation in Syntaxin 17 determines speed of greying and melanoma incidence in Grey horses.", "authors": [{"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Hodge", "given": "McKaela", "initials": "M"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "Beckman", "given": "Madeleine", "initials": "M"}, {"family": "Bellone", "given": "Rebecca R", "initials": "RR", "orcid": "0000-0001-8838-7227", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c3235fb9bc24da59f4b2685ab0924a4.json"}}, {"family": "Kallenberg", "given": "Angelica", "initials": "A", "orcid": "0000-0001-7993-6597", "researcher": {"href": "https://publications.scilifelab.se/researcher/b86eca5b3e87464ca2e00fc0f1ad44e0.json"}}, {"family": "J'Usrey", "given": "Stephanie", "initials": "S"}, {"family": "Ohmura", "given": "Hajime", "initials": "H"}, {"family": "Seki", "given": "Kazuhiro", "initials": "K"}, {"family": "Furukawa", "given": "Risako", "initials": "R", "orcid": "0009-0002-4673-0845", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5000c3c34a44dcebe85e6c8418b065e.json"}}, {"family": "Ohnuma", "given": "Aoi", "initials": "A"}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Tozaki", "given": "Teruaki", "initials": "T", "orcid": "0000-0001-8797-6644", "researcher": {"href": "https://publications.scilifelab.se/researcher/8246b65d8481438885db4d4be0691aaa.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.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": "2024-08-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7510", "issn-l": "2041-1723"}, "abstract": "The Greying with age phenotype in horses involves loss of hair pigmentation whereas skin pigmentation is not reduced, and a predisposition to melanoma. The causal mutation was initially reported as a duplication of a 4.6 kb intronic sequence in Syntaxin 17. The speed of greying varies considerably among Grey horses. Here we demonstrate the presence of two different Grey alleles, G2 carrying two tandem copies of the duplicated sequence and G3 carrying three. The latter is by far the most common allele, probably due to strong selection for the striking white phenotype. Our results reveal a remarkable dosage effect where the G3 allele is associated with fast greying and high incidence of melanoma whereas G2 is associated with slow greying and low incidence of melanoma. The copy number expansion transforms a weak enhancer to a strong melanocyte-specific enhancer that underlies hair greying (G2 and G3) and a drastically elevated risk of melanoma (G3 only). Our direct pedigree-based observation of the origin of a G2 allele from a G3 allele by copy number contraction demonstrates the dynamic evolution of this locus and provides the ultimate evidence for causality of the copy number variation of the 4.6 kb intronic sequence.", "doi": "10.1038/s41467-024-51898-2", "pmid": "39209879", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11362437"}, {"db": "pii", "key": "10.1038/s41467-024-51898-2"}], "notes": [], "created": "2024-10-21T11:17:13.688Z", "modified": "2024-11-25T10:17:52.816Z"}, {"entity": "publication", "iuid": "63f26e56ef43498c85dcb25e3bead3b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63f26e56ef43498c85dcb25e3bead3b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63f26e56ef43498c85dcb25e3bead3b0"}}, "title": "Structural basis of frizzled 7 activation and allosteric regulation.", "authors": [{"family": "Bous", "given": "Julien", "initials": "J", "orcid": "0000-0002-3459-7592", "researcher": {"href": "https://publications.scilifelab.se/researcher/523b9682aafc43c99c2c41ec70e6c030.json"}}, {"family": "Kinsolving", "given": "Julia", "initials": "J", "orcid": "0000-0002-0431-8222", "researcher": {"href": "https://publications.scilifelab.se/researcher/86addc3c2f3344f6aefd7627927b372d.json"}}, {"family": "Gr\u00e4tz", "given": "Lukas", "initials": "L", "orcid": "0000-0001-6755-0742", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f33b51487ee46f6aff0c5feaee25179.json"}}, {"family": "Scharf", "given": "Magdalena M", "initials": "MM", "orcid": "0000-0002-3305-3956", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5ac9a5b7ff4ad29ec675ba0078ff58.json"}}, {"family": "Voss", "given": "Jan Hendrik", "initials": "JH", "orcid": "0000-0003-0595-4607", "researcher": {"href": "https://publications.scilifelab.se/researcher/d631e7108d5d4f92a37c8ee33cc73bff.json"}}, {"family": "Selcuk", "given": "Berkay", "initials": "B", "orcid": "0000-0003-3206-4749", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c33902b9aa04d118a23ad0aad3ceba2.json"}}, {"family": "Adebali", "given": "Og\u00fcn", "initials": "O", "orcid": "0000-0001-9213-4070", "researcher": {"href": "https://publications.scilifelab.se/researcher/e58531eabdcc4bd19ac88d3cc51d6920.json"}}, {"family": "Schulte", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-2700-7013", "researcher": {"href": "https://publications.scilifelab.se/researcher/711448c6b6ae4cf48a899c6a8953dcd1.json"}}], "type": "journal article", "published": "2024-08-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7422", "issn-l": "2041-1723"}, "abstract": "Frizzleds (ten paralogs: FZD1-10) belong to the class F of G protein-coupled receptors (GPCRs), which remains poorly understood despite its crucial role in multiple key biological functions including embryonic development, stem cell regulation, and homeostasis in the adult. FZD7, one of the most studied members of the family, is more specifically involved in the migration of mesendoderm cells during the development and renewal of intestinal stem cells in adults. Moreover, FZD7 has been highlighted for its involvement in tumor development predominantly in the gastrointestinal tract. This study reports the structure of inactive FZD7, without any stabilizing mutations, determined by cryo-electron microscopy (cryo-EM) at 1.9 \u00c5 resolution. We characterize a fluctuating water pocket in the core of the receptor important for FZD7 dynamics. Molecular dynamics simulations are used to investigate the temporal distribution of those water molecules and their importance for potential conformational changes in FZD7. Moreover, we identify lipids interacting with the receptor core and a conserved cholesterol-binding site, which displays a key role in FZD7 association with a transducer protein, Disheveled (DVL), and initiation of downstream signaling and signalosome formation.", "doi": "10.1038/s41467-024-51664-4", "pmid": "39198452", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11358414"}, {"db": "pii", "key": "10.1038/s41467-024-51664-4"}], "notes": [], "created": "2024-11-15T17:57:12.786Z", "modified": "2025-10-25T10:14:08.828Z"}, {"entity": "publication", "iuid": "09b2174874b74c20886dd68920d6961e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09b2174874b74c20886dd68920d6961e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09b2174874b74c20886dd68920d6961e"}}, "title": "Single-cell transcriptomics reveal transcriptional programs underlying male and female cell fate during Plasmodium falciparum gametocytogenesis.", "authors": [{"family": "Mohammed", "given": "Mubasher", "initials": "M"}, {"family": "Dziedziech", "given": "Alexis", "initials": "A"}, {"family": "Macedo", "given": "Diego", "initials": "D"}, {"family": "Huppertz", "given": "Frederik", "initials": "F"}, {"family": "Veith", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-1810-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e316fdf93964e89a0606e68da08c336.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Christ", "given": "Elena", "initials": "E"}, {"family": "Scheytt", "given": "Richard", "initials": "R", "orcid": "0009-0004-1405-6360", "researcher": {"href": "https://publications.scilifelab.se/researcher/3866987412724150b6af427c16dd17cf.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2024-08-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "7177"}, "abstract": "The Plasmodium falciparum life cycle includes obligate transition between a human and mosquito host. Gametocytes are responsible for transmission from the human to the mosquito vector where gamete fusion followed by meiosis occurs. To elucidate how male and female gametocytes differentiate in the absence of sex chromosomes, we perform FACS-based cell enrichment of a P. falciparum gametocyte reporter line followed by single-cell RNA-seq. In our analyses we define the transcriptional programs and predict candidate driver genes underlying male and female development, including genes from the ApiAP2 family of transcription factors. A motif-driven, gene regulatory network analysis indicates that AP2-G5 specifically modulates male development. Additionally, genes linked to the inner membrane complex, involved in morphological changes, are uniquely expressed in the female lineage. The transcriptional programs of male and female development detailed herein allow for further exploration of the evolution of sex in eukaryotes and provide targets for future development of transmission blocking therapies.", "doi": "10.1038/s41467-024-51201-3", "pmid": "39187486", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC11347709"}, {"db": "pii", "key": "10.1038/s41467-024-51201-3"}], "notes": [], "created": "2024-11-25T10:17:42.276Z", "modified": "2025-07-18T10:45:32.069Z"}, {"entity": "publication", "iuid": "e25c443cc2a84c89b1642a768afa88b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e25c443cc2a84c89b1642a768afa88b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e25c443cc2a84c89b1642a768afa88b0"}}, "title": "BaTwa populations from Zambia retain ancestry of past hunter-gatherer groups.", "authors": [{"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "Barham", "given": "Lawrence", "initials": "L"}, {"family": "Mudenda", "given": "George", "initials": "G"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2024-08-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7307", "issn-l": "2041-1723"}, "abstract": "Sub-equatorial Africa is today inhabited predominantly by Bantu-speaking groups of Western African descent who brought agriculture to the Luangwa valley in eastern Zambia ~2000 years ago. Before their arrival the area was inhabited by hunter-gatherers, who in many cases were subsequently replaced, displaced or assimilated. In Zambia, we know little about the genetic affinities of these hunter-gatherers. We examine ancestry of two isolated communities in Zambia, known as BaTwa and possible descendants of recent hunter-gatherers. We genotype over two million genome-wide SNPs from two BaTwa populations (total of 80 individuals) and from three comparative farming populations to: (i) determine if the BaTwa carry genetic links to past hunter-gatherer-groups, and (ii) characterise the genetic affinities of past Zambian hunter-gatherer-groups. The BaTwa populations do harbour a hunter-gatherer-like genetic ancestry and Western African ancestry. The hunter-gatherer component is a unique local signature, intermediate between current-day Khoe-San ancestry from southern Africa and central African rainforest hunter-gatherer ancestry.", "doi": "10.1038/s41467-024-50733-y", "pmid": "39181874", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11344834"}, {"db": "pii", "key": "10.1038/s41467-024-50733-y"}], "notes": [], "created": "2024-10-21T11:15:04.878Z", "modified": "2024-11-25T10:17:25.391Z"}, {"entity": "publication", "iuid": "fcbd7b36b40943fc8cdd7edffb61ddc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcbd7b36b40943fc8cdd7edffb61ddc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcbd7b36b40943fc8cdd7edffb61ddc6"}}, "title": "FOXO-regulated OSER1 reduces oxidative stress and extends lifespan in multiple species.", "authors": [{"family": "Song", "given": "Jiangbo", "initials": "J", "orcid": "0000-0002-1349-632X", "researcher": {"href": "https://publications.scilifelab.se/researcher/456a6f81be6a405f9d611180a3a2ab11.json"}}, {"family": "Li", "given": "Zhiquan", "initials": "Z", "orcid": "0000-0003-3253-7606", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b4fd9aa55244f45bb6fb5aa065491b0.json"}}, {"family": "Zhou", "given": "Lei", "initials": "L", "orcid": "0000-0002-6101-6669", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f17a6beaee1412d8944e6a3866147da.json"}}, {"family": "Chen", "given": "Xin", "initials": "X", "orcid": "0000-0001-8968-2711", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11213ffc2174216aa1d9aad2d4c182c.json"}}, {"family": "Sew", "given": "Wei Qi Guinevere", "initials": "WQG"}, {"family": "Herranz", "given": "H\u00e9ctor", "initials": "H"}, {"family": "Ye", "given": "Zilu", "initials": "Z", "orcid": "0000-0001-8829-6579", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dafd75832df4a1ba72f6e8df4fbedc1.json"}}, {"family": "Olsen", "given": "Jesper Velgaard", "initials": "JV", "orcid": "0000-0002-4747-4938", "researcher": {"href": "https://publications.scilifelab.se/researcher/c537b77eb960461f8d087aa5aeaa1f71.json"}}, {"family": "Li", "given": "Yuan", "initials": "Y", "orcid": "0000-0001-8275-2916", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc11bfbd9b243dcb13459b2ebc006a1.json"}}, {"family": "Nygaard", "given": "Marianne", "initials": "M", "orcid": "0000-0003-0703-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d68eda16735460d81993dc39006d5a5.json"}}, {"family": "Christensen", "given": "Kaare", "initials": "K", "orcid": "0000-0002-5429-5292", "researcher": {"href": "https://publications.scilifelab.se/researcher/e79ea43d09544efc95351b52ac682910.json"}}, {"family": "Tong", "given": "Xiaoling", "initials": "X", "orcid": "0000-0002-2649-899X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5f43ec02e48493ba6898d502abf972e.json"}}, {"family": "Bohr", "given": "Vilhelm A", "initials": "VA", "orcid": "0000-0003-4823-6429", "researcher": {"href": "https://publications.scilifelab.se/researcher/2623c8d5da76485198b91ac4b43cfd10.json"}}, {"family": "Rasmussen", "given": "Lene Juel", "initials": "LJ", "orcid": "0000-0001-6864-963X", "researcher": {"href": "https://publications.scilifelab.se/researcher/989eb06874c845979459f2f09068f4c8.json"}}, {"family": "Dai", "given": "Fangyin", "initials": "F", "orcid": "0000-0002-0215-2177", "researcher": {"href": "https://publications.scilifelab.se/researcher/aaa81aaa281d4970bfe587d012478d03.json"}}], "type": "journal article", "published": "2024-08-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7144", "issn-l": "2041-1723"}, "abstract": "FOXO transcription factors modulate aging-related pathways and influence longevity in multiple species, but the transcriptional targets that mediate these effects remain largely unknown. Here, we identify an evolutionarily conserved FOXO target gene, Oxidative stress-responsive serine-rich protein 1 (OSER1), whose overexpression extends lifespan in silkworms, nematodes, and flies, while its depletion correspondingly shortens lifespan. In flies, overexpression of OSER1 increases resistance to oxidative stress, starvation, and heat shock, while OSER1-depleted flies are more vulnerable to these stressors. In silkworms, hydrogen peroxide both induces and is scavenged by OSER1 in vitro and in vivo. Knockdown of OSER1 in Caenorhabditis elegans leads to increased ROS production and shorter lifespan, mitochondrial fragmentation, decreased ATP production, and altered transcription of mitochondrial genes. Human proteomic analysis suggests that OSER1 plays roles in oxidative stress response, cellular senescence, and reproduction, which is consistent with the data and suggests that OSER1 could play a role in fertility in silkworms and nematodes. Human studies demonstrate that polymorphic variants in OSER1 are associated with human longevity. In summary, OSER1 is an evolutionarily conserved FOXO-regulated protein that improves resistance to oxidative stress, maintains mitochondrial functional integrity, and increases lifespan in multiple species. Additional studies will clarify the role of OSER1 as a critical effector of healthy aging.", "doi": "10.1038/s41467-024-51542-z", "pmid": "39164296", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11336091"}, {"db": "pii", "key": "10.1038/s41467-024-51542-z"}], "notes": [], "created": "2024-10-21T11:23:02.650Z", "modified": "2024-10-21T11:23:03.401Z"}, {"entity": "publication", "iuid": "c0cac7649e664f42a2dad23b77043ae7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0cac7649e664f42a2dad23b77043ae7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0cac7649e664f42a2dad23b77043ae7"}}, "title": "Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution.", "authors": [{"family": "Hildebrandt", "given": "Franziska", "initials": "F", "orcid": "0000-0002-2673-1704", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c69d2d421d64a11a719a6fd55c1977a.json"}}, {"family": "Iturritza", "given": "Miren Urrutia", "initials": "MU", "orcid": "0000-0002-3989-1803", "researcher": {"href": "https://publications.scilifelab.se/researcher/65bc5beb14634ef9af3d153c19355794.json"}}, {"family": "Zwicker", "given": "Christian", "initials": "C"}, {"family": "Vanneste", "given": "Bavo", "initials": "B"}, {"family": "Van Hul", "given": "No\u00e9mi", "initials": "N", "orcid": "0000-0003-1410-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce1f79e0359b45c9991d14649ad4bc2b.json"}}, {"family": "Semle", "given": "Elisa", "initials": "E"}, {"family": "Quin", "given": "Jaclyn", "initials": "J"}, {"family": "Pascini", "given": "Tales", "initials": "T"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6979cdfc0b4e4285f9d810c39bb7b7.json"}}, {"family": "He", "given": "Mengxiao", "initials": "M", "orcid": "0000-0001-5905-8467", "researcher": {"href": "https://publications.scilifelab.se/researcher/79045a6ac62b4f8ea64233619eb6bfc9.json"}}, {"family": "Andersson", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8608-625X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7313cdcd5f41d4a567a6c315aac3a1.json"}}, {"family": "Scott", "given": "Charlotte L", "initials": "CL", "orcid": "0000-0003-4914-6580", "researcher": {"href": "https://publications.scilifelab.se/researcher/75d25f2a77f9444bb6e57ade9a1388a3.json"}}, {"family": "Vega-Rodriguez", "given": "Joel", "initials": "J", "orcid": "0000-0002-9576-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/a89fc53ed4fb4e179636b66ae8d1caa3.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2024-08-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7105", "issn-l": "2041-1723"}, "abstract": "Upon infecting its vertebrate host, the malaria parasite initially invades the liver where it undergoes massive replication, whilst remaining clinically silent. The coordination of host responses across the complex liver tissue during malaria infection remains unexplored. Here, we perform spatial transcriptomics in combination with single-nuclei RNA sequencing over multiple time points to delineate host-pathogen interactions across Plasmodium berghei-infected liver tissues. Our data reveals significant changes in spatial gene expression in the malaria-infected tissues. These include changes related to lipid metabolism in the proximity to sites of Plasmodium infection, distinct inflammation programs between lobular zones, and regions with enrichment of different inflammatory cells, which we term 'inflammatory hotspots'. We also observe significant upregulation of genes involved in inflammation in the control liver tissues of mice injected with mosquito salivary gland components. However, this response is considerably delayed compared to that observed in P. berghei-infected mice. Our study establishes a benchmark for investigating transcriptome changes during host-parasite interactions in tissues, it provides informative insights regarding in vivo study design linked to infection and offers a useful tool for the discovery and validation of de novo intervention strategies aimed at malaria liver stage infection.", "doi": "10.1038/s41467-024-51418-2", "pmid": "39160174", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11333755"}, {"db": "pii", "key": "10.1038/s41467-024-51418-2"}], "notes": [], "created": "2024-11-25T10:17:47.545Z", "modified": "2024-11-25T10:17:47.707Z"}, {"entity": "publication", "iuid": "1e4e4601890c4a40880fd60cbab92ad8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e4e4601890c4a40880fd60cbab92ad8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e4e4601890c4a40880fd60cbab92ad8"}}, "title": "Motor innervation directs the correct development of the mouse sympathetic nervous system.", "authors": [{"family": "Erickson", "given": "Alek G", "initials": "AG", "orcid": "0000-0001-7110-9386", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fcd4f91a2fa4847a1d81bb5be2b1da9.json"}}, {"family": "Motta", "given": "Alessia", "initials": "A", "orcid": "0000-0002-1008-8347", "researcher": {"href": "https://publications.scilifelab.se/researcher/8124ce783ece4d098fcd3675145d1e53.json"}}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME", "orcid": "0000-0002-0563-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e0722d8c5484a13bb37c3a3b084ff8c.json"}}, {"family": "Edwards", "given": "Steven", "initials": "S"}, {"family": "Coulpier", "given": "Fanny", "initials": "F"}, {"family": "Th\u00e9oulle", "given": "Emy", "initials": "E"}, {"family": "Murtazina", "given": "Aliia", "initials": "A", "orcid": "0000-0003-1630-1855", "researcher": {"href": "https://publications.scilifelab.se/researcher/9590b1e2770b4dfa9233ad9bdd906deb.json"}}, {"family": "Poverennaya", "given": "Irina", "initials": "I", "orcid": "0000-0003-2562-5632", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba58765568c846ae8250bfe56eb9d56e.json"}}, {"family": "Wies", "given": "Daniel", "initials": "D"}, {"family": "Ganofsky", "given": "Jeremy", "initials": "J", "orcid": "0000-0002-2361-7869", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ee1d09bb1b34b3c800943512c13749e.json"}}, {"family": "Canu", "given": "Giovanni", "initials": "G", "orcid": "0000-0002-3349-4479", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d8a7a89ab424482a8d816dda085a7aa.json"}}, {"family": "Lallemend", "given": "Francois", "initials": "F", "orcid": "0000-0001-5484-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9494a8ea444facbf3b564670930ab5.json"}}, {"family": "Topilko", "given": "Piotr", "initials": "P"}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}, {"family": "Fried", "given": "Kaj", "initials": "K", "orcid": "0000-0002-9997-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46eaae026524ee6b9b589f12846b458.json"}}, {"family": "Ruhrberg", "given": "Christiana", "initials": "C", "orcid": "0000-0002-3212-9381", "researcher": {"href": "https://publications.scilifelab.se/researcher/71f5aeb40eb04defa937360b83f9d73a.json"}}, {"family": "Schwarz", "given": "Quenten", "initials": "Q", "orcid": "0000-0002-5958-4181", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d558c2ad5704db4a70500e1ca9bbbf2.json"}}, {"family": "Castellani", "given": "Valerie", "initials": "V", "orcid": "0000-0001-9623-9312", "researcher": {"href": "https://publications.scilifelab.se/researcher/4164c2013f294c7cb5e0c0aa7693c912.json"}}, {"family": "Bonanomi", "given": "Dario", "initials": "D", "orcid": "0000-0003-4517-1244", "researcher": {"href": "https://publications.scilifelab.se/researcher/23a9b651c23e4cfab7b7b2df4126c328.json"}}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}], "type": "journal article", "published": "2024-08-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "7065"}, "abstract": "The sympathetic nervous system controls bodily functions including vascular tone, cardiac rhythm, and the \"fight-or-flight response\". Sympathetic chain ganglia develop in parallel with preganglionic motor nerves extending from the neural tube, raising the question of whether axon targeting contributes to sympathetic chain formation. Using nerve-selective genetic ablations and lineage tracing in mouse, we reveal that motor nerve-associated Schwann cell precursors (SCPs) contribute sympathetic neurons and satellite glia after the initial seeding of sympathetic ganglia by neural crest. Motor nerve ablation causes mispositioning of SCP-derived sympathoblasts as well as sympathetic chain hypoplasia and fragmentation. Sympathetic neurons in motor-ablated embryos project precociously and abnormally towards dorsal root ganglia, eventually resulting in fusion of sympathetic and sensory ganglia. Cell interaction analysis identifies semaphorins as potential motor nerve-derived signaling molecules regulating sympathoblast positioning and outgrowth. Overall, central innervation functions both as infrastructure and regulatory niche to ensure the integrity of peripheral ganglia morphogenesis.", "doi": "10.1038/s41467-024-51290-0", "pmid": "39152112", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11329663"}, {"db": "pii", "key": "10.1038/s41467-024-51290-0"}], "notes": [], "created": "2024-08-27T07:41:28.383Z", "modified": "2024-08-27T07:42:00.559Z"}, {"entity": "publication", "iuid": "eb29b09a66a84e1081cbd8cf6eb5333a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb29b09a66a84e1081cbd8cf6eb5333a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb29b09a66a84e1081cbd8cf6eb5333a"}}, "title": "Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins.", "authors": [{"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1cd4d11f8d443e8ff305f923b8fbb0.json"}}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0002-7855-9539", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c626e0c08ca449899cebece751e79cf.json"}}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Papetti", "given": "Chiara", "initials": "C", "orcid": "0000-0002-4567-459X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1a151631ac04ec0bfd9f952781bc973.json"}}, {"family": "Gislason", "given": "Astthor", "initials": "A"}, {"family": "Glenner", "given": "Henrik", "initials": "H"}, {"family": "Cartes", "given": "Joan E", "initials": "JE"}, {"family": "Blanco-Bercial", "given": "Leocadio", "initials": "L", "orcid": "0000-0003-0658-7183", "researcher": {"href": "https://publications.scilifelab.se/researcher/5077c59ccfe8496eb534c1ef6d725e06.json"}}, {"family": "Eriksen", "given": "Elena", "initials": "E"}, {"family": "Meyer", "given": "Bettina", "initials": "B", "orcid": "0000-0001-6804-9896", "researcher": {"href": "https://publications.scilifelab.se/researcher/9347bf907b1c4b258495153b5550f3dc.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}], "type": "journal article", "published": "2024-08-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "6297"}, "abstract": "Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change.", "doi": "10.1038/s41467-024-50239-7", "pmid": "39090106", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11294593"}, {"db": "pii", "key": "10.1038/s41467-024-50239-7"}], "notes": [], "created": "2024-08-02T12:21:47.326Z", "modified": "2024-11-25T10:17:04.308Z"}, {"entity": "publication", "iuid": "c1686601bc6b4c808ba31fbb6c6d93d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1686601bc6b4c808ba31fbb6c6d93d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1686601bc6b4c808ba31fbb6c6d93d3"}}, "title": "A genetic-epigenetic interplay at 1q21.1 locus underlies CHD1L-mediated vulnerability to primary progressive multiple sclerosis.", "authors": [{"family": "Pahlevan Kakhki", "given": "Majid", "initials": "M", "orcid": "0000-0002-5407-3147", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f376c85cfbe4711ae41d9ee5ade8f09.json"}}, {"family": "Giordano", "given": "Antonino", "initials": "A"}, {"family": "Starvaggi Cucuzza", "given": "Chiara", "initials": "C", "orcid": "0000-0002-9088-7658", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ead2e8f98754d1586891eda5adb9e1a.json"}}, {"family": "Venkata S Badam", "given": "Tejaswi", "initials": "T"}, {"family": "Samudyata", "given": "Samudyata", "initials": "S"}, {"family": "Lem\u00e9e", "given": "Marianne Victoria", "initials": "MV", "orcid": "0000-0002-4897-0722", "researcher": {"href": "https://publications.scilifelab.se/researcher/361e3a91dc5245e587309759769414c8.json"}}, {"family": "Stridh", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-4855-0039", "researcher": {"href": "https://publications.scilifelab.se/researcher/613e86be4685423093de57bb83be261b.json"}}, {"family": "Gkogka", "given": "Asimenia", "initials": "A"}, {"family": "Shchetynsky", "given": "Klementy", "initials": "K"}, {"family": "Harroud", "given": "Adil", "initials": "A", "orcid": "0000-0003-2616-7274", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a769f610fb430e89258c1c30cbd23b.json"}}, {"family": "Gyllenberg", "given": "Alexandra", "initials": "A"}, {"family": "Liu", "given": "Yun", "initials": "Y"}, {"family": "Boddul", "given": "Sanjaykumar", "initials": "S"}, {"family": "James", "given": "Tojo", "initials": "T"}, {"family": "Sorosina", "given": "Melissa", "initials": "M"}, {"family": "Filippi", "given": "Massimo", "initials": "M", "orcid": "0000-0002-5485-0479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8878f32c07334124b8e3bce42c94c076.json"}}, {"family": "Esposito", "given": "Federica", "initials": "F"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9633-677X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a34df8186ba24df3b14fe9743cf546b4.json"}}, {"family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2.json"}}, {"family": "Casaccia", "given": "Patrizia", "initials": "P", "orcid": "0000-0002-4785-9264", "researcher": {"href": "https://publications.scilifelab.se/researcher/e62a7dde40bd454e9072ff43fff8a2ea.json"}}, {"family": "Hillert", "given": "Jan", "initials": "J"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Sellgren", "given": "Carl M", "initials": "CM", "orcid": "0000-0001-9103-2785", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c0740ddfd6d4c98988b2a19096a9814.json"}}, {"family": "Golzio", "given": "Christelle", "initials": "C"}, {"family": "Kular", "given": "Lara", "initials": "L", "orcid": "0000-0002-2907-6071", "researcher": {"href": "https://publications.scilifelab.se/researcher/09563004a20543dc934dd4d3b1ceebd7.json"}}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}], "type": "journal article", "published": "2024-07-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6419", "issn-l": "2041-1723"}, "abstract": "Multiple Sclerosis (MS) is a heterogeneous inflammatory and neurodegenerative disease with an unpredictable course towards progressive disability. Treating progressive MS is challenging due to limited insights into the underlying mechanisms. We examined the molecular changes associated with primary progressive MS (PPMS) using a cross-tissue (blood and post-mortem brain) and multilayered data (genetic, epigenetic, transcriptomic) from independent cohorts. In PPMS, we found hypermethylation of the 1q21.1 locus, controlled by PPMS-specific genetic variations and influencing the expression of proximal genes (CHD1L, PRKAB2) in the brain. Evidence from reporter assay and CRISPR/dCas9 experiments supports a causal link between methylation and expression and correlation network analysis further implicates these genes in PPMS brain processes. Knock-down of CHD1L in human iPSC-derived neurons and knock-out of chd1l in zebrafish led to developmental and functional deficits of neurons. Thus, several lines of evidence suggest a distinct genetic-epigenetic-transcriptional interplay in the 1q21.1 locus potentially contributing to PPMS pathogenesis.", "doi": "10.1038/s41467-024-50794-z", "pmid": "39079955", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11289459"}, {"db": "pii", "key": "10.1038/s41467-024-50794-z"}], "notes": [], "created": "2024-08-15T12:14:24.965Z", "modified": "2024-11-25T10:17:37.116Z"}, {"entity": "publication", "iuid": "d28325d47fdb47cda393a1e60d677055", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d28325d47fdb47cda393a1e60d677055.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d28325d47fdb47cda393a1e60d677055"}}, "title": "Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques.", "authors": [{"family": "Mandolesi", "given": "Marco", "initials": "M", "orcid": "0000-0003-2927-7831", "researcher": {"href": "https://publications.scilifelab.se/researcher/29e6c31be1704c97a2853aca0833f6b0.json"}}, {"family": "Das", "given": "Hrishikesh", "initials": "H", "orcid": "0000-0001-7495-7065", "researcher": {"href": "https://publications.scilifelab.se/researcher/b150c8ccf1164aaab678a9f6c1acd97b.json"}}, {"family": "de Vries", "given": "Liset", "initials": "L", "orcid": "0000-0002-4797-086X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6b05b7eec7c4120b4bee2ff15ac8035.json"}}, {"family": "Yang", "given": "Yiqiu", "initials": "Y"}, {"family": "Kim", "given": "Changil", "initials": "C"}, {"family": "Dhinakaran", "given": "Manojj", "initials": "M", "orcid": "0000-0003-2536-8699", "researcher": {"href": "https://publications.scilifelab.se/researcher/de859a6247424dd285f56b841dc23a36.json"}}, {"family": "Castro Dopico", "given": "Xaquin", "initials": "X", "orcid": "0000-0002-9005-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1d266d61654951a684193993ca53b1.json"}}, {"family": "Fischbach", "given": "Julian", "initials": "J", "orcid": "0000-0001-9411-9181", "researcher": {"href": "https://publications.scilifelab.se/researcher/20e4fea1f9f54727b1bf3ef1cb8f81a4.json"}}, {"family": "Kim", "given": "Sungyong", "initials": "S"}, {"family": "Guryleva", "given": "Mariia V", "initials": "MV"}, {"family": "\u00c0dori", "given": "Monika", "initials": "M"}, {"family": "Chernyshev", "given": "Mark", "initials": "M", "orcid": "0000-0003-1622-9240", "researcher": {"href": "https://publications.scilifelab.se/researcher/678134399edb44afac5e7eacc8622fcb.json"}}, {"family": "St\u00e5lmarck", "given": "Aron", "initials": "A"}, {"family": "Hanke", "given": "Leo", "initials": "L", "orcid": "0000-0001-5514-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece050a286f946f6807170cffc9320e7.json"}}, {"family": "McInerney", "given": "Gerald M", "initials": "GM", "orcid": "0000-0003-2257-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac2f68095fe4426b97ec070865e5091.json"}}, {"family": "Sheward", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0002-0227-5636", "researcher": {"href": "https://publications.scilifelab.se/researcher/6105f3617cdf4241bf335299ac957ee5.json"}}, {"family": "Corcoran", "given": "Martin", "initials": "M"}, {"family": "H\u00e4llberg", "given": "B Martin", "initials": "BM", "orcid": "0000-0002-6781-0345", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b7e4327d0ac48288afd6061f149156d.json"}}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB", "orcid": "0000-0001-7255-9047", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad611ac9c76e44989e585edc4d7ff713.json"}}], "type": "journal article", "published": "2024-07-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6338", "issn-l": "2041-1723"}, "abstract": "The continued evolution of SARS-CoV-2 underscores the need to understand qualitative aspects of the humoral immune response elicited by spike immunization. Here, we combine monoclonal antibody (mAb) isolation with deep B cell receptor (BCR) repertoire sequencing of rhesus macaques immunized with prefusion-stabilized spike glycoprotein. Longitudinal tracing of spike-sorted B cell lineages in multiple immune compartments demonstrates increasing somatic hypermutation and broad dissemination of vaccine-elicited B cells in draining and non-draining lymphoid compartments, including the bone marrow, spleen and, most notably, periaortic lymph nodes. Phylogenetic analysis of spike-specific monoclonal antibody lineages identified through deep repertoire sequencing delineates extensive intra-clonal diversification that shaped neutralizing activity. Structural analysis of the spike in complex with a broadly neutralizing mAb provides a molecular basis for the observed differences in neutralization breadth between clonally related antibodies. Our findings highlight that immunization leads to extensive intra-clonal B cell evolution where members of the same lineage can both retain the original epitope specificity and evolve to recognize additional spike variants not previously encountered.", "doi": "10.1038/s41467-024-50286-0", "pmid": "39068149", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11283548"}, {"db": "pii", "key": "10.1038/s41467-024-50286-0"}], "notes": [], "created": "2024-10-14T13:07:16.627Z", "modified": "2024-11-25T10:17:09.411Z"}, {"entity": "publication", "iuid": "169cd135482a4f3caa6614d91f5810b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/169cd135482a4f3caa6614d91f5810b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/169cd135482a4f3caa6614d91f5810b7"}}, "title": "Interneuron diversity in the human dorsal striatum.", "authors": [{"family": "Garma", "given": "Leonardo D", "initials": "LD", "orcid": "0000-0003-1220-8397", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fc1770f1fa24c7f82e6962f20d0839c.json"}}, {"family": "Harder", "given": "Lisbeth", "initials": "L", "orcid": "0000-0002-0637-720X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2c737f7aed64d23b90c4c445eb93040.json"}}, {"family": "Barba-Reyes", "given": "Juan M", "initials": "JM"}, {"family": "Marco Salas", "given": "Sergio", "initials": "S"}, {"family": "D\u00edez-Salguero", "given": "M\u00f3nica", "initials": "M"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Serrano-Pozo", "given": "Alberto", "initials": "A", "orcid": "0000-0003-0899-7530", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3a9c6d7c28446e8009dabf6d33050b.json"}}, {"family": "Hyman", "given": "Bradley T", "initials": "BT", "orcid": "0000-0002-7959-9401", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c3a94c8f6144fc88ec1f3f16976f5c3.json"}}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana B", "initials": "AB", "orcid": "0000-0002-1121-6072", "researcher": {"href": "https://publications.scilifelab.se/researcher/c554287bb9d84341bb45668e01bfb90d.json"}}], "type": "journal article", "published": "2024-07-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6164", "issn-l": "2041-1723"}, "abstract": "Deciphering the striatal interneuron diversity is key to understanding the basal ganglia circuit and to untangling the complex neurological and psychiatric diseases affecting this brain structure. We performed snRNA-seq and spatial transcriptomics of postmortem human caudate nucleus and putamen samples to elucidate the diversity and abundance of interneuron populations and their inherent transcriptional structure in the human dorsal striatum. We propose a comprehensive taxonomy of striatal interneurons with eight main classes and fourteen subclasses, providing their full transcriptomic identity and spatial expression profile as well as additional quantitative FISH validation for specific populations. We have also delineated the correspondence of our taxonomy with previous standardized classifications and shown the main transcriptomic and class abundance differences between caudate nucleus and putamen. Notably, based on key functional genes such as ion channels and synaptic receptors, we found matching known mouse interneuron populations for the most abundant populations, the recently described PTHLH and TAC3 interneurons. Finally, we were able to integrate other published datasets with ours, supporting the generalizability of this harmonized taxonomy.", "doi": "10.1038/s41467-024-50414-w", "pmid": "39039043", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11263574"}, {"db": "pii", "key": "10.1038/s41467-024-50414-w"}], "notes": [], "created": "2024-11-25T10:17:14.777Z", "modified": "2024-11-25T10:17:14.982Z"}, {"entity": "publication", "iuid": "833ddbd417134b2391ed6f567cb965bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/833ddbd417134b2391ed6f567cb965bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/833ddbd417134b2391ed6f567cb965bf"}}, "title": "A single-cell pan-cancer analysis to show the variability of tumor-infiltrating myeloid cells in immune checkpoint blockade.", "authors": [{"family": "Li", "given": "Weiyuan", "initials": "W"}, {"family": "Pan", "given": "Lu", "initials": "L", "orcid": "0000-0001-7467-6992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e446ee543a94babbe11f379bde2885c.json"}}, {"family": "Hong", "given": "Weifeng", "initials": "W"}, {"family": "Ginhoux", "given": "Florent", "initials": "F", "orcid": "0000-0002-2857-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/83178179295443d4a990addb88281065.json"}}, {"family": "Zhang", "given": "Xuan", "initials": "X"}, {"family": "Xiao", "given": "Chunjie", "initials": "C"}, {"family": "Li", "given": "Xuexin", "initials": "X", "orcid": "0000-0001-5824-9720", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfd5f1e6e5644a9ab922a685167f868d.json"}}], "type": "journal article", "published": "2024-07-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6142", "issn-l": "2041-1723"}, "abstract": "Myeloid cells are vital components of the immune system and have pivotal functions in orchestrating immune responses. Understanding their functions within the tumor microenvironment and their interactions with tumor-infiltrating lymphocytes presents formidable challenges across diverse cancer types, particularly with regards to cancer immunotherapies. Here, we explore tumor-infiltrating myeloid cells (TIMs) by conducting a pan-cancer analysis using single-cell transcriptomics across eight distinct cancer types, encompassing a total of 192 tumor samples from 129 patients. By examining gene expression patterns and transcriptional activities of TIMs in different cancer types, we discern notable alterations in abundance of TIMs and kinetic behaviors prior to and following immunotherapy. We also identify specific cell-cell interaction targets in immunotherapy; unique and shared regulatory profiles critical for treatment response; and TIMs associated with survival outcomes. Overall, our study illuminates the heterogeneity of TIMs and improves our understanding of tissue-specific and cancer-specific myeloid subsets within the context of tumor immunotherapies.", "doi": "10.1038/s41467-024-50478-8", "pmid": "39034339", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11271490"}, {"db": "pii", "key": "10.1038/s41467-024-50478-8"}], "notes": [], "created": "2024-11-25T10:17:20.143Z", "modified": "2024-11-25T10:17:20.268Z"}, {"entity": "publication", "iuid": "d27fb32da6774e5d88889bbc52103f9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d27fb32da6774e5d88889bbc52103f9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d27fb32da6774e5d88889bbc52103f9b"}}, "title": "The Escherichia coli chromosome moves to the replisome.", "authors": [{"family": "Gras", "given": "Konrad", "initials": "K"}, {"family": "Fange", "given": "David", "initials": "D", "orcid": "0009-0006-3981-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/195ab3e1f94e4ad39b4aa32da6b3e217.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": "2024-07-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6018", "issn-l": "2041-1723"}, "abstract": "In Escherichia coli, it is debated whether the two replisomes move independently along the two chromosome arms during replication or if they remain spatially confined. Here, we use high-throughput fluorescence microscopy to simultaneously determine the location and short-time-scale (1 s) movement of the replisome and a chromosomal locus throughout the cell cycle. The assay is performed for several loci. We find that (i) the two replisomes are confined to a region of ~250 nm and ~120 nm along the cell's long and short axis, respectively, (ii) the chromosomal loci move to and through this region sequentially based on their distance from the origin of replication, and (iii) when a locus is being replicated, its short time-scale movement slows down. This behavior is the same at different growth rates. In conclusion, our data supports a model with DNA moving towards spatially confined replisomes at replication.", "doi": "10.1038/s41467-024-50047-z", "pmid": "39019870", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11255300"}, {"db": "pii", "key": "10.1038/s41467-024-50047-z"}], "notes": [], "created": "2024-11-25T10:16:58.970Z", "modified": "2024-11-25T10:16:59.056Z"}, {"entity": "publication", "iuid": "88d3b144a82242fe917650dbb2327d3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88d3b144a82242fe917650dbb2327d3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88d3b144a82242fe917650dbb2327d3d"}}, "title": "Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex.", "authors": [{"family": "Riepl", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5641-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d319a620085414b92d1b92fb640ec72.json"}}, {"family": "Gamiz-Hernandez", "given": "Ana P", "initials": "AP", "orcid": "0000-0002-0961-328X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8021ee901c9442e792bba76d38984d4a.json"}}, {"family": "Kovalova", "given": "Terezia", "initials": "T", "orcid": "0000-0002-0144-2463", "researcher": {"href": "https://publications.scilifelab.se/researcher/28a04987c43944d788c125a1dfd15828.json"}}, {"family": "Kr\u00f3l", "given": "Sylwia M", "initials": "SM"}, {"family": "Mader", "given": "Sophie L", "initials": "SL", "orcid": "0000-0002-3011-3319", "researcher": {"href": "https://publications.scilifelab.se/researcher/23c686122cd34cfe9a4ab53c925c246d.json"}}, {"family": "Sj\u00f6strand", "given": "Dan", "initials": "D"}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M", "orcid": "0000-0001-5574-9383", "researcher": {"href": "https://publications.scilifelab.se/researcher/d968fcccace74b689185bb9fa2d33bf8.json"}}, {"family": "Brzezinski", "given": "Peter", "initials": "P", "orcid": "0000-0003-3860-4988", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3314030ecf94791a713a068d4926c20.json"}}, {"family": "Kaila", "given": "Ville R I", "initials": "VRI", "orcid": "0000-0003-4464-6324", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdcc63256cea406c9cb9cdaecc9cbcbe.json"}}], "type": "journal article", "published": "2024-06-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "5276", "issn-l": "2041-1723"}, "abstract": "Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 \u00c5) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.", "doi": "10.1038/s41467-024-49628-9", "pmid": "38902248", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11189923"}, {"db": "pii", "key": "10.1038/s41467-024-49628-9"}], "notes": [], "created": "2024-11-15T08:56:46.121Z", "modified": "2024-11-15T10:41:20.395Z"}, {"entity": "publication", "iuid": "439b4f3e6f4a4cd087c14c33e9843759", "links": {"self": {"href": "https://publications.scilifelab.se/publication/439b4f3e6f4a4cd087c14c33e9843759.json"}, "display": {"href": "https://publications.scilifelab.se/publication/439b4f3e6f4a4cd087c14c33e9843759"}}, "title": "descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques.", "authors": [{"family": "Otomo", "given": "Kohei", "initials": "K", "orcid": "0000-0002-5322-6295", "researcher": {"href": "https://publications.scilifelab.se/researcher/533d35e986ee455586e089453d6a97d9.json"}}, {"family": "Omura", "given": "Takaki", "initials": "T"}, {"family": "Nozawa", "given": "Yuki", "initials": "Y", "orcid": "0009-0002-4571-6232", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc582ce80ae24ab284c32facf997a994.json"}}, {"family": "Edwards", "given": "Steven J", "initials": "SJ"}, {"family": "Sato", "given": "Yukihiko", "initials": "Y"}, {"family": "Saito", "given": "Yuri", "initials": "Y"}, {"family": "Yagishita", "given": "Shigehiro", "initials": "S"}, {"family": "Uchida", "given": "Hitoshi", "initials": "H", "orcid": "0000-0002-8952-2061", "researcher": {"href": "https://publications.scilifelab.se/researcher/132470da90604fbb8d6f392e4302ffd5.json"}}, {"family": "Watakabe", "given": "Yuki", "initials": "Y", "orcid": "0000-0002-6580-1007", "researcher": {"href": "https://publications.scilifelab.se/researcher/6770fc27fcde42308b027f0517a38771.json"}}, {"family": "Naitou", "given": "Kiyotada", "initials": "K", "orcid": "0000-0001-8599-2528", "researcher": {"href": "https://publications.scilifelab.se/researcher/878767bc68214823b850dfb427575684.json"}}, {"family": "Yanai", "given": "Rin", "initials": "R"}, {"family": "Sahara", "given": "Naruhiko", "initials": "N"}, {"family": "Takagi", "given": "Satoshi", "initials": "S", "orcid": "0000-0001-9749-1034", "researcher": {"href": "https://publications.scilifelab.se/researcher/87d7e07cf7494536a2c70937d87f4515.json"}}, {"family": "Katayama", "given": "Ryohei", "initials": "R", "orcid": "0000-0001-7394-895X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f933af571a2044ae9929841a8f53ae83.json"}}, {"family": "Iwata", "given": "Yusuke", "initials": "Y", "orcid": "0009-0009-7203-772X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebaed40358324e2ea2a9cbb9c3b0aef3.json"}}, {"family": "Shiokawa", "given": "Toshiro", "initials": "T"}, {"family": "Hayakawa", "given": "Yoku", "initials": "Y"}, {"family": "Otsuka", "given": "Kensuke", "initials": "K"}, {"family": "Watanabe-Takano", "given": "Haruko", "initials": "H", "orcid": "0000-0002-2986-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a79a191375419fb20e671f637c0a90.json"}}, {"family": "Haneda", "given": "Yuka", "initials": "Y", "orcid": "0000-0002-6178-1109", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4accbf75ce2497988cf403c910f78fa.json"}}, {"family": "Fukuhara", "given": "Shigetomo", "initials": "S", "orcid": "0000-0003-2777-501X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0819338144444c05bfa4d05fbc0a869f.json"}}, {"family": "Fujiwara", "given": "Miku", "initials": "M"}, {"family": "Nii", "given": "Takenobu", "initials": "T"}, {"family": "Meno", "given": "Chikara", "initials": "C", "orcid": "0000-0002-0869-6642", "researcher": {"href": "https://publications.scilifelab.se/researcher/104cf925fa24479f8d8561fdc6742496.json"}}, {"family": "Takeshita", "given": "Naoki", "initials": "N", "orcid": "0000-0002-1418-9188", "researcher": {"href": "https://publications.scilifelab.se/researcher/01c6c6da90e7462087eb38accca9d997.json"}}, {"family": "Yashiro", "given": "Kenta", "initials": "K"}, {"family": "Rosales Rocabado", "given": "Juan Marcelo", "initials": "JM", "orcid": "0000-0002-8753-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/eda8249af61547319e77b66721ea8191.json"}}, {"family": "Kaku", "given": "Masaru", "initials": "M", "orcid": "0000-0002-7988-6435", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b49fea6ce3e43f3918a4ada8a55c6c4.json"}}, {"family": "Yamada", "given": "Tatsuya", "initials": "T", "orcid": "0000-0002-6906-9861", "researcher": {"href": "https://publications.scilifelab.se/researcher/727c7ecfeb4747f5aad5f8a106be8bce.json"}}, {"family": "Oishi", "given": "Yumiko", "initials": "Y"}, {"family": "Koike", "given": "Hiroyuki", "initials": "H", "orcid": "0000-0001-9934-6930", "researcher": {"href": "https://publications.scilifelab.se/researcher/99607b00ae124e13b29626412fde6f9d.json"}}, {"family": "Cheng", "given": "Yinglan", "initials": "Y"}, {"family": "Sekine", "given": "Keisuke", "initials": "K", "orcid": "0000-0001-5133-0876", "researcher": {"href": "https://publications.scilifelab.se/researcher/e87dc82e3059497d93d47fa4a7939e8a.json"}}, {"family": "Koga", "given": "Jun-Ichiro", "initials": "J"}, {"family": "Sugiyama", "given": "Kaori", "initials": "K"}, {"family": "Kimura", "given": "Kenichi", "initials": "K", "orcid": "0000-0002-0363-8865", "researcher": {"href": "https://publications.scilifelab.se/researcher/067d51f73a7745b7b61df312d75ea49d.json"}}, {"family": "Karube", "given": "Fuyuki", "initials": "F"}, {"family": "Kim", "given": "Hyeree", "initials": "H", "orcid": "0009-0007-3174-2989", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec3bb7dfa8d243fcb85f0fa7a6a28a2e.json"}}, {"family": "Manabe", "given": "Ichiro", "initials": "I", "orcid": "0000-0001-9481-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/20749719d6974fd593ae69998f2efe0b.json"}}, {"family": "Nemoto", "given": "Tomomi", "initials": "T", "orcid": "0000-0001-6102-1495", "researcher": {"href": "https://publications.scilifelab.se/researcher/824c920cbacb4cc988fd3abf6aafa08b.json"}}, {"family": "Tainaka", "given": "Kazuki", "initials": "K", "orcid": "0000-0002-5943-8723", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2ebee6e49614394880c6f5805174b46.json"}}, {"family": "Hamada", "given": "Akinobu", "initials": "A"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Susaki", "given": "Etsuo A", "initials": "EA", "orcid": "0000-0001-5621-7311", "researcher": {"href": "https://publications.scilifelab.se/researcher/97fb49e8f6e843dab92b70890dbf9dc6.json"}}], "type": "journal article", "published": "2024-06-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "4941"}, "abstract": "Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000-50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.", "doi": "10.1038/s41467-024-49131-1", "pmid": "38866781", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-024-49131-1"}], "notes": [], "created": "2024-06-14T08:32:48.936Z", "modified": "2024-11-25T17:48:31.705Z"}, {"entity": "publication", "iuid": "f3a8c5465513414e80b2ec9c5f5c4ce7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3a8c5465513414e80b2ec9c5f5c4ce7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3a8c5465513414e80b2ec9c5f5c4ce7"}}, "title": "Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice.", "authors": [{"family": "Masarapu", "given": "Yuvarani", "initials": "Y", "orcid": "0000-0002-3267-2085", "researcher": {"href": "https://publications.scilifelab.se/researcher/055fa17f6cdd490e87182c94c847c440.json"}}, {"family": "Cekanaviciute", "given": "Egle", "initials": "E", "orcid": "0000-0003-3306-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/13bfc7ccb66a4ef0b724b42eeafffedc.json"}}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/161d8b5fb6734b33ad5f5590edbc0cff.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Fallegger", "given": "Robin", "initials": "R", "orcid": "0000-0003-3264-6028", "researcher": {"href": "https://publications.scilifelab.se/researcher/59c8a7db6d314f15ab3038663f991d11.json"}}, {"family": "Badia-I-Mompel", "given": "Pau", "initials": "P", "orcid": "0000-0002-1004-3923", "researcher": {"href": "https://publications.scilifelab.se/researcher/86747ef92e0a4c14be8221a0a9f4aaf8.json"}}, {"family": "Boyko", "given": "Valery", "initials": "V", "orcid": "0000-0002-3724-9294", "researcher": {"href": "https://publications.scilifelab.se/researcher/40e46d1d14b14d0ca373aed26662ed77.json"}}, {"family": "Vasisht", "given": "Shubha", "initials": "S"}, {"family": "Saravia-Butler", "given": "Amanda", "initials": "A"}, {"family": "Gebre", "given": "Samrawit", "initials": "S"}, {"family": "L\u00e1z\u00e1r", "given": "Enik\u0151", "initials": "E", "orcid": "0000-0001-8664-7531", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd94abaf66dd407da5056c04174fc62d.json"}}, {"family": "Graziano", "given": "Marta", "initials": "M"}, {"family": "Frapard", "given": "Sol\u00e8ne", "initials": "S", "orcid": "0000-0002-2649-7225", "researcher": {"href": "https://publications.scilifelab.se/researcher/a336a6a31fae4766afbb5e376a4a12a3.json"}}, {"family": "Hinshaw", "given": "Robert G", "initials": "RG", "orcid": "0000-0003-0060-7753", "researcher": {"href": "https://publications.scilifelab.se/researcher/736bdd057fe7491885504738a1ef3341.json"}}, {"family": "Bergmann", "given": "Olaf", "initials": "O", "orcid": "0000-0003-1065-4107", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb61ad666a3427193e07c6274e8c3a1.json"}}, {"family": "Taylor", "given": "Deanne M", "initials": "DM", "orcid": "0000-0002-3302-4610", "researcher": {"href": "https://publications.scilifelab.se/researcher/862bf6178eaf4d96a9b87be21231c0be.json"}}, {"family": "Wallace", "given": "Douglas C", "initials": "DC", "orcid": "0000-0002-7480-8278", "researcher": {"href": "https://publications.scilifelab.se/researcher/da24a7104b504c6bbed58d7e5021e96c.json"}}, {"family": "Sylv\u00e9n", "given": "Christer", "initials": "C"}, {"family": "Meletis", "given": "Konstantinos", "initials": "K", "orcid": "0000-0001-5665-4781", "researcher": {"href": "https://publications.scilifelab.se/researcher/56822ffe0341444297c820580f52dfd0.json"}}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J", "orcid": "0000-0002-8552-8976", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce0043f77cad4f6e8ab9641d7f42c420.json"}}, {"family": "Galazka", "given": "Jonathan M", "initials": "JM", "orcid": "0000-0002-4153-0249", "researcher": {"href": "https://publications.scilifelab.se/researcher/c262ca6a35e74ea78350272c73202581.json"}}, {"family": "Costes", "given": "Sylvain V", "initials": "SV", "orcid": "0000-0002-8542-2389", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba1143c1d0644f239333abcce8508f38.json"}}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}], "type": "journal article", "published": "2024-06-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "4778"}, "abstract": "Impairment of the central nervous system (CNS) poses a significant health risk for astronauts during long-duration space missions. In this study, we employed an innovative approach by integrating single-cell multiomics (transcriptomics and chromatin accessibility) with spatial transcriptomics to elucidate the impact of spaceflight on the mouse brain in female mice. Our comparative analysis between ground control and spaceflight-exposed animals revealed significant alterations in essential brain processes including neurogenesis, synaptogenesis and synaptic transmission, particularly affecting the cortex, hippocampus, striatum and neuroendocrine structures. Additionally, we observed astrocyte activation and signs of immune dysfunction. At the pathway level, some spaceflight-induced changes in the brain exhibit similarities with neurodegenerative disorders, marked by oxidative stress and protein misfolding. Our integrated spatial multiomics approach serves as a stepping stone towards understanding spaceflight-induced CNS impairments at the level of individual brain regions and cell types, and provides a basis for comparison in future spaceflight studies. For broader scientific impact, all datasets from this study are available through an interactive data portal, as well as the National Aeronautics and Space Administration (NASA) Open Science Data Repository (OSDR).", "doi": "10.1038/s41467-024-48916-8", "pmid": "38862479", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11166911"}, {"db": "pii", "key": "10.1038/s41467-024-48916-8"}], "notes": [], "created": "2024-06-14T17:33:56.739Z", "modified": "2024-12-16T08:31:00.571Z"}, {"entity": "publication", "iuid": "df880e2368024d3186c599e61cf01f8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df880e2368024d3186c599e61cf01f8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df880e2368024d3186c599e61cf01f8a"}}, "title": "ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers.", "authors": [{"family": "Zhang", "given": "Yi", "initials": "Y"}, {"family": "Xie", "given": "Guojia", "initials": "G", "orcid": "0000-0002-8250-6157", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec90bde6e0a474f927615602734cd4c.json"}}, {"family": "Lee", "given": "Ji-Eun", "initials": "JE", "orcid": "0000-0002-3768-7016", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b9ee3b2ab77440c80566ad35fc02924.json"}}, {"family": "Zandian", "given": "Mohamad", "initials": "M", "orcid": "0000-0002-4967-6867", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f81558cc5d546f0bbb8b9db1456bc14.json"}}, {"family": "Sudarshan", "given": "Deepthi", "initials": "D"}, {"family": "Estavoyer", "given": "Benjamin", "initials": "B"}, {"family": "Benz", "given": "Caroline", "initials": "C", "orcid": "0000-0002-5166-3598", "researcher": {"href": "https://publications.scilifelab.se/researcher/86628e15252f4dd98f08759d59fad848.json"}}, {"family": "Viita", "given": "Tiina", "initials": "T"}, {"family": "Asgaritarghi", "given": "Golareh", "initials": "G"}, {"family": "Lachance", "given": "Catherine", "initials": "C"}, {"family": "Messmer", "given": "Cl\u00e9mence", "initials": "C"}, {"family": "Simonetti", "given": "Leandro", "initials": "L", "orcid": "0000-0003-1283-9770", "researcher": {"href": "https://publications.scilifelab.se/researcher/23530c1a3cef4f499a460ac59c674261.json"}}, {"family": "Sinha", "given": "Vikrant Kumar", "initials": "VK"}, {"family": "Lambert", "given": "Jean-Philippe", "initials": "JP", "orcid": "0000-0002-0833-1221", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea53138c672d469295549d26672f2e26.json"}}, {"family": "Chen", "given": "Yu-Wen", "initials": "YW"}, {"family": "Wang", "given": "Shu-Ping", "initials": "SP", "orcid": "0000-0002-5895-1269", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9023a2623140319f7e298758b186e1.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}, {"family": "Affar", "given": "El Bachir", "initials": "EB", "orcid": "0000-0002-6374-3683", "researcher": {"href": "https://publications.scilifelab.se/researcher/1acebd04acd94e199bebe57a10db34ff.json"}}, {"family": "C\u00f4t\u00e9", "given": "Jacques", "initials": "J", "orcid": "0000-0001-6751-555X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4db696aa49342a0b1d9c0efb38c899c.json"}}, {"family": "Ge", "given": "Kai", "initials": "K"}, {"family": "Kutateladze", "given": "Tatiana G", "initials": "TG", "orcid": "0000-0001-7375-6990", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f6b888607504d27b88684a37f4087b9.json"}}], "type": "journal article", "published": "2024-06-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "4883", "issn-l": "2041-1723"}, "abstract": "The human methyltransferase and transcriptional coactivator MLL4 and its paralog MLL3 are frequently mutated in cancer. MLL4 and MLL3 monomethylate histone H3K4 and contain a set of uncharacterized PHD fingers. Here, we report a novel function of the PHD2 and PHD3 (PHD2/3) fingers of MLL4 and MLL3 that bind to ASXL2, a component of the Polycomb repressive H2AK119 deubiquitinase (PR-DUB) complex. The structure of MLL4 PHD2/3 in complex with the MLL-binding helix (MBH) of ASXL2 and mutational analyses reveal the molecular mechanism which is conserved in homologous ASXL1 and ASXL3. The native interaction of the Trithorax MLL3/4 complexes with the PR-DUB complex in vivo depends solely on MBH of ASXL1/2, coupling the two histone modifying activities. ChIP-seq analysis in embryonic stem cells demonstrates that MBH of ASXL1/2 is required for the deubiquitinase BAP1 recruitment to MLL4-bound active enhancers. Our findings suggest an ASXL1/2-dependent functional link between the MLL3/4 and PR-DUB complexes.", "doi": "10.1038/s41467-024-49391-x", "pmid": "38849395", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11161652"}, {"db": "pii", "key": "10.1038/s41467-024-49391-x"}], "notes": [], "created": "2024-08-15T12:13:00.466Z", "modified": "2024-10-01T09:33:16.920Z"}, {"entity": "publication", "iuid": "f1fcb31fd4044e3cb4c83d56389eae4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1fcb31fd4044e3cb4c83d56389eae4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1fcb31fd4044e3cb4c83d56389eae4a"}}, "title": "Structure and mechanism of the K+/H+ exchanger KefC.", "authors": [{"family": "Gulati", "given": "Ashutosh", "initials": "A", "orcid": "0000-0003-0960-994X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b2b0aa7260492c8141083762e08125.json"}}, {"family": "Kokane", "given": "Surabhi", "initials": "S"}, {"family": "Perez-Boerema", "given": "Annemarie", "initials": "A", "orcid": "0000-0002-1180-5838", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a711071c6844bdcb4c151971774435f.json"}}, {"family": "Alleva", "given": "Claudia", "initials": "C", "orcid": "0000-0001-8595-9250", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba3dab4eb9824851b9384e58d3e2c528.json"}}, {"family": "Meier", "given": "Pascal F", "initials": "PF"}, {"family": "Matsuoka", "given": "Rei", "initials": "R"}, {"family": "Drew", "given": "David", "initials": "D", "orcid": "0000-0001-8866-6349", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc19844f8147480fb0af2e437744131b.json"}}], "type": "journal article", "published": "2024-06-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "4751", "issn-l": "2041-1723"}, "abstract": "Intracellular potassium (K+) homeostasis is fundamental to cell viability. In addition to channels, K+ levels are maintained by various ion transporters. One major family is the proton-driven K+ efflux transporters, which in gram-negative bacteria is important for detoxification and in plants is critical for efficient photosynthesis and growth. Despite their importance, the structure and molecular basis for K+-selectivity is poorly understood. Here, we report ~3.1 \u00c5 resolution cryo-EM structures of the Escherichia coli glutathione (GSH)-gated K+ efflux transporter KefC in complex with AMP, AMP/GSH and an ion-binding variant. KefC forms a homodimer similar to the inward-facing conformation of Na+/H+ antiporter NapA. By structural assignment of a coordinated K+ ion, MD simulations, and SSM-based electrophysiology, we demonstrate how ion-binding in KefC is adapted for binding a dehydrated K+ ion. KefC harbors C-terminal regulator of K+ conductance (RCK) domains, as present in some bacterial K+-ion channels. The domain-swapped helices in the RCK domains bind AMP and GSH and they inhibit transport by directly interacting with the ion-transporter module. Taken together, we propose that KefC is activated by detachment of the RCK domains and that ion selectivity exploits the biophysical properties likewise adapted by K+-ion-channels.", "doi": "10.1038/s41467-024-49082-7", "pmid": "38834573", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11150392"}, {"db": "pii", "key": "10.1038/s41467-024-49082-7"}], "notes": [], "created": "2024-11-15T10:38:25.459Z", "modified": "2024-11-15T10:38:35.847Z"}, {"entity": "publication", "iuid": "733098b953924c518563f4dc3fc01f74", "links": {"self": {"href": "https://publications.scilifelab.se/publication/733098b953924c518563f4dc3fc01f74.json"}, "display": {"href": "https://publications.scilifelab.se/publication/733098b953924c518563f4dc3fc01f74"}}, "title": "Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers.", "authors": [{"family": "De Oliveira", "given": "Danilo Hirabae", "initials": "DH"}, {"family": "Gowda", "given": "Vasantha", "initials": "V"}, {"family": "Sparrman", "given": "Tobias", "initials": "T"}, {"family": "Gustafsson", "given": "Linnea", "initials": "L", "orcid": "0000-0002-8925-2815", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e3c43a438b24bb0a6c38e280b766139.json"}}, {"family": "Sanches Pires", "given": "Rodrigo", "initials": "R", "orcid": "0000-0001-6038-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/32b029c89af144d8ab7ca1baabde8779.json"}}, {"family": "Riekel", "given": "Christian", "initials": "C", "orcid": "0000-0003-2025-5118", "researcher": {"href": "https://publications.scilifelab.se/researcher/44f44f098f6e48a9ad23b720a27eb3d7.json"}}, {"family": "Barth", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5784-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d21e415961d4237a5dcea736ca54841.json"}}, {"family": "Lendel", "given": "Christofer", "initials": "C", "orcid": "0000-0001-9238-7246", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0ef7451c7d34882b04566aa12025d00.json"}}, {"family": "Hedhammar", "given": "My", "initials": "M", "orcid": "0000-0003-0140-419X", "researcher": {"href": "https://publications.scilifelab.se/researcher/061cceecaf0e4bed8efabca146e5b235.json"}}], "type": "journal article", "published": "2024-05-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "4670", "issn-l": "2041-1723"}, "abstract": "The major ampullate Spidroin 1 (MaSp1) is the main protein of the dragline spider silk. The C-terminal (CT) domain of MaSp1 is crucial for the self-assembly into fibers but the details of how it contributes to the fiber formation remain unsolved. Here we exploit the fact that the CT domain can form silk-like fibers by itself to gain knowledge about this transition. Structural investigations of fibers from recombinantly produced CT domain from E. australis MaSp1 reveal an \u03b1-helix to \u03b2-sheet transition upon fiber formation and highlight the helix No4 segment as most likely to initiate the structural conversion. This prediction is corroborated by the finding that a peptide corresponding to helix No4 has the ability of pH-induced conversion into \u03b2-sheets and self-assembly into nanofibrils. Our results provide structural information about the CT domain in fiber form and clues about its role in triggering the structural conversion of spidroins during fiber assembly.", "doi": "10.1038/s41467-024-49111-5", "pmid": "38821983", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11143275"}, {"db": "pii", "key": "10.1038/s41467-024-49111-5"}], "notes": [], "created": "2024-11-13T19:35:22.452Z", "modified": "2025-10-17T13:03:52.955Z"}, {"entity": "publication", "iuid": "d4db29d93f3144d29d7dcb207e5ed083", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4db29d93f3144d29d7dcb207e5ed083.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4db29d93f3144d29d7dcb207e5ed083"}}, "title": "Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer.", "authors": [{"family": "Wang", "given": "Kang", "initials": "K", "orcid": "0000-0001-5401-1803", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bdb074014224910b0f34e893b15e660.json"}}, {"family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "researcher": {"href": "https://publications.scilifelab.se/researcher/f786763a4a0e4b5bb865ebb199eb6ca2.json"}}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Sarhan", "given": "Dhifaf", "initials": "D", "orcid": "0000-0003-0196-4496", "researcher": {"href": "https://publications.scilifelab.se/researcher/22a235fbd46e49ba953ea339b8b8a507.json"}}, {"family": "Sun", "given": "Yizhe", "initials": "Y"}, {"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications.scilifelab.se/researcher/0921ab7566514fb0a3cd0daf2baabe6e.json"}}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG", "orcid": "0000-0001-9919-4471", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8506000a14a4a5286aa557ab67ef690.json"}}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A"}, {"family": "Liu", "given": "Xingrong", "initials": "X"}, {"family": "Loman", "given": "Niklas", "initials": "N"}, {"family": "Hedenfalk", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6840-3397", "researcher": {"href": "https://publications.scilifelab.se/researcher/c852ed467120466f91d053425077c0b8.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd38f4f7704144ed9e3f869e197175e6.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J", "orcid": "0000-0003-2013-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0d4d98261f41268c76dd91345a1857.json"}}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af6483a77d746c2b838414692f1f4ed.json"}}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications.scilifelab.se/researcher/7683c0280e9b4145aa54305fb08936a7.json"}}], "type": "journal article", "published": "2024-05-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3837", "issn-l": "2041-1723"}, "abstract": "Although metabolic reprogramming within tumor cells and tumor microenvironment (TME) is well described in breast cancer, little is known about how the interplay of immune state and cancer metabolism evolves during treatment. Here, we characterize the immunometabolic profiles of tumor tissue samples longitudinally collected from individuals with breast cancer before, during and after neoadjuvant chemotherapy (NAC) using proteomics, genomics and histopathology. We show that the pre-, on-treatment and dynamic changes of the immune state, tumor metabolic proteins and tumor cell gene expression profiling-based metabolic phenotype are associated with treatment response. Single-cell/nucleus RNA sequencing revealed distinct tumor and immune cell states in metabolism between cold and hot tumors. Potential drivers of NAC based on above analyses were validated in vitro. In summary, the study shows that the interaction of tumor-intrinsic metabolic states and TME is associated with treatment outcome, supporting the concept of targeting tumor metabolism for immunoregulation.", "doi": "10.1038/s41467-024-47932-y", "pmid": "38714665", "labels": {"Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11076527"}, {"db": "pii", "key": "10.1038/s41467-024-47932-y"}], "notes": [], "created": "2024-11-27T13:26:50.334Z", "modified": "2024-11-27T13:26:50.959Z"}, {"entity": "publication", "iuid": "b2a30a6011bb47659582e0b4cdce2803", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2a30a6011bb47659582e0b4cdce2803.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2a30a6011bb47659582e0b4cdce2803"}}, "title": "The hinge-engineered IgG1-IgG3 hybrid subclass IgGh47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies.", "authors": [{"family": "Izadi", "given": "Arman", "initials": "A", "orcid": "0000-0002-0262-1017", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d6f1927cfc643818a0a3a1b8602af14.json"}}, {"family": "Karami", "given": "Yasaman", "initials": "Y", "orcid": "0000-0001-8413-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/a71f08b3f3794e66b7adae400c14f142.json"}}, {"family": "Bratanis", "given": "Eleni", "initials": "E", "orcid": "0000-0002-0636-6658", "researcher": {"href": "https://publications.scilifelab.se/researcher/c935953f81fc4d8eb6a9b9ddb7774c1b.json"}}, {"family": "Wrighton", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-3378-7925", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b5821cc01364325a4b9fe177e7f6e33.json"}}, {"family": "Khakzad", "given": "Hamed", "initials": "H", "orcid": "0000-0002-8556-0650", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7b030c1452c4dc9b430deffdf493e6f.json"}}, {"family": "Nyblom", "given": "Maria", "initials": "M"}, {"family": "Olofsson", "given": "Berit", "initials": "B", "orcid": "0009-0009-0602-2183", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ad483473b044b7dbc7e6c61ef1c0a73.json"}}, {"family": "Happonen", "given": "Lotta", "initials": "L", "orcid": "0000-0002-5922-4549", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7af0a6faf6a48e7937a644be472edbe.json"}}, {"family": "Tang", "given": "Di", "initials": "D", "orcid": "0000-0001-6323-9375", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2a27467c4094d9f8d8f8402efa333f4.json"}}, {"family": "Sundwall", "given": "Martin", "initials": "M", "orcid": "0000-0002-0114-6613", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0080c10aa64cd7b073813c8ebc0bc7.json"}}, {"family": "Godzwon", "given": "Magdalena", "initials": "M"}, {"family": "Chao", "given": "Yashuan", "initials": "Y", "orcid": "0000-0002-0295-3142", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed7bd7c821754977ba516c3e1c04eceb.json"}}, {"family": "Toledo", "given": "Alejandro Gomez", "initials": "AG", "orcid": "0000-0002-2103-7158", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e9d9a5e2dc148c9bcdc07f2b4a17ebc.json"}}, {"family": "Schmidt", "given": "Tobias", "initials": "T", "orcid": "0000-0001-9943-4121", "researcher": {"href": "https://publications.scilifelab.se/researcher/2eba2593dde24540a7d70aa3b593e4fc.json"}}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}, {"family": "Nilges", "given": "Michael", "initials": "M", "orcid": "0000-0002-1451-8092", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebfd5336137d4eaabde8f4f9baed470a.json"}}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad3c999da10c41e4a3afda2718815083.json"}}, {"family": "Bahnan", "given": "Wael", "initials": "W"}, {"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", "orcid": "0000-0001-9885-9312", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e99f34fb854beb8d810b05fe941057.json"}}, {"family": "Nordenfelt", "given": "Pontus", "initials": "P", "orcid": "0000-0002-9481-9951", "researcher": {"href": "https://publications.scilifelab.se/researcher/7aa3418ab23a4ec48c037d6d6ddea5b5.json"}}], "type": "journal article", "published": "2024-04-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3600", "issn-l": "2041-1723"}, "abstract": "Streptococcus pyogenes can cause invasive disease with high mortality despite adequate antibiotic treatments. To address this unmet need, we have previously generated an opsonic IgG1 monoclonal antibody, Ab25, targeting the bacterial M protein. Here, we engineer the IgG2-4 subclasses of Ab25. Despite having reduced binding, the IgG3 version promotes stronger phagocytosis of bacteria. Using atomic simulations, we show that IgG3's Fc tail has extensive movement in 3D space due to its extended hinge region, possibly facilitating interactions with immune cells. We replaced the hinge of IgG1 with four different IgG3-hinge segment subclasses, IgGhxx. Hinge-engineering does not diminish binding as with IgG3 but enhances opsonic function, where a 47 amino acid hinge is comparable to IgG3 in function. IgGh47 shows improved protection against S. pyogenes in a systemic infection mouse model, suggesting that IgGh47 has promise as a preclinical therapeutic candidate. Importantly, the enhanced opsonic function of IgGh47 is generalizable to diverse S. pyogenes strains from clinical isolates. We generated IgGh47 versions of anti-SARS-CoV-2 mAbs to broaden the biological applicability, and these also exhibit strongly enhanced opsonic function compared to the IgG1 subclass. The improved function of the IgGh47 subclass in two distant biological systems provides new insights into antibody function.", "doi": "10.1038/s41467-024-47928-8", "pmid": "38678029", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11055898"}, {"db": "pii", "key": "10.1038/s41467-024-47928-8"}], "notes": [], "created": "2024-11-08T09:49:22.468Z", "modified": "2025-10-17T13:05:07.370Z"}, {"entity": "publication", "iuid": "ee820c6646394d0990ac6db415b16eaf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee820c6646394d0990ac6db415b16eaf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee820c6646394d0990ac6db415b16eaf"}}, "title": "Loss of NEDD8 in cancer cells causes vulnerability to immune checkpoint blockade in triple-negative breast cancer.", "authors": [{"family": "Papakyriacou", "given": "Irineos", "initials": "I"}, {"family": "Kutkaite", "given": "Ginte", "initials": "G", "orcid": "0000-0002-2918-294X", "researcher": {"href": "https://publications.scilifelab.se/researcher/96c8d90120fa425a894860cb51a6fc72.json"}}, {"family": "R\u00fabies Bed\u00f3s", "given": "Marta", "initials": "M", "orcid": "0000-0003-0949-4329", "researcher": {"href": "https://publications.scilifelab.se/researcher/55c1f1948ce743af9f612f9eb8f3ad57.json"}}, {"family": "Nagarajan", "given": "Divya", "initials": "D"}, {"family": "Alford", "given": "Liam P", "initials": "LP"}, {"family": "Menden", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-0267-5792", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f8aaf0128004196a7b07998f0b3f7c2.json"}}, {"family": "Mao", "given": "Yumeng", "initials": "Y", "orcid": "0000-0001-6142-6628", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1deb3c4a48d402c9f98be90ce96d98d.json"}}], "type": "journal article", "published": "2024-04-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3581", "issn-l": "2041-1723"}, "abstract": "Immune checkpoint blockade therapy aims to activate the immune system to eliminate cancer cells. However, clinical benefits are only recorded in a subset of patients. Here, we leverage genome-wide CRISPR/Cas9 screens in a Tumor-Immune co-Culture System focusing on triple-negative breast cancer (TNBC). We reveal that NEDD8 loss in cancer cells causes a vulnerability to nivolumab (anti-PD-1). Genetic deletion of NEDD8 only delays cell division initially but cell proliferation is unaffected after recovery. Since the NEDD8 gene is commonly essential, we validate this observation with additional CRISPR screens and uncover enhanced immunogenicity in NEDD8 deficient cells using proteomics. In female immunocompetent mice, PD-1 blockade lacks efficacy against established EO771 breast cancer tumors. In contrast, we observe tumor regression mediated by CD8+ T cells against Nedd8 deficient EO771 tumors after PD-1 blockade. In essence, we provide evidence that NEDD8 is conditionally essential in TNBC and presents as a synergistic drug target for PD-1/L1 blockade therapy.", "doi": "10.1038/s41467-024-47987-x", "pmid": "38678024", "labels": {"CRISPR Functional Genomics": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11055868"}, {"db": "pii", "key": "10.1038/s41467-024-47987-x"}], "notes": [], "created": "2024-05-02T15:40:31.944Z", "modified": "2024-11-25T10:16:48.659Z"}, {"entity": "publication", "iuid": "fd3d1863ce1e404cbd824f5ec6d4f971", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd3d1863ce1e404cbd824f5ec6d4f971.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd3d1863ce1e404cbd824f5ec6d4f971"}}, "title": "The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids.", "authors": [{"family": "Holmberg", "given": "Sandra M", "initials": "SM", "orcid": "0000-0002-6290-2590", "researcher": {"href": "https://publications.scilifelab.se/researcher/7815cc43d5ee43b1b83aea417aaa7734.json"}}, {"family": "Feeney", "given": "Rachel H", "initials": "RH", "orcid": "0000-0002-7686-6279", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1e816ac8a604325b1a878b4a33dbc44.json"}}, {"family": "Prasoodanan P K", "given": "Vishnu", "initials": "V"}, {"family": "Pu\u00e9rtolas-Balint", "given": "Fabiola", "initials": "F", "orcid": "0000-0003-4898-5673", "researcher": {"href": "https://publications.scilifelab.se/researcher/52b9ecd971f64eb89d05334fe9e975bb.json"}}, {"family": "Singh", "given": "Dhirendra K", "initials": "DK"}, {"family": "Wongkuna", "given": "Supapit", "initials": "S", "orcid": "0000-0003-3766-5391", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1a42a392e642dbaaee6d5dbf6b1ef5.json"}}, {"family": "Zandbergen", "given": "Lotte", "initials": "L"}, {"family": "Hauner", "given": "Hans", "initials": "H"}, {"family": "Brandl", "given": "Beate", "initials": "B"}, {"family": "Nieminen", "given": "Anni I", "initials": "AI", "orcid": "0000-0001-8999-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/eddac59bcacb4eff9a44249cf2305779.json"}}, {"family": "Skurk", "given": "Thomas", "initials": "T", "orcid": "0000-0002-6875-1658", "researcher": {"href": "https://publications.scilifelab.se/researcher/f312550741dc4fe6b6c3064d2d8b83b7.json"}}, {"family": "Schroeder", "given": "Bjoern O", "initials": "BO", "orcid": "0000-0002-6716-8284", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2c57653fc214cbcbb242cbbc524d517.json"}}], "type": "journal article", "published": "2024-04-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3502", "issn-l": "2041-1723"}, "abstract": "Beneficial gut bacteria are indispensable for developing colonic mucus and fully establishing its protective function against intestinal microorganisms. Low-fiber diet consumption alters the gut bacterial configuration and disturbs this microbe-mucus interaction, but the specific bacteria and microbial metabolites responsible for maintaining mucus function remain poorly understood. By using human-to-mouse microbiota transplantation and ex vivo analysis of colonic mucus function, we here show as a proof-of-concept that individuals who increase their daily dietary fiber intake can improve the capacity of their gut microbiota to prevent diet-mediated mucus defects. Mucus growth, a critical feature of intact colonic mucus, correlated with the abundance of the gut commensal Blautia, and supplementation of Blautia coccoides to mice confirmed its mucus-stimulating capacity. Mechanistically, B. coccoides stimulated mucus growth through the production of the short-chain fatty acids propionate and acetate via activation of the short-chain fatty acid receptor Ffar2, which could serve as a new target to restore mucus growth during mucus-associated lifestyle diseases.", "doi": "10.1038/s41467-024-47594-w", "pmid": "38664378", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11045866"}, {"db": "pii", "key": "10.1038/s41467-024-47594-w"}], "notes": [], "created": "2024-11-25T10:16:38.017Z", "modified": "2024-11-25T10:16:38.245Z"}, {"entity": "publication", "iuid": "8acfeb033c3c459a9cff10bf8bb576c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9"}}, "title": "High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue.", "authors": [{"family": "Zhang", "given": "Ning", "initials": "N"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Verron", "given": "Quentin", "initials": "Q"}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Bellomo", "given": "Sara E", "initials": "SE"}, {"family": "Longo", "given": "Gabriel M C", "initials": "GMC", "orcid": "0000-0003-2028-1068", "researcher": {"href": "https://publications.scilifelab.se/researcher/2afe47a108d0451ebaf8269a0f18eb84.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Su", "given": "Peng", "initials": "P"}, {"family": "Han", "given": "Bo", "initials": "B"}, {"family": "Wang", "given": "Wanzhong", "initials": "W"}, {"family": "Onorato", "given": "Sofia", "initials": "S"}, {"family": "Grassini", "given": "Dora", "initials": "D"}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Giordano", "given": "Silvia", "initials": "S", "orcid": "0000-0003-1854-1086", "researcher": {"href": "https://publications.scilifelab.se/researcher/7072fc7ce1d44d0392b4ba3da82a16fb.json"}}, {"family": "Yang", "given": "Qifeng", "initials": "Q"}, {"family": "Sapino", "given": "Anna", "initials": "A", "orcid": "0000-0003-3542-9571", "researcher": {"href": "https://publications.scilifelab.se/researcher/b77045e1832b4267b330df154cbe80db.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Druid", "given": "Henrik", "initials": "H", "orcid": "0000-0002-9198-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bb7f9c706b451f9813bae017e0fad7.json"}}, {"family": "Roukos", "given": "Vassilis", "initials": "V", "orcid": "0000-0002-5065-3937", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5da3165b15741ff967e77618bd96cc1.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-04-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3475", "issn-l": "2041-1723"}, "abstract": "Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we perform multi-region, single-cell DNA sequencing to characterize the SCNA landscape across tumor-rich and normal tissue in two male patients with localized prostate cancer. We identify two distinct karyotypes: 'pseudo-diploid' cells harboring few SCNAs and highly aneuploid cells. Pseudo-diploid cells form numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones. In contrast, aneuploid cells do not form subclones and are detected throughout the prostate, including normal tissue regions. Highly localized pseudo-diploid subclones are confined within tumor-rich regions and carry deletions in multiple tumor-suppressor genes. Our study reveals that SCNAs are widespread in normal and tumor regions across the prostate in localized prostate cancer patients and suggests that a subset of pseudo-diploid cells drive tumorigenesis in the aging prostate.", "doi": "10.1038/s41467-024-47664-z", "pmid": "38658552", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11043350"}, {"db": "pii", "key": "10.1038/s41467-024-47664-z"}], "notes": [], "created": "2024-05-17T09:16:39.558Z", "modified": "2024-11-25T10:16:43.449Z"}, {"entity": "publication", "iuid": "675fb48cfa4a4d6b957ebee8caba3428", "links": {"self": {"href": "https://publications.scilifelab.se/publication/675fb48cfa4a4d6b957ebee8caba3428.json"}, "display": {"href": "https://publications.scilifelab.se/publication/675fb48cfa4a4d6b957ebee8caba3428"}}, "title": "Molecular patterns of resistance to immune checkpoint blockade in melanoma.", "authors": [{"family": "Lauss", "given": "Martin", "initials": "M"}, {"family": "Phung", "given": "Bengt", "initials": "B"}, {"family": "Borch", "given": "Troels Holz", "initials": "TH"}, {"family": "Harbst", "given": "Katja", "initials": "K", "orcid": "0000-0002-8225-1510", "researcher": {"href": "https://publications.scilifelab.se/researcher/daa5f87bad0d4e798c406854993eb7f0.json"}}, {"family": "Kaminska", "given": "Kamila", "initials": "K"}, {"family": "Ebbesson", "given": "Anna", "initials": "A"}, {"family": "Hedenfalk", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6840-3397", "researcher": {"href": "https://publications.scilifelab.se/researcher/c852ed467120466f91d053425077c0b8.json"}}, {"family": "Yuan", "given": "Joan", "initials": "J"}, {"family": "Nielsen", "given": "Kari", "initials": "K", "orcid": "0000-0002-7363-0455", "researcher": {"href": "https://publications.scilifelab.se/researcher/202c6d3ce63340c4bbcca6dab9e320b1.json"}}, {"family": "Ingvar", "given": "Christian", "initials": "C"}, {"family": "Carneiro", "given": "Ana", "initials": "A"}, {"family": "Isaksson", "given": "Karolin", "initials": "K"}, {"family": "Pietras", "given": "Kristian", "initials": "K", "orcid": "0000-0001-6738-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/5be0a3ec07654822a91df964eab1d6e4.json"}}, {"family": "Svane", "given": "Inge Marie", "initials": "IM", "orcid": "0000-0002-9451-6037", "researcher": {"href": "https://publications.scilifelab.se/researcher/c83b2b9332ba40fd90e1bce8eafa4c40.json"}}, {"family": "Donia", "given": "Marco", "initials": "M", "orcid": "0000-0003-4966-9752", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f6af601067419786f6632b185f1fbe.json"}}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-6865-0147", "researcher": {"href": "https://publications.scilifelab.se/researcher/0099af8e34f64a37a35392d32a0d357e.json"}}], "type": "journal article", "published": "2024-04-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3075", "issn-l": "2041-1723"}, "abstract": "Immune checkpoint blockade (ICB) has improved outcome for patients with metastatic melanoma but not all benefit from treatment. Several immune- and tumor intrinsic features are associated with clinical response at baseline. However, we need to further understand the molecular changes occurring during development of ICB resistance. Here, we collect biopsies from a cohort of 44 patients with melanoma after progression on anti-CTLA4 or anti-PD1 monotherapy. Genetic alterations of antigen presentation and interferon gamma signaling pathways are observed in approximately 25% of ICB resistant cases. Anti-CTLA4 resistant lesions have a sustained immune response, including immune-regulatory features, as suggested by multiplex spatial and T cell receptor (TCR) clonality analyses. One anti-PD1 resistant lesion harbors a distinct immune cell niche, however, anti-PD1 resistant tumors are generally immune poor with non-expanded TCR clones. Such immune poor microenvironments are associated with melanoma cells having a de-differentiated phenotype lacking expression of MHC-I molecules. In addition, anti-PD1 resistant tumors have reduced fractions of PD1+ CD8+ T cells as compared to ICB na\u00efve metastases. Collectively, these data show the complexity of ICB resistance and highlight differences between anti-CTLA4 and anti-PD1 resistance that may underlie differential clinical outcomes of therapy sequence and combination.", "doi": "10.1038/s41467-024-47425-y", "pmid": "38594286", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11004175"}, {"db": "pii", "key": "10.1038/s41467-024-47425-y"}], "notes": [], "created": "2024-11-25T10:16:32.724Z", "modified": "2025-11-07T13:30:42.010Z"}, {"entity": "publication", "iuid": "179851889d0d4a39a94c941c6743b19e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/179851889d0d4a39a94c941c6743b19e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/179851889d0d4a39a94c941c6743b19e"}}, "title": "Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.", "authors": [{"family": "Eisele", "given": "A S", "initials": "AS", "orcid": "0000-0001-8376-4089", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0018e1152f649dbab46ce240c5d7736.json"}}, {"family": "Tarbier", "given": "M", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications.scilifelab.se/researcher/662e96c24ee6442898ec2caab1eec25d.json"}}, {"family": "Dormann", "given": "A A", "initials": "AA"}, {"family": "Pelechano", "given": "V", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e906e11225514a289df84a2145f807fe.json"}}, {"family": "Suter", "given": "D M", "initials": "DM", "orcid": "0000-0001-5644-4899", "researcher": {"href": "https://publications.scilifelab.se/researcher/f233935422f64f96891cb2ca8e662d62.json"}}], "type": "journal article", "published": "2024-03-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "2744", "issn-l": "2041-1723"}, "abstract": "Assigning single cell transcriptomes to cellular lineage trees by lineage tracing has transformed our understanding of differentiation during development, regeneration, and disease. However, lineage tracing is technically demanding, often restricted in time-resolution, and most scRNA-seq datasets are devoid of lineage information. Here we introduce Gene Expression Memory-based Lineage Inference (GEMLI), a computational tool allowing to robustly identify small to medium-sized cell lineages solely from scRNA-seq datasets. GEMLI allows to study heritable gene expression, to discriminate symmetric and asymmetric cell fate decisions and to reconstruct individual multicellular structures from pooled scRNA-seq datasets. In human breast cancer biopsies, GEMLI reveals previously unknown gene expression changes at the onset of cancer invasiveness. The universal applicability of GEMLI allows studying the role of small cell lineages in a wide range of physiological and pathological contexts, notably in vivo. GEMLI is available as an R package on GitHub ( https://github.com/UPSUTER/GEMLI ).", "doi": "10.1038/s41467-024-47158-y", "pmid": "38553478", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10980719"}, {"db": "pii", "key": "10.1038/s41467-024-47158-y"}], "notes": [], "created": "2024-11-25T10:16:27.515Z", "modified": "2024-11-25T10:16:27.613Z"}, {"entity": "publication", "iuid": "74bf3dccedb8436ea8a05bef8c89d201", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74bf3dccedb8436ea8a05bef8c89d201.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74bf3dccedb8436ea8a05bef8c89d201"}}, "title": "Ion mobility-tandem mass spectrometry of mucin-type O-glycans.", "authors": [{"family": "Bechtella", "given": "Le\u00efla", "initials": "L", "orcid": "0000-0002-7354-3108", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bd4eb095d624ac1959d8dc16150ab8c.json"}}, {"family": "Chunsheng", "given": "Jin", "initials": "J", "orcid": "0000-0002-0229-102X", "researcher": {"href": "https://publications.scilifelab.se/researcher/458804f3f7274b8a9efe7a90469d0e56.json"}}, {"family": "Fentker", "given": "Kerstin", "initials": "K", "orcid": "0009-0005-0437-1049", "researcher": {"href": "https://publications.scilifelab.se/researcher/991a0c7c9fdf4187835f12fb4c68bdf0.json"}}, {"family": "Ert\u00fcrk", "given": "G\u00fcney R", "initials": "GR"}, {"family": "Safferthal", "given": "Marc", "initials": "M", "orcid": "0009-0006-9267-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6e1dbee77d342be876a1d7fba2732e0.json"}}, {"family": "Polewski", "given": "\u0141ukasz", "initials": "\u0141", "orcid": "0009-0001-9802-2528", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4d3ffc3ab2345478fad082496479704.json"}}, {"family": "G\u00f6tze", "given": "Michael", "initials": "M", "orcid": "0000-0003-4001-2324", "researcher": {"href": "https://publications.scilifelab.se/researcher/f049e7388fe7421099b5f38c675d3962.json"}}, {"family": "Graeber", "given": "Simon Y", "initials": "SY", "orcid": "0000-0002-1666-8924", "researcher": {"href": "https://publications.scilifelab.se/researcher/f803b57dfcbb4f3b9b60ae9947e10930.json"}}, {"family": "Vos", "given": "Ga\u00ebl M", "initials": "GM"}, {"family": "Struwe", "given": "Weston B", "initials": "WB", "orcid": "0000-0003-0594-226X", "researcher": {"href": "https://publications.scilifelab.se/researcher/193bc52c108c43d6aed7a796261202a9.json"}}, {"family": "Mall", "given": "Marcus A", "initials": "MA", "orcid": "0000-0002-4057-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a5827fb0517424b974964081ea15d19.json"}}, {"family": "Mertins", "given": "Philipp", "initials": "P", "orcid": "0000-0002-2245-528X", "researcher": {"href": "https://publications.scilifelab.se/researcher/83ca1dab03d24278ae7cddad4944f830.json"}}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Pagel", "given": "Kevin", "initials": "K", "orcid": "0000-0001-8054-4718", "researcher": {"href": "https://publications.scilifelab.se/researcher/398849274b4e45f6a6c6997026f7c5a1.json"}}], "type": "journal article", "published": "2024-03-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "2611", "issn-l": "2041-1723"}, "abstract": "The dense O-glycosylation of mucins plays an important role in the defensive properties of the mucus hydrogel. Aberrant glycosylation is often correlated with inflammation and pathology such as COPD, cancer, and Crohn's disease. The inherent complexity of glycans and the diversity in the O-core structure constitute fundamental challenges for the analysis of mucin-type O-glycans. Due to coexistence of multiple isomers, multidimensional workflows such as LC-MS are required. To separate the highly polar carbohydrates, porous graphitized carbon is often used as a stationary phase. However, LC-MS workflows are time-consuming and lack reproducibility. Here we present a rapid alternative for separating and identifying O-glycans released from mucins based on trapped ion mobility mass spectrometry. Compared to established LC-MS, the acquisition time is reduced from an hour to two minutes. To test the validity, the developed workflow was applied to sputum samples from cystic fibrosis patients to map O-glycosylation features associated with disease.", "doi": "10.1038/s41467-024-46825-4", "pmid": "38521783", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10960840"}, {"db": "pii", "key": "10.1038/s41467-024-46825-4"}], "notes": [], "created": "2024-11-27T15:32:35.327Z", "modified": "2024-11-27T15:35:26.455Z"}, {"entity": "publication", "iuid": "b2cb8fa709924974859cd7b23995e51b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2cb8fa709924974859cd7b23995e51b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2cb8fa709924974859cd7b23995e51b"}}, "title": "Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.", "authors": [{"family": "ElBeck", "given": "Zaher", "initials": "Z", "orcid": "0000-0002-2073-7988", "researcher": {"href": "https://publications.scilifelab.se/researcher/9abd18865bda4f53a1521974e6f9e46b.json"}}, {"family": "Hossain", "given": "Mohammad Bakhtiar", "initials": "MB", "orcid": "0000-0002-4251-1912", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7e91850afd945dfb91a396d843194f4.json"}}, {"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/058b6ec6390a41929dc1288f71de63d4.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Karlsson", "given": "Fredrik", "initials": "F"}, {"family": "Lindgren", "given": "Julia", "initials": "J", "orcid": "0000-0002-3566-2069", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3c465ab67924de69b7248e3acff0978.json"}}, {"family": "Walentinsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-8100-6866", "researcher": {"href": "https://publications.scilifelab.se/researcher/991f835d5cb84de6ad619c50d81d5dd1.json"}}, {"family": "Koppenh\u00f6fer", "given": "Dominique", "initials": "D", "orcid": "0000-0001-5807-9645", "researcher": {"href": "https://publications.scilifelab.se/researcher/24ab61b179f940a8853619f5a817e06a.json"}}, {"family": "Jarvis", "given": "Rebecca", "initials": "R", "orcid": "0000-0001-7583-6548", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bfea4b88ef64bebbcdf8839e4428864.json"}}, {"family": "B\u00fcrli", "given": "Roland", "initials": "R"}, {"family": "Jamier", "given": "Tanguy", "initials": "T", "orcid": "0000-0003-3014-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/eab91541aeb24d9face573899b25b19c.json"}}, {"family": "Franssen", "given": "Elske", "initials": "E"}, {"family": "Firth", "given": "Mike", "initials": "M"}, {"family": "Degasperi", "given": "Andrea", "initials": "A", "orcid": "0000-0001-6879-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/c074b0dc07bb4b779a4c20e190854594.json"}}, {"family": "Bendtsen", "given": "Claus", "initials": "C", "orcid": "0000-0002-8338-987X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21acfbf749d4f1ca0a8be226d4696ce.json"}}, {"family": "Menzies", "given": "Robert I", "initials": "RI"}, {"family": "Streckfuss-B\u00f6meke", "given": "Katrin", "initials": "K"}, {"family": "Kohlhaas", "given": "Michael", "initials": "M"}, {"family": "Nickel", "given": "Alexander G", "initials": "AG"}, {"family": "Lund", "given": "Lars H", "initials": "LH"}, {"family": "Maack", "given": "Christoph", "initials": "C", "orcid": "0000-0003-3694-4559", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee3dedbf152c4f24847d6d83b15ed1c3.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Betsholtz", "given": "Christer", "initials": "C", "orcid": "0000-0002-8494-971X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a00cfe9d521047f280978d84d7dcf1b3.json"}}], "type": "journal article", "published": "2024-03-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "2358"}, "abstract": "While excessive production of reactive oxygen species (ROS) is a characteristic hallmark of numerous diseases, clinical approaches that ameliorate oxidative stress have been unsuccessful. Here, utilizing multi-omics, we demonstrate that in cardiomyocytes, mitochondrial isocitrate dehydrogenase (IDH2) constitutes a major antioxidative defense mechanism. Paradoxically reduced expression of IDH2 associated with ventricular eccentric hypertrophy is counterbalanced by an increase in the enzyme activity. We unveil redox-dependent sex dimorphism, and extensive mutual regulation of the antioxidative activities of IDH2 and NRF2 by a feedforward network that involves 2-oxoglutarate and L-2-hydroxyglutarate and mediated in part through unconventional hydroxy-methylation of cytosine residues present in introns. Consequently, conditional targeting of ROS in a murine model of heart failure improves cardiac function in sex- and phenotype-dependent manners. Together, these insights may explain why previous attempts to treat heart failure with antioxidants have been unsuccessful and open new approaches to personalizing and, thereby, improving such treatment.", "doi": "10.1038/s41467-024-46384-8", "pmid": "38509128", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "BioImage Informatics": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10954618"}, {"db": "pii", "key": "10.1038/s41467-024-46384-8"}], "notes": [], "created": "2024-03-21T08:13:07.086Z", "modified": "2024-11-13T10:25:41.474Z"}, {"entity": "publication", "iuid": "cf7ea31e683f4c45835678b143349f84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf7ea31e683f4c45835678b143349f84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf7ea31e683f4c45835678b143349f84"}}, "title": "fhl2b mediates extraocular muscle protection in zebrafish models of muscular dystrophies and its ectopic expression ameliorates affected body muscles.", "authors": [{"family": "Dennhag", "given": "Nils", "initials": "N", "orcid": "0000-0003-0885-6586", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf9ac3fa9a504dcb877d144438ed5161.json"}}, {"family": "Kahsay", "given": "Abraha", "initials": "A", "orcid": "0000-0003-1518-9785", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b2b788339fd463fa1a2c777bcf87948.json"}}, {"family": "Nissen", "given": "Itzel", "initials": "I", "orcid": "0000-0002-0741-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4f02fa8059145bc9b17d0c1ef978ee2.json"}}, {"family": "Nord", "given": "Hanna", "initials": "H", "orcid": "0000-0002-6098-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/22d8cc445c6b41b4a8488d620995d8c3.json"}}, {"family": "Chermenina", "given": "Maria", "initials": "M"}, {"family": "Liu", "given": "Jiao", "initials": "J"}, {"family": "Arner", "given": "Anders", "initials": "A"}, {"family": "Liu", "given": "Jing-Xia", "initials": "JX", "orcid": "0000-0003-2508-9921", "researcher": {"href": "https://publications.scilifelab.se/researcher/353db8f1d54e4d0ca55b64ef7b0249d7.json"}}, {"family": "Backman", "given": "Ludvig J", "initials": "LJ"}, {"family": "Remeseiro", "given": "Silvia", "initials": "S", "orcid": "0000-0001-5343-007X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb0bc2da415e4c6aafc3f55fba80a12b.json"}}, {"family": "von Hofsten", "given": "Jonas", "initials": "J", "orcid": "0000-0003-3730-1790", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee9e4dc7b9a44b818e4c10aea633a934.json"}}, {"family": "Pedrosa Domell\u00f6f", "given": "Fatima", "initials": "F", "orcid": "0000-0002-0648-4996", "researcher": {"href": "https://publications.scilifelab.se/researcher/30143e3ec79a4f16b82495ce9e453750.json"}}], "type": "journal article", "published": "2024-03-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1950", "issn-l": "2041-1723"}, "abstract": "In muscular dystrophies, muscle fibers loose integrity and die, causing significant suffering and premature death. Strikingly, the extraocular muscles (EOMs) are spared, functioning well despite the disease progression. Although EOMs have been shown to differ from body musculature, the mechanisms underlying this inherent resistance to muscle dystrophies remain unknown. Here, we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscles in zebrafish via transcriptomic profiling. We show that the LIM-protein Fhl2 is increased in response to the knockout of desmin, plectin and obscurin, cytoskeletal proteins whose knockout causes different muscle dystrophies, and contributes to disease protection of the EOMs. Moreover, we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje, significantly improving their survival. Therefore, Fhl2 is a protective agent and a candidate target gene for therapy of muscular dystrophies.", "doi": "10.1038/s41467-024-46187-x", "pmid": "38431640", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10908798"}, {"db": "pii", "key": "10.1038/s41467-024-46187-x"}], "notes": [], "created": "2024-03-14T11:06:34.815Z", "modified": "2024-11-25T10:16:22.287Z"}, {"entity": "publication", "iuid": "f67599f2d15a446e95242e93aa672435", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f67599f2d15a446e95242e93aa672435.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f67599f2d15a446e95242e93aa672435"}}, "title": "Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer.", "authors": [{"family": "Fonseca", "given": "Nicolette M", "initials": "NM"}, {"family": "Maurice-Dror", "given": "Corinne", "initials": "C"}, {"family": "Herberts", "given": "Cameron", "initials": "C", "orcid": "0000-0002-9929-8374", "researcher": {"href": "https://publications.scilifelab.se/researcher/9042c9215bdd4bdcabd35a3c9fae37bc.json"}}, {"family": "Tu", "given": "Wilson", "initials": "W"}, {"family": "Fan", "given": "William", "initials": "W"}, {"family": "Murtha", "given": "Andrew J", "initials": "AJ", "orcid": "0000-0003-3980-7656", "researcher": {"href": "https://publications.scilifelab.se/researcher/79541aa76b734ae08142618a7ed7bdf8.json"}}, {"family": "Kollmannsberger", "given": "Catarina", "initials": "C"}, {"family": "Kwan", "given": "Edmond M", "initials": "EM"}, {"family": "Parekh", "given": "Karan", "initials": "K"}, {"family": "Sch\u00f6nlau", "given": "Elena", "initials": "E"}, {"family": "Bernales", "given": "Cecily Q", "initials": "CQ"}, {"family": "Donnellan", "given": "Gr\u00e1inne", "initials": "G"}, {"family": "Ng", "given": "Sarah W S", "initials": "SWS", "orcid": "0000-0002-7647-6940", "researcher": {"href": "https://publications.scilifelab.se/researcher/07ca842f21534e6dbbfdded47272a56a.json"}}, {"family": "Sumiyoshi", "given": "Takayuki", "initials": "T"}, {"family": "Vergidis", "given": "Joanna", "initials": "J"}, {"family": "Noonan", "given": "Krista", "initials": "K"}, {"family": "Finch", "given": "Daygen L", "initials": "DL"}, {"family": "Zulfiqar", "given": "Muhammad", "initials": "M"}, {"family": "Miller", "given": "Stacy", "initials": "S"}, {"family": "Parimi", "given": "Sunil", "initials": "S"}, {"family": "Lavoie", "given": "Jean-Michel", "initials": "JM"}, {"family": "Hardy", "given": "Edward", "initials": "E"}, {"family": "Soleimani", "given": "Maryam", "initials": "M"}, {"family": "Nappi", "given": "Lucia", "initials": "L"}, {"family": "Eigl", "given": "Bernhard J", "initials": "BJ", "orcid": "0000-0003-1653-6929", "researcher": {"href": "https://publications.scilifelab.se/researcher/f58d358ee19e454e80f2c7e71ffc7f6d.json"}}, {"family": "Kollmannsberger", "given": "Christian", "initials": "C"}, {"family": "Taavitsainen", "given": "Sinja", "initials": "S", "orcid": "0000-0001-7559-9853", "researcher": {"href": "https://publications.scilifelab.se/researcher/b89ff2079b6a4671827a92ed71a28b5e.json"}}, {"family": "Nykter", "given": "Matti", "initials": "M", "orcid": "0000-0001-6956-2843", "researcher": {"href": "https://publications.scilifelab.se/researcher/467356981d4b4379b913ae4088cb451e.json"}}, {"family": "Tolmeijer", "given": "Sofie H", "initials": "SH", "orcid": "0000-0003-4066-885X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3e2ba79e6d346f3a731e1a56d152fe3.json"}}, {"family": "Boerrigter", "given": "Emmy", "initials": "E", "orcid": "0000-0002-3041-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/c30a4a271429406aa5278eb8c4a27fb1.json"}}, {"family": "Mehra", "given": "Niven", "initials": "N", "orcid": "0000-0002-4794-1831", "researcher": {"href": "https://publications.scilifelab.se/researcher/77734ec9c50e41ac8ffab2fc6a7d0074.json"}}, {"family": "van Erp", "given": "Nielka P", "initials": "NP"}, {"family": "De Laere", "given": "Bram", "initials": "B"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H", "orcid": "0000-0002-1073-2753", "researcher": {"href": "https://publications.scilifelab.se/researcher/813ff17beb984198a103e3dbe61bae7e.json"}}, {"family": "Khalaf", "given": "Daniel J", "initials": "DJ"}, {"family": "Annala", "given": "Matti", "initials": "M"}, {"family": "Chi", "given": "Kim N", "initials": "KN"}, {"family": "Wyatt", "given": "Alexander W", "initials": "AW", "orcid": "0000-0003-2399-0329", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bd075e69bcb494696a624e89d153fd9.json"}}], "type": "journal article", "published": "2024-02-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1828", "issn-l": "2041-1723"}, "abstract": "No consensus strategies exist for prognosticating metastatic castration-resistant prostate cancer (mCRPC). Circulating tumor DNA fraction (ctDNA%) is increasingly reported by commercial and laboratory tests but its utility for risk stratification is unclear. Here, we intersect ctDNA%, treatment outcomes, and clinical characteristics across 738 plasma samples from 491 male mCRPC patients from two randomized multicentre phase II trials and a prospective province-wide blood biobanking program. ctDNA% correlates with serum and radiographic metrics of disease burden and is highest in patients with liver metastases. ctDNA% strongly predicts overall survival, progression-free survival, and treatment response independent of therapeutic context and outperformed established prognostic clinical factors. Recognizing that ctDNA-based biomarker genotyping is limited by low ctDNA% in some patients, we leverage the relationship between clinical prognostic factors and ctDNA% to develop a clinically-interpretable machine-learning tool that predicts whether a patient has sufficient ctDNA% for informative ctDNA genotyping (available online: https://www.ctDNA.org ). Our results affirm ctDNA% as an actionable tool for patient risk stratification and provide a practical framework for optimized biomarker testing.", "doi": "10.1038/s41467-024-45475-w", "pmid": "38418825", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10902374"}, {"db": "pii", "key": "10.1038/s41467-024-45475-w"}], "notes": [], "created": "2024-11-20T19:58:48.442Z", "modified": "2024-11-20T19:58:50.139Z"}, {"entity": "publication", "iuid": "80c75635458e45f883e80acd6b1c4fc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1"}}, "title": "scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.", "authors": [{"family": "Chen", "given": "Jinxin Phaedo", "initials": "JP", "orcid": "0000-0002-0729-5214", "researcher": {"href": "https://publications.scilifelab.se/researcher/25fca568763f4476b53bdf7297689a2e.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Wu", "given": "Honggui", "initials": "H", "orcid": "0000-0001-7880-0591", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9697e391fe493ab4b26d2c40e7565f.json"}}, {"family": "Chen", "given": "Chong", "initials": "C", "orcid": "0000-0002-6787-0495", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8a6778068124d7cb3dd1aca6e7cc0ec.json"}}, {"family": "Della Chiara", "given": "Giulia", "initials": "G", "orcid": "0000-0001-5211-3814", "researcher": {"href": "https://publications.scilifelab.se/researcher/3410a95b5b674fa69d2c83b479d345a8.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Georgiadis", "given": "Konstantinos L", "initials": "KL"}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM"}, {"family": "Virdi", "given": "Mohit", "initials": "M"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Bellomo", "given": "Sara Erika", "initials": "SE"}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1768", "issn-l": "2041-1723"}, "abstract": "Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.", "doi": "10.1038/s41467-024-45972-y", "pmid": "38409079", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10897160"}, {"db": "pii", "key": "10.1038/s41467-024-45972-y"}], "notes": [], "created": "2024-03-14T11:05:03.191Z", "modified": "2024-04-26T09:08:57.780Z"}, {"entity": "publication", "iuid": "72c0bcbc6ed645e4a14dd4aa365fac7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72c0bcbc6ed645e4a14dd4aa365fac7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72c0bcbc6ed645e4a14dd4aa365fac7e"}}, "title": "Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF.", "authors": [{"family": "Kvedaraite", "given": "Egle", "initials": "E", "orcid": "0000-0001-5308-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/78502177bad3453a8d3ed96d4ad334ac.json"}}, {"family": "Lourda", "given": "Magda", "initials": "M", "orcid": "0000-0003-3155-1123", "researcher": {"href": "https://publications.scilifelab.se/researcher/64d9a0bc6b5d4039af5bc308a97eaad6.json"}}, {"family": "Mouratidou", "given": "Natalia", "initials": "N"}, {"family": "D\u00fcking", "given": "Tim", "initials": "T", "orcid": "0000-0002-4347-7648", "researcher": {"href": "https://publications.scilifelab.se/researcher/6acbe8ae50d94479a37dda5f37336422.json"}}, {"family": "Padhi", "given": "Avinash", "initials": "A"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Sinha", "given": "Indranil", "initials": "I", "orcid": "0000-0002-2513-5927", "researcher": {"href": "https://publications.scilifelab.se/researcher/970cda1bb71d4ae1b36cc5628023f7d4.json"}}, {"family": "Xagoraris", "given": "Ioanna", "initials": "I"}, {"family": "Kokkinou", "given": "Efthymia", "initials": "E"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Weigel", "given": "Whitney", "initials": "W"}, {"family": "Hartwig", "given": "Olga", "initials": "O", "orcid": "0000-0001-5016-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a50cebd9533432e80d2fd284c9137eb.json"}}, {"family": "Santos", "given": "Telma E", "initials": "TE"}, {"family": "Soini", "given": "Tea", "initials": "T"}, {"family": "Van Acker", "given": "Aline", "initials": "A"}, {"family": "Rahkonen", "given": "Nelly", "initials": "N"}, {"family": "Flodstr\u00f6m Tullberg", "given": "Malin", "initials": "M", "orcid": "0000-0003-2685-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6d04afbe8141c2b9297854de64dab8.json"}}, {"family": "Ringqvist", "given": "Emma", "initials": "E"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Jorns", "given": "Carl", "initials": "C", "orcid": "0000-0001-7727-8113", "researcher": {"href": "https://publications.scilifelab.se/researcher/59d387bd893f45bdb3663a0ef3aae88a.json"}}, {"family": "Lindforss", "given": "Ulrik", "initials": "U"}, {"family": "Nordenvall", "given": "Caroline", "initials": "C"}, {"family": "Stamper", "given": "Christopher T", "initials": "CT"}, {"family": "Unnersj\u00f6-Jess", "given": "David", "initials": "D", "orcid": "0000-0002-4162-0973", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d475fc7a52a46e4abe984191c5b5b5f.json"}}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Nadisauskaite", "given": "Ruta", "initials": "R"}, {"family": "Jansson", "given": "Jessica", "initials": "J"}, {"family": "Vandamme", "given": "Niels", "initials": "N"}, {"family": "Sorini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-6803-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/975173f37f144f06b236817e224de7f0.json"}}, {"family": "Grundeken", "given": "Marijke Elise", "initials": "ME", "orcid": "0000-0001-6915-0339", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64d9493eccd419d8c8908dea19602df.json"}}, {"family": "Rolandsdotter", "given": "Helena", "initials": "H"}, {"family": "Rassidakis", "given": "George", "initials": "G"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}, {"family": "Idestr\u00f6m", "given": "Maja", "initials": "M"}, {"family": "Eulitz", "given": "Stefan", "initials": "S"}, {"family": "Arnell", "given": "Henrik", "initials": "H"}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J", "orcid": "0000-0002-1119-0976", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcca878a7f314944bf1a4290cfd5d71d.json"}}, {"family": "Henter", "given": "Jan-Inge", "initials": "JI", "orcid": "0000-0002-0629-2126", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1a0d663491c4665a32a612e423dff1b.json"}}, {"family": "Svensson", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1695-7934", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3185cf86534a96983b39dd93df454a.json"}}], "type": "journal article", "published": "2024-02-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1752", "issn-l": "2041-1723"}, "abstract": "Stromal cells support epithelial cell and immune cell homeostasis and play an important role in inflammatory bowel disease (IBD) pathogenesis. Here, we quantify the stromal response to inflammation in pediatric IBD and reveal subset-specific inflammatory responses across colon segments and intestinal layers. Using data from a murine dynamic gut injury model and human ex vivo transcriptomic, protein and spatial analyses, we report that PDGFRA+CD142-/low fibroblasts and monocytes/macrophages co-localize in the intestine. In primary human fibroblast-monocyte co-cultures, intestinal PDGFRA+CD142-/low fibroblasts foster monocyte transition to CCR2+CD206+ macrophages through granulocyte-macrophage colony-stimulating factor (GM-CSF). Monocyte-derived CCR2+CD206+ cells from co-cultures have a phenotype similar to intestinal CCR2+CD206+ macrophages from newly diagnosed pediatric IBD patients, with high levels of PD-L1 and low levels of GM-CSF receptor. The study describes subset-specific changes in stromal responses to inflammation and suggests that the intestinal stroma guides intestinal macrophage differentiation.", "doi": "10.1038/s41467-024-46076-3", "pmid": "38409190", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10897309"}, {"db": "pii", "key": "10.1038/s41467-024-46076-3"}], "notes": [], "created": "2024-03-14T11:08:33.238Z", "modified": "2024-10-31T10:36:41.256Z"}, {"entity": "publication", "iuid": "9ed2bc4b12d14102b404494a0702f799", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ed2bc4b12d14102b404494a0702f799.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ed2bc4b12d14102b404494a0702f799"}}, "title": "The role of extracellular vesicle fusion with target cells in triggering systemic inflammation.", "authors": [{"family": "Papareddy", "given": "Praveen", "initials": "P", "orcid": "0000-0002-3872-478X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bf855ae83ea40e69cd21ec66d482ae1.json"}}, {"family": "Tapken", "given": "Ines", "initials": "I", "orcid": "0000-0002-2358-0031", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0c26b93a3b94a0b89fe54ffd5c8fe97.json"}}, {"family": "Kroh", "given": "Keshia", "initials": "K", "orcid": "0000-0002-9166-0711", "researcher": {"href": "https://publications.scilifelab.se/researcher/37f74c5287c747c7b5154239172f03dc.json"}}, {"family": "Varma Bhongir", "given": "Ravi Kiran", "initials": "RK", "orcid": "0000-0001-6648-1781", "researcher": {"href": "https://publications.scilifelab.se/researcher/721676e52aeb46cd863060886c4e1011.json"}}, {"family": "Rahman", "given": "Milladur", "initials": "M", "orcid": "0000-0002-8883-4848", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7eb7c317b604e018cf31f593cfe1695.json"}}, {"family": "Baumgarten", "given": "Maria", "initials": "M"}, {"family": "Cim", "given": "Eda Irem", "initials": "EI"}, {"family": "Gy\u00f6rffy", "given": "Lilla", "initials": "L"}, {"family": "Smeds", "given": "Emanuel", "initials": "E", "orcid": "0000-0002-9689-826X", "researcher": {"href": "https://publications.scilifelab.se/researcher/82e0136645f04ee29122ae9ee54fd15a.json"}}, {"family": "Neumann", "given": "Ariane", "initials": "A", "orcid": "0000-0002-8636-730X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4b9fa9e063e4152a667e51fbbe599a9.json"}}, {"family": "Veerla", "given": "Srinivas", "initials": "S", "orcid": "0000-0001-7328-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/c203a0b3112f4f499ccc79db3e47b303.json"}}, {"family": "Olinder", "given": "Jon", "initials": "J"}, {"family": "Thorlacus", "given": "Henrik", "initials": "H"}, {"family": "Ryden", "given": "Cecilia", "initials": "C"}, {"family": "Bartakova", "given": "Eva", "initials": "E"}, {"family": "Holub", "given": "Michal", "initials": "M", "orcid": "0000-0003-1894-2605", "researcher": {"href": "https://publications.scilifelab.se/researcher/6661a0c478534b3b87d88fd5ec3d4146.json"}}, {"family": "Herwald", "given": "Heiko", "initials": "H", "orcid": "0000-0002-8111-2842", "researcher": {"href": "https://publications.scilifelab.se/researcher/2be5b2b7c94942b1824ceea02744d5dd.json"}}], "type": "journal article", "published": "2024-02-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1150", "issn-l": "2041-1723"}, "abstract": "Extracellular vesicles (EVs) play a crucial role in intercellular communication by transferring bioactive molecules from donor to recipient cells. As a result, EV fusion leads to the modulation of cellular functions and has an impact on both physiological and pathological processes in the recipient cell. This study explores the impact of EV fusion on cellular responses to inflammatory signaling. Our findings reveal that fusion renders non-responsive cells susceptible to inflammatory signaling, as evidenced by increased NF-\u03baB activation and the release of inflammatory mediators. Syntaxin-binding protein 1 is essential for the merge and activation of intracellular signaling. Subsequent analysis show that EVs transfer their functionally active receptors to target cells, making them prone to an otherwise unresponsive state. EVs in complex with their agonist, require no further stimulation of the target cells to trigger mobilization of NF-\u03baB. While receptor antagonists were unable to inhibit NF-\u03baB activation, blocking of the fusion between EVs and their target cells with heparin mitigated inflammation in mice challenged with EVs.", "doi": "10.1038/s41467-024-45125-1", "pmid": "38326335", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10850166"}, {"db": "pii", "key": "10.1038/s41467-024-45125-1"}], "notes": [], "created": "2024-11-27T15:36:01.426Z", "modified": "2024-11-27T15:36:02.077Z"}, {"entity": "publication", "iuid": "cc8ed21067814ac09b593e3f722678d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc8ed21067814ac09b593e3f722678d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc8ed21067814ac09b593e3f722678d2"}}, "title": "Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1.", "authors": [{"family": "Bacic", "given": "Luka", "initials": "L"}, {"family": "Gaullier", "given": "Guillaume", "initials": "G", "orcid": "0000-0003-3405-6021", "researcher": {"href": "https://publications.scilifelab.se/researcher/26bde2020c164cff8216338fb2d6d652.json"}}, {"family": "Mohapatra", "given": "Jugal", "initials": "J"}, {"family": "Mao", "given": "Guanzhong", "initials": "G"}, {"family": "Brackmann", "given": "Klaus", "initials": "K"}, {"family": "Panfilov", "given": "Mikhail", "initials": "M", "orcid": "0000-0003-2875-7315", "researcher": {"href": "https://publications.scilifelab.se/researcher/58d227ea91aa4b90915a7e2afeb9283e.json"}}, {"family": "Liszczak", "given": "Glen", "initials": "G"}, {"family": "Sabantsev", "given": "Anton", "initials": "A", "orcid": "0000-0002-8559-8894", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae73150df15e4730be688fc5137a1389.json"}}, {"family": "Deindl", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-6807-8654", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e45e8288a3445e2b346f29b73141738.json"}}], "type": "journal article", "published": "2024-02-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1000", "issn-l": "2041-1723"}, "abstract": "The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited by PARP1/PARP2 and their co-factor HPF1. ALC1 has emerged as a cancer drug target, but how it is recruited to ADP-ribosylated nucleosomes to affect their positioning near DNA breaks is unknown. Here we find that PARP1/HPF1 preferentially initiates ADP-ribosylation on the histone H2B tail closest to the DNA break. To dissect the consequences of such asymmetry, we generate nucleosomes with a defined ADP-ribosylated H2B tail on one side only. The cryo-electron microscopy structure of ALC1 bound to such an asymmetric nucleosome indicates preferential engagement on one side. Using single-molecule FRET, we demonstrate that this asymmetric recruitment gives rise to directed sliding away from the DNA linker closest to the ADP-ribosylation site. Our data suggest a mechanism by which ALC1 slides nucleosomes away from a DNA break to render it more accessible to repair factors.", "doi": "10.1038/s41467-024-45237-8", "pmid": "38307862", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10837151"}, {"db": "pii", "key": "10.1038/s41467-024-45237-8"}], "notes": [], "created": "2024-02-06T08:28:40.080Z", "modified": "2025-10-25T10:15:14.050Z"}, {"entity": "publication", "iuid": "bd2469b856a34c23bf93587d768559f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd2469b856a34c23bf93587d768559f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd2469b856a34c23bf93587d768559f2"}}, "title": "A two-step activation mechanism enables mast cells to differentiate their response between extracellular and invasive enterobacterial infection.", "authors": [{"family": "von Beek", "given": "Christopher", "initials": "C", "orcid": "0000-0001-6310-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ea7730832f4f45ae6583076d90418a.json"}}, {"family": "Fahlgren", "given": "Anna", "initials": "A"}, {"family": "Geiser", "given": "Petra", "initials": "P", "orcid": "0000-0003-2785-4201", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0bf10f41dc4698b19288809bae2dd6.json"}}, {"family": "Di Martino", "given": "Maria Letizia", "initials": "ML", "orcid": "0000-0002-9491-4000", "researcher": {"href": "https://publications.scilifelab.se/researcher/708eae058cb3494f8407574a666a16f0.json"}}, {"family": "Lindahl", "given": "Otto", "initials": "O", "orcid": "0000-0001-7518-9483", "researcher": {"href": "https://publications.scilifelab.se/researcher/78053dd357c3435ba53aff83f06f28a4.json"}}, {"family": "Prensa", "given": "Grisna I", "initials": "GI", "orcid": "0009-0002-7101-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d030d78925948d993999b66e1959acc.json"}}, {"family": "Mendez-Enriquez", "given": "Erika", "initials": "E", "orcid": "0000-0002-2114-2812", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae73474be904a638ec13a8f704a9154.json"}}, {"family": "Eriksson", "given": "Jens", "initials": "J", "orcid": "0000-0002-8945-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/b94e7f542841474d86d53aa48958f870.json"}}, {"family": "Hallgren", "given": "Jenny", "initials": "J", "orcid": "0000-0002-3685-5364", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe8b929dbe60446f96db17a5eb2ba6f3.json"}}, {"family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "researcher": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}}, {"family": "Pejler", "given": "Gunnar", "initials": "G"}, {"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": "2024-01-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "904", "issn-l": "2041-1723"}, "abstract": "Mast cells localize to mucosal tissues and contribute to innate immune defense against infection. How mast cells sense, differentiate between, and respond to bacterial pathogens remains a topic of ongoing debate. Using the prototype enteropathogen Salmonella Typhimurium (S.Tm) and other related enterobacteria, here we show that mast cells can regulate their cytokine secretion response to distinguish between extracellular and invasive bacterial infection. Tissue-invasive S.Tm and mast cells colocalize in the mouse gut during acute Salmonella infection. Toll-like Receptor 4 (TLR4) sensing of extracellular S.Tm, or pure lipopolysaccharide, causes a modest induction of cytokine transcripts and proteins, including IL-6, IL-13, and TNF. By contrast, type-III-secretion-system-1 (TTSS-1)-dependent S.Tm invasion of both mouse and human mast cells triggers rapid and potent inflammatory gene expression and >100-fold elevated cytokine secretion. The S.Tm TTSS-1 effectors SopB, SopE, and SopE2 here elicit a second activation signal, including Akt phosphorylation downstream of effector translocation, which combines with TLR activation to drive the full-blown mast cell response. Supernatants from S.Tm-infected mast cells boost macrophage survival and maturation from bone-marrow progenitors. Taken together, this study shows that mast cells can differentiate between extracellular and host-cell invasive enterobacteria via a two-step activation mechanism and tune their inflammatory output accordingly.", "doi": "10.1038/s41467-024-45057-w", "pmid": "38291037", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10828507"}, {"db": "pii", "key": "10.1038/s41467-024-45057-w"}], "notes": [], "created": "2024-03-21T12:10:55.423Z", "modified": "2024-03-21T12:10:55.804Z"}, {"entity": "publication", "iuid": "149b1072f1304f8789c9949d7b997492", "links": {"self": {"href": "https://publications.scilifelab.se/publication/149b1072f1304f8789c9949d7b997492.json"}, "display": {"href": "https://publications.scilifelab.se/publication/149b1072f1304f8789c9949d7b997492"}}, "title": "Apoptosis-mediated ADAM10 activation removes a mucin barrier promoting T cell efferocytosis.", "authors": [{"family": "Drexhage", "given": "Linnea Z", "initials": "LZ", "orcid": "0000-0001-7679-4466", "researcher": {"href": "https://publications.scilifelab.se/researcher/0773a617433d46ceb0ea431f60ee59d1.json"}}, {"family": "Zhang", "given": "Shengpan", "initials": "S", "orcid": "0000-0002-1134-7101", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfdfec78321d488eae1c131484d6a1f0.json"}}, {"family": "Dupont", "given": "Maeva", "initials": "M"}, {"family": "Ragaller", "given": "Franziska", "initials": "F", "orcid": "0000-0002-4148-262X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ead87aca17f476b9febf3f020567c4b.json"}}, {"family": "Sjule", "given": "Ellen", "initials": "E", "orcid": "0000-0003-0166-2826", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e0fd8926ef843a0a8db936df7209107.json"}}, {"family": "Cabezas-Caballero", "given": "Jose", "initials": "J", "orcid": "0000-0001-9871-3428", "researcher": {"href": "https://publications.scilifelab.se/researcher/460c76524cf748efabf39b555b34f9ee.json"}}, {"family": "Deimel", "given": "Lachlan P", "initials": "LP", "orcid": "0000-0003-3803-871X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc322e4e39da4a769c515a5c77b844cf.json"}}, {"family": "Robertson", "given": "Helen", "initials": "H", "orcid": "0000-0002-9190-8799", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1cbf72e1e184e91917ffe3208e9095c.json"}}, {"family": "Russell", "given": "Rebecca A", "initials": "RA", "orcid": "0000-0002-6517-6483", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ce1e727941a4626823fc4d4db07088c.json"}}, {"family": "Dushek", "given": "Omer", "initials": "O", "orcid": "0000-0001-5847-5226", "researcher": {"href": "https://publications.scilifelab.se/researcher/444272de68ea4e5fb05ca044d92fee24.json"}}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Karaji", "given": "Niloofar", "initials": "N"}, {"family": "Sattentau", "given": "Quentin J", "initials": "QJ", "orcid": "0000-0001-7170-1937", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78243e447114e179d1aef437cb35717.json"}}], "type": "journal article", "published": "2024-01-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "541", "issn-l": "2041-1723"}, "abstract": "Efferocytic clearance of apoptotic cells in general, and T cells in particular, is required for tissue and immune homeostasis. Transmembrane mucins are extended glycoproteins highly expressed in the cell glycocalyx that function as a barrier to phagocytosis. Whether and how mucins may be regulated during cell death to facilitate efferocytic corpse clearance is not well understood. Here we show that normal and transformed human T cells express a subset of mucins which are rapidly and selectively removed from the cell surface during apoptosis. This process is mediated by the ADAM10 sheddase, the activity of which is associated with XKR8-catalyzed flipping of phosphatidylserine to the outer leaflet of the plasma membrane. Mucin clearance enhances uptake of apoptotic T cells by macrophages, confirming mucins as an enzymatically-modulatable barrier to efferocytosis. Together these findings demonstrate a glycocalyx regulatory pathway with implications for therapeutic intervention in the clearance of normal and transformed apoptotic T cells.", "doi": "10.1038/s41467-023-44619-8", "pmid": "38225245", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-023-44619-8"}], "notes": [], "created": "2024-01-16T06:21:10.968Z", "modified": "2024-01-16T06:21:11.640Z"}, {"entity": "publication", "iuid": "5e2eb91347d34701b54d4c5dbe67d2c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e2eb91347d34701b54d4c5dbe67d2c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e2eb91347d34701b54d4c5dbe67d2c1"}}, "title": "Nuclear Hsp104 safeguards the dormant translation machinery during quiescence.", "authors": [{"family": "Kohler", "given": "Verena", "initials": "V", "orcid": "0000-0002-1241-162X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a12e1c1d4e71468c99fa454c7c49b72b.json"}}, {"family": "Kohler", "given": "Andreas", "initials": "A", "orcid": "0000-0001-6571-2162", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8159b879db1414f9583ce2b3184cd23.json"}}, {"family": "Berglund", "given": "Lisa Larsson", "initials": "LL"}, {"family": "Hao", "given": "Xinxin", "initials": "X", "orcid": "0000-0001-5758-6290", "researcher": {"href": "https://publications.scilifelab.se/researcher/36931f6141fe452bad02e5f576fca10e.json"}}, {"family": "Gersing", "given": "Sarah", "initials": "S"}, {"family": "Imhof", "given": "Axel", "initials": "A", "orcid": "0000-0003-2993-8249", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0e2b7576e984458839c000e40c0900b.json"}}, {"family": "Nystr\u00f6m", "given": "Thomas", "initials": "T", "orcid": "0000-0001-5489-2903", "researcher": {"href": "https://publications.scilifelab.se/researcher/de24db2a24cd451db3b8e6151957601d.json"}}, {"family": "H\u00f6\u00f6g", "given": "Johanna L", "initials": "JL", "orcid": "0000-0003-2162-3816", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1eaedff964f4060ae6e69f59cad4521.json"}}, {"family": "Ott", "given": "Martin", "initials": "M"}, {"family": "Andr\u00e9asson", "given": "Claes", "initials": "C", "orcid": "0000-0001-8948-0685", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4cf1de8575d409b821467bf515c3af6.json"}}, {"family": "B\u00fcttner", "given": "Sabrina", "initials": "S", "orcid": "0000-0002-2786-8542", "researcher": {"href": "https://publications.scilifelab.se/researcher/6be7c476049b4f3497d187cba3daad77.json"}}], "type": "journal article", "published": "2024-01-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "315", "issn-l": "2041-1723"}, "abstract": "The resilience of cellular proteostasis declines with age, which drives protein aggregation and compromises viability. The nucleus has emerged as a key quality control compartment that handles misfolded proteins produced by the cytosolic protein biosynthesis system. Here, we find that age-associated metabolic cues target the yeast protein disaggregase Hsp104 to the nucleus to maintain a functional nuclear proteome during quiescence. The switch to respiratory metabolism and the accompanying decrease in translation rates direct cytosolic Hsp104 to the nucleus to interact with latent translation initiation factor eIF2 and to suppress protein aggregation. Hindering Hsp104 from entering the nucleus in quiescent cells results in delayed re-entry into the cell cycle due to compromised resumption of protein synthesis. In sum, we report that cytosolic-nuclear partitioning of the Hsp104 disaggregase is a critical mechanism to protect the latent protein synthesis machinery during quiescence in yeast, ensuring the rapid restart of translation once nutrients are replenished.", "doi": "10.1038/s41467-023-44538-8", "pmid": "38182580", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10770042"}, {"db": "pii", "key": "10.1038/s41467-023-44538-8"}], "notes": [], "created": "2024-01-09T12:59:47.170Z", "modified": "2024-11-27T13:10:41.903Z"}, {"entity": "publication", "iuid": "b7eb97ccbb1e4b5ea42f76b086428147", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7eb97ccbb1e4b5ea42f76b086428147.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7eb97ccbb1e4b5ea42f76b086428147"}}, "title": "Blue-shift photoconversion of near-infrared fluorescent proteins for labeling and tracking in living cells and organisms.", "authors": [{"family": "Pennacchietti", "given": "Francesca", "initials": "F", "orcid": "0000-0003-1769-972X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ebc891d5d09473bba00fc49ca1c321b.json"}}, {"family": "Alvelid", "given": "Jonatan", "initials": "J", "orcid": "0000-0002-3554-9322", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf7f3ec8624f4cef96f96b3c28ffc6b8.json"}}, {"family": "Morales", "given": "Rodrigo A", "initials": "RA", "orcid": "0000-0003-4382-5777", "researcher": {"href": "https://publications.scilifelab.se/researcher/61802da2579446d5b2a73c4f06b9969e.json"}}, {"family": "Damenti", "given": "Martina", "initials": "M", "orcid": "0000-0002-4209-5381", "researcher": {"href": "https://publications.scilifelab.se/researcher/048f072498914ea9bc5fcc7d8ae0347e.json"}}, {"family": "Ollech", "given": "Dirk", "initials": "D", "orcid": "0000-0002-9490-7070", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f2a4dbad2c542bab727d53bcd065748.json"}}, {"family": "Oliinyk", "given": "Olena S", "initials": "OS"}, {"family": "Shcherbakova", "given": "Daria M", "initials": "DM"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}, {"family": "Verkhusha", "given": "Vladislav V", "initials": "VV"}, {"family": "Testa", "given": "Ilaria", "initials": "I", "orcid": "0000-0003-4005-4997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d8e8420dada49d6a4ef1da7a06e02f1.json"}}], "type": "journal article", "published": "2023-12-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8402", "issn-l": "2041-1723"}, "abstract": "Photolabeling of intracellular molecules is an invaluable approach to studying various dynamic processes in living cells with high spatiotemporal precision. Among fluorescent proteins, photoconvertible mechanisms and their products are in the visible spectrum (400-650 nm), limiting their in vivo and multiplexed applications. Here we report the phenomenon of near-infrared to far-red photoconversion in the miRFP family of near infrared fluorescent proteins engineered from bacterial phytochromes. This photoconversion is induced by near-infrared light through a non-linear process, further allowing optical sectioning. Photoconverted miRFP species emit fluorescence at 650 nm enabling photolabeling entirely performed in the near-infrared range. We use miRFPs as photoconvertible fluorescent probes to track organelles in live cells and in vivo, both with conventional and super-resolution microscopy. The spectral properties of miRFPs complement those of GFP-like photoconvertible proteins, allowing strategies for photoconversion and spectral multiplexed applications.", "doi": "10.1038/s41467-023-44054-9", "pmid": "38114484", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10730883"}, {"db": "pii", "key": "10.1038/s41467-023-44054-9"}], "notes": [], "created": "2024-01-10T11:23:28.249Z", "modified": "2024-01-10T11:23:28.386Z"}, {"entity": "publication", "iuid": "79c72c42ec3a4ac5a5ca948ca0fdc2ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79c72c42ec3a4ac5a5ca948ca0fdc2ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79c72c42ec3a4ac5a5ca948ca0fdc2ef"}}, "title": "Dissecting the genetic landscape of GPCR signaling through phenotypic profiling in C. elegans.", "authors": [{"family": "Pu", "given": "Longjun", "initials": "L"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Lu", "given": "Qiongxuan", "initials": "Q"}, {"family": "Nilsson", "given": "Lars", "initials": "L"}, {"family": "Philbrook", "given": "Alison", "initials": "A"}, {"family": "Pandey", "given": "Anjali", "initials": "A"}, {"family": "Zhao", "given": "Lina", "initials": "L"}, {"family": "Schendel", "given": "Robin van", "initials": "RV", "orcid": "0000-0001-7068-0679", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aa5a36e5b534bab8a04b4c8f040abb4.json"}}, {"family": "Koh", "given": "Alan", "initials": "A", "orcid": "0000-0002-9267-455X", "researcher": {"href": "https://publications.scilifelab.se/researcher/af8b3e661b9247bd866018357cef9436.json"}}, {"family": "Peres", "given": "Tanara V", "initials": "TV", "orcid": "0000-0003-0199-8653", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cb3594666cf4c298ca22e457ec20e28.json"}}, {"family": "Hashi", "given": "Weheliye H", "initials": "WH"}, {"family": "Myint", "given": "Si Lhyam", "initials": "SL"}, {"family": "Williams", "given": "Chloe", "initials": "C"}, {"family": "Gilthorpe", "given": "Jonathan D", "initials": "JD", "orcid": "0000-0002-6884-4774", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eb2a4f38fdc4e0db2516a17d9abdf06.json"}}, {"family": "Wai", "given": "Sun Nyunt", "initials": "SN", "orcid": "0000-0003-4793-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/261986c5cf8f48878b74c4f60cc7af69.json"}}, {"family": "Brown", "given": "Andre", "initials": "A"}, {"family": "Tijsterman", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8465-9002", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1e816845f6048e2a2c7dc29e9a13cdf.json"}}, {"family": "Sengupta", "given": "Piali", "initials": "P", "orcid": "0000-0001-7468-0035", "researcher": {"href": "https://publications.scilifelab.se/researcher/244628c8890d4399a0a98fb0f8bc5ae7.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Chen", "given": "Changchun", "initials": "C", "orcid": "0000-0003-2233-8996", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cfa009cd5bc4951bcf6d5f4265b2c68.json"}}], "type": "journal article", "published": "2023-12-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8410", "issn-l": "2041-1723"}, "abstract": "G protein-coupled receptors (GPCRs) mediate responses to various extracellular and intracellular cues. However, the large number of GPCR genes and their substantial functional redundancy make it challenging to systematically dissect GPCR functions in vivo. Here, we employ a CRISPR/Cas9-based approach, disrupting 1654 GPCR-encoding genes in 284 strains and mutating 152 neuropeptide-encoding genes in 38 strains in C. elegans. These two mutant libraries enable effective deorphanization of chemoreceptors, and characterization of receptors for neuropeptides in various cellular processes. Mutating a set of closely related GPCRs in a single strain permits the assignment of functions to GPCRs with functional redundancy. Our analyses identify a neuropeptide that interacts with three receptors in hypoxia-evoked locomotory responses, unveil a collection of regulators in pathogen-induced immune responses, and define receptors for the volatile food-related odorants. These results establish our GPCR and neuropeptide mutant libraries as valuable resources for the C. elegans community to expedite studies of GPCR signaling in multiple contexts.", "doi": "10.1038/s41467-023-44177-z", "pmid": "38110404", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10728192"}, {"db": "pii", "key": "10.1038/s41467-023-44177-z"}], "notes": [], "created": "2024-01-02T13:26:28.816Z", "modified": "2024-11-25T10:16:17.175Z"}, {"entity": "publication", "iuid": "abba2963b1494fd99261f53318783d0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abba2963b1494fd99261f53318783d0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abba2963b1494fd99261f53318783d0c"}}, "title": "CENP-A and CENP-B collaborate to create an open centromeric chromatin state.", "authors": [{"family": "Nagpal", "given": "Harsh", "initials": "H"}, {"family": "Ali-Ahmad", "given": "Ahmad", "initials": "A", "orcid": "0000-0002-9021-5405", "researcher": {"href": "https://publications.scilifelab.se/researcher/de1dff855d3a464ebfaa688560e1070f.json"}}, {"family": "Hirano", "given": "Yasuhiro", "initials": "Y", "orcid": "0000-0001-7339-4053", "researcher": {"href": "https://publications.scilifelab.se/researcher/62b67aa9b7ac42779562ace608d27ba2.json"}}, {"family": "Cai", "given": "Wei", "initials": "W", "orcid": "0000-0001-7482-7033", "researcher": {"href": "https://publications.scilifelab.se/researcher/93eaa15b823a48abb3f876db3e72bc5b.json"}}, {"family": "Halic", "given": "Mario", "initials": "M", "orcid": "0000-0002-0061-7372", "researcher": {"href": "https://publications.scilifelab.se/researcher/12af3cfa4f55436ea4fc7d64c378229e.json"}}, {"family": "Fukagawa", "given": "Tatsuo", "initials": "T", "orcid": "0000-0001-8564-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a66fb662b5440fb9e1116ecf15403cf.json"}}, {"family": "Sekuli\u0107", "given": "Nikolina", "initials": "N", "orcid": "0000-0002-8027-9114", "researcher": {"href": "https://publications.scilifelab.se/researcher/711df7e0192f4434a448deec7e5c1c14.json"}}, {"family": "Fierz", "given": "Beat", "initials": "B", "orcid": "0000-0002-2991-3044", "researcher": {"href": "https://publications.scilifelab.se/researcher/28e2af5e821949aea4ef24d1572be652.json"}}], "type": "journal article", "published": "2023-12-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8227", "issn-l": "2041-1723"}, "abstract": "Centromeres are epigenetically defined via the presence of the histone H3 variant CENP-A. Contacting CENP-A nucleosomes, the constitutive centromere associated network (CCAN) and the kinetochore assemble, connecting the centromere to spindle microtubules during cell division. The DNA-binding centromeric protein CENP-B is involved in maintaining centromere stability and, together with CENP-A, shapes the centromeric chromatin state. The nanoscale organization of centromeric chromatin is not well understood. Here, we use single-molecule fluorescence and cryoelectron microscopy (cryoEM) to show that CENP-A incorporation establishes a dynamic and open chromatin state. The increased dynamics of CENP-A chromatin create an opening for CENP-B DNA access. In turn, bound CENP-B further opens the chromatin fiber structure and induces nucleosomal DNA unwrapping. Finally, removal of CENP-A increases CENP-B mobility in cells. Together, our studies show that the two centromere-specific proteins collaborate to reshape chromatin structure, enabling the binding of centromeric factors and establishing a centromeric chromatin state.", "doi": "10.1038/s41467-023-43739-5", "pmid": "38086807", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10716449"}, {"db": "pii", "key": "10.1038/s41467-023-43739-5"}], "notes": [], "created": "2023-12-22T11:43:10.070Z", "modified": "2024-11-27T14:50:35.560Z"}, {"entity": "publication", "iuid": "cf4eea7dc9114c88a4492dde1a35c646", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf4eea7dc9114c88a4492dde1a35c646.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf4eea7dc9114c88a4492dde1a35c646"}}, "title": "Genes with epigenetic alterations in human pancreatic islets impact mitochondrial function, insulin secretion, and type 2 diabetes", "authors": [{"family": "R\u00f6nn", "given": "Tina", "initials": "T", "orcid": "0000-0001-7622-800X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d24f13a3d6e4538a6584634beabe5d3.json"}}, {"family": "Ofori", "given": "Jones K", "initials": "JK", "orcid": "0000-0001-6484-1544", "researcher": {"href": "https://publications.scilifelab.se/researcher/31b7b1843fd94a99b488eaf653c6385b.json"}}, {"family": "Perfilyev", "given": "Alexander", "initials": "A", "orcid": "0000-0003-1136-8946", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d86c6fc2d684b4dbc93c2c66e4c4b88.json"}}, {"family": "Hamilton", "given": "Alexander", "initials": "A", "orcid": "0000-0001-5203-9220", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f077dfd61a44eddb403c972994cd3e7.json"}}, {"family": "Pircs", "given": "Karolina", "initials": "K", "orcid": "0000-0001-8281-4785", "researcher": {"href": "https://publications.scilifelab.se/researcher/070f9eb7abde403697f7e8ba0f9ac40e.json"}}, {"family": "Eichelmann", "given": "Fabian", "initials": "F", "orcid": "0000-0002-3975-5596", "researcher": {"href": "https://publications.scilifelab.se/researcher/810ca03b2e8c4adf888cf694facbb38a.json"}}, {"family": "Garcia-Calzon", "given": "Sonia", "initials": "S"}, {"family": "Karagiannopoulos", "given": "Alexandros", "initials": "A", "orcid": "0000-0001-8458-1065", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8c0cfd9fd9741729f91d5dd554c199d.json"}}, {"family": "Stenlund", "given": "Hans", "initials": "H", "orcid": "0000-0001-9943-296X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5259d6369f564651ace11d8bff689535.json"}}, {"family": "Wendt", "given": "Anna", "initials": "A"}, {"family": "Volkov", "given": "Petr", "initials": "P"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}, {"family": "Mulder", "given": "Hindrik", "initials": "H"}, {"family": "Eliasson", "given": "Lena", "initials": "L", "orcid": "0000-0002-6467-5029", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6567e3b86e42c8bb5ef008b665f2de.json"}}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"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": "2023-12-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8040", "issn-l": "2041-1723"}, "abstract": "Epigenetic dysregulation may influence disease progression. Here we explore whether epigenetic alterations in human pancreatic islets impact insulin secretion and type 2 diabetes (T2D). In islets, 5,584 DNA methylation sites exhibit alterations in T2D cases versus controls and are associated with HbA1c in individuals not diagnosed with T2D. T2D-associated methylation changes are found in enhancers and regions bound by \u03b2-cell-specific transcription factors and associated with reduced expression of e.g. CABLES1, FOXP1, GABRA2, GLR1A, RHOT1, and TBC1D4. We find RHOT1 (MIRO1) to be a key regulator of insulin secretion in human islets. Rhot1-deficiency in \u03b2-cells leads to reduced insulin secretion, ATP/ADP ratio, mitochondrial mass, Ca2+, and respiration. Regulators of mitochondrial dynamics and metabolites, including L-proline, glycine, GABA, and carnitines, are altered in Rhot1-deficient \u03b2-cells. Islets from diabetic GK rats present Rhot1-deficiency. Finally, RHOT1methylation in blood is associated with future T2D. Together, individuals with T2D exhibit epigenetic alterations linked to mitochondrial dysfunction in pancreatic islets.", "doi": "10.1038/s41467-023-43719-9", "pmid": "38086799", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10716521"}, {"db": "pii", "key": "10.1038/s41467-023-43719-9"}], "notes": [], "created": "2024-01-10T09:59:46.931Z", "modified": "2025-10-17T13:03:13.252Z"}, {"entity": "publication", "iuid": "f3a2e9a2ed934057bcdb6be6711ac846", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3a2e9a2ed934057bcdb6be6711ac846.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3a2e9a2ed934057bcdb6be6711ac846"}}, "title": "Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes.", "authors": [{"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Pold", "given": "Grace", "initials": "G"}, {"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": "2023-12-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8249", "issn-l": "2041-1723"}, "abstract": "Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.", "doi": "10.1038/s41467-023-44022-3", "pmid": "38086813", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10716430"}, {"db": "pii", "key": "10.1038/s41467-023-44022-3"}], "notes": [], "created": "2024-11-25T10:16:12.005Z", "modified": "2024-11-25T10:16:12.056Z"}, {"entity": "publication", "iuid": "a6edd515f3214f8594dc78220571aa36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6edd515f3214f8594dc78220571aa36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6edd515f3214f8594dc78220571aa36"}}, "title": "The formation of the Indo-Pacific montane avifauna.", "authors": [{"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Kennedy", "given": "Jonathan David", "initials": "JD"}, {"family": "Pujolar", "given": "Jos\u00e9 Mart\u00edn", "initials": "JM"}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA", "orcid": "0000-0001-8940-456X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f54d4c39cdd74208ad03500bd22b7609.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": "2023-12-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8215", "issn-l": "2041-1723"}, "abstract": "The processes generating the earth's montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species' ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region's montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.", "doi": "10.1038/s41467-023-43964-y", "pmid": "38081809", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10713610"}, {"db": "pii", "key": "10.1038/s41467-023-43964-y"}], "notes": [], "created": "2024-01-02T13:39:08.815Z", "modified": "2024-11-25T10:16:06.008Z"}, {"entity": "publication", "iuid": "e51b393a38794d448b63eda5594d8adf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e51b393a38794d448b63eda5594d8adf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e51b393a38794d448b63eda5594d8adf"}}, "title": "Evaluation of circulating plasma proteins in breast cancer using Mendelian randomisation.", "authors": [{"family": "M\u00e4larstig", "given": "Anders", "initials": "A", "orcid": "0000-0003-2608-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70c845d32264b448e0b4631b826be6d.json"}}, {"family": "Grassmann", "given": "Felix", "initials": "F"}, {"family": "Dahl", "given": "Leo", "initials": "L", "orcid": "0000-0003-1492-3052", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4df506f315c4289935b935a503efd56.json"}}, {"family": "Dimitriou", "given": "Marios", "initials": "M", "orcid": "0000-0001-8362-2099", "researcher": {"href": "https://publications.scilifelab.se/researcher/531c153359bb400fb48c7324a3bd69ad.json"}}, {"family": "McLeod", "given": "Dianna", "initials": "D"}, {"family": "Gabrielson", "given": "Marike", "initials": "M"}, {"family": "Smith-Byrne", "given": "Karl", "initials": "K"}, {"family": "Thomas", "given": "Cecilia E", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1156f987764218af202efbd76c31fd.json"}}, {"family": "Huang", "given": "Tzu-Hsuan", "initials": "TH", "orcid": "0000-0003-0650-582X", "researcher": {"href": "https://publications.scilifelab.se/researcher/009096335007406698aba18720a4455a.json"}}, {"family": "Forsberg", "given": "Simon K G", "initials": "SKG", "orcid": "0000-0002-7451-9222", "researcher": {"href": "https://publications.scilifelab.se/researcher/e97a399d54a94d56aa6cbd62425e27f6.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P", "orcid": "0000-0001-7633-403X", "researcher": {"href": "https://publications.scilifelab.se/researcher/97fea086745a40e9a3a20baba08bb7b8.json"}}, {"family": "Ulfstedt", "given": "Mikael", "initials": "M"}, {"family": "Johansson", "given": "Mattias", "initials": "M"}, {"family": "Sokolov", "given": "Aleksandr V", "initials": "AV"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0001-5413-204X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b9eaa6a5dfc4ecf8bf82ece793cd457.json"}}], "type": "journal article", "published": "2023-11-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "7680", "issn-l": "2041-1723"}, "abstract": "Biomarkers for early detection of breast cancer may complement population screening approaches to enable earlier and more precise treatment. The blood proteome is an important source for biomarker discovery but so far, few proteins have been identified with breast cancer risk. Here, we measure 2929 unique proteins in plasma from 598 women selected from the Karolinska Mammography Project to explore the association between protein levels, clinical characteristics, and gene variants, and to identify proteins with a causal role in breast cancer. We present 812 cis-acting protein quantitative trait loci for 737 proteins which are used as instruments in Mendelian randomisation analyses of breast cancer risk. Of those, we present five proteins (CD160, DNPH1, LAYN, LRRC37A2 and TLR1) that show a potential causal role in breast cancer risk with confirmatory results in independent cohorts. Our study suggests that these proteins should be further explored as biomarkers and potential drug targets in breast cancer.", "doi": "10.1038/s41467-023-43485-8", "pmid": "37996402", "labels": {"Affinity Proteomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10667261"}, {"db": "pii", "key": "10.1038/s41467-023-43485-8"}], "notes": [], "created": "2023-11-29T18:54:00.962Z", "modified": "2024-01-16T13:48:31.653Z"}, {"entity": "publication", "iuid": "7d95af839fa143759ce68c732ed930c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d95af839fa143759ce68c732ed930c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d95af839fa143759ce68c732ed930c2"}}, "title": "The heat shock protein LarA activates the Lon protease in response to proteotoxic stress.", "authors": [{"family": "Omnus", "given": "Deike J", "initials": "DJ", "orcid": "0000-0002-4091-4291", "researcher": {"href": "https://publications.scilifelab.se/researcher/4012e43cedf04b19be7a7edfa227aa8f.json"}}, {"family": "Fink", "given": "Matthias J", "initials": "MJ", "orcid": "0000-0002-4620-2009", "researcher": {"href": "https://publications.scilifelab.se/researcher/16ee1108730641498bcf0d38b116cb18.json"}}, {"family": "Kallazhi", "given": "Aswathy", "initials": "A", "orcid": "0009-0003-4585-2792", "researcher": {"href": "https://publications.scilifelab.se/researcher/df59bcc8d7524fdfaad0b6b43abe4e86.json"}}, {"family": "Xandri Zaragoza", "given": "Maria", "initials": "M"}, {"family": "Leppert", "given": "Axel", "initials": "A", "orcid": "0000-0001-6223-3350", "researcher": {"href": "https://publications.scilifelab.se/researcher/e89c2b7f8a294cfdae4848e96be7520b.json"}}, {"family": "Landreh", "given": "Michael", "initials": "M", "orcid": "0000-0002-7958-4074", "researcher": {"href": "https://publications.scilifelab.se/researcher/87494f4204c04be9bce5e9ddcdc92d8a.json"}}, {"family": "Jonas", "given": "Kristina", "initials": "K", "orcid": "0000-0002-1469-4424", "researcher": {"href": "https://publications.scilifelab.se/researcher/3351b638c7904141b4ae20dd41929e26.json"}}], "type": "journal article", "published": "2023-11-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "7636", "issn-l": "2041-1723"}, "abstract": "The Lon protease is a highly conserved protein degradation machine that has critical regulatory and protein quality control functions in cells from the three domains of life. Here, we report the discovery of a \u03b1-proteobacterial heat shock protein, LarA, that functions as a dedicated Lon regulator. We show that LarA accumulates at the onset of proteotoxic stress and allosterically activates Lon-catalysed degradation of a large group of substrates through a five amino acid sequence at its C-terminus. Further, we find that high levels of LarA cause growth inhibition in a Lon-dependent manner and that Lon-mediated degradation of LarA itself ensures low LarA levels in the absence of stress. We suggest that the temporal LarA-dependent activation of Lon helps to meet an increased proteolysis demand in response to protein unfolding stress. Our study defines a regulatory interaction of a conserved protease with a heat shock protein, serving as a paradigm of how protease activity can be tuned under changing environmental conditions.", "doi": "10.1038/s41467-023-43385-x", "pmid": "37993443", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10665427"}, {"db": "pii", "key": "10.1038/s41467-023-43385-x"}], "notes": [], "created": "2023-11-29T12:37:38.523Z", "modified": "2023-11-29T12:37:38.620Z"}, {"entity": "publication", "iuid": "8bfe93edf9d64769a9d6fef06df316a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8bfe93edf9d64769a9d6fef06df316a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8bfe93edf9d64769a9d6fef06df316a3"}}, "title": "Development of mesothelioma-specific oncolytic immunotherapy enabled by immunopeptidomics of murine and human mesothelioma tumors.", "authors": [{"family": "Chiaro", "given": "Jacopo", "initials": "J"}, {"family": "Antignani", "given": "Gabriella", "initials": "G"}, {"family": "Feola", "given": "Sara", "initials": "S", "orcid": "0000-0002-4012-4310", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9d2c4168aa541b5ad9a7e5155dc1069.json"}}, {"family": "Feodoroff", "given": "Michaela", "initials": "M", "orcid": "0000-0002-6094-9838", "researcher": {"href": "https://publications.scilifelab.se/researcher/b828ef2f6621496cbc6ac77cc8413c14.json"}}, {"family": "Martins", "given": "Beatriz", "initials": "B"}, {"family": "Cojoc", "given": "Hanne", "initials": "H"}, {"family": "Russo", "given": "Salvatore", "initials": "S"}, {"family": "Fusciello", "given": "Manlio", "initials": "M", "orcid": "0000-0002-7166-3018", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c74e3317cd646c1989a49b281c3e8e7.json"}}, {"family": "Hamdan", "given": "Firas", "initials": "F", "orcid": "0000-0003-4678-7382", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f991da24d5c4c02945f0bfb614558a2.json"}}, {"family": "Ferrari", "given": "Valentina", "initials": "V"}, {"family": "Ciampi", "given": "Daniele", "initials": "D", "orcid": "0000-0001-6523-3049", "researcher": {"href": "https://publications.scilifelab.se/researcher/3161ddeb6095464fbd04afed3d7e56ee.json"}}, {"family": "Ilonen", "given": "Ilkka", "initials": "I", "orcid": "0000-0002-8149-3550", "researcher": {"href": "https://publications.scilifelab.se/researcher/8409282fff6b479daec8aa4e898a3aee.json"}}, {"family": "R\u00e4s\u00e4nen", "given": "Jari", "initials": "J"}, {"family": "M\u00e4yr\u00e4np\u00e4\u00e4", "given": "Mikko", "initials": "M", "orcid": "0000-0002-0877-9640", "researcher": {"href": "https://publications.scilifelab.se/researcher/63d6deb5a00141b0bb2c2f031ef8d53a.json"}}, {"family": "Partanen", "given": "Jukka", "initials": "J", "orcid": "0000-0001-6681-4734", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f3b7cf9d4874b63b92556eccf060493.json"}}, {"family": "Koskela", "given": "Satu", "initials": "S", "orcid": "0000-0001-9258-9163", "researcher": {"href": "https://publications.scilifelab.se/researcher/478c0a65a147450bb5c5a7ba7d196b41.json"}}, {"family": "Honkanen", "given": "Jarno", "initials": "J"}, {"family": "Halonen", "given": "Jussi", "initials": "J"}, {"family": "Kuryk", "given": "Lukasz", "initials": "L", "orcid": "0000-0003-1887-6361", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa535fd845648f5ab10d0e1a407f8f9.json"}}, {"family": "Rescigno", "given": "Maria", "initials": "M", "orcid": "0000-0002-6464-509X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee52150f5c1c4140aaf8758fff64572c.json"}}, {"family": "Gr\u00f6nholm", "given": "Mikaela", "initials": "M"}, {"family": "Branca", "given": "Rui M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Cerullo", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4901-3796", "researcher": {"href": "https://publications.scilifelab.se/researcher/6404cf54a990420fb0b63d626aa783fb.json"}}], "type": "journal article", "published": "2023-11-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "7056", "issn-l": "2041-1723"}, "abstract": "Malignant pleural mesothelioma (MPM) is an aggressive tumor with a poor prognosis. As the available therapeutic options show a lack of efficacy, novel therapeutic strategies are urgently needed. Given its T-cell infiltration, we hypothesized that MPM is a suitable target for therapeutic cancer vaccination. To date, research on mesothelioma has focused on the identification of molecular signatures to better classify and characterize the disease, and little is known about therapeutic targets that engage cytotoxic (CD8+) T cells. In this study we investigate the immunopeptidomic antigen-presented landscape of MPM in both murine (AB12 cell line) and human cell lines (H28, MSTO-211H, H2452, and JL1), as well as in patients' primary tumors. Applying state-of-the-art immuno-affinity purification methodologies, we identify MHC I-restricted peptides presented on the surface of malignant cells. We characterize in vitro the immunogenicity profile of the eluted peptides using T cells from human healthy donors and cancer patients. Furthermore, we use the most promising peptides to formulate an oncolytic virus-based precision immunotherapy (PeptiCRAd) and test its efficacy in a mouse model of mesothelioma in female mice. Overall, we demonstrate that the use of immunopeptidomic analysis in combination with oncolytic immunotherapy represents a feasible and effective strategy to tackle untreatable tumors.", "doi": "10.1038/s41467-023-42668-7", "pmid": "37923723", "labels": {"Global Proteomics and Proteogenomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC10624665"}, {"db": "pii", "key": "10.1038/s41467-023-42668-7"}], "notes": [], "created": "2023-11-30T10:26:49.610Z", "modified": "2023-11-30T10:26:49.935Z"}, {"entity": "publication", "iuid": "df5638c2c3d442cd861fa36a108950d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df5638c2c3d442cd861fa36a108950d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df5638c2c3d442cd861fa36a108950d6"}}, "title": "Proteomics reveal biomarkers for diagnosis, disease activity and long-term disability outcomes in multiple sclerosis.", "authors": [{"family": "\u00c5kesson", "given": "Julia", "initials": "J", "orcid": "0000-0002-9276-0546", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba1adc3a1e614b87808e3b1b5d4d9cb1.json"}}, {"family": "Hojjati", "given": "Sara", "initials": "S"}, {"family": "Hellberg", "given": "Sandra", "initials": "S"}, {"family": "Raffetseder", "given": "Johanna", "initials": "J", "orcid": "0000-0001-8871-2560", "researcher": {"href": "https://publications.scilifelab.se/researcher/604da06820f542ef84b97cf0e4641e2c.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Rynkowski", "given": "Robert", "initials": "R"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Altafini", "given": "Claudio", "initials": "C", "orcid": "0000-0003-4142-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/397523f1994046fdb4c462d5127e4c1d.json"}}, {"family": "Lubovac-Pilav", "given": "Zelmina", "initials": "Z", "orcid": "0000-0001-6427-0315", "researcher": {"href": "https://publications.scilifelab.se/researcher/af98c65fa2964875bd6d46f9c2488e6b.json"}}, {"family": "Mellerg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-0120-3734", "researcher": {"href": "https://publications.scilifelab.se/researcher/f471bdcfc7fc4c2fb282484ac7e148bd.json"}}, {"family": "Jenmalm", "given": "Maria C", "initials": "MC", "orcid": "0000-0002-2117-5366", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf1f485192744e0c95ccecdb5471b577.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Ernerudh", "given": "Jan", "initials": "J", "orcid": "0000-0001-9456-2044", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc016a1ad2b14e91b97b65d5aaae7f59.json"}}, {"family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2.json"}}], "type": "journal article", "published": "2023-10-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6903", "issn-l": "2041-1723"}, "abstract": "Sensitive and reliable protein biomarkers are needed to predict disease trajectory and personalize treatment strategies for multiple sclerosis (MS). Here, we use the highly sensitive proximity-extension assay combined with next-generation sequencing (Olink Explore) to quantify 1463 proteins in cerebrospinal fluid (CSF) and plasma from 143 people with early-stage MS and 43 healthy controls. With longitudinally followed discovery and replication cohorts, we identify CSF proteins that consistently predicted both short- and long-term disease progression. Lower levels of neurofilament light chain (NfL) in CSF is superior in predicting the absence of disease activity two years after sampling (replication AUC = 0.77) compared to all other tested proteins. Importantly, we also identify a combination of 11 CSF proteins (CXCL13, LTA, FCN2, ICAM3, LY9, SLAMF7, TYMP, CHI3L1, FYB1, TNFRSF1B and NfL) that predict the severity of disability worsening according to the normalized age-related MS severity score (replication AUC = 0.90). The identification of these proteins may help elucidate pathogenetic processes and might aid decisions on treatment strategies for persons with MS.", "doi": "10.1038/s41467-023-42682-9", "pmid": "37903821", "labels": {"NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10616092"}, {"db": "pii", "key": "10.1038/s41467-023-42682-9"}], "notes": [], "created": "2023-11-23T07:26:00.330Z", "modified": "2023-11-29T18:44:34.331Z"}, {"entity": "publication", "iuid": "397f0c6069f74329b30503eecca169d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/397f0c6069f74329b30503eecca169d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/397f0c6069f74329b30503eecca169d2"}}, "title": "Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.", "authors": [{"family": "Sendell-Price", "given": "Ashley T", "initials": "AT", "orcid": "0000-0002-1227-8929", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2d5fb40391442c8a62c20b1ca9a3295.json"}}, {"family": "Tulenko", "given": "Frank J", "initials": "FJ"}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Kang", "given": "Du", "initials": "D", "orcid": "0000-0002-1497-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eda8755c14042289ac7196edeffca01.json"}}, {"family": "Montandon", "given": "Margo", "initials": "M", "orcid": "0000-0002-1707-0190", "researcher": {"href": "https://publications.scilifelab.se/researcher/db6f9463614b43c1aa3d41114a8f5086.json"}}, {"family": "Winkler", "given": "Sylke", "initials": "S", "orcid": "0000-0002-0915-3316", "researcher": {"href": "https://publications.scilifelab.se/researcher/f292bbf542f244278bef19506b21b031.json"}}, {"family": "Kulb", "given": "Kathleen", "initials": "K"}, {"family": "Naylor", "given": "Gavin P", "initials": "GP"}, {"family": "Phillippy", "given": "Adam", "initials": "A", "orcid": "0000-0003-2983-8934", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadfad6b448a4438abee6a1b2f842b35.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O"}, {"family": "Mountcastle", "given": "Jacquelyn", "initials": "J"}, {"family": "Balacco", "given": "Jennifer R", "initials": "JR"}, {"family": "Dutra", "given": "Amalia", "initials": "A"}, {"family": "Dale", "given": "Rebecca E", "initials": "RE"}, {"family": "Haase", "given": "Bettina", "initials": "B"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Myers", "given": "Gene", "initials": "G", "orcid": "0000-0002-6580-7839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9e5a63cadcf4ab995f3e989bc38c024.json"}}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76.json"}}, {"family": "Currie", "given": "Peter D", "initials": "PD", "orcid": "0000-0001-8874-8862", "researcher": {"href": "https://publications.scilifelab.se/researcher/13638faa71f94e13b088922cdfa01bb3.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f97783b5013409ebc1a6bd2df5ca92c.json"}}], "type": "journal article", "published": "2023-10-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6628", "issn-l": "2041-1723"}, "abstract": "Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum). We generate a high-quality reference genome, and resequence the whole genomes of parents and nine offspring to detect de novo mutations. Using stringent criteria, we estimate a mutation rate of 7\u00d710-10 per base pair, per generation. This represents one of the lowest directly estimated mutation rates for any vertebrate clade, indicating that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by a low mutation rate.", "doi": "10.1038/s41467-023-42238-x", "pmid": "37857613", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10587355"}, {"db": "pii", "key": "10.1038/s41467-023-42238-x"}], "notes": [], "created": "2023-12-18T15:04:16.059Z", "modified": "2024-01-16T13:48:31.927Z"}, {"entity": "publication", "iuid": "46075f3ed1084d18863bd3e5bdf68fa1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46075f3ed1084d18863bd3e5bdf68fa1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46075f3ed1084d18863bd3e5bdf68fa1"}}, "title": "Design, structure and plasma binding of ancestral \u03b2-CoV scaffold antigens.", "authors": [{"family": "Hueting", "given": "David", "initials": "D"}, {"family": "Schriever", "given": "Karen", "initials": "K", "orcid": "0000-0002-3677-5508", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9d0ab1663284759bdf74f9478fe009d.json"}}, {"family": "Sun", "given": "Rui", "initials": "R"}, {"family": "Vlachiotis", "given": "Stelios", "initials": "S"}, {"family": "Zuo", "given": "Fanglei", "initials": "F", "orcid": "0000-0002-4545-1265", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec0d27f8a674ebb89d95e59e99364e3.json"}}, {"family": "Du", "given": "Likun", "initials": "L"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Hofstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}, {"family": "Walld\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Marcotte", "given": "Harold", "initials": "H", "orcid": "0000-0002-7168-349X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d328d037bc844b29398959d350e0053.json"}}, {"family": "Pan-Hammarstr\u00f6m", "given": "Qiang", "initials": "Q", "orcid": "0000-0003-1990-8804", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9d3baa27411425a8b8f63f3c3230964.json"}}, {"family": "Andr\u00e9ll", "given": "Juni", "initials": "J", "orcid": "0000-0003-2313-9155", "researcher": {"href": "https://publications.scilifelab.se/researcher/be8a8574a94e42e18cf54c207ec66643.json"}}, {"family": "Syr\u00e9n", "given": "Per-Olof", "initials": "PO", "orcid": "0000-0002-4066-2776", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0ff76fed92947a8912df63248f3f1af.json"}}], "type": "journal article", "published": "2023-10-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6527", "issn-l": "2041-1723"}, "abstract": "We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma of patients recovered from COVID-19 but do not bind to the human angiotensin-converting enzyme 2 (ACE2) receptor. Cryo-EM analysis of the AnSAs yield high resolution structures (2.6-2.8 \u00c5) indicating a closed pre-fusion conformation in which all three receptor-binding domains (RBDs) are facing downwards. The structures reveal an intricate hydrogen-bonding network mediated by well-resolved loops, both within and across monomers, tethering the N-terminal domain and RBD together. We show that AnSA-5 can induce and boost a broad-spectrum immune response against the wild-type RBD as well as circulating variants of concern in an immune organoid model derived from tonsils. Finally, we highlight how AnSAs are potent scaffolds by replacing the ancestral RBD with the wild-type sequence, which restores ACE2 binding and increases the interaction with convalescent plasma.", "doi": "10.1038/s41467-023-42200-x", "pmid": "37845250", "labels": {"Cryo-EM": "Service", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10579346"}, {"db": "pii", "key": "10.1038/s41467-023-42200-x"}], "notes": [], "created": "2023-11-26T16:00:58.067Z", "modified": "2025-10-17T13:05:07.471Z"}, {"entity": "publication", "iuid": "61870ecf000246d1bfc7c1a38844d67c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61870ecf000246d1bfc7c1a38844d67c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61870ecf000246d1bfc7c1a38844d67c"}}, "title": "Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale.", "authors": [{"family": "Sounart", "given": "Hailey", "initials": "H", "orcid": "0009-0000-5772-3961", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d2d0007b3d643588c5196d482cb2089.json"}}, {"family": "Voronin", "given": "Denis", "initials": "D"}, {"family": "Masarapu", "given": "Yuvarani", "initials": "Y", "orcid": "0000-0002-3267-2085", "researcher": {"href": "https://publications.scilifelab.se/researcher/055fa17f6cdd490e87182c94c847c440.json"}}, {"family": "Chung", "given": "Matthew", "initials": "M"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6979cdfc0b4e4285f9d810c39bb7b7.json"}}, {"family": "Ghedin", "given": "Elodie", "initials": "E", "orcid": "0000-0002-1515-725X", "researcher": {"href": "https://publications.scilifelab.se/researcher/999da8f68b344372874fec159e5a986b.json"}}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}], "type": "journal article", "published": "2023-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6500", "issn-l": "2041-1723"}, "abstract": "Several important human infectious diseases are caused by microscale-sized parasitic nematodes like filarial worms. Filarial worms have their own spatial tissue organization; to uncover this tissue structure, we need methods that can spatially resolve these miniature specimens. Most filarial worms evolved a mutualistic association with endosymbiotic bacteria Wolbachia. However, the mechanisms underlying the dependency of filarial worms on the fitness of these bacteria remain unknown. As Wolbachia is essential for the development, reproduction, and survival of filarial worms, we spatially explored how Wolbachia interacts with the worm's reproductive system by performing a spatial characterization using Spatial Transcriptomics (ST) across a posterior region containing reproductive tissue and developing embryos of adult female Brugia malayi worms. We provide a proof-of-concept for miniature-ST to explore spatial gene expression patterns in small sample types, demonstrating the method's ability to uncover nuanced tissue region expression patterns, observe the spatial localization of key B. malayi - Wolbachia pathway genes, and co-localize the B. malayi spatial transcriptome in Wolbachia tissue regions, also under antibiotic treatment. We envision our approach will open up new avenues for the study of infectious diseases caused by micro-scale parasitic worms.", "doi": "10.1038/s41467-023-42237-y", "pmid": "37838705", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10576761"}, {"db": "pii", "key": "10.1038/s41467-023-42237-y"}], "notes": [], "created": "2024-11-25T10:16:00.794Z", "modified": "2024-11-25T10:16:00.902Z"}, {"entity": "publication", "iuid": "5c111fe17f824fe289df7e8e78c1cf8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c111fe17f824fe289df7e8e78c1cf8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c111fe17f824fe289df7e8e78c1cf8a"}}, "title": "Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication.", "authors": [{"family": "Chakraborty", "given": "Chaitali", "initials": "C"}, {"family": "Nissen", "given": "Itzel", "initials": "I", "orcid": "0000-0002-0741-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4f02fa8059145bc9b17d0c1ef978ee2.json"}}, {"family": "Vincent", "given": "Craig A", "initials": "CA"}, {"family": "H\u00e4gglund", "given": "Anna-Carin", "initials": "AC"}, {"family": "H\u00f6rnblad", "given": "Andreas", "initials": "A", "orcid": "0000-0003-1283-0784", "researcher": {"href": "https://publications.scilifelab.se/researcher/59e1f49dc64841d097fb0cddfcd660c9.json"}}, {"family": "Remeseiro", "given": "Silvia", "initials": "S", "orcid": "0000-0001-5343-007X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb0bc2da415e4c6aafc3f55fba80a12b.json"}}], "type": "journal article", "published": "2023-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6446", "issn-l": "2041-1723"}, "abstract": "Chromatin organization controls transcription by modulating 3D-interactions between enhancers and promoters in the nucleus. Alterations in epigenetic states and 3D-chromatin organization result in gene expression changes contributing to cancer. Here, we map the promoter-enhancer interactome and regulatory landscape of glioblastoma, the most aggressive primary brain tumour. Our data reveals profound rewiring of promoter-enhancer interactions, chromatin accessibility and redistribution of histone marks in glioblastoma. This leads to loss of long-range regulatory interactions and overall activation of promoters, which orchestrate changes in the expression of genes associated to glutamatergic synapses, axon guidance, axonogenesis and chromatin remodelling. SMAD3 and PITX1 emerge as major transcription factors controlling genes related to synapse organization and axon guidance. Inhibition of SMAD3 and neuronal activity stimulation cooperate to promote proliferation of glioblastoma cells in co-culture with glutamatergic neurons, and in mice bearing patient-derived xenografts. Our findings provide mechanistic insight into the regulatory networks that mediate neurogliomal synaptic communication.", "doi": "10.1038/s41467-023-41919-x", "pmid": "37833281", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10576091"}, {"db": "pii", "key": "10.1038/s41467-023-41919-x"}], "notes": [], "created": "2023-12-01T13:22:54.419Z", "modified": "2024-11-25T10:15:55.539Z"}, {"entity": "publication", "iuid": "58ed0fc0d058426ca2f18b39c8fdd6bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58ed0fc0d058426ca2f18b39c8fdd6bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58ed0fc0d058426ca2f18b39c8fdd6bb"}}, "title": "Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs.", "authors": [{"family": "Petruk", "given": "Ganna", "initials": "G", "orcid": "0000-0003-1336-2900", "researcher": {"href": "https://publications.scilifelab.se/researcher/496c3fa062e34cd2a92941720fe62b5a.json"}}, {"family": "Puthia", "given": "Manoj", "initials": "M", "orcid": "0000-0001-6048-7234", "researcher": {"href": "https://publications.scilifelab.se/researcher/f794b8d0d66a4bab964e915ff71a7023.json"}}, {"family": "Samsudin", "given": "Firdaus", "initials": "F"}, {"family": "Petrlova", "given": "Jitka", "initials": "J", "orcid": "0000-0002-7554-3945", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f5e9799bbd647309b383de9f754df00.json"}}, {"family": "Olm", "given": "Franziska", "initials": "F", "orcid": "0000-0001-5222-6130", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5b929c8316a43b7938fbc6cd2bf330e.json"}}, {"family": "Mittendorfer", "given": "Margareta", "initials": "M"}, {"family": "Hyll\u00e9n", "given": "Snejana", "initials": "S", "orcid": "0000-0003-1253-4969", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ce81a1e114d4de08470ee8c44d7e15d.json"}}, {"family": "Edstr\u00f6m", "given": "Dag", "initials": "D"}, {"family": "Str\u00f6mdahl", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Diehl", "given": "Carl", "initials": "C"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S", "orcid": "0000-0002-7694-285X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6416b323664f4126b70067193d7b8347.json"}}, {"family": "Walse", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-1513-9040", "researcher": {"href": "https://publications.scilifelab.se/researcher/216f98091f43414eae8cd583dcd9a24d.json"}}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S", "orcid": "0000-0003-4646-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfae5f64ec9d45e282cdfd038539fe25.json"}}, {"family": "Bond", "given": "Peter J", "initials": "PJ", "orcid": "0000-0003-2900-098X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34efd0fc1d104a839dced094addd4d91.json"}}, {"family": "Lindstedt", "given": "Sandra", "initials": "S"}, {"family": "Schmidtchen", "given": "Artur", "initials": "A", "orcid": "0000-0001-9209-3141", "researcher": {"href": "https://publications.scilifelab.se/researcher/406510dc3844487e9c45f713ea173b8e.json"}}], "type": "journal article", "published": "2023-09-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6097", "issn-l": "2041-1723"}, "abstract": "There is a clinical need for conceptually new treatments that target the excessive activation of inflammatory pathways during systemic infection. Thrombin-derived C-terminal peptides (TCPs) are endogenous anti-infective immunomodulators interfering with CD14-mediated TLR-dependent immune responses. Here we describe the development of a peptide-based compound for systemic use, sHVF18, expressing the evolutionarily conserved innate structural fold of natural TCPs. Using a combination of structure- and in silico-based design, nuclear magnetic resonance spectroscopy, biophysics, mass spectrometry, cellular, and in vivo studies, we here elucidate the structure, CD14 interactions, protease stability, transcriptome profiling, and therapeutic efficacy of sHVF18. The designed peptide displays a conformationally stabilized, protease resistant active innate fold and targets the LPS-binding groove of CD14. In vivo, it shows therapeutic efficacy in experimental models of endotoxin shock in mice and pigs and increases survival in mouse models of systemic polymicrobial infection. The results provide a drug class based on Nature\u00b4s own anti-infective principles.", "doi": "10.1038/s41467-023-41702-y", "pmid": "37773180", "labels": {"Clinical Genomics Lund": "Service", "Structural Proteomics": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10541425"}, {"db": "pii", "key": "10.1038/s41467-023-41702-y"}], "notes": [], "created": "2023-11-21T18:39:47.348Z", "modified": "2023-12-01T13:27:00.432Z"}, {"entity": "publication", "iuid": "474e326bac8c485b94882e2b5810d0c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/474e326bac8c485b94882e2b5810d0c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/474e326bac8c485b94882e2b5810d0c5"}}, "title": "A subset of type-II collagen-binding antibodies prevents experimental arthritis by inhibiting FCGR3 signaling in neutrophils.", "authors": [{"family": "Xu", "given": "Zhongwei", "initials": "Z", "orcid": "0000-0001-5178-3437", "researcher": {"href": "https://publications.scilifelab.se/researcher/f056000b3af842bda8cdd411da7d44ad.json"}}, {"family": "Xu", "given": "Bingze", "initials": "B"}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "Moreno-Gir\u00f3", "given": "\u00c0lex", "initials": "\u00c0", "orcid": "0000-0002-4655-1639", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f7cba46c513494683d27e8212f2f7ea.json"}}, {"family": "Zhao", "given": "Danxia", "initials": "D"}, {"family": "Martin", "given": "Myriam", "initials": "M", "orcid": "0000-0003-1526-8678", "researcher": {"href": "https://publications.scilifelab.se/researcher/98b90b41b1504b199dc3c4e2d2abec9b.json"}}, {"family": "L\u00f6nnblom", "given": "Erik", "initials": "E", "orcid": "0000-0002-1311-2541", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f5683b51d554ff482bd76c0ded3aaa2.json"}}, {"family": "Li", "given": "Qixing", "initials": "Q", "orcid": "0000-0003-4115-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a08486ecf2d48c89419e65bdc67d5b0.json"}}, {"family": "Kr\u00e4mer", "given": "Alexander", "initials": "A"}, {"family": "Ge", "given": "Changrong", "initials": "C"}, {"family": "Cheng", "given": "Lei", "initials": "L", "orcid": "0000-0002-0984-6964", "researcher": {"href": "https://publications.scilifelab.se/researcher/392a8eb7957841be9608b8507cddd9f0.json"}}, {"family": "Liang", "given": "Bibo", "initials": "B"}, {"family": "Tong", "given": "Dongmei", "initials": "D", "orcid": "0000-0002-3468-5293", "researcher": {"href": "https://publications.scilifelab.se/researcher/08057adc31904e8a8dc58eb4c6f3dec0.json"}}, {"family": "Stawikowska", "given": "Roma", "initials": "R"}, {"family": "Blom", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-1348-1734", "researcher": {"href": "https://publications.scilifelab.se/researcher/c18466d1f5614ecbb63c5d4136a02466.json"}}, {"family": "Fields", "given": "Gregg B", "initials": "GB", "orcid": "0000-0003-3573-1527", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37314f6aead44d7a4de9a21024e0cd5.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}, {"family": "Holmdahl", "given": "Rikard", "initials": "R", "orcid": "0000-0002-4969-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/49e60d22dd1a4dd1a4ca5a50d9fc4fc7.json"}}], "type": "journal article", "published": "2023-09-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5949", "issn-l": "2041-1723"}, "abstract": "Rheumatoid arthritis (RA) involves several classes of pathogenic autoantibodies, some of which react with type-II collagen (COL2) in articular cartilage. We previously described a subset of COL2 antibodies targeting the F4 epitope (ERGLKGHRGFT) that could be regulatory. Here, using phage display, we developed recombinant antibodies against this epitope and examined the underlying mechanism of action. One of these antibodies, R69-4, protected against cartilage antibody- and collagen-induced arthritis in mice, but not autoimmune disease models independent of arthritogenic autoantibodies. R69-4 was further shown to cross-react with a large range of proteins within the inflamed synovial fluid, such as the complement protein C1q. Complexed R69-4 inhibited neutrophil FCGR3 signaling, thereby impairing downstream IL-1\u03b2 secretion and neutrophil self-orchestrated recruitment. Likewise, human isotypes of R69-4 protected against arthritis with comparable efficiency. We conclude that R69-4 abrogates autoantibody-mediated arthritis mainly by hindering FCGR3 signaling, highlighting its potential clinical utility in acute RA.", "doi": "10.1038/s41467-023-41561-7", "pmid": "37741824", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10517938"}, {"db": "pii", "key": "10.1038/s41467-023-41561-7"}], "notes": [], "created": "2024-05-13T07:50:30.661Z", "modified": "2025-10-17T13:05:07.506Z"}, {"entity": "publication", "iuid": "e100499748ca4919a43efecd22554d70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e100499748ca4919a43efecd22554d70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e100499748ca4919a43efecd22554d70"}}, "title": "Comprehensive proteomics and meta-analysis of COVID-19 host response.", "authors": [{"family": "Baba\u010di\u0107", "given": "Haris", "initials": "H", "orcid": "0000-0003-0813-0005", "researcher": {"href": "https://publications.scilifelab.se/researcher/45a1c5d3d2d34a9e96d112877632784c.json"}}, {"family": "Christ", "given": "Wanda", "initials": "W", "orcid": "0000-0003-3886-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe3a44fdb547b885cce5b6f490b2bc.json"}}, {"family": "Ara\u00fajo", "given": "Jos\u00e9 Eduardo", "initials": "JE"}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Sharma", "given": "Nidhi", "initials": "N"}, {"family": "Tynell", "given": "Janne", "initials": "J", "orcid": "0000-0001-6930-5230", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb43fb2383e047679010f0969a115f2f.json"}}, {"family": "Garc\u00eda", "given": "Marina", "initials": "M", "orcid": "0000-0002-9130-3933", "researcher": {"href": "https://publications.scilifelab.se/researcher/20fa6d5f40764b32a70f792f29d97e60.json"}}, {"family": "Varnaite", "given": "Renata", "initials": "R"}, {"family": "Asgeirsson", "given": "Hilmir", "initials": "H", "orcid": "0000-0003-3869-8021", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc2be98322a74715a21f56ce31217d84.json"}}, {"family": "Glans", "given": "Hedvig", "initials": "H"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Gredmark-Russ", "given": "Sara", "initials": "S"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}], "type": "meta-analysis", "published": "2023-09-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5921", "issn-l": "2041-1723"}, "abstract": "COVID-19 is characterised by systemic immunological perturbations in the human body, which can lead to multi-organ damage. Many of these processes are considered to be mediated by the blood. Therefore, to better understand the systemic host response to SARS-CoV-2 infection, we performed systematic analyses of the circulating, soluble proteins in the blood through global proteomics by mass-spectrometry (MS) proteomics. Here, we show that a large part of the soluble blood proteome is altered in COVID-19, among them elevated levels of interferon-induced and proteasomal proteins. Some proteins that have alternating levels in human cells after a SARS-CoV-2 infection in vitro and in different organs of COVID-19 patients are deregulated in the blood, suggesting shared infection-related changes.The availability of different public proteomic resources on soluble blood proteome alterations leaves uncertainty about the change of a given protein during COVID-19. Hence, we performed a systematic review and meta-analysis of MS global proteomics studies of soluble blood proteomes, including up to 1706 individuals (1039 COVID-19 patients), to provide concluding estimates for the alteration of 1517 soluble blood proteins in COVID-19. Finally, based on the meta-analysis we developed CoViMAPP, an open-access resource for effect sizes of alterations and diagnostic potential of soluble blood proteins in COVID-19, which is publicly available for the research, clinical, and academic community.", "doi": "10.1038/s41467-023-41159-z", "pmid": "37739942", "labels": {"Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10516886"}, {"db": "pii", "key": "10.1038/s41467-023-41159-z"}], "notes": [], "created": "2023-11-29T11:54:56.281Z", "modified": "2023-11-29T11:54:56.390Z"}, {"entity": "publication", "iuid": "4555fc7b277b4c99b53435715afcc6a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4555fc7b277b4c99b53435715afcc6a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4555fc7b277b4c99b53435715afcc6a2"}}, "title": "Prosaposin maintains lipid homeostasis in dopamine neurons and counteracts experimental parkinsonism in rodents.", "authors": [{"family": "He", "given": "Yachao", "initials": "Y", "orcid": "0000-0002-0241-2901", "researcher": {"href": "https://publications.scilifelab.se/researcher/80733d0ca6fa45d7b9133ac217de6e18.json"}}, {"family": "Kaya", "given": "Ibrahim", "initials": "I", "orcid": "0000-0003-3345-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/99a00a900df8419f96fafa97344e56ea.json"}}, {"family": "Shariatgorji", "given": "Reza", "initials": "R", "orcid": "0000-0001-9484-0921", "researcher": {"href": "https://publications.scilifelab.se/researcher/7762e9f6779c4780a4077c557eb7a3b6.json"}}, {"family": "Lundkvist", "given": "Johan", "initials": "J"}, {"family": "Wahlberg", "given": "Lars U", "initials": "LU"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Mamula", "given": "Dejan", "initials": "D"}, {"family": "Kehr", "given": "Jan", "initials": "J"}, {"family": "Zareba-Paslawska", "given": "Justyna", "initials": "J", "orcid": "0000-0001-6193-5908", "researcher": {"href": "https://publications.scilifelab.se/researcher/632ee1b0b103420ea8c98cefb18244a4.json"}}, {"family": "Biverst\u00e5l", "given": "Henrik", "initials": "H", "orcid": "0000-0002-2097-7658", "researcher": {"href": "https://publications.scilifelab.se/researcher/e599409acaaf45b880fc45a65e9bd664.json"}}, {"family": "Chergui", "given": "Karima", "initials": "K"}, {"family": "Zhang", "given": "Xiaoqun", "initials": "X"}, {"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": "2023-09-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "5804"}, "abstract": "Prosaposin (PSAP) modulates glycosphingolipid metabolism and variants have been linked to Parkinson's disease (PD). Here, we find altered PSAP levels in the plasma, CSF and post-mortem brain of PD patients. Altered plasma and CSF PSAP levels correlate with PD-related motor impairments. Dopaminergic PSAP-deficient (cPSAPDAT) mice display hypolocomotion and depression/anxiety-like symptoms with mildly impaired dopaminergic neurotransmission, while serotonergic PSAP-deficient (cPSAPSERT) mice behave normally. Spatial lipidomics revealed an accumulation of highly unsaturated and shortened lipids and reduction of sphingolipids throughout the brains of cPSAPDAT mice. The overexpression of \u03b1-synuclein via AAV lead to more severe dopaminergic degeneration and higher p-Ser129 \u03b1-synuclein levels in cPSAPDAT mice compared to WT mice. Overexpression of PSAP via AAV and encapsulated cell biodelivery protected against 6-OHDA and \u03b1-synuclein toxicity in wild-type rodents. Thus, these findings suggest PSAP may maintain dopaminergic lipid homeostasis, which is dysregulated in PD, and counteract experimental parkinsonism.", "doi": "10.1038/s41467-023-41539-5", "pmid": "37726325", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10509278"}, {"db": "pii", "key": "10.1038/s41467-023-41539-5"}], "notes": [], "created": "2023-11-30T10:50:10.413Z", "modified": "2024-02-09T14:28:28.286Z"}, {"entity": "publication", "iuid": "a7779ca0e6794082a6fb16d84f023606", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7779ca0e6794082a6fb16d84f023606.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7779ca0e6794082a6fb16d84f023606"}}, "title": "Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.", "authors": [{"family": "Mihali\u010d", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Benz", "given": "Caroline", "initials": "C", "orcid": "0000-0002-5166-3598", "researcher": {"href": "https://publications.scilifelab.se/researcher/86628e15252f4dd98f08759d59fad848.json"}}, {"family": "Kassa", "given": "Eszter", "initials": "E"}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Simonetti", "given": "Leandro", "initials": "L", "orcid": "0000-0003-1283-9770", "researcher": {"href": "https://publications.scilifelab.se/researcher/23530c1a3cef4f499a460ac59c674261.json"}}, {"family": "Inturi", "given": "Raviteja", "initials": "R"}, {"family": "Aronsson", "given": "Hanna", "initials": "H"}, {"family": "Andersson", "given": "Eva", "initials": "E"}, {"family": "Chi", "given": "Celestine N", "initials": "CN"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}, {"family": "Jemth", "given": "Per", "initials": "P", "orcid": "0000-0003-1516-7228", "researcher": {"href": "https://publications.scilifelab.se/researcher/91bb46ceba74462498354a328886b982.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2023-09-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5636", "issn-l": "2041-1723"}, "abstract": "The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD \u223c 7-300 \u03bcM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.", "doi": "10.1038/s41467-023-41312-8", "pmid": "37704626", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10499821"}, {"db": "pii", "key": "10.1038/s41467-023-41312-8"}], "notes": [], "created": "2023-10-19T13:57:45.671Z", "modified": "2024-11-12T10:39:14.679Z"}, {"entity": "publication", "iuid": "755e7f7e5104445e87f7735a04e84157", "links": {"self": {"href": "https://publications.scilifelab.se/publication/755e7f7e5104445e87f7735a04e84157.json"}, "display": {"href": "https://publications.scilifelab.se/publication/755e7f7e5104445e87f7735a04e84157"}}, "title": "Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development.", "authors": [{"family": "Witman", "given": "Nevin", "initials": "N"}, {"family": "Zhou", "given": "Chikai", "initials": "C"}, {"family": "H\u00e4neke", "given": "Timm", "initials": "T"}, {"family": "Xiao", "given": "Yao", "initials": "Y"}, {"family": "Huang", "given": "Xiaoting", "initials": "X"}, {"family": "Rohner", "given": "Eduarde", "initials": "E", "orcid": "0000-0001-8411-3720", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7bb51a667fd4c79968aec99cf52ff58.json"}}, {"family": "Sohlm\u00e9r", "given": "Jesper", "initials": "J", "orcid": "0000-0003-2607-7500", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e770e2f774bb68ed8059bc6aa2aef.json"}}, {"family": "Grote Beverborg", "given": "Niels", "initials": "N", "orcid": "0000-0003-4629-9960", "researcher": {"href": "https://publications.scilifelab.se/researcher/4209163c007f4c7cb94cdf9777ee90cc.json"}}, {"family": "Chien", "given": "Kenneth R", "initials": "KR", "orcid": "0000-0002-2759-8378", "researcher": {"href": "https://publications.scilifelab.se/researcher/971382878b474966bbe58acaa1585999.json"}}, {"family": "Sahara", "given": "Makoto", "initials": "M", "orcid": "0000-0002-6281-5454", "researcher": {"href": "https://publications.scilifelab.se/researcher/db8ed12692374718a5a07fc52e9c5c33.json"}}], "type": "journal article", "published": "2023-09-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5435", "issn-l": "2041-1723"}, "abstract": "Cardiogenic growth factors play important roles in heart development. Placental growth factor (PLGF) has previously been reported to have angiogenic effects; however, its potential role in cardiogenesis has not yet been determined. We analyze single-cell RNA-sequencing data derived from human and primate embryonic hearts and find PLGF shows a biphasic expression pattern, as it is expressed specifically on ISL1+ second heart field progenitors at an earlier stage and on vascular smooth muscle cells (SMCs) and endothelial cells (ECs) at later stages. Using chemically modified mRNAs (modRNAs), we generate a panel of cardiogenic growth factors and test their effects on enhancing cardiomyocyte (CM) and EC induction during different stages of human embryonic stem cell (hESC) differentiations. We discover that only the application of PLGF modRNA at early time points of hESC-CM differentiation can increase both CM and EC production. Conversely, genetic deletion of PLGF reduces generation of CMs, SMCs and ECs in vitro. We also confirm in vivo beneficial effects of PLGF modRNA for development of human heart progenitor-derived cardiac muscle grafts on murine kidney capsules. Further, we identify the previously unrecognized PLGF-related transcriptional networks driven by EOMES and SOX17. These results shed light on the dual cardiomyogenic and vasculogenic effects of PLGF during heart development.", "doi": "10.1038/s41467-023-41305-7", "pmid": "37669989", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10480216"}, {"db": "pii", "key": "10.1038/s41467-023-41305-7"}], "notes": [], "created": "2023-10-11T09:07:02.839Z", "modified": "2023-10-19T12:34:41.339Z"}, {"entity": "publication", "iuid": "cc8c5c5984f945c3b508e69505674009", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc8c5c5984f945c3b508e69505674009.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc8c5c5984f945c3b508e69505674009"}}, "title": "The interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis.", "authors": [{"family": "Schoeler", "given": "Marc", "initials": "M", "orcid": "0000-0001-8363-1016", "researcher": {"href": "https://publications.scilifelab.se/researcher/d788d9e049e648b1b11fa35f7228e191.json"}}, {"family": "Ellero-Simatos", "given": "Sandrine", "initials": "S", "orcid": "0000-0002-9282-1804", "researcher": {"href": "https://publications.scilifelab.se/researcher/1045a2d3f9e74aa49bc6b6be0c48ba55.json"}}, {"family": "Birkner", "given": "Till", "initials": "T", "orcid": "0000-0003-2656-2821", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdd65718e0a41fc995619186fd7f440.json"}}, {"family": "Mayneris-Perxachs", "given": "Jordi", "initials": "J", "orcid": "0000-0003-3788-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8f06af30c4d4bb5b047a999bbbe9994.json"}}, {"family": "Olsson", "given": "Lisa", "initials": "L", "orcid": "0000-0001-9730-1915", "researcher": {"href": "https://publications.scilifelab.se/researcher/2460963d77ee4eee9409fbd8c257d910.json"}}, {"family": "Brolin", "given": "Harald", "initials": "H"}, {"family": "Loeber", "given": "Ulrike", "initials": "U", "orcid": "0000-0001-7468-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/7180811b734042c0b3b8fb3f2ee03e5e.json"}}, {"family": "Kraft", "given": "Jamie D", "initials": "JD"}, {"family": "Polizzi", "given": "Arnaud", "initials": "A", "orcid": "0000-0003-1986-2770", "researcher": {"href": "https://publications.scilifelab.se/researcher/67bf8bbabc554e90a5cb32f4752bca07.json"}}, {"family": "Mart\u00ed-Navas", "given": "Marian", "initials": "M"}, {"family": "Puig", "given": "Josep", "initials": "J"}, {"family": "Moschetta", "given": "Antonio", "initials": "A", "orcid": "0000-0003-2123-6074", "researcher": {"href": "https://publications.scilifelab.se/researcher/e34bdbb78ebc40a487d0e8c5a189709b.json"}}, {"family": "Montagner", "given": "Alexandra", "initials": "A"}, {"family": "Gourdy", "given": "Pierre", "initials": "P"}, {"family": "Heymes", "given": "Christophe", "initials": "C"}, {"family": "Guillou", "given": "Herv\u00e9", "initials": "H"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Fern\u00e1ndez-Real", "given": "Jos\u00e9 Manuel", "initials": "JM", "orcid": "0000-0002-7442-9323", "researcher": {"href": "https://publications.scilifelab.se/researcher/93e21b9322504231959a987578ab2099.json"}}, {"family": "Forslund", "given": "Sofia K", "initials": "SK", "orcid": "0000-0003-4285-6993", "researcher": {"href": "https://publications.scilifelab.se/researcher/bde445b76979400ab4543b9391007ff3.json"}}, {"family": "Burcelin", "given": "Remy", "initials": "R", "orcid": "0000-0002-7942-8346", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f8b823dbccc4a8ea0f9fac633de306e.json"}}, {"family": "Caesar", "given": "Robert", "initials": "R", "orcid": "0000-0003-1017-2933", "researcher": {"href": "https://publications.scilifelab.se/researcher/b93a81d0ccb7489cae0fbb2b6ab6464d.json"}}], "type": "journal article", "published": "2023-09-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5329", "issn-l": "2041-1723"}, "abstract": "Dietary lipids can affect metabolic health through gut microbiota-mediated mechanisms, but the influence of lipid-microbiota interaction on liver steatosis is largely unknown. We investigate the impact of dietary lipids on human gut microbiota composition and the effects of microbiota-lipid interactions on steatosis in male mice. In humans, low intake of saturated fatty acids (SFA) is associated with increased microbial diversity independent of fiber intake. In mice, poorly absorbed dietary long-chain SFA, particularly stearic acid, induce a shift in bile acid profile and improved metabolism and steatosis. These benefits are dependent on the gut microbiota, as they are transmitted by microbial transfer. Diets enriched in polyunsaturated fatty acids are protective against steatosis but have minor influence on the microbiota. In summary, we find that diets enriched in poorly absorbed long-chain SFA modulate gut microbiota profiles independent of fiber intake, and this interaction is relevant to improve metabolism and decrease liver steatosis.", "doi": "10.1038/s41467-023-41074-3", "pmid": "37658064", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10474162"}, {"db": "pii", "key": "10.1038/s41467-023-41074-3"}], "notes": [], "created": "2023-12-05T06:30:29.902Z", "modified": "2024-01-03T13:12:49.382Z"}, {"entity": "publication", "iuid": "b6d7787be6f54069811e84189b52b7ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6d7787be6f54069811e84189b52b7ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6d7787be6f54069811e84189b52b7ab"}}, "title": "Long-read whole-genome analysis of human single cells.", "authors": [{"family": "H\u00e5rd", "given": "Joanna", "initials": "J"}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C", "orcid": "0000-0003-0502-3693", "researcher": {"href": "https://publications.scilifelab.se/researcher/982873aade554b38b26b877298db5115.json"}}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Contreras-Lopez", "given": "Orlando", "initials": "O"}, {"family": "Chin", "given": "Chen-Shan", "initials": "CS", "orcid": "0000-0003-4394-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/58952eb371364939acef96efba96a143.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}], "type": "journal article", "published": "2023-08-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "5164"}, "abstract": "Long-read sequencing has dramatically increased our understanding of human genome variation. Here, we demonstrate that long-read technology can give new insights into the genomic architecture of individual cells. Clonally expanded CD8+ T-cells from a human donor were subjected to droplet-based multiple displacement amplification (dMDA) to generate long molecules with reduced bias. PacBio sequencing generated up to 40% genome coverage per single-cell, enabling detection of single nucleotide variants (SNVs), structural variants (SVs), and tandem repeats, also in regions inaccessible by short reads. 28 somatic SNVs were detected, including one case of mitochondrial heteroplasmy. 5473 high-confidence SVs/cell were discovered, a sixteen-fold increase compared to Illumina-based results from clonally related cells. Single-cell de novo assembly generated a genome size of up to 598 Mb and 1762 (12.8%) complete gene models. In summary, our work shows the promise of long-read sequencing toward characterization of the full spectrum of genetic variation in single cells.", "doi": "10.1038/s41467-023-40898-3", "pmid": "37620373", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Long read": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "NGI Single cell": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC10449900"}, {"db": "pii", "key": "10.1038/s41467-023-40898-3"}], "notes": [], "created": "2023-09-04T11:21:18.412Z", "modified": "2024-11-25T10:15:50.528Z"}, {"entity": "publication", "iuid": "f844bbd67bf042fb8e38b6243c0285ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f844bbd67bf042fb8e38b6243c0285ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f844bbd67bf042fb8e38b6243c0285ef"}}, "title": "Atomic-level structure determination of amorphous molecular solids by NMR.", "authors": [{"family": "Cordova", "given": "Manuel", "initials": "M", "orcid": "0000-0002-8722-6541", "researcher": {"href": "https://publications.scilifelab.se/researcher/edb1d673895f4e54a2c6c15c4e632c53.json"}}, {"family": "Moutzouri", "given": "Pinelopi", "initials": "P"}, {"family": "Nilsson Lill", "given": "Sten O", "initials": "SO"}, {"family": "Cousen", "given": "Alexander", "initials": "A"}, {"family": "Kearns", "given": "Martin", "initials": "M"}, {"family": "Norberg", "given": "Stefan T", "initials": "ST", "orcid": "0000-0003-4556-1920", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2f3c395447c4a20b9a2bcf6e2defa60.json"}}, {"family": "Svensk Ankarberg", "given": "Anna", "initials": "A", "orcid": "0000-0003-1092-4453", "researcher": {"href": "https://publications.scilifelab.se/researcher/de3c12490dd1421dbdc28cff6ef5ece0.json"}}, {"family": "McCabe", "given": "James", "initials": "J"}, {"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": "Emsley", "given": "Lyndon", "initials": "L", "orcid": "0000-0003-1360-2572", "researcher": {"href": "https://publications.scilifelab.se/researcher/d035a7c9c3c34fbda5feaa334a550910.json"}}], "type": "journal article", "published": "2023-08-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5138", "issn-l": "2041-1723"}, "abstract": "Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder leads to a high degree of overlap between measured signals, and prevents the unambiguous identification of a single modeled periodic structure as representative of the whole material. Here, we determine the atomic-level ensemble structure of the amorphous form of the drug AZD4625 by combining solid-state NMR experiments with molecular dynamics (MD) simulations and machine-learned chemical shifts. By considering the combined shifts of all 1H and 13C atomic sites in the molecule, we determine the structure of the amorphous form by identifying an ensemble of local molecular environments that are in agreement with experiment. We then extract and analyze preferred conformations and intermolecular interactions in the amorphous sample in terms of the stabilization of the amorphous form of the drug.", "doi": "10.1038/s41467-023-40853-2", "pmid": "37612269", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10447443"}, {"db": "pii", "key": "10.1038/s41467-023-40853-2"}], "notes": [], "created": "2023-12-04T09:35:32.277Z", "modified": "2025-10-17T13:03:53.564Z"}, {"entity": "publication", "iuid": "36f146b5c7b14bbca774b45612b1d3ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36f146b5c7b14bbca774b45612b1d3ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36f146b5c7b14bbca774b45612b1d3ec"}}, "title": "An idiosyncratic zonated stroma encapsulates desmoplastic liver metastases and originates from injured liver.", "authors": [{"family": "Fern\u00e1ndez Moro", "given": "Carlos", "initials": "C", "orcid": "0000-0001-6863-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/216d382919954ccfb4b47458bb3d9b08.json"}}, {"family": "Geyer", "given": "Natalie", "initials": "N"}, {"family": "Harrizi", "given": "Sara", "initials": "S"}, {"family": "Hamidi", "given": "Yousra", "initials": "Y"}, {"family": "S\u00f6derqvist", "given": "Sara", "initials": "S"}, {"family": "Kuznyecov", "given": "Danyil", "initials": "D", "orcid": "0009-0007-8218-557X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b48e050665d04e4da8484bcf6da5cc96.json"}}, {"family": "Tidholm Qvist", "given": "Evelina", "initials": "E"}, {"family": "Salmonson Schaad", "given": "Media", "initials": "M"}, {"family": "Hermann", "given": "Laura", "initials": "L"}, {"family": "Lindberg", "given": "Amanda", "initials": "A"}, {"family": "Heuchel", "given": "Rainer L", "initials": "RL", "orcid": "0000-0002-2782-585X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf96c4ef4e8c4d64bcbffdcaa994258b.json"}}, {"family": "Mart\u00edn-Bernab\u00e9", "given": "Alfonso", "initials": "A"}, {"family": "Dhanjal", "given": "Soniya", "initials": "S"}, {"family": "Navis", "given": "Anna C", "initials": "AC", "orcid": "0000-0002-5267-4678", "researcher": {"href": "https://publications.scilifelab.se/researcher/e89ad1a255984dd2ba50d83c3c0c628f.json"}}, {"family": "Villard", "given": "Christina", "initials": "C"}, {"family": "Del Valle", "given": "Andrea C", "initials": "AC", "orcid": "0000-0002-1698-9533", "researcher": {"href": "https://publications.scilifelab.se/researcher/52990e30c09c48cbbd0f39f90ab25994.json"}}, {"family": "Boz\u00f3ky", "given": "Lorand", "initials": "L"}, {"family": "Sparrelid", "given": "Ernesto", "initials": "E"}, {"family": "Dirix", "given": "Luc", "initials": "L", "orcid": "0000-0002-6248-1677", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f1a10889290412e9257e79899aef2e9.json"}}, {"family": "Strell", "given": "Carina", "initials": "C"}, {"family": "\u00d6stman", "given": "Arne", "initials": "A", "orcid": "0000-0003-3993-0021", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa382835e9554f5db45fa6cd86f04eab.json"}}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Vermeulen", "given": "Peter B", "initials": "PB"}, {"family": "Engstrand", "given": "Jennie", "initials": "J", "orcid": "0000-0003-1123-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef6292473b94b3b90e78745841cdeaa.json"}}, {"family": "Boz\u00f3ky", "given": "B\u00e9la", "initials": "B"}, {"family": "Gerling", "given": "Marco", "initials": "M", "orcid": "0000-0002-1810-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f9aa5d37124e379eb160737d657bab.json"}}], "type": "journal article", "published": "2023-08-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5024", "issn-l": "2041-1723"}, "abstract": "A perimetastatic capsule is a strong positive prognostic factor in liver metastases, but its origin remains unclear. Here, we systematically quantify the capsule's extent and cellular composition in 263 patients with colorectal cancer liver metastases to investigate its clinical significance and origin. We show that survival improves proportionally with increasing encapsulation and decreasing tumor-hepatocyte contact. Immunostaining reveals the gradual zonation of the capsule, transitioning from benign-like NGFRhigh stroma at the liver edge to FAPhigh stroma towards the tumor. Encapsulation correlates with decreased tumor viability and preoperative chemotherapy. In mice, chemotherapy and tumor cell ablation induce capsule formation. Our results suggest that encapsulation develops where tumor invasion into the liver plates stalls, representing a reparative process rather than tumor-induced desmoplasia. We propose a model of metastases growth, where the efficient tumor colonization of the liver parenchyma and a reparative liver injury reaction are opposing determinants of metastasis aggressiveness.", "doi": "10.1038/s41467-023-40688-x", "pmid": "37596278", "labels": {"CRISPR Functional Genomics": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10439160"}, {"db": "pii", "key": "10.1038/s41467-023-40688-x"}], "notes": [], "created": "2023-08-20T11:51:56.440Z", "modified": "2023-10-19T12:56:35.044Z"}, {"entity": "publication", "iuid": "5695e3006598431b9d0bd2133b29f905", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5695e3006598431b9d0bd2133b29f905.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5695e3006598431b9d0bd2133b29f905"}}, "title": "GATA2 mitotic bookmarking is required for definitive haematopoiesis.", "authors": [{"family": "Silv\u00e9rio-Alves", "given": "Rita", "initials": "R", "orcid": "0000-0002-4630-171X", "researcher": {"href": "https://publications.scilifelab.se/researcher/95cc1af96c174d469798042f673c9fed.json"}}, {"family": "Kurochkin", "given": "Ilia", "initials": "I", "orcid": "0000-0003-3100-0903", "researcher": {"href": "https://publications.scilifelab.se/researcher/215e3195c7a943578f6fc51e367fb3af.json"}}, {"family": "Rydstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0002-3404-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c074907dfd84c9c9d90a21fe426f1af.json"}}, {"family": "Vazquez Echegaray", "given": "Camila", "initials": "C", "orcid": "0000-0001-8849-6853", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8be89104abe46fd9367798bf0861392.json"}}, {"family": "Haider", "given": "Jakob", "initials": "J", "orcid": "0009-0004-8878-829X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4feef9203389416c8e27e5fe0a90a3f8.json"}}, {"family": "Nicholls", "given": "Matthew", "initials": "M", "orcid": "0000-0003-1161-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/52e5c2ab1a6745b8873f2b29f3dfbb73.json"}}, {"family": "Rode", "given": "Christina", "initials": "C"}, {"family": "Thelaus", "given": "Louise", "initials": "L"}, {"family": "Lindgren", "given": "Aida Yifter", "initials": "AY"}, {"family": "Ferreira", "given": "Alexandra Gabriela", "initials": "AG", "orcid": "0000-0001-8918-1183", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec9f547e3c394728bbd4c87c63560d0c.json"}}, {"family": "Brand\u00e3o", "given": "Rafael", "initials": "R"}, {"family": "Larsson", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9198-7434", "researcher": {"href": "https://publications.scilifelab.se/researcher/89b5caecc2ec48edb49d37e08a7665e1.json"}}, {"family": "de Bruijn", "given": "Marella F T R", "initials": "MFTR", "orcid": "0000-0002-4934-4125", "researcher": {"href": "https://publications.scilifelab.se/researcher/f30aeb359f684a509ceb4fe00559bc13.json"}}, {"family": "Martin-Gonzalez", "given": "Javier", "initials": "J", "orcid": "0000-0002-7075-6028", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d3fc746a9444e15a5051d22c4271f28.json"}}, {"family": "Pereira", "given": "Carlos-Filipe", "initials": "CF", "orcid": "0000-0002-9724-1382", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b298bb485b744fdb87f51ad579d0a79.json"}}], "type": "journal article", "published": "2023-08-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "4645", "issn-l": "2041-1723"}, "abstract": "In mitosis, most transcription factors detach from chromatin, but some are retained and bookmark genomic sites. Mitotic bookmarking has been implicated in lineage inheritance, pluripotency and reprogramming. However, the biological significance of this mechanism in vivo remains unclear. Here, we address mitotic retention of the hemogenic factors GATA2, GFI1B and FOS during haematopoietic specification. We show that GATA2 remains bound to chromatin throughout mitosis, in contrast to GFI1B and FOS, via C-terminal zinc finger-mediated DNA binding. GATA2 bookmarks a subset of its interphase targets that are co-enriched for RUNX1 and other regulators of definitive haematopoiesis. Remarkably, homozygous mice harbouring the cyclin B1 mitosis degradation domain upstream Gata2 partially phenocopy knockout mice. Degradation of GATA2 at mitotic exit abolishes definitive haematopoiesis at aorta-gonad-mesonephros, placenta and foetal liver, but does not impair yolk sac haematopoiesis. Our findings implicate GATA2-mediated mitotic bookmarking as critical for definitive haematopoiesis and highlight a dependency on bookmarkers for lineage commitment.", "doi": "10.1038/s41467-023-40391-x", "pmid": "37580379", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10425459"}, {"db": "pii", "key": "10.1038/s41467-023-40391-x"}], "notes": [], "created": "2023-11-21T18:57:44.537Z", "modified": "2024-11-26T09:11:59.518Z"}, {"entity": "publication", "iuid": "0f4b2f133342404c882907cf77fe61be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f4b2f133342404c882907cf77fe61be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f4b2f133342404c882907cf77fe61be"}}, "title": "Complementarity-determining region clustering may cause CAR-T cell dysfunction.", "authors": [{"family": "Sar\u00e9n", "given": "Tina", "initials": "T", "orcid": "0000-0001-5227-6779", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8f06b113565445f8dc2882a926229b6.json"}}, {"family": "Saronio", "given": "Giulia", "initials": "G"}, {"family": "Marti Torrell", "given": "Paula", "initials": "P"}, {"family": "Zhu", "given": "Xu", "initials": "X"}, {"family": "Thelander", "given": "Josefin", "initials": "J"}, {"family": "Andersson", "given": "Yasmin", "initials": "Y"}, {"family": "Hofstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Nestor", "given": "Marika", "initials": "M"}, {"family": "Dimberg", "given": "Anna", "initials": "A", "orcid": "0000-0003-4422-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/c53166298a214331866c8cbf3bb9a3b9.json"}}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M", "orcid": "0000-0003-2685-0575", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3fefc78a0b040faa998efb8fde7b920.json"}}, {"family": "Yu", "given": "Di", "initials": "D", "orcid": "0000-0002-8636-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfc1c71920c74292b4392a2ee108998d.json"}}, {"family": "Essand", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9725-0422", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5afc47ab0814c09909af3c66217a3a6.json"}}], "type": "journal article", "published": "2023-08-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4732"}, "abstract": "Chimeric antigen receptor (CAR)-T cell therapy is rapidly advancing as cancer treatment, however, designing an optimal CAR remains challenging. A single-chain variable fragment (scFv) is generally used as CAR targeting moiety, wherein the complementarity-determining regions (CDRs) define its specificity. We report here that the CDR loops can cause CAR clustering, leading to antigen-independent tonic signalling and subsequent CAR-T cell dysfunction. We show via CARs incorporating scFvs with identical framework and varying CDR sequences that CARs may cluster on the T cell surface, which leads to antigen-independent CAR-T cell activation, characterized by increased cell size and interferon (IFN)-\u03b3 secretion. This results in CAR-T cell exhaustion, activation-induced cell death and reduced responsiveness to target-antigen-expressing tumour cells. CDR mutagenesis confirms that the CAR-clustering is mediated by CDR-loops. In summary, antigen-independent tonic signalling can be induced by CDR-mediated CAR clustering, which could not be predicted from the scFv sequences, but could be tested for by evaluating the activity of unstimulated CAR-T cells.", "doi": "10.1038/s41467-023-40303-z", "pmid": "37563127", "labels": {"Global Proteomics and Proteogenomics": "Service", "Bioinformatics Support for Computational Resources": "Service", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10415375"}, {"db": "pii", "key": "10.1038/s41467-023-40303-z"}], "notes": [], "created": "2023-08-14T06:46:42.174Z", "modified": "2025-10-17T13:05:07.543Z"}, {"entity": "publication", "iuid": "f33c20d74f204c0e85888aad80e6bae6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f33c20d74f204c0e85888aad80e6bae6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f33c20d74f204c0e85888aad80e6bae6"}}, "title": "Genetic insights into resting heart rate and its role in cardiovascular disease.", "authors": [{"family": "van de Vegte", "given": "Yordi J", "initials": "YJ", "orcid": "0000-0002-6689-0144", "researcher": {"href": "https://publications.scilifelab.se/researcher/9edbd70a05e140da86f8a115a8cfa913.json"}}, {"family": "Eppinga", "given": "Ruben N", "initials": "RN"}, {"family": "van der Ende", "given": "M Yldau", "initials": "MY"}, {"family": "Hagemeijer", "given": "Yanick P", "initials": "YP", "orcid": "0000-0001-6036-3741", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3c9fe93b0e04102b0298e2d08a7503c.json"}}, {"family": "Mahendran", "given": "Yuvaraj", "initials": "Y"}, {"family": "Salfati", "given": "Elias", "initials": "E"}, {"family": "Smith", "given": "Albert V", "initials": "AV", "orcid": "0000-0003-1942-5845", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b28739aa7d746718d670363d7c18a40.json"}}, {"family": "Tan", "given": "Vanessa Y", "initials": "VY"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Appel", "given": "Emil V", "initials": "EV"}, {"family": "Schurmann", "given": "Claudia", "initials": "C", "orcid": "0000-0003-4158-9192", "researcher": {"href": "https://publications.scilifelab.se/researcher/357aae1711d34a0e993b10c93c73cfb4.json"}}, {"family": "Brody", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0001-8509-148X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e137fc0192e4fa295a88589d57e3498.json"}}, {"family": "Rueedi", "given": "Rico", "initials": "R"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Sveinbjornsson", "given": "Gardar", "initials": "G", "orcid": "0000-0003-2429-9468", "researcher": {"href": "https://publications.scilifelab.se/researcher/edcfa2e1ad7f44d883bb2de28708bf50.json"}}, {"family": "Lecoeur", "given": "Cecile", "initials": "C", "orcid": "0000-0003-0075-6417", "researcher": 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"https://publications.scilifelab.se/researcher/7e9bdbf58ae94fc8b455bbbcbcaa50ce.json"}}, {"family": "Hicks", "given": "Andrew A", "initials": "AA", "orcid": "0000-0001-6320-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/a679db3cfdb6408b8f1a009534d7b902.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Kiemeney", "given": "Lambertus A L M", "initials": "LALM", "orcid": "0000-0002-2368-1326", "researcher": {"href": "https://publications.scilifelab.se/researcher/b174fc0d7ae44de6bba97a2f816ba695.json"}}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Wilson", "given": "James F", "initials": "JF", "orcid": "0000-0001-5751-9178", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39e6e0f7210494cb4f80be0f7413b6f.json"}}, {"family": "Burgess", "given": "Stephen", "initials": "S", "orcid": "0000-0001-5365-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd2dcaf4dbb4e4c91c2af460b8fa98f.json"}}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "Lieb", "given": "Wolfgang", "initials": "W", "orcid": "0000-0003-2544-4460", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6b229457c2c4b25ae9c7d2cf029b82b.json"}}, {"family": "Jukema", "given": "J Wouter", "initials": "JW", "orcid": "0000-0002-3246-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479b794031d4df7bed96340b3470c19.json"}}, {"family": "Eijgelsheim", "given": "Mark", "initials": "M"}, {"family": "Lakatta", "given": "Edward L M", "initials": "ELM", "orcid": "0000-0002-4772-0035", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc797241e3fa45d7b9d8438568414f2a.json"}}, {"family": "Cheng", "given": "Ching-Yu", "initials": "C"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M", "orcid": "0000-0001-7471-475X", "researcher": {"href": "https://publications.scilifelab.se/researcher/346fa1fbeb2e474b94f189d52d7cfb1c.json"}}, {"family": "Wong", "given": "Tien-Yin", "initials": "T"}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C", "orcid": "0000-0002-4042-4719", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5ac2397f6b14194949f4dbb92a21eba.json"}}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ", "orcid": "0000-0003-3925-3913", "researcher": {"href": "https://publications.scilifelab.se/researcher/65ee5f9938f547bcbe51cbaf5fd7a9ba.json"}}, {"family": "Riese", "given": "Harriette", "initials": "H"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T", "orcid": "0000-0002-2555-4427", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ed59707dae4c8fb9e63ac1f7c398e3.json"}}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}], "type": "meta-analysis", "published": "2023-08-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4646"}, "abstract": "Resting heart rate is associated with cardiovascular diseases and mortality in observational and Mendelian randomization studies. The aims of this study are to extend the number of resting heart rate associated genetic variants and to obtain further insights in resting heart rate biology and its clinical consequences. A genome-wide meta-analysis of 100 studies in up to 835,465 individuals reveals 493 independent genetic variants in 352 loci, including 68 genetic variants outside previously identified resting heart rate associated loci. We prioritize 670 genes and in silico annotations point to their enrichment in cardiomyocytes and provide insights in their ECG signature. Two-sample Mendelian randomization analyses indicate that higher genetically predicted resting heart rate increases risk of dilated cardiomyopathy, but decreases risk of developing atrial fibrillation, ischemic stroke, and cardio-embolic stroke. We do not find evidence for a linear or non-linear genetic association between resting heart rate and all-cause mortality in contrast to our previous Mendelian randomization study. Systematic alteration of key differences between the current and previous Mendelian randomization study indicates that the most likely cause of the discrepancy between these studies arises from false positive findings in previous one-sample MR analyses caused by weak-instrument bias at lower P-value thresholds. The results extend our understanding of resting heart rate biology and give additional insights in its role in cardiovascular disease development.", "doi": "10.1038/s41467-023-39521-2", "pmid": "37532724", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10397318"}, {"db": "pii", "key": "10.1038/s41467-023-39521-2"}], "notes": [], "created": "2023-08-14T06:18:27.304Z", "modified": "2023-11-30T22:39:21.180Z"}, {"entity": "publication", "iuid": "cac2b2a5dca44746b91a68788dce04df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cac2b2a5dca44746b91a68788dce04df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cac2b2a5dca44746b91a68788dce04df"}}, "title": "Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age.", "authors": [{"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P", "orcid": "0000-0003-4452-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/035ae0d32cf649f6a82c6e4df78cc122.json"}}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Ehler", "given": "Edvard", "initials": "E", "orcid": "0000-0003-1774-0091", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d5e30a4e46e47d8b800d5242e23d7de.json"}}, {"family": "Breszka", "given": "Agnieszka", "initials": "A"}, {"family": "G\u00f3rski", "given": "Jacek", "initials": "J"}, {"family": "Taras", "given": "Halina", "initials": "H"}, {"family": "Szczepanek", "given": "Anita", "initials": "A"}, {"family": "Pola\u0144ska", "given": "Marta", "initials": "M"}, {"family": "W\u0142odarczak", "given": "Piotr", "initials": "P", "orcid": "0000-0003-0359-7386", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4581e4213be44969693180b26b3f263.json"}}, {"family": "Lasota-Ku\u015b", "given": "Anna", "initials": "A", "orcid": "0000-0002-0603-846X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8716e836f3894e28bee1bcacffb7245a.json"}}, {"family": "W\u00f3jcik", "given": "Irena", "initials": "I"}, {"family": "Romaniszyn", "given": "Jan", "initials": "J"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Ko\u015bko", "given": "Aleksander", "initials": "A"}, {"family": "Ignaczak", "given": "Marcin", "initials": "M"}, {"family": "Sadowski", "given": "Sylwester", "initials": "S"}, {"family": "Matoga", "given": "Andrzej", "initials": "A"}, {"family": "Grossman", "given": "Anna", "initials": "A"}, {"family": "Ilchyshyn", "given": "Vasyl", "initials": "V"}, {"family": "Yahodinska", "given": "Maryna O", "initials": "MO"}, {"family": "Roma\u0144ska", "given": "Adriana", "initials": "A"}, {"family": "Tunia", "given": "Krzysztof", "initials": "K"}, {"family": "Przyby\u0142a", "given": "Marcin", "initials": "M"}, {"family": "Grygiel", "given": "Ryszard", "initials": "R"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}], "type": "historical article", "published": "2023-08-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4395"}, "abstract": "The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.", "doi": "10.1038/s41467-023-40072-9", "pmid": "37528090", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10393988"}, {"db": "pii", "key": "10.1038/s41467-023-40072-9"}], "notes": [], "created": "2023-10-19T12:43:53.699Z", "modified": "2024-01-16T13:48:32.641Z"}, {"entity": "publication", "iuid": "295aef354d21417f9b1d254f7f751005", "links": {"self": {"href": "https://publications.scilifelab.se/publication/295aef354d21417f9b1d254f7f751005.json"}, "display": {"href": "https://publications.scilifelab.se/publication/295aef354d21417f9b1d254f7f751005"}}, "title": "Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature.", "authors": [{"family": "Lihavainen", "given": "Jenna", "initials": "J", "orcid": "0000-0001-7979-8876", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab4d87f8aed74a9794dea29912031a93.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J"}, {"family": "Bag", "given": "Pushan", "initials": "P", "orcid": "0000-0003-3858-4606", "researcher": {"href": "https://publications.scilifelab.se/researcher/033b97dc712047a294d3e801ba750787.json"}}, {"family": "Fataftah", "given": "Nazeer", "initials": "N"}, {"family": "Robinson", "given": "Kathryn Megan", "initials": "KM", "orcid": "0000-0002-5249-604X", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d40626e73d49799c175a2ea14f5626.json"}}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "4288", "issn-l": "2041-1723"}, "abstract": "Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive \"switches\"; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.", "doi": "10.1038/s41467-023-39564-5", "pmid": "37463905", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10354028"}, {"db": "pii", "key": "10.1038/s41467-023-39564-5"}], "notes": [], "created": "2023-08-30T07:04:20.536Z", "modified": "2025-10-17T13:03:13.717Z"}, {"entity": "publication", "iuid": "bd7e4686333d489495edae6e2cb9e54a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a"}}, "title": "Next generation pan-cancer blood proteome profiling using proximity extension assay.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Lundin", "given": "Emma", "initials": "E", "orcid": "0009-0000-7711-1962", "researcher": {"href": "https://publications.scilifelab.se/researcher/06761839da88443e9098d9562810fb7f.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N", "orcid": "0000-0002-7835-4357", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1b2d0ce6ea452b82a35c603a073eb1.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Lindman", "given": "Henrik", "initials": "H"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9613-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/978fc6fea7d54f5b81a8b5a87efa083a.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Enblad", "given": "Malin", "initials": "M", "orcid": "0000-0001-5900-0900", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e801966db544e6286fb2b4037980dba.json"}}, {"family": "Simonson", "given": "Oscar E", "initials": "OE", "orcid": "0000-0002-3552-5558", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a52b4426da84787aeb56b8d6232ba87.json"}}, {"family": "H\u00e4ggman", "given": "Michael", "initials": "M"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.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": "2023-07-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4308"}, "abstract": "A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.", "doi": "10.1038/s41467-023-39765-y", "pmid": "37463882", "labels": {"Affinity Proteomics Uppsala": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10354027"}, {"db": "pii", "key": "10.1038/s41467-023-39765-y"}], "notes": [], "created": "2023-11-29T19:16:18.991Z", "modified": "2024-01-16T13:48:32.880Z"}, {"entity": "publication", "iuid": "1e042f602f324b7eb585860df4f9dcc5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e042f602f324b7eb585860df4f9dcc5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e042f602f324b7eb585860df4f9dcc5"}}, "title": "Unmodified rabies mRNA vaccine elicits high cross-neutralizing antibody titers and diverse B cell memory responses.", "authors": [{"family": "Hellgren", "given": "Fredrika", "initials": "F"}, {"family": "Cagigi", "given": "Alberto", "initials": "A"}, {"family": "Arcoverde Cerveira", "given": "Rodrigo", "initials": "R", "orcid": "0000-0002-1145-2534", "researcher": {"href": "https://publications.scilifelab.se/researcher/df30915fb0e849609871f5237a33ff2b.json"}}, {"family": "Ols", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-9784-7176", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1343e56a87f49c4abc7beb6f36b87c1.json"}}, {"family": "Kern", "given": "Theresa", "initials": "T", "orcid": "0009-0000-0151-5442", "researcher": {"href": "https://publications.scilifelab.se/researcher/da58a11a6fcc47babadfd35a7fdae808.json"}}, {"family": "Lin", "given": "Ang", "initials": "A"}, {"family": "Eriksson", "given": "Bengt", "initials": "B"}, {"family": "Dodds", "given": "Michael G", "initials": "MG"}, {"family": "Jasny", "given": "Edith", "initials": "E"}, {"family": "Schwendt", "given": "Kim", "initials": "K"}, {"family": "Freuling", "given": "Conrad", "initials": "C"}, {"family": "M\u00fcller", "given": "Thomas", "initials": "T"}, {"family": "Corcoran", "given": "Martin", "initials": "M"}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB"}, {"family": "Petsch", "given": "Benjamin", "initials": "B"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K", "orcid": "0000-0001-7679-9494", "researcher": {"href": "https://publications.scilifelab.se/researcher/737245a5bc2144bd90be71487cbb3192.json"}}], "type": "journal article", "published": "2023-06-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "3713", "issn-l": "2041-1723"}, "abstract": "Licensed rabies virus vaccines based on whole inactivated virus are effective in humans. However, there is a lack of detailed investigations of the elicited immune response, and whether responses can be improved using novel vaccine platforms. Here we show that two doses of a lipid nanoparticle-formulated unmodified mRNA vaccine encoding the rabies virus glycoprotein (RABV-G) induces higher levels of RABV-G specific plasmablasts and T cells in blood, and plasma cells in the bone marrow compared to two doses of Rabipur in non-human primates. The mRNA vaccine also generates higher RABV-G binding and neutralizing antibody titers than Rabipur, while the degree of somatic hypermutation and clonal diversity of the response are similar for the two vaccines. The higher overall antibody titers induced by the mRNA vaccine translates into improved cross-neutralization of related lyssavirus strains, suggesting that this platform has potential for the development of a broadly protective vaccine against these viruses.", "doi": "10.1038/s41467-023-39421-5", "pmid": "37349310", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10287699"}, {"db": "pii", "key": "10.1038/s41467-023-39421-5"}], "notes": [], "created": "2023-12-01T12:29:38.796Z", "modified": "2024-01-16T13:48:33.121Z"}, {"entity": "publication", "iuid": "fe2a0c6262d54bd08331f61bf5aa938e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe2a0c6262d54bd08331f61bf5aa938e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe2a0c6262d54bd08331f61bf5aa938e"}}, "title": "Flavodiiron-mediated O2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring.", "authors": [{"family": "Bag", "given": "Pushan", "initials": "P", "orcid": "0000-0003-3858-4606", "researcher": {"href": "https://publications.scilifelab.se/researcher/033b97dc712047a294d3e801ba750787.json"}}, {"family": "Shutova", "given": "Tatyana", "initials": "T"}, {"family": "Shevela", "given": "Dmitry", "initials": "D", "orcid": "0000-0002-5174-083X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2fe5ffea7ec45e3a9fa3e6a0f0854d8.json"}}, {"family": "Lihavainen", "given": "Jenna", "initials": "J", "orcid": "0000-0001-7979-8876", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab4d87f8aed74a9794dea29912031a93.json"}}, {"family": "Nanda", "given": "Sanchali", "initials": "S", "orcid": "0000-0002-6694-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e8ebdfe862142b39a0ebb0a5946a516.json"}}, {"family": "Ivanov", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-7910-5494", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cc5e19a40374d67a3ae74182c5dae6f.json"}}, {"family": "Messinger", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2790-7721", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d8388d9249849f4b45d7a891c71c0ff.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}], "type": "journal article", "published": "2023-06-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "3210", "issn-l": "2041-1723"}, "abstract": "Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.", "doi": "10.1038/s41467-023-38938-z", "pmid": "37270605", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10239515"}, {"db": "pii", "key": "10.1038/s41467-023-38938-z"}], "notes": [], "created": "2023-12-03T19:50:55.791Z", "modified": "2025-10-17T13:03:13.797Z"}, {"entity": "publication", "iuid": "dd973b0ce8ea40e58c5a41de25f1b570", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd973b0ce8ea40e58c5a41de25f1b570.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd973b0ce8ea40e58c5a41de25f1b570"}}, "title": "Directionality of developing skeletal muscles is set by mechanical forces.", "authors": [{"family": "Sunadome", "given": "Kazunori", "initials": "K"}, {"family": "Erickson", "given": "Alek G", "initials": "AG"}, {"family": "Kah", "given": "Delf", "initials": "D", "orcid": "0000-0002-3800-2461", "researcher": {"href": "https://publications.scilifelab.se/researcher/2feb3ab785af4c0991d02ee953a18b8c.json"}}, {"family": "Fabry", "given": "Ben", "initials": "B", "orcid": "0000-0003-1737-0465", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f391e2904d14618830d1f3cb993bf60.json"}}, {"family": "Adori", "given": "Csaba", "initials": "C"}, {"family": "Kameneva", "given": "Polina", "initials": "P"}, {"family": "Faure", "given": "Louis", "initials": "L", "orcid": "0000-0003-4621-586X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbf218e53c854d69a1b474a61480c33f.json"}}, {"family": "Kanatani", "given": "Shigeaki", "initials": "S", "orcid": "0000-0003-2226-4288", "researcher": {"href": "https://publications.scilifelab.se/researcher/355335d5d964416883ccf63a312b69db.json"}}, {"family": "Kaucka", "given": "Marketa", "initials": "M", "orcid": "0000-0002-8781-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/933187e42ddc4ab6a29c46d5cca411e6.json"}}, {"family": "Dehnisch Ellstr\u00f6m", "given": "Ivar", "initials": "I"}, {"family": "Tesarova", "given": "Marketa", "initials": "M", "orcid": "0000-0002-5200-7365", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad2bf55bfa2240458ad9a4d73fe9baff.json"}}, {"family": "Zikmund", "given": "Tomas", "initials": "T", "orcid": "0000-0003-2948-5198", "researcher": {"href": "https://publications.scilifelab.se/researcher/7648df9d2584437d8388fab4a130d4eb.json"}}, {"family": "Kaiser", "given": "Jozef", "initials": "J", "orcid": "0000-0002-7397-125X", "researcher": {"href": "https://publications.scilifelab.se/researcher/98b611052bed483eb58f6ac51b35e003.json"}}, {"family": "Edwards", "given": "Steven", "initials": "S"}, {"family": "Maki", "given": "Koichiro", "initials": "K"}, {"family": "Adachi", "given": "Taiji", "initials": "T", "orcid": "0000-0001-5280-4156", "researcher": {"href": "https://publications.scilifelab.se/researcher/a13e752761974a339df29fd35873a6f2.json"}}, {"family": "Yamamoto", "given": "Takuya", "initials": "T"}, {"family": "Fried", "given": "Kaj", "initials": "K", "orcid": "0000-0002-9997-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46eaae026524ee6b9b589f12846b458.json"}}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}], "type": "journal article", "published": "2023-05-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "3060", "issn-l": "2041-1723"}, "abstract": "Formation of oriented myofibrils is a key event in musculoskeletal development. However, the mechanisms that drive myocyte orientation and fusion to control muscle directionality in adults remain enigmatic. Here, we demonstrate that the developing skeleton instructs the directional outgrowth of skeletal muscle and other soft tissues during limb and facial morphogenesis in zebrafish and mouse. Time-lapse live imaging reveals that during early craniofacial development, myoblasts condense into round clusters corresponding to future muscle groups. These clusters undergo oriented stretch and alignment during embryonic growth. Genetic perturbation of cartilage patterning or size disrupts the directionality and number of myofibrils in vivo. Laser ablation of musculoskeletal attachment points reveals tension imposed by cartilage expansion on the forming myofibers. Application of continuous tension using artificial attachment points, or stretchable membrane substrates, is sufficient to drive polarization of myocyte populations in vitro. Overall, this work outlines a biomechanical guidance mechanism that is potentially useful for engineering functional skeletal muscle.", "doi": "10.1038/s41467-023-38647-7", "pmid": "37244931", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10224984"}, {"db": "pii", "key": "10.1038/s41467-023-38647-7"}], "notes": [], "created": "2023-06-07T08:57:26.323Z", "modified": "2023-06-07T08:57:26.672Z"}, {"entity": "publication", "iuid": "8e4409137b2d4a079106e80bc6f25610", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e4409137b2d4a079106e80bc6f25610.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e4409137b2d4a079106e80bc6f25610"}}, "title": "Cisplatin toxicity is counteracted by the activation of the p38/ATF-7 signaling pathway in post-mitotic C. elegans.", "authors": [{"family": "Raj", "given": "Dorota", "initials": "D", "orcid": "0000-0002-7357-2902", "researcher": {"href": "https://publications.scilifelab.se/researcher/23ff7c388c2b43e3a9d3a3514fe5e049.json"}}, {"family": "Kraish", "given": "Bashar", "initials": "B"}, {"family": "Martikainen", "given": "Jari", "initials": "J", "orcid": "0000-0003-0366-1683", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfd56b6dfb74494890131a51097996d8.json"}}, {"family": "Podraza-Farhanieh", "given": "Agnieszka", "initials": "A", "orcid": "0000-0002-1120-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/8244c5dad7974bc0a2a4ec38cc3e58ce.json"}}, {"family": "Kao", "given": "Gautam", "initials": "G", "orcid": "0000-0003-1313-3024", "researcher": {"href": "https://publications.scilifelab.se/researcher/4575b678a90740428136c9f5e1bdd53b.json"}}, {"family": "Naredi", "given": "Peter", "initials": "P", "orcid": "0000-0002-5652-0422", "researcher": {"href": "https://publications.scilifelab.se/researcher/a41ccd84008a4a94a29410451bc012c9.json"}}], "type": "journal article", "published": "2023-05-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "2886"}, "abstract": "Cisplatin kills proliferating cells via DNA damage but also has profound effects on post-mitotic cells in tumors, kidneys, and neurons. However, the effects of cisplatin on post-mitotic cells are still poorly understood. Among model systems, C. elegans adults are unique in having completely post-mitotic somatic tissues. The p38 MAPK pathway controls ROS detoxification via SKN-1/NRF and immune responses via ATF-7/ATF2. Here, we show that p38 MAPK pathway mutants are sensitive to cisplatin, but while cisplatin exposure increases ROS levels, skn-1 mutants are resistant. Cisplatin exposure leads to phosphorylation of PMK-1/MAPK and ATF-7 and the IRE-1/TRF-1 signaling module functions upstream of the p38 MAPK pathway to activate signaling. We identify the response proteins whose increased abundance depends on IRE-1/p38 MAPK activity as well as cisplatin exposure. Four of these proteins are necessary for protection from cisplatin toxicity, which is characterized by necrotic death. We conclude that the p38 MAPK pathway-driven proteins are crucial for adult cisplatin resilience.", "doi": "10.1038/s41467-023-38568-5", "pmid": "37210583", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Integrated Microscopy Technologies Gothenburg": "Service", "Glycoproteomics and MS Proteomics": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10199892"}, {"db": "pii", "key": "10.1038/s41467-023-38568-5"}], "notes": [], "created": "2023-11-30T22:37:44.515Z", "modified": "2024-01-16T13:46:27.417Z"}, {"entity": "publication", "iuid": "c763cc0d6be544df8e6de1820f63e0f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c763cc0d6be544df8e6de1820f63e0f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c763cc0d6be544df8e6de1820f63e0f9"}}, "title": "Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins.", "authors": [{"family": "Elliott", "given": "Kerryn", "initials": "K", "orcid": "0000-0001-9238-7879", "researcher": {"href": "https://publications.scilifelab.se/researcher/43d0bf4d07f44363ab3a0b97ecb22e36.json"}}, {"family": "Singh", "given": "Vinod Kumar", "initials": "VK", "orcid": "0000-0002-7556-2505", "researcher": {"href": "https://publications.scilifelab.se/researcher/944f79abc5034c889bf3086d20499997.json"}}, {"family": "Bostr\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0001-8199-8922", "researcher": {"href": "https://publications.scilifelab.se/researcher/22c73409ff7c49ccb84f63bb39480ec9.json"}}, {"family": "Larsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-1400-0119", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b196318c09a46d48ece9c8417be01ff.json"}}], "type": "journal article", "published": "2023-05-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "2701", "issn-l": "2041-1723"}, "abstract": "Decades ago, it was shown that proteins binding to DNA can quantitatively alter the formation of DNA damage by UV light. This established the principle of UV footprinting for non-intrusive study of protein-DNA contacts in living cells, albeit at limited scale and precision. Here, we perform deep base-resolution quantification of the principal UV damage lesion, the cyclobutane pyrimidine dimer (CPD), at select human promoter regions using targeted CPD sequencing. Several transcription factors exhibited distinctive and repeatable damage signatures indicative of site occupancy, involving strong (up to 17-fold) position-specific elevations and reductions in CPD formation frequency relative to naked DNA. Positive damage modulation at some ETS transcription factor binding sites coincided at base level with melanoma somatic mutation hotspots. Our work provides proof of concept for the study of protein-DNA interactions at individual loci using light and sequencing, and reveals widespread and potent modulation of UV damage in regulatory regions.", "doi": "10.1038/s41467-023-38266-2", "pmid": "37169761", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10175305"}, {"db": "pii", "key": "10.1038/s41467-023-38266-2"}], "notes": [], "created": "2023-10-04T12:37:44.184Z", "modified": "2023-10-19T11:55:43.881Z"}, {"entity": "publication", "iuid": "b04dac4df10a4c7091ec0ad6daefaba9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b04dac4df10a4c7091ec0ad6daefaba9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b04dac4df10a4c7091ec0ad6daefaba9"}}, "title": "Identification of three bacterial species associated with increased appendicular lean mass: the HUNT study.", "authors": [{"family": "Grahnemo", "given": "Louise", "initials": "L", "orcid": "0000-0001-5276-6612", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb1ac8fe74954a5db43e8e6538cf8235.json"}}, {"family": "Nethander", "given": "Maria", "initials": "M", "orcid": "0000-0003-3688-906X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53d61951f51c4d40bef24672866382cb.json"}}, {"family": "Coward", "given": "Eivind", "initials": "E"}, {"family": "Gabrielsen", "given": "Maiken Elvestad", "initials": "ME"}, {"family": "Sree", "given": "Satya", "initials": "S"}, {"family": "Billod", "given": "Jean-Marc", "initials": "J"}, {"family": "Sj\u00f6gren", "given": "Klara", "initials": "K"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Langhammer", "given": "Arnulf", "initials": "A"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}], "type": "journal article", "published": "2023-04-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "2250"}, "abstract": "Appendicular lean mass (ALM) associates with mobility and bone mineral density (BMD). While associations between gut microbiota composition and ALM have been reported, previous studies rely on relatively small sample sizes. Here, we determine the associations between prevalent gut microbes and ALM in large discovery and replication cohorts with information on relevant confounders within the population-based Norwegian HUNT cohort (n = 5196, including women and men). We show that the presence of three bacterial species - Coprococcus comes, Dorea longicatena, and Eubacterium ventriosum - are reproducibly associated with higher ALM. When combined into an anabolic species count, participants with all three anabolic species have 0.80 kg higher ALM than those without any. In an exploratory analysis, the anabolic species count is positively associated with femoral neck and total hip BMD. We conclude that the anabolic species count may be used as a marker of ALM and BMD. The therapeutic potential of these anabolic species to prevent sarcopenia and osteoporosis needs to be determined.", "doi": "10.1038/s41467-023-37978-9", "pmid": "37080991", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10119287"}, {"db": "pii", "key": "10.1038/s41467-023-37978-9"}], "notes": [], "created": "2023-06-16T15:12:34.469Z", "modified": "2023-11-30T22:34:44.953Z"}, {"entity": "publication", "iuid": "579194408fda4d8c9e4324e8a98dd4e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/579194408fda4d8c9e4324e8a98dd4e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/579194408fda4d8c9e4324e8a98dd4e1"}}, "title": "Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19.", "authors": [{"family": "Yu", "given": "Meng", "initials": "M", "orcid": "0000-0002-9798-6624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e0d4b3b53994166af0f2f7fd0679c6b.json"}}, {"family": "Charles", "given": "Afandi", "initials": "A", "orcid": "0000-0003-0022-3303", "researcher": {"href": "https://publications.scilifelab.se/researcher/29721279f6fb4c50a2f96d86a0ce9686.json"}}, {"family": "Cagigi", "given": "Alberto", "initials": "A"}, {"family": "Christ", "given": "Wanda", "initials": "W", "orcid": "0000-0003-3886-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe3a44fdb547b885cce5b6f490b2bc.json"}}, {"family": "\u00d6sterberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Falck-Jones", "given": "Sara", "initials": "S"}, {"family": "Azizmohammadi", "given": "Lida", "initials": "L"}, {"family": "\u00c5hlberg", "given": "Eric", "initials": "E"}, {"family": "Falck-Jones", "given": "Ryan", "initials": "R", "orcid": "0000-0002-0985-8658", "researcher": {"href": "https://publications.scilifelab.se/researcher/addfd2bdc37b4f7cb7bf4cb65183b153.json"}}, {"family": "Svensson", "given": "Julia", "initials": "J"}, {"family": "Nie", "given": "Mu", "initials": "M"}, {"family": "Warnqvist", "given": "Anna", "initials": "A"}, {"family": "Hellgren", "given": "Fredrika", "initials": "F"}, {"family": "Lenart", "given": "Klara", "initials": "K", "orcid": "0000-0002-4984-2618", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2e93a7400934289947153f095273178.json"}}, {"family": "Arcoverde Cerveira", "given": "Rodrigo", "initials": "R", "orcid": "0000-0002-1145-2534", "researcher": {"href": "https://publications.scilifelab.se/researcher/df30915fb0e849609871f5237a33ff2b.json"}}, {"family": "Ols", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-9784-7176", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1343e56a87f49c4abc7beb6f36b87c1.json"}}, {"family": "Lindgren", "given": "Gustaf", "initials": "G"}, {"family": "Lin", "given": "Ang", "initials": "A"}, {"family": "Maecker", "given": "Holden", "initials": "H", "orcid": "0000-0003-0795-9946", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3bcc923a42f4137a30d6ba7cb850d7f.json"}}, {"family": "Bell", "given": "Max", "initials": "M", "orcid": "0000-0001-7464-0324", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bf2fb404fae432aa21aa9eb34098efc.json"}}, {"family": "Johansson", "given": "Niclas", "initials": "N"}, {"family": "Albert", "given": "Jan", "initials": "J", "orcid": "0000-0001-9020-0521", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23f55d392eb411d90a53c2fb22aced3.json"}}, {"family": "Sundling", "given": "Christopher", "initials": "C", "orcid": "0000-0002-6138-690X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89c1e689a46b4b14adb0dc99e1c0a58c.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "F\u00e4rnert", "given": "Anna", "initials": "A"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K", "orcid": "0000-0001-7679-9494", "researcher": {"href": "https://publications.scilifelab.se/researcher/737245a5bc2144bd90be71487cbb3192.json"}}, {"family": "Smed-S\u00f6rensen", "given": "Anna", "initials": "A", "orcid": "0000-0001-6966-7039", "researcher": {"href": "https://publications.scilifelab.se/researcher/b874ce1e1fd4455e9d681c3d3db74ed0.json"}}], "type": "journal article", "published": "2023-04-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "2164"}, "abstract": "Effective humoral immune responses require well-orchestrated B and T follicular helper (Tfh) cell interactions. Whether these interactions are impaired and associated with COVID-19 disease severity is unclear. Here, longitudinal blood samples across COVID-19 disease severity are analysed. We find that during acute infection SARS-CoV-2-specific circulating Tfh (cTfh) cells expand with disease severity. SARS-CoV-2-specific cTfh cell frequencies correlate with plasmablast frequencies and SARS-CoV-2 antibody titers, avidity and neutralization. Furthermore, cTfh cells but not other memory CD4 T cells, from severe patients better induce plasmablast differentiation and antibody production compared to cTfh cells from mild patients. However, virus-specific cTfh cell development is delayed in patients that display or later develop severe disease compared to those with mild disease, which correlates with delayed induction of high-avidity neutralizing antibodies. Our study suggests that impaired generation of functional virus-specific cTfh cells delays high-quality antibody production at an early stage, potentially enabling progression to severe disease.", "doi": "10.1038/s41467-023-37835-9", "pmid": "37061513", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10105364"}, {"db": "pii", "key": "10.1038/s41467-023-37835-9"}], "notes": [], "created": "2023-04-21T13:16:11.901Z", "modified": "2023-11-16T14:36:19.050Z"}, {"entity": "publication", "iuid": "dfa9a3ae70d6467682de5c56e5f50b63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfa9a3ae70d6467682de5c56e5f50b63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfa9a3ae70d6467682de5c56e5f50b63"}}, "title": "Type I interferon shapes brain distribution and tropism of tick-borne flavivirus", "authors": [{"family": "Chotiwan", "given": "Nunya", "initials": "N", "orcid": "0000-0003-3214-6605", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba9da05817a4a8ea7037131000d6a7f.json"}}, {"family": "Rosendal", "given": "Ebba", "initials": "E"}, {"family": "Willekens", "given": "Stefanie M A", "initials": "SMA", "orcid": "0000-0003-3445-7829", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c73f555fa4948fcaed3377742873725.json"}}, {"family": "Schexnaydre", "given": "Erin", "initials": "E", "orcid": "0000-0002-2993-8647", "researcher": {"href": "https://publications.scilifelab.se/researcher/f643b7350ed5404aac418ce43d907f27.json"}}, {"family": "Nilsson", "given": "Emma", "initials": "E", "orcid": "0000-0001-8123-3292", "researcher": {"href": "https://publications.scilifelab.se/researcher/6070627ce8644379afe4a239a23c0f93.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Hahn", "given": "Max", "initials": "M", "orcid": "0000-0002-0712-8256", "researcher": {"href": "https://publications.scilifelab.se/researcher/563182c6e86b4107adf691eb73fdf31f.json"}}, {"family": "Mihai", "given": "Ionut Sebastian", "initials": "IS"}, {"family": "Morini", "given": "Federico", "initials": "F"}, {"family": "Zhang", "given": "Jianguo", "initials": "J"}, {"family": "Ebel", "given": "Gregory D", "initials": "GD", "orcid": "0000-0002-4458-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/f22f43706da74da783697a1d11c6d965.json"}}, {"family": "Carlson", "given": "Lars Anders", "initials": "LA", "orcid": "0000-0003-2342-6488", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba0e366ce21e49b48212bbed5a0a7bd1.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Ahlgren", "given": "Ulf", "initials": "U", "orcid": "0000-0001-5923-8572", "researcher": {"href": "https://publications.scilifelab.se/researcher/373ea8fda2264851aecc0078161884c8.json"}}, {"family": "Marcellino", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4618-7267", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8a6551237324a3f80a39921078d4183.json"}}, {"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": "2023-04-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-023-37698-0", "pmid": null, "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-19T14:40:58.557Z", "modified": "2024-01-19T14:40:58.874Z"}, {"entity": "publication", "iuid": "02b285ce5bce4603802f481d83ee7f79", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02b285ce5bce4603802f481d83ee7f79.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02b285ce5bce4603802f481d83ee7f79"}}, "title": "The intestinal MUC2 mucin C-terminus is stabilized by an extra disulfide bond in comparison to von Willebrand factor and other gel-forming mucins.", "authors": [{"family": "Gallego", "given": "Pablo", "initials": "P"}, {"family": "Garcia-Bonete", "given": "Maria-Jose", "initials": "MJ", "orcid": "0000-0002-8832-4338", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca1f7997b83b4b2398d08c2b2a927e5e.json"}}, {"family": "Trillo-Muyo", "given": "Sergio", "initials": "S", "orcid": "0000-0002-3135-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e6b6b830e9145a2ae3e6c10895acbee.json"}}, {"family": "Recktenwald", "given": "Christian V", "initials": "CV", "orcid": "0000-0003-1710-1863", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f82f923a04c4369aef10e6cf4e6c7f1.json"}}, {"family": "Johansson", "given": "Malin E V", "initials": "MEV", "orcid": "0000-0002-4237-6677", "researcher": {"href": "https://publications.scilifelab.se/researcher/520dab35c19049c8b3f1083a92e60d56.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": "2023-04-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1969", "issn-l": "2041-1723"}, "abstract": "The MUC2 mucin polymer is the main building unit of the intestinal mucus layers separating intestinal microbiota from the host epithelium. The MUC2 mucin is a large glycoprotein with a C-terminal domain similar to the MUC5AC and MUC5B mucins and the von Willebrand factor (VWF). A structural model of the C-terminal part of MUC2, MUC2-C, was generated by combining Cryo-electron microscopy, AlphaFold prediction, information of its glycosylation, and small angle X-ray scattering information. The globular VWD4 assembly in the N-terminal of MUC2-C is followed by 3.5 linear VWC domains that form an extended flexible structure before the C-terminal cystine-knot. All gel-forming mucins and VWF form tail-tail disulfide-bonded dimers in their C-terminal cystine-knot domain, but interestingly the MUC2 mucin has an extra stabilizing disulfide bond on the N-terminal side of the VWD4 domain, likely essential for a stable intestinal mucus barrier.", "doi": "10.1038/s41467-023-37666-8", "pmid": "37031240", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10082768"}, {"db": "pii", "key": "10.1038/s41467-023-37666-8"}], "notes": [], "created": "2023-11-28T13:06:35.939Z", "modified": "2023-11-28T13:06:36.019Z"}, {"entity": "publication", "iuid": "937420beed3f45248f9e846261358e94", "links": {"self": {"href": "https://publications.scilifelab.se/publication/937420beed3f45248f9e846261358e94.json"}, "display": {"href": "https://publications.scilifelab.se/publication/937420beed3f45248f9e846261358e94"}}, "title": "Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria.", "authors": [{"family": "Shuoker", "given": "Bashar", "initials": "B"}, {"family": "Pichler", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-3408-652X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89029dfd93c148a0b9c16a66edecf0fb.json"}}, {"family": "Jin", "given": "Chunsheng", "initials": "C", "orcid": "0000-0002-0229-102X", "researcher": {"href": "https://publications.scilifelab.se/researcher/458804f3f7274b8a9efe7a90469d0e56.json"}}, {"family": "Sakanaka", "given": "Hiroka", "initials": "H"}, {"family": "Wu", "given": "Haiyang", "initials": "H"}, {"family": "Gascue\u00f1a", "given": "Ana Mart\u00ednez", "initials": "AM", "orcid": "0000-0002-6245-5823", "researcher": {"href": "https://publications.scilifelab.se/researcher/77cdc688e98a4bf1a7590ea86d644b62.json"}}, {"family": "Liu", "given": "Jining", "initials": "J"}, {"family": "Nielsen", "given": "Tine Sofie", "initials": "TS"}, {"family": "Holgersson", "given": "Jan", "initials": "J"}, {"family": "Nordberg Karlsson", "given": "Eva", "initials": "E", "orcid": "0000-0002-8597-7050", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddb4af1ad5f344eebef11432ed7ee4df.json"}}, {"family": "Juge", "given": "Nathalie", "initials": "N", "orcid": "0000-0001-8515-1315", "researcher": {"href": "https://publications.scilifelab.se/researcher/a155db7bbffc48429fb2e68ab7b0c306.json"}}, {"family": "Meier", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-3761-3217", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d38fd89c1be4714b927c7c10a2117a5.json"}}, {"family": "Morth", "given": "Jens Preben", "initials": "JP", "orcid": "0000-0003-4077-0192", "researcher": {"href": "https://publications.scilifelab.se/researcher/d16ea8a43be84cdba3e41cbaec91940e.json"}}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG", "orcid": "0000-0002-3045-2628", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e0b7440ff1447c9611d938d185fbc7.json"}}, {"family": "Abou Hachem", "given": "Maher", "initials": "M", "orcid": "0000-0001-8250-1842", "researcher": {"href": "https://publications.scilifelab.se/researcher/c422215c0fb242f08e9b101521ba8f64.json"}}], "type": "journal article", "published": "2023-04-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "1833"}, "abstract": "The mucolytic human gut microbiota specialist Akkermansia muciniphila is proposed to boost mucin-secretion by the host, thereby being a key player in mucus turnover. Mucin glycan utilization requires the removal of protective caps, notably fucose and sialic acid, but the enzymatic details of this process remain largely unknown. Here, we describe the specificities of ten A. muciniphila glycoside hydrolases, which collectively remove all known sialyl and fucosyl mucin caps including those on double-sulfated epitopes. Structural analyses revealed an unprecedented fucosidase modular arrangement and explained the sialyl T-antigen specificity of a sialidase of a previously unknown family. Cell-attached sialidases and fucosidases displayed mucin-binding and their inhibition abolished growth of A. muciniphila on mucin. Remarkably, neither the sialic acid nor fucose contributed to A. muciniphila growth, but instead promoted butyrate production by co-cultured Clostridia. This study brings unprecedented mechanistic insight into the initiation of mucin O-glycan degradation by A. muciniphila and nutrient sharing between mucus-associated bacteria.", "doi": "10.1038/s41467-023-37533-6", "pmid": "37005422", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10067855"}, {"db": "pii", "key": "10.1038/s41467-023-37533-6"}], "notes": [], "created": "2023-12-04T10:22:14.448Z", "modified": "2024-01-16T13:46:27.512Z"}, {"entity": "publication", "iuid": "8c62fc49e69343088f6622db30a0504a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c62fc49e69343088f6622db30a0504a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c62fc49e69343088f6622db30a0504a"}}, "title": "Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukaemia.", "authors": [{"family": "Woodward", "given": "Eleanor L", "initials": "EL"}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Moura-Castro", "given": "Larissa H", "initials": "LH", "orcid": "0000-0001-9063-5592", "researcher": {"href": "https://publications.scilifelab.se/researcher/d326f608c7744622a92cc73768f23afb.json"}}, {"family": "van den Bos", "given": "Hilda", "initials": "H"}, {"family": "Gunnarsson", "given": "Rebeqa", "initials": "R"}, {"family": "Olsson-Arvidsson", "given": "Linda", "initials": "L"}, {"family": "Spierings", "given": "Diana C J", "initials": "DCJ", "orcid": "0000-0001-8403-474X", "researcher": {"href": "https://publications.scilifelab.se/researcher/62825465dc084c7ebd10b71e274d5eb2.json"}}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Duployez", "given": "Nicolas", "initials": "N"}, {"family": "Zaliova", "given": "Marketa", "initials": "M", "orcid": "0000-0002-1639-7124", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc439d4e47984c11a566df2d4e1a1dcd.json"}}, {"family": "Zuna", "given": "Jan", "initials": "J", "orcid": "0000-0002-0887-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/34c778d142f84ee3add0199b823ed356.json"}}, {"family": "Johansson", "given": "Bertil", "initials": "B", "orcid": "0000-0001-8829-4813", "researcher": {"href": "https://publications.scilifelab.se/researcher/fed657adae7f49f2b8d052cff36eac07.json"}}, {"family": "Foijer", "given": "Floris", "initials": "F", "orcid": "0000-0003-0989-3127", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ef3e70e2b5249029ff65894fd11b851.json"}}, {"family": "Paulsson", "given": "Kajsa", "initials": "K", "orcid": "0000-0001-7950-222X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2033b23811f1432c90ad860dd993e7a8.json"}}], "type": "journal article", "published": "2023-03-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1658", "issn-l": "2041-1723"}, "abstract": "High hyperdiploid acute lymphoblastic leukemia (HeH ALL), one of the most common childhood malignancies, is driven by nonrandom aneuploidy (abnormal chromosome numbers) mainly comprising chromosomal gains. In this study, we investigate how aneuploidy in HeH ALL arises. Single cell whole genome sequencing of 2847 cells from nine primary cases and one normal bone marrow reveals that HeH ALL generally display low chromosomal heterogeneity, indicating that they are not characterized by chromosomal instability and showing that aneuploidy-driven malignancies are not necessarily chromosomally heterogeneous. Furthermore, most chromosomal gains are present in all leukemic cells, suggesting that they arose early during leukemogenesis. Copy number data from 577 primary cases reveals selective pressures that were used for in silico modeling of aneuploidy development. This shows that the aneuploidy in HeH ALL likely arises by an initial tripolar mitosis in a diploid cell followed by clonal evolution, in line with a punctuated evolution model.", "doi": "10.1038/s41467-023-37356-5", "pmid": "36966135", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10039905"}, {"db": "pii", "key": "10.1038/s41467-023-37356-5"}], "notes": [], "created": "2024-01-07T09:05:55.224Z", "modified": "2024-01-07T09:05:55.466Z"}, {"entity": "publication", "iuid": "b5c8c85e130e40d7984d2c097b23a4ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5c8c85e130e40d7984d2c097b23a4ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5c8c85e130e40d7984d2c097b23a4ea"}}, "title": "Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants.", "authors": [{"family": "M\u00e4kel\u00e4", "given": "Anna R", "initials": "AR"}, {"family": "U\u011furlu", "given": "Hasan", "initials": "H", "orcid": "0000-0002-3849-7847", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa26094fded848c685b7ad9d2355b4dc.json"}}, {"family": "Hannula", "given": "Liina", "initials": "L"}, {"family": "Kant", "given": "Ravi", "initials": "R", "orcid": "0000-0003-3878-9775", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ee44aebd7174ab9bb5fc741c0a13e2b.json"}}, {"family": "Salminen", "given": "Petja", "initials": "P"}, {"family": "Fagerlund", "given": "Riku", "initials": "R"}, {"family": "M\u00e4ki", "given": "Sanna", "initials": "S"}, {"family": "Haveri", "given": "Anu", "initials": "A", "orcid": "0000-0003-4620-7536", "researcher": {"href": "https://publications.scilifelab.se/researcher/981b0b4c9c9e47138958c7d8753d3340.json"}}, {"family": "Strandin", "given": "Tomas", "initials": "T"}, {"family": "Kareinen", "given": "Lauri", "initials": "L"}, {"family": "Hepojoki", "given": "Jussi", "initials": "J", "orcid": "0000-0001-5699-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/90f4bea163f34c08ade5950650ef9566.json"}}, {"family": "Kuivanen", "given": "Suvi", "initials": "S"}, {"family": "Levanov", "given": "Lev", "initials": "L"}, {"family": "Pasternack", "given": "Arja", "initials": "A", "orcid": "0000-0002-6088-4245", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e8c1a42861e49a99be70101486ed3b1.json"}}, {"family": "Naves", "given": "Rauno A", "initials": "RA"}, {"family": "Ritvos", "given": "Olli", "initials": "O"}, {"family": "\u00d6sterlund", "given": "Pamela", "initials": "P", "orcid": "0000-0002-2229-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4657c21b1c1489eb139604a276b8738.json"}}, {"family": "Sironen", "given": "Tarja", "initials": "T", "orcid": "0000-0002-2344-2755", "researcher": {"href": "https://publications.scilifelab.se/researcher/8060fb77390f429e862149edf1435b5c.json"}}, {"family": "Vapalahti", "given": "Olli", "initials": "O", "orcid": "0000-0003-2270-6824", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddd242b27ab54495aa9e135590938eaf.json"}}, {"family": "Kipar", "given": "Anja", "initials": "A", "orcid": "0000-0001-7289-3459", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b82e8542b104dd79e189137733305e1.json"}}, {"family": "Huiskonen", "given": "Juha T", "initials": "JT", "orcid": "0000-0002-0348-7323", "researcher": {"href": "https://publications.scilifelab.se/researcher/c858a2e60971462f9e53653320c9eb0f.json"}}, {"family": "Rissanen", "given": "Ilona", "initials": "I", "orcid": "0000-0003-4937-1825", "researcher": {"href": "https://publications.scilifelab.se/researcher/20befd1e39cc4530b46c4f961c9a435c.json"}}, {"family": "Saksela", "given": "Kalle", "initials": "K", "orcid": "0000-0003-0827-122X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5615e2d363d84510bd0e70b80f886f5f.json"}}], "type": "journal article", "published": "2023-03-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1637", "issn-l": "2041-1723"}, "abstract": "The emergence of increasingly immunoevasive SARS-CoV-2 variants emphasizes the need for prophylactic strategies to complement vaccination in fighting the COVID-19 pandemic. Intranasal administration of neutralizing antibodies has shown encouraging protective potential but there remains a need for SARS-CoV-2 blocking agents that are less vulnerable to mutational viral variation and more economical to produce in large scale. Here we describe TriSb92, a highly manufacturable and stable trimeric antibody-mimetic sherpabody targeted against a conserved region of the viral spike glycoprotein. TriSb92 potently neutralizes SARS-CoV-2, including the latest Omicron variants like BF.7, XBB, and BQ.1.1. In female Balb/c mice intranasal administration of just 5 or 50 micrograms of TriSb92 as early as 8 h before but also 4 h after SARS-CoV-2 challenge can protect from infection. Cryo-EM and biochemical studies reveal triggering of a conformational shift in the spike trimer as the inhibitory mechanism of TriSb92. The potency and robust biochemical properties of TriSb92 together with its resistance against viral sequence evolution suggest that TriSb92 could be useful as a nasal spray for protecting susceptible individuals from SARS-CoV-2 infection.", "doi": "10.1038/s41467-023-37290-6", "pmid": "36964125", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10037368"}, {"db": "pii", "key": "10.1038/s41467-023-37290-6"}], "notes": [], "created": "2023-06-08T20:24:47.138Z", "modified": "2023-11-26T14:06:35.516Z"}, {"entity": "publication", "iuid": "3c1a67cd94f74385986c48e143426831", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c1a67cd94f74385986c48e143426831.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c1a67cd94f74385986c48e143426831"}}, "title": "Correlates of protection and viral load trajectories in omicron breakthrough infections in triple vaccinated healthcare workers.", "authors": [{"family": "Marking", "given": "Ulrika", "initials": "U"}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Norin", "given": "Nina Greilert", "initials": "NG"}, {"family": "Bladh", "given": "Oscar", "initials": "O"}, {"family": "Christ", "given": "Wanda", "initials": "W", "orcid": "0000-0003-3886-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe3a44fdb547b885cce5b6f490b2bc.json"}}, {"family": "Gordon", "given": "Max", "initials": "M", "orcid": "0000-0002-8080-5815", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3f1f5ca4e2a4f17bf9454cd7b5a259d.json"}}, {"family": "Ng", "given": "Henry", "initials": "H"}, {"family": "Blom", "given": "Kim", "initials": "K"}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}, {"family": "Mangsbo", "given": "Sara", "initials": "S"}, {"family": "Alm", "given": "Jessica J", "initials": "JJ"}, {"family": "Smed-S\u00f6rensen", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2023-03-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "1577"}, "abstract": "Vaccination offers protection against severe COVID-19 caused by SARS-CoV-2 omicron but is less effective against infection. Characteristics such as serum antibody titer correlation to protection, viral abundance and clearance of omicron infection in vaccinated individuals are scarce. We present a 4-week twice-weekly SARS-CoV-2 qPCR screening in 368 triple vaccinated healthcare workers. Spike-specific IgG levels, neutralization titers and mucosal spike-specific IgA-levels were determined at study start and qPCR-positive participants were sampled repeatedly for two weeks. 81 (cumulative incidence 22%) BA.1, BA.1.1 and BA.2 infections were detected. High serum antibody titers are shown to be protective against infection (p < 0.01), linked to reduced viral load (p < 0.01) and time to viral clearance (p < 0.05). Pre-omicron SARS-CoV-2 infection is independently associated to increased protection against omicron, largely mediated by mucosal spike specific IgA responses (nested models lr test p = 0.02 and 0.008). Only 10% of infected participants remain asymptomatic through the course of their infection. We demonstrate that high levels of vaccine-induced spike-specific WT antibodies are linked to increased protection against infection and to reduced viral load if infected, and suggest that the additional protection offered by pre-omicron SARS-CoV-2 infection largely is mediated by mucosal spike-specific IgA.", "doi": "10.1038/s41467-023-36984-1", "pmid": "36949041", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10031702"}, {"db": "pii", "key": "10.1038/s41467-023-36984-1"}], "notes": [], "created": "2023-04-08T19:28:16.337Z", "modified": "2024-11-27T22:32:10.979Z"}, {"entity": "publication", "iuid": "146c0055084542878ac0e9cb73932a95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/146c0055084542878ac0e9cb73932a95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/146c0055084542878ac0e9cb73932a95"}}, "title": "An integrated single cell and spatial transcriptomic map of human white adipose tissue.", "authors": [{"family": "Massier", "given": "Lucas", "initials": "L"}, {"family": "Jalkanen", "given": "Jutta", "initials": "J", "orcid": "0000-0002-0219-1096", "researcher": {"href": "https://publications.scilifelab.se/researcher/96620636aff142c484d07894c573f3d2.json"}}, {"family": "Elmastas", "given": "Merve", "initials": "M", "orcid": "0000-0002-1346-5080", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4055754f8cb4035ac1e160cc3cad356.json"}}, {"family": "Zhong", "given": "Jiawei", "initials": "J", "orcid": "0000-0002-2802-0770", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d30cbe9680a42c1b6478921e4b63287.json"}}, {"family": "Wang", "given": "Tongtong", "initials": "T"}, {"family": "Nono Nankam", "given": "Pamela A", "initials": "PA", "orcid": "0000-0001-9301-4556", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff19be55f9dd48f6becb1a0c47000d68.json"}}, {"family": "Frendo-Cumbo", "given": "Scott", "initials": "S", "orcid": "0000-0002-9047-4650", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bfa1b27416e47fd90a77657fcb0a34e.json"}}, {"family": "B\u00e4ckdahl", "given": "Jesper", "initials": "J"}, {"family": "Subramanian", "given": "Narmadha", "initials": "N"}, {"family": "Sekine", "given": "Takuya", "initials": "T"}, {"family": "Kerr", "given": "Alastair G", "initials": "AG", "orcid": "0000-0003-2085-1542", "researcher": {"href": "https://publications.scilifelab.se/researcher/076ba1b03b78451ba1ddb95b04e74b27.json"}}, {"family": "Tseng", "given": "Ben T P", "initials": "BTP"}, {"family": "Laurencikiene", "given": "Jurga", "initials": "J"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Lourda", "given": "Magda", "initials": "M", "orcid": "0000-0003-3155-1123", "researcher": {"href": "https://publications.scilifelab.se/researcher/64d9a0bc6b5d4039af5bc308a97eaad6.json"}}, {"family": "Kublickiene", "given": "Karolina", "initials": "K", "orcid": "0000-0002-4841-6836", "researcher": {"href": "https://publications.scilifelab.se/researcher/42acd99d04974333989f148a1f960207.json"}}, {"family": "Bhalla", "given": "Nayanika", "initials": "N", "orcid": "0000-0002-6800-0432", "researcher": {"href": "https://publications.scilifelab.se/researcher/add89d1454ce490ab138768993411d70.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Valsesia", "given": "Armand", "initials": "A", "orcid": "0000-0003-0746-9664", "researcher": {"href": "https://publications.scilifelab.se/researcher/b480c6022f2f43bdb95e7a37e11d5235.json"}}, {"family": "Astrup", "given": "Arne", "initials": "A", "orcid": "0000-0001-8968-8996", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa3d74e15326474282c62b26c4c1507b.json"}}, {"family": "Blaak", "given": "Ellen E", "initials": "EE", "orcid": "0000-0002-2496-3464", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fa433d6fe8d4b6b811c20a88378e4eb.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea50cf03c6748c086846c3a28882979.json"}}, {"family": "Viguerie", "given": "Nathalie", "initials": "N", "orcid": "0000-0002-1730-9915", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1b76daf0c9e478b974d0fa9fb4aa5a1.json"}}, {"family": "Langin", "given": "Dominique", "initials": "D", "orcid": "0000-0002-2669-7825", "researcher": {"href": "https://publications.scilifelab.se/researcher/689d03a8a3614168bc04d897a7cfd0c2.json"}}, {"family": "Wolfrum", "given": "Christian", "initials": "C", "orcid": "0000-0002-3862-6805", "researcher": {"href": "https://publications.scilifelab.se/researcher/43777b7ae29b470793e30b6d32d2674f.json"}}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M", "orcid": "0000-0003-4785-1876", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab61ac66c36749019ce5066fb1a5061e.json"}}, {"family": "Mejhert", "given": "Niklas", "initials": "N", "orcid": "0000-0003-1785-833X", "researcher": {"href": "https://publications.scilifelab.se/researcher/81eb60b84ea14ad9ba7e4d3433c37a3e.json"}}], "type": "meta-analysis", "published": "2023-03-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1438", "issn-l": "2041-1723"}, "abstract": "To date, single-cell studies of human white adipose tissue (WAT) have been based on small cohort sizes and no cellular consensus nomenclature exists. Herein, we performed a comprehensive meta-analysis of publicly available and newly generated single-cell, single-nucleus, and spatial transcriptomic results from human subcutaneous, omental, and perivascular WAT. Our high-resolution map is built on data from ten studies and allowed us to robustly identify >60 subpopulations of adipocytes, fibroblast and adipogenic progenitors, vascular, and immune cells. Using these results, we deconvolved spatial and bulk transcriptomic data from nine additional cohorts to provide spatial and clinical dimensions to the map. This identified cell-cell interactions as well as relationships between specific cell subtypes and insulin resistance, dyslipidemia, adipocyte volume, and lipolysis upon long-term weight changes. Altogether, our meta-map provides a rich resource defining the cellular and microarchitectural landscape of human WAT and describes the associations between specific cell types and metabolic states.", "doi": "10.1038/s41467-023-36983-2", "pmid": "36922516", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10017705"}, {"db": "pii", "key": "10.1038/s41467-023-36983-2"}], "notes": [], "created": "2023-10-04T12:19:09.279Z", "modified": "2023-10-19T10:08:08.367Z"}, {"entity": "publication", "iuid": "549ae9e85a6d41c6be8acdeb3cfbf660", "links": {"self": {"href": "https://publications.scilifelab.se/publication/549ae9e85a6d41c6be8acdeb3cfbf660.json"}, "display": {"href": "https://publications.scilifelab.se/publication/549ae9e85a6d41c6be8acdeb3cfbf660"}}, "title": "Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization.", "authors": [{"family": "Amselem", "given": "Elias", "initials": "E", "orcid": "0000-0003-2846-9225", "researcher": {"href": "https://publications.scilifelab.se/researcher/b36dcc99173f461e84941241665eaedf.json"}}, {"family": "Broadwater", "given": "Bo", "initials": "B", "orcid": "0000-0002-5870-2457", "researcher": {"href": "https://publications.scilifelab.se/researcher/327b8749f1a4415781ab6bca7554a367.json"}}, {"family": "H\u00e4vermark", "given": "Tora", "initials": "T", "orcid": "0000-0002-3794-3243", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8aca0712dea4996a8ba3f51b0a5d126.json"}}, {"family": "Johansson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8811-2629", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7c7f4a540fa4bc2b5176c48bde2b0d7.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": "2023-03-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1336", "issn-l": "2041-1723"}, "abstract": "Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.", "doi": "10.1038/s41467-023-36879-1", "pmid": "36906676", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10008558"}, {"db": "pii", "key": "10.1038/s41467-023-36879-1"}], "notes": [], "created": "2023-11-27T21:47:54.647Z", "modified": "2024-01-16T13:48:33.841Z"}, {"entity": "publication", "iuid": "0834b002d95d4369a2817a82baf8a196", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0834b002d95d4369a2817a82baf8a196.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0834b002d95d4369a2817a82baf8a196"}}, "title": "ARF suppression by MYC but not MYCN confers increased malignancy of aggressive pediatric brain tumors.", "authors": [{"family": "Mainwaring", "given": "Oliver J", "initials": "OJ", "orcid": "0000-0002-7973-9849", "researcher": {"href": "https://publications.scilifelab.se/researcher/494a0479041f41149902feb34f668043.json"}}, {"family": "Weishaupt", "given": "Holger", "initials": "H"}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G"}, {"family": "Borgenvik", "given": "Anna", "initials": "A"}, {"family": "Breinschmid", "given": "Laura", "initials": "L"}, {"family": "Verbaan", "given": "Annemieke D", "initials": "AD"}, {"family": "Richardson", "given": "Stacey", "initials": "S"}, {"family": "Thompson", "given": "Dean", "initials": "D"}, {"family": "Clifford", "given": "Steven C", "initials": "SC"}, {"family": "Hill", "given": "Rebecca M", "initials": "RM"}, {"family": "Annusver", "given": "Karl", "initials": "K", "orcid": "0000-0002-9515-7216", "researcher": {"href": "https://publications.scilifelab.se/researcher/941902f72c214c868d0136cf433442a7.json"}}, {"family": "Sundstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Holmberg", "given": "Karl O", "initials": "KO"}, {"family": "Kasper", "given": "Maria", "initials": "M", "orcid": "0000-0002-6117-2717", "researcher": {"href": "https://publications.scilifelab.se/researcher/b036a8a125ca4f0896f2e832e1248dc0.json"}}, {"family": "Hutter", "given": "Sonja", "initials": "S"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1221", "issn-l": "2041-1723"}, "abstract": "Medulloblastoma, the most common malignant pediatric brain tumor, often harbors MYC amplifications. Compared to high-grade gliomas, MYC-amplified medulloblastomas often show increased photoreceptor activity and arise in the presence of a functional ARF/p53 suppressor pathway. Here, we generate an immunocompetent transgenic mouse model with regulatable MYC that develop clonal tumors that molecularly resemble photoreceptor-positive Group 3 medulloblastoma. Compared to MYCN-expressing brain tumors driven from the same promoter, pronounced ARF silencing is present in our MYC-expressing model and in human medulloblastoma. While partial Arf suppression causes increased malignancy in MYCN-expressing tumors, complete Arf depletion promotes photoreceptor-negative high-grade glioma formation. Computational models and clinical data further identify drugs targeting MYC-driven tumors with a suppressed but functional ARF pathway. We show that the HSP90 inhibitor, Onalespib, significantly targets MYC-driven but not MYCN-driven tumors in an ARF-dependent manner. The treatment increases cell death in synergy with cisplatin and demonstrates potential for targeting MYC-driven medulloblastoma.", "doi": "10.1038/s41467-023-36847-9", "pmid": "36869047", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9984535"}, {"db": "pii", "key": "10.1038/s41467-023-36847-9"}], "notes": [], "created": "2023-05-22T20:23:04.680Z", "modified": "2024-01-16T13:48:33.867Z"}, {"entity": "publication", "iuid": "43be4b7ebdd343f88b86e31d874b86f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43be4b7ebdd343f88b86e31d874b86f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43be4b7ebdd343f88b86e31d874b86f0"}}, "title": "Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter.", "authors": [{"family": "Davies", "given": "James S", "initials": "JS", "orcid": "0000-0003-4029-1650", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9d11e818c243d58bc8ea333ee04801.json"}}, {"family": "Currie", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1509-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/aeb1a8b434304b38a08cb52b1cb7fdb7.json"}}, {"family": "North", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-5011-1567", "researcher": {"href": "https://publications.scilifelab.se/researcher/068cd0053ad3414b96003075cb6df2f6.json"}}, {"family": "Scalise", "given": "Mariafrancesca", "initials": "M", "orcid": "0000-0003-3860-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b7d7db24b1b4e51859f8ccb72ec6753.json"}}, {"family": "Wright", "given": "Joshua D", "initials": "JD"}, {"family": "Copping", "given": "Jack M", "initials": "JM"}, {"family": "Remus", "given": "Daniela M", "initials": "DM"}, {"family": "Gulati", "given": "Ashutosh", "initials": "A", "orcid": "0000-0003-0960-994X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b2b0aa7260492c8141083762e08125.json"}}, {"family": "Morado", "given": "Dustin R", "initials": "DR", "orcid": "0000-0003-4693-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/eef09b7a95b64a699900bae6a5390e31.json"}}, {"family": "Jamieson", "given": "Sam A", "initials": "SA", "orcid": "0000-0003-0120-4737", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e8f6f753c6c49b3a45a35c12e21a9b5.json"}}, {"family": "Newton-Vesty", "given": "Michael C", "initials": "MC"}, {"family": "Abeysekera", "given": "Gayan S", "initials": "GS"}, {"family": "Ramaswamy", "given": "Subramanian", "initials": "S", "orcid": "0000-0002-6709-190X", "researcher": {"href": "https://publications.scilifelab.se/researcher/93f6a58622ed4c7d88b0f860e9de996b.json"}}, {"family": "Friemann", "given": "Rosmarie", "initials": "R"}, {"family": "Wakatsuki", "given": "Soichi", "initials": "S", "orcid": "0000-0001-5896-7968", "researcher": {"href": "https://publications.scilifelab.se/researcher/f86677d7e3174fed807d7010e41bf746.json"}}, {"family": "Allison", "given": "Jane R", "initials": "JR", "orcid": "0000-0002-5699-1726", "researcher": {"href": "https://publications.scilifelab.se/researcher/3800a6052323474992cb0e0d80a93bcf.json"}}, {"family": "Indiveri", "given": "Cesare", "initials": "C"}, {"family": "Drew", "given": "David", "initials": "D", "orcid": "0000-0001-8866-6349", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc19844f8147480fb0af2e437744131b.json"}}, {"family": "Mace", "given": "Peter D", "initials": "PD", "orcid": "0000-0003-2175-9537", "researcher": {"href": "https://publications.scilifelab.se/researcher/1535ee428bb94c8ba958cfac2bb009c5.json"}}, {"family": "Dobson", "given": "Renwick C J", "initials": "RCJ", "orcid": "0000-0002-5506-4939", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c8622c295ef40cea6238cd5b8fba026.json"}}], "type": "journal article", "published": "2023-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1120", "issn-l": "2041-1723"}, "abstract": "In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 \u00c5 resolution. SiaM comprises a \"transport\" domain and a \"scaffold\" domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na+ and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an 'elevator-with-an-operator' mechanism.", "doi": "10.1038/s41467-023-36590-1", "pmid": "36849793", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9971032"}, {"db": "pii", "key": "10.1038/s41467-023-36590-1"}], "notes": [], "created": "2023-11-27T08:12:34.925Z", "modified": "2023-12-04T10:03:04.596Z"}, {"entity": "publication", "iuid": "972a9d48ef104e73a8766b8630ade5af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/972a9d48ef104e73a8766b8630ade5af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/972a9d48ef104e73a8766b8630ade5af"}}, "title": "Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.", "authors": [{"family": "Jun", "given": "Seong-Hwan", "initials": "S"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "O'Flanagan", "given": "Ciara", "initials": "C"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Aparicio", "given": "Samuel", "initials": "S", "orcid": "0000-0002-0487-9599", "researcher": {"href": "https://publications.scilifelab.se/researcher/8665401549d749ea8c1ab814dbfe5061.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Roth", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3422-8823", "researcher": {"href": "https://publications.scilifelab.se/researcher/55d6b9360321440ca1bc9199a42b624a.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications.scilifelab.se/researcher/b956941833b843f6ace483bf4c21e643.json"}}], "type": "journal article", "published": "2023-02-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "982"}, "abstract": "Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.", "doi": "10.1038/s41467-023-36202-y", "pmid": "36813776", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9946941"}, {"db": "pii", "key": "10.1038/s41467-023-36202-y"}], "notes": [], "created": "2023-03-06T13:47:42.947Z", "modified": "2023-11-29T11:39:09.375Z"}, {"entity": "publication", "iuid": "bad5b686c16e48c0a5d5984892016a93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bad5b686c16e48c0a5d5984892016a93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bad5b686c16e48c0a5d5984892016a93"}}, "title": "Reproducing extracellular matrix adverse remodelling of non-ST myocardial infarction in a large animal model.", "authors": [{"family": "Contessotto", "given": "Paolo", "initials": "P", "orcid": "0000-0002-6990-9883", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd9eff0e573f4f7097fb575bf6479f8e.json"}}, {"family": "Spelat", "given": "Renza", "initials": "R", "orcid": "0000-0001-5794-8976", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7974e486fb24bbf979eb920f9d49380.json"}}, {"family": "Ferro", "given": "Federico", "initials": "F", "orcid": "0000-0002-6023-8227", "researcher": {"href": "https://publications.scilifelab.se/researcher/27810903638948feb4391fa537a7eda3.json"}}, {"family": "Vysockas", "given": "Vaidas", "initials": "V", "orcid": "0000-0002-2179-2348", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c01194476544942a0fd0c153a44487e.json"}}, {"family": "Krivickien\u0117", "given": "Au\u0161ra", "initials": "A", "orcid": "0000-0003-4978-2915", "researcher": {"href": "https://publications.scilifelab.se/researcher/29901a96314b4fc489e3aa1712004ae7.json"}}, {"family": "Jin", "given": "Chunsheng", "initials": "C", "orcid": "0000-0002-0229-102X", "researcher": {"href": "https://publications.scilifelab.se/researcher/458804f3f7274b8a9efe7a90469d0e56.json"}}, {"family": "Chantepie", "given": "Sandrine", "initials": "S"}, {"family": "Chinello", "given": "Clizia", "initials": "C"}, {"family": "Pauza", "given": "Audrys G", "initials": "AG", "orcid": "0000-0001-9635-8872", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb08209745534c21878f607cc414aab8.json"}}, {"family": "Valente", "given": "Camilla", "initials": "C", "orcid": "0000-0003-3084-1102", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cf678853015478daf234ab0f854584e.json"}}, {"family": "Rackauskas", "given": "Mindaugas", "initials": "M", "orcid": "0000-0002-2503-3437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2edbecde7f94bcfbea7f0776b69bbb2.json"}}, {"family": "Casara", "given": "Alvise", "initials": "A", "orcid": "0000-0002-5056-8732", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3bfb0f2394e44cda5c96d23c6c3b32e.json"}}, {"family": "Zigmantait\u0117", "given": "Vilma", "initials": "V", "orcid": "0000-0002-0410-1533", "researcher": {"href": "https://publications.scilifelab.se/researcher/baa4c86fec6e4f0bbdd6e980a9796ff6.json"}}, {"family": "Magni", "given": "Fulvio", "initials": "F", "orcid": "0000-0002-8663-0374", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d2bb884997b4437924cc2659b823637.json"}}, {"family": "Papy-Garcia", "given": "Dulce", "initials": "D", "orcid": "0000-0003-2225-9331", "researcher": {"href": "https://publications.scilifelab.se/researcher/697039fd70604a79804beb2e8179d9cf.json"}}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG", "orcid": "0000-0002-3045-2628", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e0b7440ff1447c9611d938d185fbc7.json"}}, {"family": "Ereminien\u0117", "given": "Egl\u0117", "initials": "E", "orcid": "0000-0002-8332-788X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ab7bba2798e40f3b67a791e6be512bc.json"}}, {"family": "Pandit", "given": "Abhay", "initials": "A"}, {"family": "Da Costa", "given": "Mark", "initials": "M", "orcid": "0000-0001-7713-2608", "researcher": {"href": "https://publications.scilifelab.se/researcher/a18320fbed7b43299aedc829736f4eb9.json"}}], "type": "journal article", "published": "2023-02-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "995", "issn-l": "2041-1723"}, "abstract": "The rising incidence of non-ST-segment elevation myocardial infarction (NSTEMI) and associated long-term high mortality constitutes an urgent clinical issue. Unfortunately, the study of possible interventions to treat this pathology lacks a reproducible pre-clinical model. Indeed, currently adopted small and large animal models of MI mimic only full-thickness, ST-segment-elevation (STEMI) infarcts, and hence cater only for an investigation into therapeutics and interventions directed at this subset of MI. Thus, we develop an ovine model of NSTEMI by ligating the myocardial muscle at precise intervals parallel to the left anterior descending coronary artery. Upon histological and functional investigation to validate the proposed model and comparison with STEMI full ligation model, RNA-seq and proteomics show the distinctive features of post-NSTEMI tissue remodelling. Transcriptome and proteome-derived pathway analyses at acute (7 days) and late (28 days) post-NSTEMI pinpoint specific alterations in cardiac post-ischaemic extracellular matrix. Together with the rise of well-known markers of inflammation and fibrosis, NSTEMI ischaemic regions show distinctive patterns of complex galactosylated and sialylated N-glycans in cellular membranes and extracellular matrix. Identifying such changes in molecular moieties accessible to infusible and intra-myocardial injectable drugs sheds light on developing targeted pharmacological solutions to contrast adverse fibrotic remodelling.", "doi": "10.1038/s41467-023-36350-1", "pmid": "36813782", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9945840"}, {"db": "pii", "key": "10.1038/s41467-023-36350-1"}], "notes": [], "created": "2023-12-04T10:23:03.795Z", "modified": "2024-01-16T13:46:27.924Z"}, {"entity": "publication", "iuid": "6d83dd5dfa2b47619e8d8fbc33006340", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d83dd5dfa2b47619e8d8fbc33006340.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d83dd5dfa2b47619e8d8fbc33006340"}}, "title": "Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria.", "authors": [{"family": "Parajuli", "given": "Narayan Prasad", "initials": "NP", "orcid": "0000-0002-3228-9908", "researcher": {"href": "https://publications.scilifelab.se/researcher/2166eb5331f14d61b59573dd7fb466c8.json"}}, {"family": "Emmerich", "given": "Andrew", "initials": "A", "orcid": "0000-0002-0908-9924", "researcher": {"href": "https://publications.scilifelab.se/researcher/688f9a82f69b42cfa5bd9a8e9f8df20c.json"}}, {"family": "Mandava", "given": "Chandra Sekhar", "initials": "CS"}, {"family": "Pavlov", "given": "Michael Y", "initials": "MY"}, {"family": "Sanyal", "given": "Suparna", "initials": "S", "orcid": "0000-0002-7124-792X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c5ffabce284f28885f6594da1460d6.json"}}], "type": "journal article", "published": "2023-02-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "918", "issn-l": "2041-1723"}, "abstract": "Thermorubin (THB) is a long-known broad-spectrum ribosome-targeting antibiotic, but the molecular mechanism of its action was unclear. Here, our precise fast-kinetics assays in a reconstituted Escherichia coli translation system and 1.96 \u00c5 resolution cryo-EM structure of THB-bound 70S ribosome with mRNA and initiator tRNA, independently suggest that THB binding at the intersubunit bridge B2a near decoding center of the ribosome interferes with the binding of A-site substrates aminoacyl-tRNAs and class-I release factors, thereby inhibiting elongation and termination steps of bacterial translation. Furthermore, THB acts as an anti-dissociation agent that tethers the ribosomal subunits and blocks ribosome recycling, subsequently reducing the pool of active ribosomes. Our results show that THB does not inhibit translation initiation as proposed earlier and provide a complete mechanism of how THB perturbs bacterial protein synthesis. This in-depth characterization will hopefully spur efforts toward the design of THB analogs with improved solubility and effectivity against multidrug-resistant bacteria.", "doi": "10.1038/s41467-023-36528-7", "pmid": "36806263", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9938272"}, {"db": "pii", "key": "10.1038/s41467-023-36528-7"}], "notes": [], "created": "2023-03-22T16:16:18.652Z", "modified": "2023-11-27T09:34:18.279Z"}, {"entity": "publication", "iuid": "9ba59eb622564ea2b2d31daad09424ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ba59eb622564ea2b2d31daad09424ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ba59eb622564ea2b2d31daad09424ab"}}, "title": "Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation.", "authors": [{"family": "Li", "given": "Bingnan", "initials": "B", "orcid": "0000-0001-8143-4035", "researcher": {"href": "https://publications.scilifelab.se/researcher/08106e5753c749d88bcc4c1b4094d98c.json"}}, {"family": "Zeis", "given": "Patrice", "initials": "P", "orcid": "0000-0001-7615-2201", "researcher": {"href": "https://publications.scilifelab.se/researcher/61486627ad2d47bea298be5db287ae38.json"}}, {"family": "Zhang", "given": "Yujie", "initials": "Y"}, {"family": "Alekseenko", "given": "Alisa", "initials": "A"}, {"family": "F\u00fcrst", "given": "Eliska", "initials": "E", "orcid": "0000-0001-7101-5347", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6e6424c3604b298d0c9c5e4d96c88f.json"}}, {"family": "Sanchez", "given": "Yerma Pareja", "initials": "YP"}, {"family": "Lin", "given": "Gen", "initials": "G", "orcid": "0000-0001-9969-8418", "researcher": {"href": "https://publications.scilifelab.se/researcher/97d352875a5f4fa1b7171f6488a9ff99.json"}}, {"family": "Tekkedil", "given": "Manu M", "initials": "MM"}, {"family": "Piazza", "given": "Ilaria", "initials": "I"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e906e11225514a289df84a2145f807fe.json"}}], "type": "journal article", "published": "2023-02-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "910", "issn-l": "2041-1723"}, "abstract": "Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Chromatin organization has been shown to play a role in the faster response of primed cells. However, the contribution of post-transcriptional regulation is not yet explored. Here we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose. We find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. Our work shows that gene-specific differences in intrinsic nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that primed cells present altered levels of RNA degradation machinery and that both nuclear and cytoplasmic mRNA decay modulate transcriptional memory. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.", "doi": "10.1038/s41467-023-36586-x", "pmid": "36801853", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9936472"}, {"db": "pii", "key": "10.1038/s41467-023-36586-x"}], "notes": [], "created": "2023-11-27T21:47:43.577Z", "modified": "2024-01-16T13:48:33.947Z"}, {"entity": "publication", "iuid": "cbf0d01af2ae416bb9cbe604da19514f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbf0d01af2ae416bb9cbe604da19514f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbf0d01af2ae416bb9cbe604da19514f"}}, "title": "Cryo-EM structure supports a role of AQP7 as a junction protein.", "authors": [{"family": "Huang", "given": "Peng", "initials": "P", "orcid": "0000-0001-8556-5606", "researcher": {"href": "https://publications.scilifelab.se/researcher/b73b858f0d164fb0937ac36c0bbc414f.json"}}, {"family": "Venskutonyt\u0117", "given": "Raminta", "initials": "R", "orcid": "0000-0003-0650-0180", "researcher": {"href": "https://publications.scilifelab.se/researcher/757980f162074076b0b9d4696cae6a95.json"}}, {"family": "Prasad", "given": "Rashmi B", "initials": "RB", "orcid": "0000-0002-4400-6741", "researcher": {"href": "https://publications.scilifelab.se/researcher/313aa9ded0c946c3b986e856a62ae85a.json"}}, {"family": "Ardalani", "given": "Hamidreza", "initials": "H", "orcid": "0000-0002-3245-7991", "researcher": {"href": "https://publications.scilifelab.se/researcher/3596a601d5414415a13306f1af2fb1b5.json"}}, {"family": "de Mar\u00e9", "given": "Sofia W", "initials": "SW"}, {"family": "Fan", "given": "Xiao", "initials": "X"}, {"family": "Li", "given": "Ping", "initials": "P"}, {"family": "Sp\u00e9gel", "given": "Peter", "initials": "P", "orcid": "0000-0002-6092-2387", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e06a5bbd6114a248eafb168782d0b27.json"}}, {"family": "Yan", "given": "Nieng", "initials": "N", "orcid": "0000-0003-4829-7416", "researcher": {"href": "https://publications.scilifelab.se/researcher/16c64456639a4e18bd52a9d884d7b6df.json"}}, {"family": "Gourdon", "given": "Pontus", "initials": "P", "orcid": "0000-0002-8631-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dc6cdbbcab048fab7a65df6cb796aab.json"}}, {"family": "Artner", "given": "Isabella", "initials": "I", "orcid": "0000-0002-2895-5664", "researcher": {"href": "https://publications.scilifelab.se/researcher/587d8c34847549f899d8354182f0a94f.json"}}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}], "type": "journal article", "published": "2023-02-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "600", "issn-l": "2041-1723"}, "abstract": "Aquaglyceroporin 7 (AQP7) facilitates glycerol flux across the plasma membrane with a critical physiological role linked to metabolism, obesity, and associated diseases. Here, we present the single-particle cryo-EM structure of AQP7 determined at 2.55 \u00c5 resolution adopting two adhering tetramers, stabilized by extracellularly exposed loops, in a configuration like that of the well-characterized interaction of AQP0 tetramers. The central pore, in-between the four monomers, displays well-defined densities restricted by two leucine filters. Gas chromatography mass spectrometry (GC/MS) results show that the AQP7 sample contains glycerol 3-phosphate (Gro3P), which is compatible with the identified features in the central pore. AQP7 is shown to be highly expressed in human pancreatic \u03b1- and \u03b2- cells suggesting that the identified AQP7 octamer assembly, in addition to its function as glycerol channel, may serve as junction proteins within the endocrine pancreas.", "doi": "10.1038/s41467-023-36272-y", "pmid": "36737436", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9898259"}, {"db": "pii", "key": "10.1038/s41467-023-36272-y"}], "notes": [], "created": "2023-10-05T08:15:21.786Z", "modified": "2023-11-27T08:29:09.523Z"}, {"entity": "publication", "iuid": "6679c4b418fa47b3a6bf6e9d7539b0f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6679c4b418fa47b3a6bf6e9d7539b0f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6679c4b418fa47b3a6bf6e9d7539b0f1"}}, "title": "Inversions maintain differences between migratory phenotypes of a songbird.", "authors": [{"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Mackintosh", "given": "Alexander", "initials": "A"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Bensch", "given": "Staffan", "initials": "S", "orcid": "0000-0002-0082-0899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b925a620a68049928c3dc0cbc87948ba.json"}}], "type": "journal article", "published": "2023-01-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "452"}, "abstract": "Structural rearrangements have been shown to be important in local adaptation and speciation, but have been difficult to reliably identify and characterize in non-model species. Here we combine long reads, linked reads and optical mapping to characterize three divergent chromosome regions in the willow warbler Phylloscopus trochilus, of which two are associated with differences in migration and one with an environmental gradient. We show that there are inversions (0.4-13 Mb) in each of the regions and that the divergence times between inverted and non-inverted haplotypes are similar across the regions (~1.2 Myrs), which is compatible with a scenario where inversions arose in either of two allopatric populations that subsequently hybridized. The improved genomes allow us to detect additional functional differences in the divergent regions, providing candidate genes for migration and adaptations to environmental gradients.", "doi": "10.1038/s41467-023-36167-y", "pmid": "36707538", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9883250"}, {"db": "pii", "key": "10.1038/s41467-023-36167-y"}], "notes": [], "created": "2023-03-06T13:47:37.052Z", "modified": "2024-01-16T13:48:34.085Z"}, {"entity": "publication", "iuid": "477434a47b94448f836521f7892ec2be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/477434a47b94448f836521f7892ec2be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/477434a47b94448f836521f7892ec2be"}}, "title": "Early response evaluation by single cell signaling profiling in acute myeloid leukemia.", "authors": [{"family": "Tislevoll", "given": "Benedicte Sjo", "initials": "BS", "orcid": "0000-0003-4962-997X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6874ed44ded94d709e1d11fc62af6b43.json"}}, {"family": "Helles\u00f8y", "given": "Monica", "initials": "M", "orcid": "0000-0002-0115-7427", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2df980a59134a4e82c3ac5e0edfecc9.json"}}, {"family": "Fagerholt", "given": "Oda Helen Eck", "initials": "OHE", "orcid": "0000-0002-5712-8860", "researcher": {"href": "https://publications.scilifelab.se/researcher/38167da5fcd94d14856785c8dd3319e9.json"}}, {"family": "Gullaksen", "given": "Stein-Erik", "initials": "SE"}, {"family": "Srivastava", "given": "Aashish", "initials": "A", "orcid": "0000-0003-0532-3979", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69d8575b0dd4fc99fe8e6a601706a90.json"}}, {"family": "Birkeland", "given": "Even", "initials": "E"}, {"family": "Kleftogiannis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0003-1086-821X", "researcher": {"href": "https://publications.scilifelab.se/researcher/88b8cce357b54b3cb0d22e5dd995d8d0.json"}}, {"family": "Ayuda-Dur\u00e1n", "given": "Pilar", "initials": "P", "orcid": "0000-0002-9799-3680", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c39b575f5e1485b98e6271d56da8751.json"}}, {"family": "Piechaczyk", "given": "Laure", "initials": "L"}, {"family": "Tadele", "given": "Dagim Shiferaw", "initials": "DS", "orcid": "0000-0001-8319-678X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b2524c8c8754beda75c6118d372b56e.json"}}, {"family": "Skavland", "given": "J\u00f8rn", "initials": "J"}, {"family": "Baliakas", "given": "Panagotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Hovland", "given": "Randi", "initials": "R", "orcid": "0000-0001-8543-2213", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0ea76c7a8a349b9b4c367f294d455f5.json"}}, {"family": "Andresen", "given": "Vibeke", "initials": "V", "orcid": "0000-0002-2368-2978", "researcher": {"href": "https://publications.scilifelab.se/researcher/43af3d6b0a4a432796443809e2facaaf.json"}}, {"family": "Seternes", "given": "Ole Morten", "initials": "OM", "orcid": "0000-0001-8537-3612", "researcher": {"href": "https://publications.scilifelab.se/researcher/843d4ab66cf04591aa1ec42503ebd6bf.json"}}, {"family": "Tvedt", "given": "Tor Henrik Anderson", "initials": "THA"}, {"family": "Aghaeepour", "given": "Nima", "initials": "N", "orcid": "0000-0002-6117-8764", "researcher": {"href": "https://publications.scilifelab.se/researcher/a61941f98d9e43e289e94dc59ff9dfcc.json"}}, {"family": "Gavasso", "given": "Sonia", "initials": "S"}, {"family": "Porkka", "given": "Kimmo", "initials": "K", "orcid": "0000-0003-4112-5902", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f4ebafb55b34613af79c4d16a3eb75c.json"}}, {"family": "Jonassen", "given": "Inge", "initials": "I", "orcid": "0000-0003-4110-0748", "researcher": {"href": "https://publications.scilifelab.se/researcher/c609d886fc37469196e4bb639a0a89bb.json"}}, {"family": "Fl\u00f8isand", "given": "Yngvar", "initials": "Y", "orcid": "0000-0001-7267-1944", "researcher": {"href": "https://publications.scilifelab.se/researcher/f221b95eed9649618358528c075e4da2.json"}}, {"family": "Enserink", "given": "Jorrit", "initials": "J", "orcid": "0000-0002-2394-5387", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0f0fc1c8ab142d39502e5b3df86b1bc.json"}}, {"family": "Blaser", "given": "Nello", "initials": "N", "orcid": "0000-0001-9489-1657", "researcher": {"href": "https://publications.scilifelab.se/researcher/22c9faae544a4d188acd34946ead8647.json"}}, {"family": "Gjertsen", "given": "Bj\u00f8rn Tore", "initials": "BT", "orcid": "0000-0001-9358-9704", "researcher": {"href": "https://publications.scilifelab.se/researcher/96c4d4aadc5f4ffb85df2176935b77db.json"}}], "type": "journal article", "published": "2023-01-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "115", "issn-l": "2041-1723"}, "abstract": "Aberrant pro-survival signaling is a hallmark of cancer cells, but the response to chemotherapy is poorly understood. In this study, we investigate the initial signaling response to standard induction chemotherapy in a cohort of 32 acute myeloid leukemia (AML) patients, using 36-dimensional mass cytometry. Through supervised and unsupervised machine learning approaches, we find that reduction of extracellular-signal-regulated kinase (ERK) 1/2 and p38 mitogen-activated protein kinase (MAPK) phosphorylation in the myeloid cell compartment 24 h post-chemotherapy is a significant predictor of patient 5-year overall survival in this cohort. Validation by RNA sequencing shows induction of MAPK target gene expression in patients with high phospho-ERK1/2 24 h post-chemotherapy, while proteomics confirm an increase of the p38 prime target MAPK activated protein kinase 2 (MAPKAPK2). In this study, we demonstrate that mass cytometry can be a valuable tool for early response evaluation in AML and elucidate the potential of functional signaling analyses in precision oncology diagnostics.", "doi": "10.1038/s41467-022-35624-4", "pmid": "36611026", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9825407"}, {"db": "pii", "key": "10.1038/s41467-022-35624-4"}], "notes": [], "created": "2023-11-29T08:27:28.554Z", "modified": "2023-11-29T08:27:29.154Z"}, {"entity": "publication", "iuid": "0d5b8a5532a44405aa335c790cd39459", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d5b8a5532a44405aa335c790cd39459.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d5b8a5532a44405aa335c790cd39459"}}, "title": "Upper gut heat shock proteins HSP70 and GRP78 promote insulin resistance, hyperglycemia, and non-alcoholic steatohepatitis.", "authors": [{"family": "Angelini", "given": "Giulia", "initials": "G"}, {"family": "Castagneto-Gissey", "given": "Lidia", "initials": "L", "orcid": "0000-0002-3800-167X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cb38fc0358c4cc5999ac3e719badee0.json"}}, {"family": "Salinari", "given": "Serenella", "initials": "S"}, {"family": "Bertuzzi", "given": "Alessandro", "initials": "A"}, {"family": "Anello", "given": "Danila", "initials": "D"}, {"family": "Pradhan", "given": "Meenakshi", "initials": "M", "orcid": "0000-0002-4908-8512", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c48850ad9c94450bf9ec8d21e6ce6f1.json"}}, {"family": "Zsch\u00e4tzsch", "given": "Marlen", "initials": "M"}, {"family": "Ritter", "given": "Paul", "initials": "P"}, {"family": "Le Roux", "given": "Carel W", "initials": "CW", "orcid": "0000-0001-5521-5445", "researcher": {"href": "https://publications.scilifelab.se/researcher/3def373e973945889670140361ad8ee5.json"}}, {"family": "Rubino", "given": "Francesco", "initials": "F"}, {"family": "Basso", "given": "Nicola", "initials": "N", "orcid": "0000-0001-7529-630X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a1b89803c234056ba8260b8567666d1.json"}}, {"family": "Casella", "given": "Giovanni", "initials": "G", "orcid": "0000-0002-1535-7198", "researcher": {"href": "https://publications.scilifelab.se/researcher/1964d8f975714c0db6ba9c36a38794ec.json"}}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR", "orcid": "0000-0002-5211-2536", "researcher": {"href": "https://publications.scilifelab.se/researcher/99881f50c4a443ec9178c1df90047e88.json"}}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Mingrone", "given": "Geltrude", "initials": "G", "orcid": "0000-0003-2021-528X", "researcher": {"href": "https://publications.scilifelab.se/researcher/896980ae262f4f669297ec7889c7cc77.json"}}], "type": "journal article", "published": "2022-12-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "7715", "issn-l": "2041-1723"}, "abstract": "A high-fat diet increases the risk of insulin resistance, type-2 diabetes, and non-alcoholic steato-hepatitis. Here we identified two heat-shock proteins, Heat-Shock-Protein70 and Glucose-Regulated Protein78, which are increased in the jejunum of rats on a high-fat diet. We demonstrated a causal link between these proteins and hepatic and whole-body insulin-resistance, as well as the metabolic response to bariatric/metabolic surgery. Long-term continuous infusion of Heat-Shock-Protein70 and Glucose-Regulated Protein78 caused insulin-resistance, hyperglycemia, and non-alcoholic steato-hepatitis in rats on a chow diet, while in rats on a high-fat diet continuous infusion of monoclonal antibodies reversed these phenotypes, mimicking metabolic surgery. Infusion of these proteins or their antibodies was also associated with shifts in fecal microbiota composition. Serum levels of Heat-Shock-Protein70 and Glucose-Regulated Protein78were elevated in patients with non-alcoholic steato-hepatitis, but decreased following metabolic surgery. Understanding the intestinal regulation of metabolism may provide options to reverse metabolic diseases.", "doi": "10.1038/s41467-022-35310-5", "pmid": "36513656", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9748124"}, {"db": "pii", "key": "10.1038/s41467-022-35310-5"}], "notes": [], "created": "2023-11-27T21:47:32.497Z", "modified": "2024-01-16T13:48:34.302Z"}, {"entity": "publication", "iuid": "376ba41322394bb49764039bc6081e06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/376ba41322394bb49764039bc6081e06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/376ba41322394bb49764039bc6081e06"}}, "title": "Structural mechanism of signal transduction in a phytochrome histidine kinase.", "authors": [{"family": "Wahlgren", "given": "Weixiao Yuan", "initials": "WY"}, {"family": "Claesson", "given": "Elin", "initials": "E"}, {"family": "Tuure", "given": "Iida", "initials": "I", "orcid": "0000-0002-9754-6848", "researcher": {"href": "https://publications.scilifelab.se/researcher/70e380355782434ca0c2bd050a108786.json"}}, {"family": "Trillo-Muyo", "given": "Sergio", "initials": "S", "orcid": "0000-0002-3135-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e6b6b830e9145a2ae3e6c10895acbee.json"}}, {"family": "B\u00f3dizs", "given": "Szabolcs", "initials": "S", "orcid": "0000-0002-3303-5897", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9848a63af6e4d019bbce45745b2bd8c.json"}}, {"family": "Ihalainen", "given": "Janne A", "initials": "JA", "orcid": "0000-0002-8741-1587", "researcher": {"href": "https://publications.scilifelab.se/researcher/4730f17c203e496bb52a8812767bf37b.json"}}, {"family": "Takala", "given": "Heikki", "initials": "H", "orcid": "0000-0003-2518-8583", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf65baa23c3349caa07bc0f44cb52d88.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": "2022-12-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "7673", "issn-l": "2041-1723"}, "abstract": "Phytochrome proteins detect red/far-red light to guide the growth, motion, development and reproduction in plants, fungi, and bacteria. Bacterial phytochromes commonly function as an entrance signal in two-component sensory systems. Despite the availability of three-dimensional structures of phytochromes and other two-component proteins, the conformational changes, which lead to activation of the protein, are not understood. We reveal cryo electron microscopy structures of the complete phytochrome from Deinoccocus radiodurans in its resting and photoactivated states at 3.6 \u00c5 and 3.5 \u00c5 resolution, respectively. Upon photoactivation, the photosensory core module hardly changes its tertiary domain arrangement, but the connector helices between the photosensory and the histidine kinase modules open up like a zipper, causing asymmetry and disorder in the effector domains. The structures provide a framework for atom-scale understanding of signaling in phytochromes, visualize allosteric communication over several nanometers, and suggest that disorder in the dimeric arrangement of the effector domains is important for phosphatase activity in a two-component system. The results have implications for the development of optogenetic applications.", "doi": "10.1038/s41467-022-34893-3", "pmid": "36509762", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9744887"}, {"db": "pii", "key": "10.1038/s41467-022-34893-3"}], "notes": [], "created": "2023-11-26T14:06:55.998Z", "modified": "2023-11-26T14:06:56.176Z"}, {"entity": "publication", "iuid": "452f9e423170414ea771ee32215c63e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/452f9e423170414ea771ee32215c63e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/452f9e423170414ea771ee32215c63e1"}}, "title": "Sphingosine 1-phosphate mediates adiponectin receptor signaling essential for lipid homeostasis and embryogenesis.", "authors": [{"family": "Ruiz", "given": "Mario", "initials": "M", "orcid": "0000-0002-7149-6600", "researcher": {"href": "https://publications.scilifelab.se/researcher/35ea5372ccf64bad864d90e4b3698a24.json"}}, {"family": "Devkota", "given": "Ranjan", "initials": "R"}, {"family": "Panagaki", "given": "Dimitra", "initials": "D"}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO", "orcid": "0000-0001-9993-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/28c1f37dc6cc4ed98c8e8eb1a621fa2c.json"}}, {"family": "Kaper", "given": "Delaney", "initials": "D", "orcid": "0000-0002-9929-8104", "researcher": {"href": "https://publications.scilifelab.se/researcher/e96d29226c884ec496240844de56499a.json"}}, {"family": "Henricsson", "given": "Marcus", "initials": "M", "orcid": "0000-0002-4202-0339", "researcher": {"href": "https://publications.scilifelab.se/researcher/01a323cbf0a24269bd32bfc34539e021.json"}}, {"family": "Nik", "given": "Ali", "initials": "A"}, {"family": "Petkevicius", "given": "Kasparas", "initials": "K", "orcid": "0000-0003-2295-6065", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807cea22e324d8297776e90d31ed636.json"}}, {"family": "H\u00f6\u00f6g", "given": "Johanna L", "initials": "JL", "orcid": "0000-0003-2162-3816", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1eaedff964f4060ae6e69f59cad4521.json"}}, {"family": "Bohlooly-Y", "given": "Mohammad", "initials": "M"}, {"family": "Carlsson", "given": "Peter", "initials": "P"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Pilon", "given": "Marc", "initials": "M", "orcid": "0000-0003-3919-2882", "researcher": {"href": "https://publications.scilifelab.se/researcher/d45c4ecf9afe463c971af2de53a770a8.json"}}], "type": "journal article", "published": "2022-11-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "7162", "issn-l": "2041-1723"}, "abstract": "Cells and organisms require proper membrane composition to function and develop. Phospholipids are the major component of membranes and are primarily acquired through the diet. Given great variability in diet composition, cells must be able to deploy mechanisms that correct deviations from optimal membrane composition and properties. Here, using lipidomics and unbiased proteomics, we found that the embryonic lethality in mice lacking the fluidity regulators Adiponectin Receptors 1 and 2 (AdipoR1/2) is associated with aberrant high saturation of the membrane phospholipids. Using mouse embryonic fibroblasts (MEFs) derived from AdipoR1/2-KO embryos, human cell lines and the model organism C. elegans we found that, mechanistically, AdipoR1/2-derived sphingosine 1-phosphate (S1P) signals in parallel through S1PR3-SREBP1 and PPAR\u03b3 to sustain the expression of the fatty acid desaturase SCD and maintain membrane properties. Thus, our work identifies an evolutionary conserved pathway by which cells and organisms achieve membrane homeostasis and adapt to a variable environment.", "doi": "10.1038/s41467-022-34931-0", "pmid": "36418331", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9684441"}, {"db": "pii", "key": "10.1038/s41467-022-34931-0"}], "notes": [], "created": "2023-03-07T14:34:55.175Z", "modified": "2024-01-16T13:46:28.029Z"}, {"entity": "publication", "iuid": "20542f90f1d64447bba7fb7b1daf8db8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20542f90f1d64447bba7fb7b1daf8db8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20542f90f1d64447bba7fb7b1daf8db8"}}, "title": "Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores.", "authors": [{"family": "Jespersen", "given": "Nathan", "initials": "N"}, {"family": "Ehrenbolger", "given": "Kai", "initials": "K", "orcid": "0000-0003-1312-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/3acfe2f8d3914170a9eb6515a0c7976c.json"}}, {"family": "Winiger", "given": "Rahel R", "initials": "RR"}, {"family": "Svedberg", "given": "Dennis", "initials": "D"}, {"family": "Vossbrinck", "given": "Charles R", "initials": "CR"}, {"family": "Barandun", "given": "Jonas", "initials": "J", "orcid": "0000-0003-2971-8190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2456fbe0b6bf406889842ab9f0267c22.json"}}], "type": "journal article", "published": "2022-11-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6962", "issn-l": "2041-1723"}, "abstract": "Proteasomes play an essential role in the life cycle of intracellular pathogens with extracellular stages by ensuring proteostasis in environments with limited resources. In microsporidia, divergent parasites with extraordinarily streamlined genomes, the proteasome complexity and structure are unknown, which limits our understanding of how these unique pathogens adapt and compact essential eukaryotic complexes. We present cryo-electron microscopy structures of the microsporidian 20S and 26S proteasome isolated from dormant or germinated Vairimorpha necatrix spores. The discovery of PI31-like peptides, known to inhibit proteasome activity, bound simultaneously to all six active sites within the central cavity of the dormant spore proteasome, suggests reduced activity in the environmental stage. In contrast, the absence of the PI31-like peptides and the existence of 26S particles post-germination in the presence of ATP indicates that proteasomes are reactivated in nutrient-rich conditions. Structural and phylogenetic analyses reveal that microsporidian proteasomes have undergone extensive reductive evolution, lost at least two regulatory proteins, and compacted nearly every subunit. The highly derived structure of the microsporidian proteasome, and the minimized version of PI31 presented here, reinforce the feasibility of the development of specific inhibitors and provide insight into the unique evolution and biology of these medically and economically important pathogens.", "doi": "10.1038/s41467-022-34691-x", "pmid": "36379934", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9666519"}, {"db": "pii", "key": "10.1038/s41467-022-34691-x"}], "notes": [], "created": "2022-11-28T12:56:29.301Z", "modified": "2022-11-28T12:56:29.317Z"}, {"entity": "publication", "iuid": "1a8578beca9d4f599daedc3b45656e0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a8578beca9d4f599daedc3b45656e0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a8578beca9d4f599daedc3b45656e0e"}}, "title": "A multivesicular body-like organelle mediates stimulus-regulated trafficking of olfactory ciliary transduction proteins.", "authors": [{"family": "Maurya", "given": "Devendra Kumar", "initials": "DK", "orcid": "0000-0001-6052-4314", "researcher": {"href": "https://publications.scilifelab.se/researcher/7538f712473945629fe5371a5ff4fc73.json"}}, {"family": "Berghard", "given": "Anna", "initials": "A", "orcid": "0000-0001-8367-9589", "researcher": {"href": "https://publications.scilifelab.se/researcher/234eeb58a90642e7827db9c9d61abc18.json"}}, {"family": "Bohm", "given": "Staffan", "initials": "S", "orcid": "0000-0001-9950-7597", "researcher": {"href": "https://publications.scilifelab.se/researcher/c97bf7c882f6472a904f283c67929ae8.json"}}], "type": "journal article", "published": "2022-11-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6889", "issn-l": "2041-1723"}, "abstract": "Stimulus transduction in cilia of olfactory sensory neurons is mediated by odorant receptors, G\u03b1olf, adenylate cyclase-3, cyclic nucleotide-gated and chloride ion channels. Mechanisms regulating trafficking and localization of these proteins in the dendrite are unknown. By lectin/immunofluorescence staining and in vivo correlative light-electron microscopy (CLEM), we identify a retinitis pigmentosa-2 (RP2), ESCRT-0 and synaptophysin-containing multivesicular organelle that is not part of generic recycling/degradative/exosome pathways. The organelle's intraluminal vesicles contain the olfactory transduction proteins except for Golf subunits G\u03b313 and G\u03b21. Instead, G\u03b21 colocalizes with RP2 on the organelle's outer membrane. The organelle accumulates in response to stimulus deprivation, while odor stimuli or adenylate cyclase activation cause outer membrane disintegration, release of intraluminal vesicles, and RP2/G\u03b21 translocation to the base of olfactory cilia. Together, these findings reveal the existence of a dendritic organelle that mediates both stimulus-regulated storage of olfactory ciliary transduction proteins and membrane-delimited sorting important for G protein heterotrimerization.", "doi": "10.1038/s41467-022-34604-y", "pmid": "36371422", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9653401"}, {"db": "pii", "key": "10.1038/s41467-022-34604-y"}], "notes": [], "created": "2022-12-05T17:14:23.375Z", "modified": "2022-12-05T17:14:23.472Z"}, {"entity": "publication", "iuid": "176af94247064339a6083776c29a51fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/176af94247064339a6083776c29a51fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/176af94247064339a6083776c29a51fb"}}, "title": "Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits.", "authors": [{"family": "Liu", "given": "Lili", "initials": "L", "orcid": "0000-0002-2622-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/763a2755eb5540a2a92d6dc59754fb97.json"}}, {"family": "Khan", "given": "Atlas", "initials": "A", "orcid": "0000-0002-6651-2725", "researcher": {"href": "https://publications.scilifelab.se/researcher/5058de1650d3456993dcf3ab02a8f9bb.json"}}, {"family": "Sanchez-Rodriguez", "given": "Elena", "initials": "E", "orcid": "0000-0002-7041-5485", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2ee1321f3514835b7e48e794edf9283.json"}}, {"family": "Zanoni", "given": "Francesca", "initials": "F"}, {"family": "Li", "given": "Yifu", "initials": "Y"}, {"family": "Steers", "given": "Nicholas", "initials": "N"}, {"family": "Balderes", "given": "Olivia", "initials": "O"}, {"family": "Zhang", "given": "Junying", "initials": "J", "orcid": "0000-0003-4996-8699", "researcher": {"href": "https://publications.scilifelab.se/researcher/31ced250baba47f5ae40d6b0730ac75b.json"}}, {"family": "Krithivasan", "given": "Priya", "initials": "P"}, {"family": "LeDesma", "given": "Robert A", "initials": "RA"}, {"family": "Fischman", "given": "Clara", "initials": "C"}, {"family": "Hebbring", "given": "Scott J", "initials": "SJ"}, {"family": "Harley", "given": "John B", "initials": "JB"}, {"family": "Moncrieffe", "given": "Halima", "initials": "H", "orcid": "0000-0001-9744-4879", "researcher": {"href": "https://publications.scilifelab.se/researcher/97d79764251c4ac790c01b7cbcc7fe86.json"}}, {"family": "Kottyan", "given": "Leah C", "initials": "LC", "orcid": "0000-0003-3979-2220", "researcher": {"href": "https://publications.scilifelab.se/researcher/661ee875ca2445cb96d30e95bb8a7728.json"}}, {"family": "Namjou-Khales", "given": "Bahram", "initials": "B", "orcid": "0000-0003-4452-7878", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e21a127ed014c01bce3c1136648307c.json"}}, {"family": "Walunas", "given": "Theresa L", "initials": "TL", "orcid": "0000-0002-7653-3650", "researcher": {"href": "https://publications.scilifelab.se/researcher/e41f13951de944f6a5d1537cb4fb1de6.json"}}, {"family": "Knevel", "given": "Rachel", "initials": "R"}, {"family": "Raychaudhuri", "given": "Soumya", "initials": "S"}, {"family": "Karlson", "given": "Elizabeth W", "initials": "EW"}, {"family": "Denny", "given": "Joshua C", "initials": "JC"}, {"family": "Stanaway", "given": "Ian B", "initials": "IB", "orcid": "0000-0002-0783-0918", "researcher": {"href": "https://publications.scilifelab.se/researcher/390eac8ddd9b4d308f347311f45d63d9.json"}}, {"family": "Crosslin", "given": "David", "initials": "D"}, {"family": "Rauen", "given": "Thomas", "initials": "T"}, {"family": "Floege", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Eitner", "given": "Frank", "initials": "F"}, {"family": "Moldoveanu", "given": "Zina", "initials": "Z"}, {"family": "Reily", "given": "Colin", "initials": "C"}, {"family": "Knoppova", "given": "Barbora", "initials": "B", "orcid": "0000-0003-2997-4952", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1ae8af419664853903c2af954425155.json"}}, {"family": "Hall", "given": "Stacy", "initials": "S"}, {"family": "Sheff", "given": "Justin T", "initials": "JT"}, {"family": "Julian", "given": "Bruce A", "initials": "BA"}, {"family": "Wyatt", "given": "Robert J", "initials": "RJ"}, {"family": "Suzuki", "given": "Hitoshi", "initials": "H", "orcid": "0000-0002-1901-2111", "researcher": {"href": "https://publications.scilifelab.se/researcher/e033cc3f91d14466895f025044a1ec2e.json"}}, {"family": "Xie", "given": "Jingyuan", "initials": "J"}, {"family": "Chen", "given": "Nan", "initials": "N"}, {"family": "Zhou", "given": "Xujie", "initials": "X", "orcid": "0000-0002-7215-707X", "researcher": {"href": "https://publications.scilifelab.se/researcher/04c7801d74fb4056ad7a48824413bbce.json"}}, {"family": "Zhang", "given": "Hong", "initials": "H"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Viktorin", "given": "Alexander", "initials": "A", "orcid": "0000-0003-2141-2816", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f02b9aad56348c28f639bf231748096.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Shang", "given": "Ning", "initials": "N", "orcid": "0000-0001-7040-5204", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c4b535488448c9a911ce8db475f830.json"}}, {"family": "Hripcsak", "given": "George", "initials": "G"}, {"family": "Weng", "given": "Chunhua", "initials": "C", "orcid": "0000-0002-9624-0214", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ea1b4a4132242e3abac469d5f85d58c.json"}}, {"family": "Rundek", "given": "Tatjana", "initials": "T", "orcid": "0000-0002-7115-9815", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ebc54256244a76a59f4eef9540522c.json"}}, {"family": "Elkind", "given": "Mitchell S V", "initials": "MSV", "orcid": "0000-0003-2562-1156", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f1771d64184c9db275c6308ea92c67.json"}}, {"family": "Oelsner", "given": "Elizabeth C", "initials": "EC", "orcid": "0000-0002-7481-9671", "researcher": {"href": "https://publications.scilifelab.se/researcher/afb61a7c022d4d24890446aa80c447b3.json"}}, {"family": "Barr", "given": "R Graham", "initials": "RG"}, {"family": "Ionita-Laza", "given": "Iuliana", "initials": "I"}, {"family": "Novak", "given": "Jan", "initials": "J", "orcid": "0000-0002-9211-6670", "researcher": {"href": "https://publications.scilifelab.se/researcher/e44350372d7947c9b2e4c9d2c9baab4f.json"}}, {"family": "Gharavi", "given": "Ali G", "initials": "AG", "orcid": "0000-0003-2801-233X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fe768273c7343098d829bcd64038707.json"}}, {"family": "Kiryluk", "given": "Krzysztof", "initials": "K", "orcid": "0000-0002-5047-6715", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6e7b5668c0141728599d5ebb68c8929.json"}}], "type": "journal article", "published": "2022-11-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6859", "issn-l": "2041-1723"}, "abstract": "Immunoglobulin A (IgA) mediates mucosal responses to food antigens and the intestinal microbiome and is involved in susceptibility to mucosal pathogens, celiac disease, inflammatory bowel disease, and IgA nephropathy. We performed a genome-wide association study of serum IgA levels in 41,263 individuals of diverse ancestries and identified 20 genome-wide significant loci, including 9 known and 11 novel loci. Co-localization analyses with expression QTLs prioritized candidate genes for 14 of 20 significant loci. Most loci encoded genes that produced immune defects and IgA abnormalities when genetically manipulated in mice. We also observed positive genetic correlations of serum IgA levels with IgA nephropathy, type 2 diabetes, and body mass index, and negative correlations with celiac disease, inflammatory bowel disease, and several infections. Mendelian randomization supported elevated serum IgA as a causal factor in IgA nephropathy. African ancestry was consistently associated with higher serum IgA levels and greater frequency of IgA-increasing alleles compared to other ancestries. Our findings provide novel insights into the genetic regulation of IgA levels and its potential role in human disease.", "doi": "10.1038/s41467-022-34456-6", "pmid": "36369178", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9651905"}, {"db": "pii", "key": "10.1038/s41467-022-34456-6"}], "notes": [], "created": "2023-02-24T13:14:55.508Z", "modified": "2023-06-19T13:19:40.686Z"}, {"entity": "publication", "iuid": "6448eef2b2ba45f08ede2ebd059ea9d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6448eef2b2ba45f08ede2ebd059ea9d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6448eef2b2ba45f08ede2ebd059ea9d8"}}, "title": "FRET-FISH probes chromatin compaction at individual genomic loci in single cells.", "authors": [{"family": "Mota", "given": "Ana", "initials": "A", "orcid": "0000-0001-8592-9764", "researcher": {"href": "https://publications.scilifelab.se/researcher/508960cbe03d4490a6e4594fc76e3510.json"}}, {"family": "Berezicki", "given": "Szymon", "initials": "S", "orcid": "0000-0003-3980-6290", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8794ceeb3bf405a8125545b49f7ebc7.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Li-Wang", "given": "Xiaoze", "initials": "X"}, {"family": "Gradin", "given": "Katarina", "initials": "K"}, {"family": "Peuckert", "given": "Christiane", "initials": "C"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2022-11-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6680"}, "abstract": "Chromatin compaction is a key biophysical property that influences multiple DNA transactions. Lack of chromatin accessibility is frequently used as proxy for chromatin compaction. However, we currently lack tools for directly probing chromatin compaction at individual genomic loci. To fill this gap, here we present FRET-FISH, a method combining fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at select loci in single cells. We first validate FRET-FISH by comparing it with ATAC-seq, demonstrating that local compaction and accessibility are strongly correlated. FRET-FISH also detects expected differences in compaction upon treatment with drugs perturbing global chromatin condensation. We then leverage FRET-FISH to study local chromatin compaction on the active and inactive X chromosome, along the nuclear radius, in different cell cycle phases, and during increasing passage number. FRET-FISH is a robust tool for probing local chromatin compaction in single cells.", "doi": "10.1038/s41467-022-34183-y", "pmid": "36335096", "labels": {"Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9637210"}, {"db": "pii", "key": "10.1038/s41467-022-34183-y"}], "notes": [], "created": "2023-06-26T12:49:38.233Z", "modified": "2023-11-29T16:29:33.698Z"}, {"entity": "publication", "iuid": "c11542cd240549aeb057f59e221c23d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c11542cd240549aeb057f59e221c23d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c11542cd240549aeb057f59e221c23d1"}}, "title": "Proteogenomics refines the molecular classification of chronic lymphocytic leukemia", "authors": [{"family": "Herbst", "given": "Sophie A", "initials": "SA", "orcid": "0000-0001-8502-0366", "researcher": {"href": "https://publications.scilifelab.se/researcher/760334e16daa4899b4abbb38f07e7a5f.json"}}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Helmboldt", "given": "Alexander J", "initials": "AJ", "orcid": "0000-0002-0807-7518", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e7cc6012b6f4ad98bb8767293f676ee.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/481b2a2329634f9086cf52fb808edea5.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Stahl", "given": "Matthias", "initials": "M", "orcid": "0000-0002-0176-9386", "researcher": {"href": "https://publications.scilifelab.se/researcher/f113f8aa6e77444d9492b5fed0067b25.json"}}, {"family": "Schitter", "given": "Eva C", "initials": "EC"}, {"family": "Liebers", "given": "Nora", "initials": "N"}, {"family": "Brinkmann", "given": "Berit J", "initials": "BJ", "orcid": "0000-0002-0457-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce4155b57a554aa0a105c4245ae265eb.json"}}, {"family": "Czernilofsky", "given": "Felix", "initials": "F", "orcid": "0000-0001-5868-2890", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f8a18192669486b9b05dfc57d453770.json"}}, {"family": "Roider", "given": "Tobias", "initials": "T", "orcid": "0000-0002-6973-3531", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39f6a40851c48a19a3cfb0b20bbcfbd.json"}}, {"family": "Bruch", "given": "Peter Martin", "initials": "PM", "orcid": "0000-0002-9992-3109", "researcher": {"href": "https://publications.scilifelab.se/researcher/01d972f1ca834f4eb0f3a9a949a85f97.json"}}, {"family": "Iskar", "given": "Murat", "initials": "M", "orcid": "0000-0001-8603-4313", "researcher": {"href": "https://publications.scilifelab.se/researcher/a94f83023a4b49488cd5d657604c5b78.json"}}, {"family": "Kittai", "given": "Adam", "initials": "A"}, {"family": "Huang", "given": "Ying", "initials": "Y"}, {"family": "Lu", "given": "Junyan", "initials": "J", "orcid": "0000-0002-9211-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/08813991edd84a809d5a3e0e0bfaaa2e.json"}}, {"family": "Richter", "given": "Sarah", "initials": "S"}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Umer", "given": "Husen Muhammad", "initials": "HM", "orcid": "0000-0003-3971-2462", "researcher": {"href": "https://publications.scilifelab.se/researcher/db1b83fca3c740f7a20e8dc9f2a1331c.json"}}, {"family": "Knoll", "given": "Mareike", "initials": "M"}, {"family": "Kolb", "given": "Carolin", "initials": "C"}, {"family": "Lenze", "given": "Angela", "initials": "A"}, {"family": "Cao", "given": "Xiaofang", "initials": "X"}, {"family": "\u00d6sterholm", "given": "Cecilia", "initials": "C"}, {"family": "Wahnschaffe", "given": "Linus", "initials": "L"}, {"family": "Herling", "given": "Carmen", "initials": "C"}, {"family": "Scheinost", "given": "Sebastian", "initials": "S"}, {"family": "Ganzinger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-2716-5425", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a168f3da3b48adadad47cafd3f3f64.json"}}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Kriegsmann", "given": "Katharina", "initials": "K"}, {"family": "Kriegsmann", "given": "Mark", "initials": "M"}, {"family": "Anders", "given": "Simon", "initials": "S", "orcid": "0000-0003-4868-1805", "researcher": {"href": "https://publications.scilifelab.se/researcher/c11e0cc8bbb846ac821dcd782024c0cc.json"}}, {"family": "Zapatka", "given": "Marc", "initials": "M", "orcid": "0000-0001-8287-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f34c95a849a4a2e8e48dd98034cba88.json"}}, {"family": "Del Poeta", "given": "Giovanni", "initials": "G"}, {"family": "Zucchetto", "given": "Antonella", "initials": "A"}, {"family": "Bomben", "given": "Riccardo", "initials": "R", "orcid": "0000-0002-8746-9404", "researcher": {"href": "https://publications.scilifelab.se/researcher/72fc218ceb84460ca0eece578e06593e.json"}}, {"family": "Gattei", "given": "Valter", "initials": "V", "orcid": "0000-0001-5933-9680", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2d6143330194f1d99705b0d60808f74.json"}}, {"family": "Dreger", "given": "Peter", "initials": "P"}, {"family": "Woyach", "given": "Jennifer", "initials": "J", "orcid": "0000-0002-3403-9144", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd77b10bbd084fed98ab2f647a247bf3.json"}}, {"family": "Herling", "given": "Marco", "initials": "M"}, {"family": "M\u00fcller-Tidow", "given": "Carsten", "initials": "C", "orcid": "0000-0002-7166-5232", "researcher": {"href": "https://publications.scilifelab.se/researcher/16f6edb14cb74bbdb221ea2ae0e1ab27.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}, {"family": "Stilgenbauer", "given": "Stephan", "initials": "S"}, {"family": "Zenz", "given": "Thorsten", "initials": "T", "orcid": "0000-0001-7890-9845", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f6b107b1ec94de7bbc260f92f2dcc9f.json"}}, {"family": "Huber", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-0474-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dacd52a252743b09b7f7383b95aaf36.json"}}, {"family": "Tausch", "given": "Eugen", "initials": "E"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Dietrich", "given": "Sascha", "initials": "S", "orcid": "0000-0002-0648-1832", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ddfd067d9b34285bd51eb0c08f4b73f.json"}}], "type": "journal-article", "published": "2022-10-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6226"}, "abstract": "Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic-based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterize the proteome and transcriptome alongside genetic and ex-vivo drug response profiling in a clinically annotated CLL discovery cohort (n = 68). Unsupervised clustering of the proteome data reveals six subgroups. Five of these proteomic groups are associated with genetic features, while one group is only detectable at the proteome level. This new group is characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). Classifiers developed to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n = 165, n = 169) confirm that ASB-CLL comprises about 20% of CLL patients. The inferior overall survival in ASB-CLL is also independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling.", "doi": "10.1038/s41467-022-33385-8", "pmid": "36266272", "labels": {"Global Proteomics and Proteogenomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC9584885"}, {"db": "pii", "key": "10.1038/s41467-022-33385-8"}], "notes": [], "created": "2023-06-07T14:08:49.429Z", "modified": "2023-06-19T10:57:58.320Z"}, {"entity": "publication", "iuid": "fb8cd6b0ed8d494bbafb1456c1c54e25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb8cd6b0ed8d494bbafb1456c1c54e25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb8cd6b0ed8d494bbafb1456c1c54e25"}}, "title": "Rapid antibiotic susceptibility testing and species identification for mixed samples.", "authors": [{"family": "Kandavalli", "given": "Vinodh", "initials": "V"}, {"family": "Karempudi", "given": "Praneeth", "initials": "P"}, {"family": "Larsson", "given": "Jimmy", "initials": "J"}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.json"}}], "type": "journal article", "published": "2022-10-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6215", "issn-l": "2041-1723"}, "abstract": "Antimicrobial resistance is an increasing problem on a global scale. Rapid antibiotic susceptibility testing (AST) is urgently needed in the clinic to enable personalized prescriptions in high-resistance environments and to limit the use of broad-spectrum drugs. Current rapid phenotypic AST methods do not include species identification (ID), leaving time-consuming plating or culturing as the only available option when ID is needed to make the sensitivity call. Here we describe a method to perform phenotypic AST at the single-cell level in a microfluidic chip that allows subsequent genotyping by in situ FISH. By stratifying the phenotypic AST response on the species of individual cells, it is possible to determine the susceptibility profile for each species in a mixed sample in 2 h. In this proof-of-principle study, we demonstrate the operation with four antibiotics and mixed samples with combinations of seven species.", "doi": "10.1038/s41467-022-33659-1", "pmid": "36266330", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9584937"}, {"db": "pii", "key": "10.1038/s41467-022-33659-1"}], "notes": [], "created": "2023-11-27T21:47:27.042Z", "modified": "2024-01-16T13:48:34.710Z"}, {"entity": "publication", "iuid": "675091121e4145f5934b9aa1f15f6b64", "links": {"self": {"href": "https://publications.scilifelab.se/publication/675091121e4145f5934b9aa1f15f6b64.json"}, "display": {"href": "https://publications.scilifelab.se/publication/675091121e4145f5934b9aa1f15f6b64"}}, "title": "Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.", "authors": [{"family": "Tobiasson", "given": "Victor", "initials": "V", "orcid": "0000-0001-8920-017X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5208789057a94d0d9575476bf9c88d5a.json"}}, {"family": "Berzina", "given": "Ieva", "initials": "I", "orcid": "0000-0003-2120-7580", "researcher": {"href": "https://publications.scilifelab.se/researcher/575d868bdeef4e318503564bb8a37e08.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal article", "published": "2022-10-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6132", "issn-l": "2041-1723"}, "abstract": "Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 \u00c5 resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.", "doi": "10.1038/s41467-022-33582-5", "pmid": "36253367", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9576764"}, {"db": "pii", "key": "10.1038/s41467-022-33582-5"}], "notes": [], "created": "2022-11-30T09:55:59.103Z", "modified": "2022-11-30T09:55:59.346Z"}, {"entity": "publication", "iuid": "8b71ca4979984436acd61a92e09fef83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b71ca4979984436acd61a92e09fef83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b71ca4979984436acd61a92e09fef83"}}, "title": "TLCD1 and TLCD2 regulate cellular phosphatidylethanolamine composition and promote the progression of non-alcoholic steatohepatitis", "authors": [{"family": "Petkevicius", "given": "Kasparas", "initials": "K", "orcid": "0000-0003-2295-6065", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807cea22e324d8297776e90d31ed636.json"}}, {"family": "Palmgren", "given": "Henrik", "initials": "H"}, {"family": "Glover", "given": "Matthew S", "initials": "MS"}, {"family": "Ahnmark", "given": "Andrea", "initials": "A"}, {"family": "Andr\u00e9asson", "given": "Anne Christine", "initials": "AC"}, {"family": "Madeyski-Bengtson", "given": "Katja", "initials": "K"}, {"family": "Kawana", "given": "Hiroki", "initials": "H"}, {"family": "Allman", "given": "Erik L", "initials": "EL"}, {"family": "Kaper", "given": "Delaney", "initials": "D", "orcid": "0000-0002-9929-8104", "researcher": {"href": "https://publications.scilifelab.se/researcher/e96d29226c884ec496240844de56499a.json"}}, {"family": "Uhrbom", "given": "Martin", "initials": "M"}, {"family": "Andersson", "given": "Liselotte", "initials": "L"}, {"family": "Aasehaug", "given": "Leif", "initials": "L"}, {"family": "Forsstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Wallin", "given": "Simonetta", "initials": "S", "orcid": "0000-0001-5668-1229", "researcher": {"href": "https://publications.scilifelab.se/researcher/bab022f6c191457993878dd9a5983f41.json"}}, {"family": "Ahlstedt", "given": "Ingela", "initials": "I"}, {"family": "Leke", "given": "Renata", "initials": "R"}, {"family": "Karlsson", "given": "Daniel", "initials": "D"}, {"family": "Gonz\u00e1lez-King", "given": "Hern\u00e1n", "initials": "H", "orcid": "0000-0003-4344-9484", "researcher": {"href": "https://publications.scilifelab.se/researcher/58cbb7a64622479f97f2df3e955bed91.json"}}, {"family": "L\u00f6fgren", "given": "Lars", "initials": "L"}, {"family": "Nilsson", "given": "Ralf", "initials": "R"}, {"family": "Pellegrini", "given": "Giovanni", "initials": "G"}, {"family": "Kono", "given": "Nozomu", "initials": "N", "orcid": "0000-0002-0871-8477", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea71ace9343b4d418c78d7cc4bbff16a.json"}}, {"family": "Aoki", "given": "Junken", "initials": "J"}, {"family": "Hess", "given": "Sonja", "initials": "S"}, {"family": "Sienski", "given": "Grzegorz", "initials": "G", "orcid": "0000-0002-2730-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2301dc9b57540e28fa02738caa8f8f3.json"}}, {"family": "Pilon", "given": "Marc", "initials": "M", "orcid": "0000-0003-3919-2882", "researcher": {"href": "https://publications.scilifelab.se/researcher/d45c4ecf9afe463c971af2de53a770a8.json"}}, {"family": "Bohlooly-Y", "given": "Mohammad", "initials": "M"}, {"family": "Maresca", "given": "Marcello", "initials": "M", "orcid": "0000-0003-0796-661X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3bd1ebf0013464894b127b184a4dca5.json"}}, {"family": "Peng", "given": "Xiao Rong", "initials": "XR"}], "type": "journal-article", "published": "2022-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6020", "issn-l": "2041-1723"}, "abstract": "The fatty acid composition of phosphatidylethanolamine (PE) determines cellular metabolism, oxidative stress, and inflammation. However, our understanding of how cells regulate PE composition is limited. Here, we identify a genetic locus on mouse chromosome 11, containing two poorly characterized genes Tlcd1 and Tlcd2, that strongly influences PE composition. We generated Tlcd1/2 double-knockout (DKO) mice and found that they have reduced levels of hepatic monounsaturated fatty acid (MUFA)-containing PE species. Mechanistically, TLCD1/2 proteins act cell intrinsically to promote the incorporation of MUFAs into PEs. Furthermore, TLCD1/2 interact with the mitochondria in an evolutionarily conserved manner and regulate mitochondrial PE composition. Lastly, we demonstrate the biological relevance of our findings in dietary models of metabolic disease, where Tlcd1/2 DKO mice display attenuated development of non-alcoholic steatohepatitis compared to controls. Overall, we identify TLCD1/2 proteins as key regulators of cellular PE composition, with our findings having broad implications in understanding and treating disease.", "doi": "10.1038/s41467-022-33735-6", "pmid": "36241646", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9568529"}, {"db": "pii", "key": "10.1038/s41467-022-33735-6"}], "notes": [], "created": "2022-12-05T08:13:47.856Z", "modified": "2025-10-17T13:03:14.568Z"}, {"entity": "publication", "iuid": "341fe4a6a6984eeba43a776db1cab7f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/341fe4a6a6984eeba43a776db1cab7f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/341fe4a6a6984eeba43a776db1cab7f0"}}, "title": "Manganese-driven CoQ deficiency.", "authors": [{"family": "Diessl", "given": "Jutta", "initials": "J", "orcid": "0000-0002-4044-5413", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b925cae1aaa4aa5bf79c931a2a68f39.json"}}, {"family": "Berndtsson", "given": "Jens", "initials": "J", "orcid": "0000-0001-6627-8134", "researcher": {"href": "https://publications.scilifelab.se/researcher/7620a5c7c0f245a28771d57d7179abbd.json"}}, {"family": "Broeskamp", "given": "Filomena", "initials": "F", "orcid": "0000-0002-6955-3901", "researcher": {"href": "https://publications.scilifelab.se/researcher/1539ac59d86c4b41bfb719f8e3874d0e.json"}}, {"family": "Habernig", "given": "Lukas", "initials": "L"}, {"family": "Kohler", "given": "Verena", "initials": "V"}, {"family": "Vazquez-Calvo", "given": "Carmela", "initials": "C"}, {"family": "Nandy", "given": "Arpita", "initials": "A"}, {"family": "Peselj", "given": "Carlotta", "initials": "C"}, {"family": "Drobysheva", "given": "Sofia", "initials": "S"}, {"family": "Pelosi", "given": "Ludovic", "initials": "L"}, {"family": "V\u00f6gtle", "given": "F-Nora", "initials": "FN"}, {"family": "Pierrel", "given": "Fabien", "initials": "F", "orcid": "0000-0003-2083-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ba624854b0343a5b46f5fc86cc2672b.json"}}, {"family": "Ott", "given": "Martin", "initials": "M", "orcid": "0000-0001-6367-3091", "researcher": {"href": "https://publications.scilifelab.se/researcher/b27b582dbd2a47bcbb0fb3194277902a.json"}}, {"family": "B\u00fcttner", "given": "Sabrina", "initials": "S", "orcid": "0000-0002-2786-8542", "researcher": {"href": "https://publications.scilifelab.se/researcher/6be7c476049b4f3497d187cba3daad77.json"}}], "type": "journal article", "published": "2022-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6061", "issn-l": "2041-1723"}, "abstract": "Overexposure to manganese disrupts cellular energy metabolism across species, but the molecular mechanism underlying manganese toxicity remains enigmatic. Here, we report that excess cellular manganese selectively disrupts coenzyme Q (CoQ) biosynthesis, resulting in failure of mitochondrial bioenergetics. While respiratory chain complexes remain intact, the lack of CoQ as lipophilic electron carrier precludes oxidative phosphorylation and leads to premature cell and organismal death. At a molecular level, manganese overload causes mismetallation and proteolytic degradation of Coq7, a diiron hydroxylase that catalyzes the penultimate step in CoQ biosynthesis. Coq7 overexpression or supplementation with a CoQ headgroup analog that bypasses Coq7 function fully corrects electron transport, thus restoring respiration and viability. We uncover a unique sensitivity of a diiron enzyme to mismetallation and define the molecular mechanism for manganese-induced bioenergetic failure that is conserved across species.", "doi": "10.1038/s41467-022-33641-x", "pmid": "36229432", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9563070"}, {"db": "pii", "key": "10.1038/s41467-022-33641-x"}], "notes": [], "created": "2022-11-24T11:24:25.189Z", "modified": "2022-11-24T11:24:25.349Z"}, {"entity": "publication", "iuid": "c27764ed4c514f2592c156cc59d23608", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608"}}, "title": "Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.", "authors": [{"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2cb6f3cce5f4919959e18074d51256d.json"}}, {"family": "Lillie", "given": "Mette", "initials": "M", "orcid": "0000-0001-8714-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce02b2116c0417e8a4dcd578f45983b.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}], "type": "journal article", "published": "2022-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6033"}, "abstract": "Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin's finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin's finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin's finches' radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin's finches.", "doi": "10.1038/s41467-022-33723-w", "pmid": "36229469", "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/s41467-022-33723-w"}, {"db": "pmc", "key": "PMC9562234"}], "notes": [], "created": "2022-11-09T16:00:11.231Z", "modified": "2024-01-16T13:48:34.742Z"}, {"entity": "publication", "iuid": "d2a9f88fa2d643ab84958a4a42f02b20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2a9f88fa2d643ab84958a4a42f02b20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2a9f88fa2d643ab84958a4a42f02b20"}}, "title": "Membrane-assisted assembly and selective secretory autophagy of enteroviruses.", "authors": [{"family": "Dahmane", "given": "Selma", "initials": "S"}, {"family": "Kerviel", "given": "Adeline", "initials": "A"}, {"family": "Morado", "given": "Dustin R", "initials": "DR", "orcid": "0000-0003-4693-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/eef09b7a95b64a699900bae6a5390e31.json"}}, {"family": "Shankar", "given": "Kasturika", "initials": "K"}, {"family": "Ahlman", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lazarou", "given": "Michael", "initials": "M", "orcid": "0000-0003-2150-5545", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebf4d61948b64fbabf01d1f3999bd817.json"}}, {"family": "Altan-Bonnet", "given": "Nihal", "initials": "N", "orcid": "0000-0002-5546-6452", "researcher": {"href": "https://publications.scilifelab.se/researcher/790dc32e658e48239e687bea0b616b6e.json"}}, {"family": "Carlson", "given": "Lars-Anders", "initials": "LA", "orcid": "0000-0003-2342-6488", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba0e366ce21e49b48212bbed5a0a7bd1.json"}}], "type": "journal article", "published": "2022-10-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "5986", "issn-l": "2041-1723"}, "abstract": "Enteroviruses are non-enveloped positive-sense RNA viruses that cause diverse diseases in humans. Their rapid multiplication depends on remodeling of cytoplasmic membranes for viral genome replication. It is unknown how virions assemble around these newly synthesized genomes and how they are then loaded into autophagic membranes for release through secretory autophagy. Here, we use cryo-electron tomography of infected cells to show that poliovirus assembles directly on replication membranes. Pharmacological untethering of capsids from membranes abrogates RNA encapsidation. Our data directly visualize a membrane-bound half-capsid as a prominent virion assembly intermediate. Assembly progression past this intermediate depends on the class III phosphatidylinositol 3-kinase VPS34, a key host-cell autophagy factor. On the other hand, the canonical autophagy initiator ULK1 is shown to restrict virion production since its inhibition leads to increased accumulation of virions in vast intracellular arrays, followed by an increased vesicular release at later time points. Finally, we identify multiple layers of selectivity in virus-induced autophagy, with a strong selection for RNA-loaded virions over empty capsids and the segregation of virions from other types of autophagosome contents. These findings provide an integrated structural framework for multiple stages of the poliovirus life cycle.", "doi": "10.1038/s41467-022-33483-7", "pmid": "36216808", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9550805"}, {"db": "pii", "key": "10.1038/s41467-022-33483-7"}], "notes": [], "created": "2022-11-30T08:19:56.916Z", "modified": "2022-11-30T08:23:14.288Z"}, {"entity": "publication", "iuid": "362c451c88124be69c423cc4853c5216", "links": {"self": {"href": "https://publications.scilifelab.se/publication/362c451c88124be69c423cc4853c5216.json"}, "display": {"href": "https://publications.scilifelab.se/publication/362c451c88124be69c423cc4853c5216"}}, "title": "Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.", "authors": [{"family": "Marklund", "given": "Maja", "initials": "M", "orcid": "0000-0003-2627-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a238f7adbc242398a46fd24190a2811.json"}}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Friedrich", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-3889-5589", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e1de4177ae649aba93a633ca451ebdb.json"}}, {"family": "Berglund", "given": "Emelie", "initials": "E", "orcid": "0000-0003-1857-307X", "researcher": {"href": "https://publications.scilifelab.se/researcher/87df6f4e3aed48938e7bee3acf27847e.json"}}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Tanoglidi", "given": "Anna", "initials": "A"}, {"family": "Liu", "given": "Yao", "initials": "Y", "orcid": "0000-0001-5572-723X", "researcher": {"href": "https://publications.scilifelab.se/researcher/08bfef572b6e4c7287380d8a5783bd9c.json"}}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L", "orcid": "0000-0002-5108-4481", "researcher": {"href": "https://publications.scilifelab.se/researcher/98234e5e06c241879f6f986ded3ab6f9.json"}}, {"family": "Erickson", "given": "Andrew", "initials": "A"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Lamb", "given": "Alastair D", "initials": "AD", "orcid": "0000-0002-2968-7155", "researcher": {"href": "https://publications.scilifelab.se/researcher/798d88b3df1e4a7d994e90b5d60372e6.json"}}, {"family": "Sonnhammer", "given": "Erik", "initials": "E", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d7888c298484f958c2c5f7fe0a8a9ba.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": "2022-09-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "5475"}, "abstract": "The molecular mechanisms underlying lethal castration-resistant prostate cancer remain poorly understood, with intratumoral heterogeneity a likely contributing factor. To examine the temporal aspects of resistance, we analyze tumor heterogeneity in needle biopsies collected before and after treatment with androgen deprivation therapy. By doing so, we are able to couple clinical responsiveness and morphological information such as Gleason score to transcriptome-wide data. Our data-driven analysis of transcriptomes identifies several distinct intratumoral cell populations, characterized by their unique gene expression profiles. Certain cell populations present before treatment exhibit gene expression profiles that match those of resistant tumor cell clusters, present after treatment. We confirm that these clusters are resistant by the localization of active androgen receptors to the nuclei in cancer cells post-treatment. Our data also demonstrates that most stromal cells adjacent to resistant clusters do not express the androgen receptor, and we identify differentially expressed genes for these cells. Altogether, this study shows the potential to increase the power in predicting resistant tumors.", "doi": "10.1038/s41467-022-33069-3", "pmid": "36115838", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Spatial omics": null}, "xrefs": [{"db": "pmc", "key": "PMC9482614"}, {"db": "pii", "key": "10.1038/s41467-022-33069-3"}], "notes": [], "created": "2022-12-19T10:35:54.516Z", "modified": "2023-10-23T09:22:51.156Z"}, {"entity": "publication", "iuid": "998efaa46c9942f3a499d5dba6686f2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/998efaa46c9942f3a499d5dba6686f2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/998efaa46c9942f3a499d5dba6686f2e"}}, "title": "Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield.", "authors": [{"family": "Osterholz", "given": "Helena", "initials": "H", "orcid": "0000-0002-2858-9799", "researcher": {"href": "https://publications.scilifelab.se/researcher/2049c163450b4ad48ab5efc5b11cd50e.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Alakangas", "given": "Linda J", "initials": "LJ"}, {"family": "Tullborg", "given": "Eva-Lena", "initials": "EL"}, {"family": "Dittmar", "given": "Thorsten", "initials": "T"}, {"family": "Kalinowski", "given": "Birgitta E", "initials": "BE"}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2022-08-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "4837"}, "abstract": "The deep terrestrial biosphere encompasses the life below the photosynthesis-fueled surface that perseveres in typically nutrient and energy depleted anoxic groundwaters. The composition and cycling of this vast dissolved organic matter (DOM) reservoir relevant to the global carbon cycle remains to be deciphered. Here we show that recent Baltic Sea-influenced to ancient pre-Holocene saline Fennoscandian Shield deep bedrock fracture waters carried DOM with a strong terrigenous signature and varying contributions from abiotic and biotic processes. Removal of easily degraded carbon at the surface-to-groundwater transition and corresponding microbial community assembly processes likely resulted in the highly similar DOM signatures across the notably different water types that selected for a core microbiome. In combination with the aliphatic character, depleted \u03b413C signatures in DOM indicated recent microbial production in the oldest, saline groundwater. Our study revealed the persistence of terrestrially-sourced carbon in severely energy limited deep continental groundwaters supporting deep microbial life.", "doi": "10.1038/s41467-022-32457-z", "pmid": "35977924", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9385861"}, {"db": "pii", "key": "10.1038/s41467-022-32457-z"}], "notes": [], "created": "2022-12-19T10:30:02.867Z", "modified": "2024-01-16T13:48:35.176Z"}, {"entity": "publication", "iuid": "058e4ab4248b4f38bf463af3cb986da6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/058e4ab4248b4f38bf463af3cb986da6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/058e4ab4248b4f38bf463af3cb986da6"}}, "title": "A method for Boolean analysis of protein interactions at a molecular level.", "authors": [{"family": "Raykova", "given": "Doroteya", "initials": "D", "orcid": "0000-0001-6452-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a81c40491e349178167f148f2351875.json"}}, {"family": "Kermpatsou", "given": "Despoina", "initials": "D", "orcid": "0000-0001-5872-4472", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfafe1fe67374c25ac5111ecd42c2fd4.json"}}, {"family": "Malmqvist", "given": "Tony", "initials": "T", "orcid": "0000-0003-0609-2009", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee835b51354e4cb5aff5dfbf43964dc8.json"}}, {"family": "Harrison", "given": "Philip J", "initials": "PJ"}, {"family": "Sander", "given": "Marie Rubin", "initials": "MR", "orcid": "0000-0002-9783-5682", "researcher": {"href": "https://publications.scilifelab.se/researcher/68a774625f6948d693bf4ad09eaba273.json"}}, {"family": "Stiller", "given": "Christiane", "initials": "C", "orcid": "0000-0002-6552-8426", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f8bb525e1094fbfbfb71dbbff62cbc7.json"}}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Leino", "given": "Mattias", "initials": "M"}, {"family": "Ricardo", "given": "Sara", "initials": "S", "orcid": "0000-0003-4091-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5599dd22d9e44a5af16850baf14e10e.json"}}, {"family": "Klemm", "given": "Anna", "initials": "A", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ae78afb2a424b0ab70d49871f361d13.json"}}, {"family": "David", "given": "Leonor", "initials": "L", "orcid": "0000-0003-4207-9258", "researcher": {"href": "https://publications.scilifelab.se/researcher/510030f8783044e8b644277783308bf6.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Vemuri", "given": "Kalyani", "initials": "K", "orcid": "0000-0003-2544-5412", "researcher": {"href": "https://publications.scilifelab.se/researcher/b74c149757644aa5a0997af9ca583a45.json"}}, {"family": "Dimberg", "given": "Anna", "initials": "A", "orcid": "0000-0003-4422-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/c53166298a214331866c8cbf3bb9a3b9.json"}}, {"family": "Sundqvist", "given": "Anders", "initials": "A"}, {"family": "Norlin", "given": "Maria", "initials": "M", "orcid": "0000-0003-4348-6269", "researcher": {"href": "https://publications.scilifelab.se/researcher/a10ffe5af28b4398b8d19743f7927e34.json"}}, {"family": "Klaesson", "given": "Axel", "initials": "A"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"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": "2022-08-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "4755", "issn-l": "2041-1723"}, "abstract": "Determining the levels of protein-protein interactions is essential for the analysis of signaling within the cell, characterization of mutation effects, protein function and activation in health and disease, among others. Herein, we describe MolBoolean - a method to detect interactions between endogenous proteins in various subcellular compartments, utilizing antibody-DNA conjugates for identification and signal amplification. In contrast to proximity ligation assays, MolBoolean simultaneously indicates the relative abundances of protein A and B not interacting with each other, as well as the pool of A and B proteins that are proximal enough to be considered an AB complex. MolBoolean is applicable both in fixed cells and tissue sections. The specific and quantifiable data that the method generates provide opportunities for both diagnostic use and medical research.", "doi": "10.1038/s41467-022-32395-w", "pmid": "35963857", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-32395-w"}, {"db": "pmc", "key": "PMC9375095"}], "notes": [], "created": "2022-08-30T09:04:56.787Z", "modified": "2022-08-30T09:04:57.234Z"}, {"entity": "publication", "iuid": "4a39ef47f4934674913793b770201d23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a39ef47f4934674913793b770201d23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a39ef47f4934674913793b770201d23"}}, "title": "Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data.", "authors": [{"family": "Dhapola", "given": "Parashar", "initials": "P", "orcid": "0000-0002-8070-7238", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b747086d7b04853bc1cca89d4a71bd2.json"}}, {"family": "Rodhe", "given": "Johan", "initials": "J"}, {"family": "Olofzon", "given": "Rasmus", "initials": "R", "orcid": "0000-0001-8079-8718", "researcher": {"href": "https://publications.scilifelab.se/researcher/1aa88864460e41a2a0fcd4f0e94b0172.json"}}, {"family": "Bonald", "given": "Thomas", "initials": "T"}, {"family": "Erlandsson", "given": "Eva", "initials": "E"}, {"family": "Soneji", "given": "Shamit", "initials": "S"}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2022-08-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "4616", "issn-l": "2041-1723"}, "abstract": "As the scale of single-cell genomics experiments grows into the millions, the computational requirements to process this data are beyond the reach of many. Herein we present Scarf, a modularly designed Python package that seamlessly interoperates with other single-cell toolkits and allows for memory-efficient single-cell analysis of millions of cells on a laptop or low-cost devices like single-board computers. We demonstrate Scarf's memory and compute-time efficiency by applying it to the largest existing single-cell RNA-Seq and ATAC-Seq datasets. Scarf wraps memory-efficient implementations of a graph-based t-stochastic neighbour embedding and hierarchical clustering algorithm. Moreover, Scarf performs accurate reference-anchored mapping of datasets while maintaining memory efficiency. By implementing a subsampling algorithm, Scarf additionally has the capacity to generate representative sampling of cells from a given dataset wherein rare cell populations and lineage differentiation trajectories are conserved. Together, Scarf provides a framework wherein any researcher can perform advanced processing, subsampling, reanalysis, and integration of atlas-scale datasets on standard laptop computers. Scarf is available on Github: https://github.com/parashardhapola/scarf .", "doi": "10.1038/s41467-022-32097-3", "pmid": "35941103", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9360040"}, {"db": "pii", "key": "10.1038/s41467-022-32097-3"}], "notes": [], "created": "2024-01-23T09:21:51.995Z", "modified": "2024-01-23T09:21:52.327Z"}, {"entity": "publication", "iuid": "59703b9ad74143418dad82d98296265a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59703b9ad74143418dad82d98296265a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59703b9ad74143418dad82d98296265a"}}, "title": "Structures of Atm1 provide insight into [2Fe-2S] cluster export from mitochondria.", "authors": [{"family": "Li", "given": "Ping", "initials": "P", "orcid": "0000-0002-7364-3301", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cc17e1d61cb498b88038a9f5dfa6aff.json"}}, {"family": "Hendricks", "given": "Amber L", "initials": "AL"}, {"family": "Wang", "given": "Yong", "initials": "Y"}, {"family": "Villones", "given": "Rhiza Lyne E", "initials": "RLE"}, {"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": "Cowan", "given": "J A", "initials": "JA"}, {"family": "Wang", "given": "Kaituo", "initials": "K", "orcid": "0000-0002-5922-7109", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d8ad9a00c1c47fdbf1cadc149914823.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": "2022-07-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "4339", "issn-l": "2041-1723"}, "abstract": "In eukaryotes, iron-sulfur clusters are essential cofactors for numerous physiological processes, but these clusters are primarily biosynthesized in mitochondria. Previous studies suggest mitochondrial ABCB7-type exporters are involved in maturation of cytosolic iron-sulfur proteins. However, the molecular mechanism for how the ABCB7-type exporters participate in this process remains elusive. Here, we report a series of cryo-electron microscopy structures of a eukaryotic homolog of human ABCB7, CtAtm1, determined at average resolutions ranging from 2.8 to 3.2 \u00c5, complemented by functional characterization and molecular docking in silico. We propose that CtAtm1 accepts delivery from glutathione-complexed iron-sulfur clusters. A partially occluded state links cargo-binding to residues at the mitochondrial matrix interface that line a positively charged cavity, while the binding region becomes internalized and is partially divided in an early occluded state. Collectively, our findings substantially increase the understanding of the transport mechanism of eukaryotic ABCB7-type proteins.", "doi": "10.1038/s41467-022-32006-8", "pmid": "35896548", "labels": {"Cryo-EM": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-32006-8"}, {"db": "pmc", "key": "PMC9329353"}], "notes": [], "created": "2022-08-01T10:18:17.525Z", "modified": "2024-11-07T08:45:00.230Z"}, {"entity": "publication", "iuid": "72892165f88842119e37a0f4bdf0fbd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72892165f88842119e37a0f4bdf0fbd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72892165f88842119e37a0f4bdf0fbd2"}}, "title": "Genome-wide association study identifies Sj\u00f6gren's risk loci with functional implications in immune and glandular cells.", "authors": [{"family": "Khatri", "given": "Bhuwan", "initials": "B", "orcid": "0000-0001-5456-2963", "researcher": {"href": "https://publications.scilifelab.se/researcher/babac1d62a5c4e929151c502d43362aa.json"}}, {"family": "Tessneer", "given": "Kandice L", "initials": "KL"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Aghakhanian", "given": "Farhang", "initials": "F"}, {"family": "Reksten", "given": "Tove Ragna", "initials": "TR", "orcid": "0000-0001-8704-4943", "researcher": {"href": "https://publications.scilifelab.se/researcher/2097777ee53f41339a0e5b407aac739b.json"}}, {"family": "Adler", "given": "Adam", "initials": "A"}, {"family": "Alevizos", "given": "Ilias", "initials": "I"}, {"family": "Anaya", "given": "Juan-Manuel", "initials": "JM", "orcid": "0000-0002-6444-1249", "researcher": {"href": "https://publications.scilifelab.se/researcher/00723e72bf0e4333a503614c07dc718e.json"}}, {"family": "Aqrawi", "given": "Lara A", "initials": "LA"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Brun", "given": "Johan G", "initials": "JG"}, {"family": "Bucher", "given": "Sara Magnusson", "initials": "SM"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Engelke", "given": "Fiona", "initials": "F", "orcid": "0000-0002-5673-1705", "researcher": {"href": "https://publications.scilifelab.se/researcher/77af0d191e65475fb24a088ad1ea8cae.json"}}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Glenn", "given": "Stuart B", "initials": "SB"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Jensen", "given": "Janicke Liaaen", "initials": "JL", "orcid": "0000-0003-4276-9611", "researcher": {"href": "https://publications.scilifelab.se/researcher/773434ab6d4845d187376dd8cc972d8b.json"}}, {"family": "Johnsen", "given": "Svein Joar Augl\u00e6nd", "initials": "SJA", "orcid": "0000-0002-1591-9250", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fcaa1c5f1164f9d87e856a6eafb9e2c.json"}}, {"family": "Jonsson", "given": "Malin V", "initials": "MV", "orcid": "0000-0001-5655-5513", "researcher": {"href": "https://publications.scilifelab.se/researcher/11e3b5d3254449b69d2fca5fc5f5738a.json"}}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M", "orcid": "0000-0002-4948-8380", "researcher": {"href": "https://publications.scilifelab.se/researcher/24d1313454704814b6f591a63dc5d5cb.json"}}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Li", "given": "He", "initials": "H"}, {"family": "Mandl", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7143-7088", "researcher": {"href": "https://publications.scilifelab.se/researcher/b72a91b349c148c9b9b59028d079217d.json"}}, {"family": "Mart\u00edn", "given": "Javier", "initials": "J"}, {"family": "Nocturne", "given": "Ga\u00e9tane", "initials": "G", "orcid": "0000-0001-6809-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/74e763eb9c864a6a84259f807a381725.json"}}, {"family": "Norheim", "given": "Katrine Br\u00e6kke", "initials": "KB"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Skarstein", "given": "Kathrine", "initials": "K"}, {"family": "Stolarczyk", "given": "Anna M", "initials": "AM"}, {"family": "Taylor", "given": "Kimberly E", "initials": "KE"}, {"family": "Teruel", "given": "Maria", "initials": "M", "orcid": "0000-0002-5315-2660", "researcher": {"href": "https://publications.scilifelab.se/researcher/025b474fb4a34fe68e52ebf2455d1cf0.json"}}, {"family": "Theander", "given": "Elke", "initials": "E"}, {"family": "Venuturupalli", "given": "Swamy", "initials": "S"}, {"family": "Wallace", "given": "Daniel J", "initials": "DJ"}, {"family": "Grundahl", "given": "Kiely M", "initials": "KM"}, {"family": "Hefner", "given": "Kimberly S", "initials": "KS"}, {"family": "Radfar", "given": "Lida", "initials": "L"}, {"family": "Lewis", "given": "David M", "initials": "DM"}, {"family": "Stone", "given": "Donald U", "initials": "DU"}, {"family": "Kaufman", "given": "C Erick", "initials": "CE"}, {"family": "Brennan", "given": "Michael T", "initials": "MT"}, {"family": "Guthridge", "given": "Joel M", "initials": "JM"}, {"family": "James", "given": "Judith A", "initials": "JA", "orcid": "0000-0002-9574-7355", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ac95ea8fa4f43939f8e4a94bc422ffd.json"}}, {"family": "Scofield", "given": "R Hal", "initials": "RH"}, {"family": "Gaffney", "given": "Patrick M", "initials": "PM"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA", "orcid": "0000-0002-0761-7543", "researcher": {"href": "https://publications.scilifelab.se/researcher/e36beb11c7a7495290765a85d81928fd.json"}}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"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", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Warner", "given": "Blake", "initials": "B", "orcid": "0000-0002-4961-018X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a00e0cef8794b4e8d13cb963539e1fe.json"}}, {"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", "orcid": "0000-0002-4244-5417", "researcher": {"href": "https://publications.scilifelab.se/researcher/13855fe7b68b4235a48a8dda9a0d5fd6.json"}}, {"family": "Alarcon-Riquelme", "given": "Marta E", "initials": "ME", "orcid": "0000-0002-7632-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/61acb7fc644c42d9ba02804f58b1eeee.json"}}, {"family": "PRECISESADS Clinical Consortium", "given": "", "initials": ""}, {"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", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"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": "Adrianto", "given": "Indra", "initials": "I", "orcid": "0000-0002-9973-3057", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d109293e1044471b8cefff69b1b3f67.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Lessard", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0003-2440-3843", "researcher": {"href": "https://publications.scilifelab.se/researcher/c476c83630ad4fe6acbd1930cfedffa8.json"}}], "type": "journal article", "published": "2022-07-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "4287", "issn-l": "2041-1723"}, "abstract": "Sj\u00f6gren's disease is a complex autoimmune disease with twelve established susceptibility loci. This genome-wide association study (GWAS) identifies ten novel genome-wide significant (GWS) regions in Sj\u00f6gren's cases of European ancestry: CD247, NAB1, PTTG1-MIR146A, PRDM1-ATG5, TNFAIP3, XKR6, MAPT-CRHR1, RPTOR-CHMP6-BAIAP6, TYK2, SYNGR1. Polygenic risk scores yield predictability (AUROC = 0.71) and relative risk of 12.08. Interrogation of bioinformatics databases refine the associations, define local regulatory networks of GWS SNPs from the 95% credible set, and expand the implicated gene list to >40. Many GWS SNPs are eQTLs for genes within topologically associated domains in immune cells and/or eQTLs in the main target tissue, salivary glands.", "doi": "10.1038/s41467-022-30773-y", "pmid": "35896530", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-30773-y"}, {"db": "pmc", "key": "PMC9329286"}], "notes": [], "created": "2022-08-16T13:29:32.951Z", "modified": "2022-08-16T13:29:33.688Z"}, {"entity": "publication", "iuid": "c2eb6231b5e54b648bdaf3fb9a000dba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2eb6231b5e54b648bdaf3fb9a000dba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2eb6231b5e54b648bdaf3fb9a000dba"}}, "title": "Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp.", "authors": [{"family": "Kuhl", "given": "Heiner", "initials": "H", "orcid": "0000-0001-7623-9227", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3326add41974413be16c8a2bed157f8.json"}}, {"family": "Du", "given": "Kang", "initials": "K", "orcid": "0000-0002-1497-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eda8755c14042289ac7196edeffca01.json"}}, {"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f97783b5013409ebc1a6bd2df5ca92c.json"}}, {"family": "Kalous", "given": "Luk\u00e1\u0161", "initials": "L", "orcid": "0000-0001-5518-1505", "researcher": {"href": "https://publications.scilifelab.se/researcher/c086140440e54f3793c444182f695216.json"}}, {"family": "St\u00f6ck", "given": "Matthias", "initials": "M", "orcid": "0000-0003-4888-8371", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a4dc450751436d9b552ce68da65fd9.json"}}, {"family": "Lamatsch", "given": "Dunja K", "initials": "DK", "orcid": "0000-0002-6023-4381", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f2363dc6d8417b88455ec1aadec818.json"}}], "type": "journal article", "published": "2022-07-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "4092"}, "abstract": "Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a 'collapsed' representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.", "doi": "10.1038/s41467-022-31515-w", "pmid": "35835759", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Short read": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9283417"}, {"db": "pii", "key": "10.1038/s41467-022-31515-w"}], "notes": [], "created": "2022-08-19T08:38:44.948Z", "modified": "2024-01-16T13:48:35.681Z"}, {"entity": "publication", "iuid": "dd96a7bdf07c4932b365bacb73e0b18f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd96a7bdf07c4932b365bacb73e0b18f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd96a7bdf07c4932b365bacb73e0b18f"}}, "title": "Ultra-sensitive monitoring of leukemia patients using superRCA mutation detection assays.", "authors": [{"family": "Chen", "given": "Lei", "initials": "L", "orcid": "0000-0002-5226-1427", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd94830305334239a13ecf6528620480.json"}}, {"family": "Eriksson", "given": "Anna", "initials": "A"}, {"family": "Westr\u00f6m", "given": "Simone", "initials": "S"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Landegren", "given": "Ulf", "initials": "U", "orcid": "0000-0002-7820-1000", "researcher": {"href": "https://publications.scilifelab.se/researcher/87392e51288f4ef9a38fe3989d10d180.json"}}], "type": "journal article", "published": "2022-07-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "4033", "issn-l": "2041-1723"}, "abstract": "Rare tumor-specific mutations in patient samples serve as excellent markers to monitor the course of malignant disease and responses to therapy in clinical routine, and improved assay techniques are needed for broad adoption. We describe herein a highly sensitive and selective molecule amplification technology - superRCA assays - for rapid and highly specific detection of DNA sequence variants present at very low frequencies in DNA samples. Using a standard flow cytometer we demonstrate precise, ultra-sensitive detection of single-nucleotide mutant sequences from malignant cells against up to a 100,000-fold excess of DNA from normal cells in either bone marrow or peripheral blood, to follow the course of patients treated for acute myeloid leukemia (AML). We also demonstrate that sequence variants located in a high-GC region may be sensitively detected, and we illustrate the potential of the technology for early detection of disease recurrence as a basis for prompt change of therapy.", "doi": "10.1038/s41467-022-31397-y", "pmid": "35821208", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9276831"}, {"db": "pii", "key": "10.1038/s41467-022-31397-y"}], "notes": [], "created": "2022-11-28T12:43:37.924Z", "modified": "2024-01-16T13:48:35.784Z"}, {"entity": "publication", "iuid": "3e65ed75308b49efab3cff693834b734", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e65ed75308b49efab3cff693834b734.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e65ed75308b49efab3cff693834b734"}}, "title": "Single-cell RNA-sequencing analysis of the developing mouse inner ear identifies molecular logic of auditory neuron diversification.", "authors": [{"family": "Petitpr\u00e9", "given": "Charles", "initials": "C"}, {"family": "Faure", "given": "Louis", "initials": "L", "orcid": "0000-0003-4621-586X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbf218e53c854d69a1b474a61480c33f.json"}}, {"family": "Uhl", "given": "Phoebe", "initials": "P", "orcid": "0000-0002-5521-7261", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed69ade5f1bc491385c66f6e9df66adf.json"}}, {"family": "Fontanet", "given": "Paula", "initials": "P", "orcid": "0000-0002-5324-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe102480cb7458a941fc70fe7f5cb9b.json"}}, {"family": "Filova", "given": "Iva", "initials": "I"}, {"family": "Pavlinkova", "given": "Gabriela", "initials": "G"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}, {"family": "Lallemend", "given": "Francois", "initials": "F", "orcid": "0000-0001-5484-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9494a8ea444facbf3b564670930ab5.json"}}], "type": "journal article", "published": "2022-07-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "3878"}, "abstract": "Different types of spiral ganglion neurons (SGNs) are essential for auditory perception by transmitting complex auditory information from hair cells (HCs) to the brain. Here, we use deep, single cell transcriptomics to study the molecular mechanisms that govern their identity and organization in mice. We identify a core set of temporally patterned genes and gene regulatory networks that may contribute to the diversification of SGNs through sequential binary decisions and demonstrate a role for NEUROD1 in driving specification of a Ic-SGN phenotype. We also find that each trajectory of the decision tree is defined by initial co-expression of alternative subtype molecular controls followed by gradual shifts toward cell fate resolution. Finally, analysis of both developing SGN and HC types reveals cell-cell signaling potentially playing a role in the differentiation of SGNs. Our results indicate that SGN identities are drafted prior to birth and reveal molecular principles that shape their differentiation and will facilitate studies of their development, physiology, and dysfunction.", "doi": "10.1038/s41467-022-31580-1", "pmid": "35790771", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9256748"}, {"db": "pii", "key": "10.1038/s41467-022-31580-1"}], "notes": [], "created": "2022-08-19T08:38:31.468Z", "modified": "2023-10-16T11:38:03.441Z"}, {"entity": "publication", "iuid": "f1f9f62fd9604400bd6c0577e660f552", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1f9f62fd9604400bd6c0577e660f552.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1f9f62fd9604400bd6c0577e660f552"}}, "title": "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.", "authors": [{"family": "Domenzain", "given": "Iv\u00e1n", "initials": "I", "orcid": "0000-0002-5322-2040", "researcher": {"href": "https://publications.scilifelab.se/researcher/3793e87625584ee2a31301297263a12a.json"}}, {"family": "S\u00e1nchez", "given": "Benjam\u00edn", "initials": "B", "orcid": "0000-0001-6093-4110", "researcher": {"href": "https://publications.scilifelab.se/researcher/def9067db1624ff49e94cc67ba5d4208.json"}}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a28ecc2261e436ea5884ada5e512aed.json"}}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications.scilifelab.se/researcher/0df361f8014144e79479631fcbffad53.json"}}, {"family": "Mill\u00e1n-Oropeza", "given": "Aar\u00f3n", "initials": "A"}, {"family": "Henry", "given": "C\u00e9line", "initials": "C", "orcid": "0000-0002-2355-1791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cf23e6c84ff4fe0a0055f39bcf0b1bf.json"}}, {"family": "Siewers", "given": "Verena", "initials": "V", "orcid": "0000-0002-9502-9804", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0.json"}}, {"family": "Morrissey", "given": "John P", "initials": "JP", "orcid": "0000-0001-7960-2001", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf59d720c3b34732949d72b0ada6512e.json"}}, {"family": "Sonnenschein", "given": "Nikolaus", "initials": "N"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2022-06-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "3766"}, "abstract": "Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. With this, enzyme-constrained models for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus are generated to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions reveal that upregulation and high saturation of enzymes in amino acid metabolism are common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO is expanded with an automated framework for continuous and version-controlled update of enzyme-constrained GEMs, also producing such models for Escherichia coli and Homo sapiens. In this work, we facilitate the utilization of enzyme-constrained GEMs in basic science, metabolic engineering and synthetic biology purposes.", "doi": "10.1038/s41467-022-31421-1", "pmid": "35773252", "labels": {"Systems Biology": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9246944"}, {"db": "pii", "key": "10.1038/s41467-022-31421-1"}], "notes": [], "created": "2023-05-17T11:26:17.072Z", "modified": "2023-05-17T11:35:04.659Z"}, {"entity": "publication", "iuid": "2034709ecac646fe9f1ac1a71faa2c00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2034709ecac646fe9f1ac1a71faa2c00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2034709ecac646fe9f1ac1a71faa2c00"}}, "title": "Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite.", "authors": [{"family": "Kotila", "given": "Tommi", "initials": "T", "orcid": "0000-0002-9046-5834", "researcher": {"href": "https://publications.scilifelab.se/researcher/d530363e23ac4e3e8e24e7cdecfd0fe5.json"}}, {"family": "Wioland", "given": "Hugo", "initials": "H", "orcid": "0000-0001-5254-9642", "researcher": {"href": "https://publications.scilifelab.se/researcher/578f075141c245deb2f4c08702ef5090.json"}}, {"family": "Selvaraj", "given": "Muniyandi", "initials": "M", "orcid": "0000-0001-7793-6323", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e74a48173fa4365897dd74ab6143c97.json"}}, {"family": "Kogan", "given": "Konstantin", "initials": "K", "orcid": "0000-0003-3270-9391", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c6ce8d9a1474d5b9532650d2f5014d0.json"}}, {"family": "Antenucci", "given": "Lina", "initials": "L"}, {"family": "J\u00e9gou", "given": "Antoine", "initials": "A", "orcid": "0000-0003-0356-3127", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e53291bfb224bfcb856be6e8ad06d9d.json"}}, {"family": "Huiskonen", "given": "Juha T", "initials": "JT", "orcid": "0000-0002-0348-7323", "researcher": {"href": "https://publications.scilifelab.se/researcher/c858a2e60971462f9e53653320c9eb0f.json"}}, {"family": "Romet-Lemonne", "given": "Guillaume", "initials": "G"}, {"family": "Lappalainen", "given": "Pekka", "initials": "P", "orcid": "0000-0001-6227-0354", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9125bfd659d4e0784ce349140f84f5f.json"}}], "type": "journal article", "published": "2022-06-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "3442", "issn-l": "2041-1723"}, "abstract": "Actin polymerization generates forces for cellular processes throughout the eukaryotic kingdom, but our understanding of the 'ancient' actin turnover machineries is limited. We show that, despite > 1 billion years of evolution, pathogenic Leishmania major parasite and mammalian actins share the same overall fold and co-polymerize with each other. Interestingly, Leishmania harbors a simple actin-regulatory machinery that lacks cofilin 'cofactors', which accelerate filament disassembly in higher eukaryotes. By applying single-filament biochemistry we discovered that, compared to mammalian proteins, Leishmania actin filaments depolymerize more rapidly from both ends, and are severed > 100-fold more efficiently by cofilin. Our high-resolution cryo-EM structures of Leishmania ADP-, ADP-Pi- and cofilin-actin filaments identify specific features at actin subunit interfaces and cofilin-actin interactions that explain the unusually rapid dynamics of parasite actin filaments. Our findings reveal how divergent parasites achieve rapid actin dynamics using a remarkably simple set of actin-binding proteins, and elucidate evolution of the actin cytoskeleton.", "doi": "10.1038/s41467-022-31068-y", "pmid": "35705539", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9200798"}, {"db": "pii", "key": "10.1038/s41467-022-31068-y"}], "notes": [], "created": "2022-11-30T09:31:12.829Z", "modified": "2023-11-26T14:07:44.750Z"}, {"entity": "publication", "iuid": "ba91bf6dc93d4c4cbf2dbac15a58363f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba91bf6dc93d4c4cbf2dbac15a58363f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba91bf6dc93d4c4cbf2dbac15a58363f"}}, "title": "Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery.", "authors": [{"family": "Hatano", "given": "Tomoyuki", "initials": "T", "orcid": "0000-0002-9092-3989", "researcher": {"href": "https://publications.scilifelab.se/researcher/1906b7863eb94d6cb153a7dc39e7e490.json"}}, {"family": "Palani", "given": "Saravanan", "initials": "S"}, {"family": "Papatziamou", "given": "Dimitra", "initials": "D"}, {"family": "Salzer", "given": "Ralf", "initials": "R"}, {"family": "Souza", "given": "Diorge P", "initials": "DP", "orcid": "0000-0003-1303-1765", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6c15a9ff70f4245b70a5c97c69d3cff.json"}}, {"family": "Tamarit", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4940-719X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b6e6e8715ff4f76985f2e09972e1013.json"}}, {"family": "Makwana", "given": "Mehul", "initials": "M"}, {"family": "Potter", "given": "Antonia", "initials": "A"}, {"family": "Haig", "given": "Alexandra", "initials": "A", "orcid": "0000-0001-7116-3163", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6cf9191dc344a02b3bc2d7247732451.json"}}, {"family": "Xu", "given": "Wenjue", "initials": "W", "orcid": "0000-0003-1313-3980", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a7d5f1bb9024cad8512cb2f3b8ff851.json"}}, {"family": "Townsend", "given": "David", "initials": "D", "orcid": "0000-0003-2687-6767", "researcher": {"href": "https://publications.scilifelab.se/researcher/c41cc03f15c343298defb1010c34f4e0.json"}}, {"family": "Rochester", "given": "David", "initials": "D"}, {"family": "Bellini", "given": "Dom", "initials": "D", "orcid": "0000-0003-0576-3413", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcdde1deac6147bf917ed1840d98fbf6.json"}}, {"family": "Hussain", "given": "Hamdi M A", "initials": "HMA"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG", "orcid": "0000-0002-6898-6377", "researcher": {"href": "https://publications.scilifelab.se/researcher/42fc4acc111f4c488b23fa41341705e2.json"}}, {"family": "L\u00f6we", "given": "Jan", "initials": "J", "orcid": "0000-0002-5218-6615", "researcher": {"href": "https://publications.scilifelab.se/researcher/55205fc3ea4142ea8d17d442a41a7666.json"}}, {"family": "Baum", "given": "Buzz", "initials": "B", "orcid": "0000-0002-9201-6186", "researcher": {"href": "https://publications.scilifelab.se/researcher/352c640451904a16ae7a371f1fb35ab7.json"}}, {"family": "Robinson", "given": "Nicholas P", "initials": "NP", "orcid": "0000-0002-6094-1924", "researcher": {"href": "https://publications.scilifelab.se/researcher/4da6bae3aae84633b7ee7d7a06346864.json"}}, {"family": "Balasubramanian", "given": "Mohan", "initials": "M", "orcid": "0000-0002-1292-8602", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a39a61162d140f48cd793d6de54ed78.json"}}], "type": "journal article", "published": "2022-06-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "3398", "issn-l": "2041-1723"}, "abstract": "The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, in processes that include ubiquitin-mediated multivesicular body formation, membrane repair, cytokinetic abscission, and virus exit from host cells. This ESCRT system appears to have simpler, ancient origins, since many archaeal species possess homologues of ESCRT-III and Vps4, the components that execute the final membrane scission reaction, where they have been shown to play roles in cytokinesis, extracellular vesicle formation and viral egress. Remarkably, metagenome assemblies of Asgard archaea, the closest known living relatives of eukaryotes, were recently shown to encode homologues of the entire cascade involved in ubiquitin-mediated membrane remodelling, including ubiquitin itself, components of the ESCRT-I and ESCRT-II subcomplexes, and ESCRT-III and Vps4. Here, we explore the phylogeny, structure, and biochemistry of Asgard homologues of the ESCRT machinery and the associated ubiquitylation system. We provide evidence for the ESCRT-I and ESCRT-II subcomplexes being involved in ubiquitin-directed recruitment of ESCRT-III, as it is in eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin for the ubiquitin-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.", "doi": "10.1038/s41467-022-30656-2", "pmid": "35697693", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-30656-2"}, {"db": "pmc", "key": "PMC9192718"}], "notes": [], "created": "2022-11-09T15:57:28.056Z", "modified": "2024-01-16T13:48:36.143Z"}, {"entity": "publication", "iuid": "8688bf4021944174a60cf4a78486b2ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8688bf4021944174a60cf4a78486b2ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8688bf4021944174a60cf4a78486b2ce"}}, "title": "Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery.", "authors": [{"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78aae6139714fa3ae8221f3fb380b5a.json"}}, {"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/82499805c5c24c46b8c2ec6427345c89.json"}}, {"family": "Adler", "given": "Andrew F", "initials": "AF"}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M"}, {"family": "van Lunteren", "given": "Josina Anna", "initials": "JA"}, {"family": "Nolbrant", "given": "Sara", "initials": "S", "orcid": "0000-0003-2184-1741", "researcher": {"href": "https://publications.scilifelab.se/researcher/91ab50f5e5874992a0703470230a8462.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A"}, {"family": "Vasylovska", "given": "Svitlana", "initials": "S", "orcid": "0000-0003-0682-3449", "researcher": {"href": "https://publications.scilifelab.se/researcher/e24070d9f82243b8a3159739b054aa90.json"}}, {"family": "Yoshitake", "given": "Takashi", "initials": "T"}, {"family": "Kehr", "given": "Jan", "initials": "J"}, {"family": "Carl\u00e9n", "given": "Marie", "initials": "M", "orcid": "0000-0003-1658-1631", "researcher": {"href": "https://publications.scilifelab.se/researcher/88931dd9e39c48e2820b89080c3945ad.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Parmar", "given": "Malin", "initials": "M", "orcid": "0000-0001-5002-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48b5aaff3bc4832a96fda4f2cf127cb.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0002-8019-7127", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a093b1609b74f74a8a8546f02946782.json"}}], "type": "journal article", "published": "2022-06-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "3046"}, "abstract": "Stem cell therapies for Parkinson's disease (PD) have entered first-in-human clinical trials using a set of technically related methods to produce mesencephalic dopamine (mDA) neurons from human pluripotent stem cells (hPSCs). Here, we outline an approach for high-yield derivation of mDA neurons that principally differs from alternative technologies by utilizing retinoic acid (RA) signaling, instead of WNT and FGF8 signaling, to specify mesencephalic fate. Unlike most morphogen signals, where precise concentration determines cell fate, it is the duration of RA exposure that is the key-parameter for mesencephalic specification. This concentration-insensitive patterning approach provides robustness and reduces the need for protocol-adjustments between hPSC-lines. RA-specified progenitors promptly differentiate into functional mDA neurons in vitro, and successfully engraft and relieve motor deficits after transplantation in a rat PD model. Our study provides a potential alternative route for cell therapy and disease modelling that due to its robustness could be particularly expedient when use of autologous- or immunologically matched cells is considered.", "doi": "10.1038/s41467-022-30777-8", "pmid": "35650213", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9160024"}, {"db": "pii", "key": "10.1038/s41467-022-30777-8"}], "notes": [], "created": "2022-08-19T08:37:46.809Z", "modified": "2024-01-16T13:48:36.237Z"}, {"entity": "publication", "iuid": "7c2be66358fe4a249888dc529c7b6921", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c2be66358fe4a249888dc529c7b6921.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c2be66358fe4a249888dc529c7b6921"}}, "title": "Nitrogen represses haustoria formation through abscisic acid in the parasitic plant Phtheirospermum japonicum.", "authors": [{"family": "Kokla", "given": "Anna", "initials": "A", "orcid": "0000-0002-2185-326X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae2e3351e11842eba5ea207a59d61d9e.json"}}, {"family": "Leso", "given": "Martina", "initials": "M", "orcid": "0000-0003-4192-8027", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ec4323cecc7419a8bcf1b8bd98c58e6.json"}}, {"family": "Zhang", "given": "Xiang", "initials": "X"}, {"family": "Simura", "given": "Jan", "initials": "J"}, {"family": "Serivichyaswat", "given": "Phanu T", "initials": "PT"}, {"family": "Cui", "given": "Songkui", "initials": "S", "orcid": "0000-0001-7777-6681", "researcher": {"href": "https://publications.scilifelab.se/researcher/d27f3c541a4a47cc9d2f4c4c1a5d9e3a.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Yoshida", "given": "Satoko", "initials": "S"}, {"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": "2022-05-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "2976", "issn-l": "2041-1723"}, "abstract": "Parasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. The external environment including nutrient availability affects the extent of parasitism and to understand this phenomenon, we investigated the role of nutrients and found that nitrogen is sufficient to repress haustoria formation in the root parasite Phtheirospermum japonicum. Nitrogen increases levels of abscisic acid (ABA) in P. japonicum and prevents the activation of hundreds of genes including cell cycle and xylem development genes. Blocking ABA signaling overcomes nitrogen's inhibitory effects indicating that nitrogen represses haustoria formation by increasing ABA. The effect of nitrogen appears more widespread since nitrogen also inhibits haustoria in the obligate root parasite Striga hermonthica. Together, our data show that nitrogen acts as a haustoria repressing factor and suggests a mechanism whereby parasitic plants use nitrogen availability in the external environment to regulate the extent of parasitism.", "doi": "10.1038/s41467-022-30550-x", "pmid": "35624089", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9142502"}, {"db": "pii", "key": "10.1038/s41467-022-30550-x"}], "notes": [], "created": "2022-11-09T15:52:04.586Z", "modified": "2025-10-17T13:03:14.993Z"}, {"entity": "publication", "iuid": "c49fb3031a2347bab3efed79c9599ec6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c49fb3031a2347bab3efed79c9599ec6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c49fb3031a2347bab3efed79c9599ec6"}}, "title": "The long noncoding RNA ADIPINT regulates human adipocyte metabolism via pyruvate carboxylase.", "authors": [{"family": "Kerr", "given": "Alastair G", "initials": "AG", "orcid": "0000-0003-2085-1542", "researcher": {"href": "https://publications.scilifelab.se/researcher/076ba1b03b78451ba1ddb95b04e74b27.json"}}, {"family": "Wang", "given": "Zuoneng", "initials": "Z"}, {"family": "Wang", "given": "Na", "initials": "N"}, {"family": "Kwok", "given": "Kelvin H M", "initials": "KHM"}, {"family": "Jalkanen", "given": "Jutta", "initials": "J"}, {"family": "Ludzki", "given": "Alison", "initials": "A", "orcid": "0000-0002-6967-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a028bc21724a99a71d57b3012b7b2e.json"}}, {"family": "Lecoutre", "given": "Simon", "initials": "S"}, {"family": "Langin", "given": "Dominique", "initials": "D", "orcid": "0000-0002-2669-7825", "researcher": {"href": "https://publications.scilifelab.se/researcher/689d03a8a3614168bc04d897a7cfd0c2.json"}}, {"family": "Bergo", "given": "Martin O", "initials": "MO", "orcid": "0000-0002-6915-7140", "researcher": {"href": "https://publications.scilifelab.se/researcher/76de893bff9f4f77868b03ea8b1027db.json"}}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Mim", "given": "Carsten", "initials": "C"}, {"family": "Arner", "given": "Peter", "initials": "P", "orcid": "0000-0002-6208-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b10e9b283e4806a8d97755a43e4cec.json"}}, {"family": "Gao", "given": "Hui", "initials": "H", "orcid": "0000-0002-7306-7471", "researcher": {"href": "https://publications.scilifelab.se/researcher/c212c77475f042e284e0cbe9ae4c38fa.json"}}], "type": "journal article", "published": "2022-05-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "2958", "issn-l": "2041-1723"}, "abstract": "The pleiotropic function of long noncoding RNAs is well recognized, but their direct role in governing metabolic homeostasis is less understood. Here, we describe a human adipocyte-specific lncRNA, ADIPINT, that regulates pyruvate carboxylase, a pivotal enzyme in energy metabolism. We developed an approach, Targeted RNA-protein identification using Orthogonal Organic Phase Separation, which identifies that ADIPINT binds to pyruvate carboxylase and validated the interaction with electron microscopy. ADIPINT knockdown alters the interactome and decreases the abundance and enzymatic activity of pyruvate carboxylase in the mitochondria. Reduced ADIPINT or pyruvate carboxylase expression lowers adipocyte lipid synthesis, breakdown, and lipid content. In human white adipose tissue, ADIPINT expression is increased in obesity and linked to fat cell size, adipose insulin resistance, and pyruvate carboxylase activity. Thus, we identify ADIPINT as a regulator of lipid metabolism in human white adipocytes, which at least in part is mediated through its interaction with pyruvate carboxylase.", "doi": "10.1038/s41467-022-30620-0", "pmid": "35618718", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-30620-0"}, {"db": "pmc", "key": "PMC9135762"}], "notes": [], "created": "2022-09-05T06:57:37.974Z", "modified": "2022-09-05T06:57:38.155Z"}, {"entity": "publication", "iuid": "7da5a92f39cc4ce2a269162f66b0d2e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7da5a92f39cc4ce2a269162f66b0d2e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7da5a92f39cc4ce2a269162f66b0d2e7"}}, "title": "A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases.", "authors": [{"family": "Rozman Grinberg", "given": "Inna", "initials": "I", "orcid": "0000-0003-3094-1998", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d4a64db2f9544b2bde744b063dc5247.json"}}, {"family": "Mart\u00ednez-Carranza", "given": "Markel", "initials": "M", "orcid": "0000-0003-0192-9762", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ad7db8205c847a5bf56843d600e5ce1.json"}}, {"family": "Bimai", "given": "Ornella", "initials": "O", "orcid": "0000-0003-0562-7251", "researcher": {"href": "https://publications.scilifelab.se/researcher/9545ade4d51c4c4089d97eb74841deec.json"}}, {"family": "Noua\u00efria", "given": "Ghada", "initials": "G"}, {"family": "Shahid", "given": "Saher", "initials": "S"}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Logan", "given": "Derek T", "initials": "DT", "orcid": "0000-0002-0098-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/da2734243cdb4142be696e5a82e788ae.json"}}, {"family": "Sj\u00f6berg", "given": "Britt-Marie", "initials": "BM", "orcid": "0000-0001-5953-3360", "researcher": {"href": "https://publications.scilifelab.se/researcher/fab276f213364c2eaa6fe3dc5c9b01ff.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": "2022-05-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "2700", "issn-l": "2041-1723"}, "abstract": "Ribonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of RNR genes and, often, its own, in most bacteria and some archaea. NrdR senses the concentration of nucleotides through its ATP-cone, an evolutionarily mobile domain that also regulates the enzymatic activity of many RNRs, while a Zn-ribbon domain mediates binding to NrdR boxes upstream of and overlapping the transcription start site of RNR genes. Here, we combine biochemical and cryo-EM studies of NrdR from Streptomyces coelicolor to show, at atomic resolution, how NrdR binds to DNA. The suggested mechanism involves an initial dodecamer loaded with two ATP molecules that cannot bind to DNA. When dATP concentrations increase, an octamer forms that is loaded with one molecule each of dATP and ATP per monomer. A tetramer derived from this octamer then binds to DNA and represses transcription of RNR. In many bacteria - including well-known pathogens such as Mycobacterium tuberculosis - NrdR simultaneously controls multiple RNRs and hence DNA synthesis, making it an excellent target for novel antibiotics development.", "doi": "10.1038/s41467-022-30328-1", "pmid": "35577776", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-30328-1"}, {"db": "pmc", "key": "PMC9110341"}], "notes": [], "created": "2022-05-30T08:19:29.322Z", "modified": "2023-12-04T10:19:23.813Z"}, {"entity": "publication", "iuid": "3e40e251c3564aabaf1ab72b93c372c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e40e251c3564aabaf1ab72b93c372c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e40e251c3564aabaf1ab72b93c372c0"}}, "title": "Large differences in carbohydrate degradation and transport potential among lichen fungal symbionts.", "authors": [{"family": "Resl", "given": "Philipp", "initials": "P", "orcid": "0000-0002-7841-6060", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e29faa9509a45f6acc8b699db338c54.json"}}, {"family": "Bujold", "given": "Adina R", "initials": "AR", "orcid": "0000-0002-2355-5899", "researcher": {"href": "https://publications.scilifelab.se/researcher/60efe898779247548d08384ab337f523.json"}}, {"family": "Tagirdzhanova", "given": "Gulnara", "initials": "G", "orcid": "0000-0002-8493-2387", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1ae9c7945ff48a5ba31fe6cee3375d7.json"}}, {"family": "Meidl", "given": "Peter", "initials": "P"}, {"family": "Freire Rallo", "given": "Sandra", "initials": "S", "orcid": "0000-0003-1576-0507", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a8750cc7da44685908dd10dfb009d7d.json"}}, {"family": "Kono", "given": "Mieko", "initials": "M"}, {"family": "Fern\u00e1ndez-Brime", "given": "Samantha", "initials": "S", "orcid": "0000-0003-3846-5033", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b251299082145e29390ac967f0a3a69.json"}}, {"family": "Gu\u00f0mundsson", "given": "H\u00f6r\u00f0ur", "initials": "H", "orcid": "0000-0003-0731-3141", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfb6faf550b5471f988fc66ad71148ce.json"}}, {"family": "Andr\u00e9sson", "given": "\u00d3lafur Sigmar", "initials": "\u00d3S", "orcid": "0000-0002-8451-5671", "researcher": {"href": "https://publications.scilifelab.se/researcher/db8f1296040b4d23bec851e01bb3bf85.json"}}, {"family": "Muggia", "given": "Lucia", "initials": "L", "orcid": "0000-0003-0390-6169", "researcher": {"href": "https://publications.scilifelab.se/researcher/d313fb6557784dfa96900ca797921e11.json"}}, {"family": "Mayrhofer", "given": "Helmut", "initials": "H", "orcid": "0000-0002-9433-3847", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bcdb8a0a3234259b9c822dabfb3d5ff.json"}}, {"family": "McCutcheon", "given": "John P", "initials": "JP"}, {"family": "Wedin", "given": "Mats", "initials": "M", "orcid": "0000-0002-8295-5198", "researcher": {"href": "https://publications.scilifelab.se/researcher/54e34140f23c4da9a26bf11fa4271abe.json"}}, {"family": "Werth", "given": "Silke", "initials": "S"}, {"family": "Willis", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-6204-033X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b55bfe205184f8388dfb83b24409df2.json"}}, {"family": "Spribille", "given": "Toby", "initials": "T"}], "type": "journal article", "published": "2022-05-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "2634", "issn-l": "2041-1723"}, "abstract": "Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with reductions in plant cell wall-degrading enzymes, but whether this is true of lichen fungal symbionts (LFSs) is unknown. Here, we predict genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 46 genomes from the Lecanoromycetes, the largest extant clade of LFSs. All LFSs possess a robust CAZyme arsenal including enzymes acting on cellulose and hemicellulose, confirmed by experimental assays. However, the number of genes and predicted functions of CAZymes vary widely, with some fungal symbionts possessing arsenals on par with well-known saprotrophic fungi. These results suggest that stable fungal association with a phototroph does not in itself result in fungal CAZyme loss, and lends support to long-standing hypotheses that some lichens may augment fixed CO2 with carbon from external sources.", "doi": "10.1038/s41467-022-30218-6", "pmid": "35551185", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-30218-6"}, {"db": "pmc", "key": "PMC9098629"}, {"db": "Dryad", "key": "10.5061/dryad.3xsj3txjb"}], "notes": [], "created": "2022-11-09T15:45:53.677Z", "modified": "2024-01-16T13:48:36.523Z"}, {"entity": "publication", "iuid": "9c25f649010d4c10b0c89f067f250b61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c25f649010d4c10b0c89f067f250b61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c25f649010d4c10b0c89f067f250b61"}}, "title": "Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.", "authors": [{"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "H\u00f6glund", "given": "Julia", "initials": "J", "orcid": "0000-0001-8061-3947", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b02049b625d47a69324be23e35f5b58.json"}}, {"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H", "orcid": "0000-0001-9807-1082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4143a879fa2043e7873be9e2aa72d051.json"}}, {"family": "Lo Faro", "given": "Valeria", "initials": "V", "orcid": "0000-0003-4931-7327", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e77657632e1469d9f0382673f54d071.json"}}, {"family": "Schmitz", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4480-891X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b1d0c4505854c7d9ab7a2ed3116b7ae.json"}}, {"family": "Ek", "given": "Weronica E", "initials": "WE", "orcid": "0000-0003-2194-496X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7398a2bfa9154e15a4295828bc0f5bb8.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Karlsson", "given": "Torgny", "initials": "T", "orcid": "0000-0001-8095-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/691d6823b8e04c5abf1613513da32b08.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": "2022-05-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "2532"}, "abstract": "Despite the success of genome-wide association studies, much of the genetic contribution to complex traits remains unexplained. Here, we analyse high coverage whole-genome sequencing data, to evaluate the contribution of rare genetic variants to 414 plasma proteins. The frequency distribution of genetic variants is skewed towards the rare spectrum, and damaging variants are more often rare. We estimate that less than 4.3% of the narrow-sense heritability is expected to be explained by rare variants in our cohort. Using a gene-based approach, we identify Cis-associations for 237 of the proteins, which is slightly more compared to a GWAS (N = 213), and we identify 34 associated loci in Trans. Several associations are driven by rare variants, which have larger effects, on average. We therefore conclude that rare variants could be of importance for precision medicine applications, but have a more limited contribution to the missing heritability of complex diseases.", "doi": "10.1038/s41467-022-30208-8", "pmid": "35534486", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9085767"}, {"db": "pii", "key": "10.1038/s41467-022-30208-8"}], "notes": [], "created": "2022-06-10T08:49:57.584Z", "modified": "2024-01-16T13:48:36.679Z"}, {"entity": "publication", "iuid": "d42d2a62ff4a4fd492c94539d79ed06f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d42d2a62ff4a4fd492c94539d79ed06f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d42d2a62ff4a4fd492c94539d79ed06f"}}, "title": "Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival.", "authors": [{"family": "Lu", "given": "Xi", "initials": "X", "orcid": "0000-0002-1650-9974", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2fc905a0497492c964e10e0f1f82f4c.json"}}, {"family": "Maturi", "given": "Naga Prathyusha", "initials": "NP", "orcid": "0000-0002-7726-8617", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f69dfe618f48c9bd4aa6075525975c.json"}}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Yildirim", "given": "Irem", "initials": "I", "orcid": "0000-0003-3602-5544", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29421803962496880443d5772f4c97a.json"}}, {"family": "Dang", "given": "Yonglong", "initials": "Y"}, {"family": "Zhao", "given": "Linxuan", "initials": "L"}, {"family": "Xie", "given": "Yuan", "initials": "Y"}, {"family": "Tan", "given": "E-Jean", "initials": "EJ", "orcid": "0000-0002-4631-174X", "researcher": {"href": "https://publications.scilifelab.se/researcher/03d12f8cf5714430a7297ed0c3f0e1f6.json"}}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Uhrbom", "given": "Lene", "initials": "L", "orcid": "0000-0001-8595-5698", "researcher": {"href": "https://publications.scilifelab.se/researcher/67bb8672ad514a9bb5f86c8d6b494269.json"}}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}], "type": "journal article", "published": "2022-04-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "2236", "issn-l": "2041-1723"}, "abstract": "There is ample support for developmental regulation of glioblastoma stem cells. To examine how cell lineage controls glioblastoma stem cell function, we present a cross-species epigenome analysis of mouse and human glioblastoma stem cells. We analyze and compare the chromatin-accessibility landscape of nine mouse glioblastoma stem cell cultures of three defined origins and 60 patient-derived glioblastoma stem cell cultures by assay for transposase-accessible chromatin using sequencing. This separates the mouse cultures according to cell of origin and identifies three human glioblastoma stem cell clusters that show overlapping characteristics with each of the mouse groups, and a distribution along an axis of proneural to mesenchymal phenotypes. The epigenetic-based human glioblastoma stem cell clusters display distinct functional properties and can separate patient survival. Cross-species analyses reveals conserved epigenetic regulation of mouse and human glioblastoma stem cells. We conclude that epigenetic control of glioblastoma stem cells primarily is dictated by developmental origin which impacts clinically relevant glioblastoma stem cell properties and patient survival.", "doi": "10.1038/s41467-022-29912-2", "pmid": "35469026", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-29912-2"}], "notes": [], "created": "2022-04-29T09:50:33.950Z", "modified": "2022-04-29T09:50:34.131Z"}, {"entity": "publication", "iuid": "3bc3b796af9941b69a98378c93874072", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bc3b796af9941b69a98378c93874072.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bc3b796af9941b69a98378c93874072"}}, "title": "App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden.", "authors": [{"family": "Kennedy", "given": "Beatrice", "initials": "B"}, {"family": "Fitipaldi", "given": "Hugo", "initials": "H", "orcid": "0000-0001-5352-2134", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca2f9fb4ba1a42c59104097626568a97.json"}}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Maziarz", "given": "Marlena", "initials": "M", "orcid": "0000-0003-1417-6050", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc7c22bcfc043adbcc6e58b05d1d064.json"}}, {"family": "Tsereteli", "given": "Neli", "initials": "N"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Varotsis", "given": "Georgios", "initials": "G"}, {"family": "Franks", "given": "Camilla A", "initials": "CA"}, {"family": "Nguyen", "given": "Diem", "initials": "D", "orcid": "0000-0002-9680-5772", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78958133e474831ac76dacc36f68cbb.json"}}, {"family": "Spiliopoulos", "given": "Lampros", "initials": "L"}, {"family": "Adami", "given": "Hans-Olov", "initials": "HO", "orcid": "0000-0001-9592-5791", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe682f1ff3694b96bf55e56bb8b29f80.json"}}, {"family": "Bj\u00f6rk", "given": "Jonas", "initials": "J", "orcid": "0000-0003-1883-2000", "researcher": {"href": "https://publications.scilifelab.se/researcher/a76633f634bf4c62818c717a685d26b4.json"}}, {"family": "Engblom", "given": "Stefan", "initials": "S", "orcid": "0000-0002-3614-1732", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a9c5783fd24592b0764b877d6a4df5.json"}}, {"family": "Fall", "given": "Katja", "initials": "K"}, {"family": "Grimby-Ekman", "given": "Anna", "initials": "A"}, {"family": "Litton", "given": "Jan-Eric", "initials": "JE"}, {"family": "Martinell", "given": "Mats", "initials": "M"}, {"family": "Oudin", "given": "Anna", "initials": "A"}, {"family": "Sj\u00f6str\u00f6m", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Timpka", "given": "Toomas", "initials": "T", "orcid": "0000-0001-6049-5402", "researcher": {"href": "https://publications.scilifelab.se/researcher/6952064d600343a6b3a6762972084523.json"}}, {"family": "Sudre", "given": "Carole H", "initials": "CH"}, {"family": "Graham", "given": "Mark S", "initials": "MS"}, {"family": "du Cadet", "given": "Julien Lavigne", "initials": "JL"}, {"family": "Chan", "given": "Andrew T", "initials": "AT"}, {"family": "Davies", "given": "Richard", "initials": "R", "orcid": "0000-0003-2050-3994", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e41bf0999a04f4688ec39d1c012d419.json"}}, {"family": "Ganesh", "given": "Sajaysurya", "initials": "S"}, {"family": "May", "given": "Anna", "initials": "A"}, {"family": "Ourselin", "given": "S\u00e9bastien", "initials": "S"}, {"family": "Pujol", "given": "Joan Capdevila", "initials": "JC"}, {"family": "Selvachandran", "given": "Somesh", "initials": "S"}, {"family": "Wolf", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-0530-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/fec4c1ff366146c5aaa69747c8e18617.json"}}, {"family": "Spector", "given": "Tim D", "initials": "TD", "orcid": "0000-0002-9795-0365", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3b149961364ccbb448a8cc3cdd6687.json"}}, {"family": "Steves", "given": "Claire J", "initials": "CJ", "orcid": "0000-0002-4910-0489", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d337d31e10465d93646ef8dba63050.json"}}, {"family": "Gomez", "given": "Maria F", "initials": "MF", "orcid": "0000-0001-6210-3142", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0879aded2d14b26b6a70a60d96f7e97.json"}}, {"family": "Franks", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-0520-7604", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebbf40c0f7e49dd8c75a2b6cbf27276.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": "2022-04-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "2110", "issn-l": "2041-1723"}, "abstract": "The app-based COVID Symptom Study was launched in Sweden in April 2020 to contribute to real-time COVID-19 surveillance. We enrolled 143,531 study participants (\u226518 years) who contributed 10.6 million daily symptom reports between April 29, 2020 and February 10, 2021. Here, we include data from 19,161 self-reported PCR tests to create a symptom-based model to estimate the individual probability of symptomatic COVID-19, with an AUC of 0.78 (95% CI 0.74-0.83) in an external dataset. These individual probabilities are employed to estimate daily regional COVID-19 prevalence, which are in turn used together with current hospital data to predict next week COVID-19 hospital admissions. We show that this hospital prediction model demonstrates a lower median absolute percentage error (MdAPE: 25.9%) across the five most populated regions in Sweden during the first pandemic wave than a model based on case notifications (MdAPE: 30.3%). During the second wave, the error rates are similar. When we apply the same model to an English dataset, not including local COVID-19 test data, we observe MdAPEs of 22.3% and 19.0% during the first and second pandemic waves, respectively, highlighting the transferability of the prediction model.", "doi": "10.1038/s41467-022-29608-7", "pmid": "35449172", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9023535"}, {"db": "pii", "key": "10.1038/s41467-022-29608-7"}], "notes": [], "created": "2022-05-09T20:18:19.396Z", "modified": "2024-01-16T13:48:37.037Z"}, {"entity": "publication", "iuid": "0ae342fa95624219a707ae26e188890c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ae342fa95624219a707ae26e188890c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ae342fa95624219a707ae26e188890c"}}, "title": "Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics.", "authors": [{"family": "Crowe-McAuliffe", "given": "Caillan", "initials": "C"}, {"family": "Murina", "given": "Victoriia", "initials": "V"}, {"family": "Turnbull", "given": "Kathryn Jane", "initials": "KJ"}, {"family": "Huch", "given": "Susanne", "initials": "S"}, {"family": "Kasari", "given": "Marje", "initials": "M", "orcid": "0000-0002-2177-3753", "researcher": {"href": "https://publications.scilifelab.se/researcher/878f3508ac344958a0fea57329d67274.json"}}, {"family": "Takada", "given": "Hiraku", "initials": "H"}, {"family": "Nersisyan", "given": "Lilit", "initials": "L"}, {"family": "Sundsfjord", "given": "Arnfinn", "initials": "A"}, {"family": "Hegstad", "given": "Kristin", "initials": "K", "orcid": "0000-0002-1314-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ba3d809302499593f4a315ae867e1e.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e906e11225514a289df84a2145f807fe.json"}}, {"family": "Wilson", "given": "Daniel N", "initials": "DN", "orcid": "0000-0003-3816-3828", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd50ba35f7c74d7e9d4f42fbc49739f2.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications.scilifelab.se/researcher/17ea83b1d20f43f9872edbf89b275e5d.json"}}], "type": "journal article", "published": "2022-04-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1860", "issn-l": "2041-1723"}, "abstract": "PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF). They confer resistance to oxazolidinone and phenicol antibiotics, such as linezolid and chloramphenicol, which stall translating ribosomes when certain amino acids are present at a defined position in the nascent polypeptide chain. These proteins are often encoded on mobile genetic elements, facilitating their rapid spread amongst Gram-positive bacteria, and are thought to confer resistance by binding to the ribosome and dislodging the bound antibiotic. However, the mechanistic basis of this resistance remains unclear. Here we refine the PoxtA spectrum of action, demonstrate alleviation of linezolid-induced context-dependent translational stalling, and present cryo-electron microscopy structures of PoxtA in complex with the Enterococcus faecalis 70S ribosome. PoxtA perturbs the CCA-end of the P-site tRNA, causing it to shift by \u223c4 \u00c5 out of the ribosome, corresponding to a register shift of approximately one amino acid for an attached nascent polypeptide chain. We postulate that the perturbation of the P-site tRNA by PoxtA thereby alters the conformation of the attached nascent chain to disrupt the drug binding site.", "doi": "10.1038/s41467-022-29274-9", "pmid": "35387982", "labels": {"Cryo-EM": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8987054"}, {"db": "pii", "key": "10.1038/s41467-022-29274-9"}], "notes": [], "created": "2022-11-09T15:58:01.251Z", "modified": "2024-01-16T13:48:37.095Z"}, {"entity": "publication", "iuid": "792a618f6c4e43b998c86cf7cb80f5be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/792a618f6c4e43b998c86cf7cb80f5be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/792a618f6c4e43b998c86cf7cb80f5be"}}, "title": "Direct measurements of mRNA translation kinetics in living cells.", "authors": [{"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": "Gynn\u00e5", "given": "Arvid H", "initials": "AH", "orcid": "0000-0001-8087-7715", "researcher": {"href": "https://publications.scilifelab.se/researcher/818582a582334117bd83e47dbb555db3.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.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": "2022-04-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1852", "issn-l": "2041-1723"}, "abstract": "Ribosome mediated mRNA translation is central to life. The cycle of translation, however, has been characterized mostly using reconstituted systems, with only few techniques applicable for studies in the living cell. Here we describe a live-cell ribosome-labeling method, which allows us to characterize the whole processes of finding and translating an mRNA, using single-molecule tracking techniques. We find that more than 90% of both bacterial ribosomal subunits are engaged in translation at any particular time, and that the 30S and 50S ribosomal subunits spend the same average time bound to an mRNA, revealing that 30S re-initiation on poly-cistronic mRNAs is not prevalent in E. coli. Instead, our results are best explained by substantial 70S re-initiation of translation of poly-cistronic mRNAs, which is further corroborated by experiments with translation initiation inhibitors. Finally, we find that a variety of previously described orthogonal ribosomes, with altered anti-Shine-Dalgarno sequences, show significant binding to endogenous mRNAs.", "doi": "10.1038/s41467-022-29515-x", "pmid": "35388013", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-29515-x"}, {"db": "pmc", "key": "PMC8986856"}], "notes": [], "created": "2022-11-09T15:50:13.299Z", "modified": "2024-01-16T13:48:37.128Z"}, {"entity": "publication", "iuid": "9ebcad7df6fc4b52a1198f4a36faeb0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ebcad7df6fc4b52a1198f4a36faeb0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ebcad7df6fc4b52a1198f4a36faeb0e"}}, "title": "Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines.", "authors": [{"family": "Leo", "given": "Isabelle Rose", "initials": "IR", "orcid": "0000-0002-7627-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/21185d9c6a2343f189397cbbb95c6e71.json"}}, {"family": "Aswad", "given": "Luay", "initials": "L", "orcid": "0000-0002-8730-9208", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01cefe048a541c7bdab2727d9cfc79d.json"}}, {"family": "Stahl", "given": "Matthias", "initials": "M", "orcid": "0000-0002-0176-9386", "researcher": {"href": "https://publications.scilifelab.se/researcher/f113f8aa6e77444d9492b5fed0067b25.json"}}, {"family": "Kunold", "given": "Elena", "initials": "E"}, {"family": "Post", "given": "Frederik", "initials": "F", "orcid": "0000-0003-0376-1326", "researcher": {"href": "https://publications.scilifelab.se/researcher/439eb72d3314446da93915e854774caf.json"}}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Struyf", "given": "Nona", "initials": "N", "orcid": "0000-0002-6975-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/1295c3be31024c4fa2da10cffe42c406.json"}}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Joshi", "given": "Rubin Narayan", "initials": "RN"}, {"family": "Gracia-Villacampa", "given": "Eva", "initials": "E", "orcid": "0000-0003-0353-2101", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaf72d81feea4b7899197c67131a85ba.json"}}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Kallioniemi", "given": "Olli P", "initials": "OP"}, {"family": "Tamm", "given": "Katja Pokrovskaja", "initials": "KP", "orcid": "0000-0001-6359-1256", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ec3ee706764024bd748c7a77443845.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"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", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/481b2a2329634f9086cf52fb808edea5.json"}}], "type": "journal article", "published": "2022-03-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "1691"}, "abstract": "Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Although standard-of-care chemotherapeutics are sufficient for most ALL cases, there are subsets of patients with poor response who relapse in disease. The biology underlying differences between subtypes and their response to therapy has only partially been explained by genetic and transcriptomic profiling. Here, we perform comprehensive multi-omic analyses of 49 readily available childhood ALL cell lines, using proteomics, transcriptomics, and pharmacoproteomic characterization. We connect the molecular phenotypes with drug responses to 528 oncology drugs, identifying drug correlations as well as lineage-dependent correlations. We also identify the diacylglycerol-analog bryostatin-1 as a therapeutic candidate in the MEF2D-HNRNPUL1 fusion high-risk subtype, for which this drug activates pro-apoptotic ERK signaling associated with molecular mediators of pre-B cell negative selection. Our data is the foundation for the interactive online Functional Omics Resource of ALL (FORALL) with navigable proteomics, transcriptomics, and drug sensitivity profiles at https://proteomics.se/forall .", "doi": "10.1038/s41467-022-29224-5", "pmid": "35354797", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8967900"}, {"db": "pii", "key": "10.1038/s41467-022-29224-5"}], "notes": [], "created": "2022-08-19T08:37:13.488Z", "modified": "2024-01-16T13:48:37.216Z"}, {"entity": "publication", "iuid": "f500c2ecf0914043995e5fcdca528787", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f500c2ecf0914043995e5fcdca528787.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f500c2ecf0914043995e5fcdca528787"}}, "title": "Norway spruce postglacial recolonization of Fennoscandia.", "authors": [{"family": "Nota", "given": "Kevin", "initials": "K", "orcid": "0000-0002-4744-5205", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac25364b12745a392b4d682cb723ccb.json"}}, {"family": "Klaminder", "given": "Jonatan", "initials": "J", "orcid": "0000-0001-8814-0013", "researcher": {"href": "https://publications.scilifelab.se/researcher/17201e4f705047d3a00d196bf05e7e77.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Bindler", "given": "Richard", "initials": "R", "orcid": "0000-0002-7900-309X", "researcher": {"href": "https://publications.scilifelab.se/researcher/27d5a93ec44f40ada25fab09497837cd.json"}}, {"family": "Nobile", "given": "Alessandro", "initials": "A"}, {"family": "van Steijn", "given": "Tamara", "initials": "T"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Svensson", "given": "Brita", "initials": "B"}, {"family": "Hirota", "given": "Shun K", "initials": "SK", "orcid": "0000-0002-6104-1119", "researcher": {"href": "https://publications.scilifelab.se/researcher/68947bb450e140a09d6b3211231d4528.json"}}, {"family": "Matsuo", "given": "Ayumi", "initials": "A"}, {"family": "Gunnarsson", "given": "Urban", "initials": "U", "orcid": "0000-0002-6511-942X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11fbbf2b75b4b838e74e19839c818f2.json"}}, {"family": "Sepp\u00e4", "given": "Heikki", "initials": "H", "orcid": "0000-0003-2494-7955", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fb9f7f563b41b5b79a67937d2a8918.json"}}, {"family": "V\u00e4liranta", "given": "Minna M", "initials": "MM", "orcid": "0000-0003-0129-7240", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbd5c145cac9423690a3610d40f26236.json"}}, {"family": "Wohlfarth", "given": "Barbara", "initials": "B"}, {"family": "Suyama", "given": "Yoshihisa", "initials": "Y", "orcid": "0000-0002-3136-5489", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d0147a6816d4025a4a982926f1e9bbe.json"}}, {"family": "Parducci", "given": "Laura", "initials": "L", "orcid": "0000-0003-1956-4757", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed4c737e2c7c4266b598a89aa2116a91.json"}}], "type": "journal article", "published": "2022-03-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1333", "issn-l": "2041-1723"}, "abstract": "Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 \u00b1 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.", "doi": "10.1038/s41467-022-28976-4", "pmid": "35288569", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-28976-4"}, {"db": "pmc", "key": "PMC8921311"}], "notes": [], "created": "2022-11-09T15:50:23.857Z", "modified": "2024-01-16T13:48:37.254Z"}, {"entity": "publication", "iuid": "ec581b66240c426ca45bd1ab1951a61a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec581b66240c426ca45bd1ab1951a61a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec581b66240c426ca45bd1ab1951a61a"}}, "title": "The spatial transcriptomic landscape of the healing mouse intestine following damage.", "authors": [{"family": "Parigi", "given": "Sara M", "initials": "SM"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Ramirez Flores", "given": "Ricardo O", "initials": "RO", "orcid": "0000-0003-0087-371X", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f01d7b57044e628850bb9705e03ed0.json"}}, {"family": "Frede", "given": "Annika", "initials": "A"}, {"family": "Tripathi", "given": "Kumar P", "initials": "KP"}, {"family": "Diaz", "given": "Oscar E", "initials": "OE", "orcid": "0000-0001-7622-7832", "researcher": {"href": "https://publications.scilifelab.se/researcher/9aae40d7294841989eee4629596395d3.json"}}, {"family": "Selin", "given": "Katja", "initials": "K", "orcid": "0000-0002-8888-0529", "researcher": {"href": "https://publications.scilifelab.se/researcher/64550a7d2143443dbf3f1575ab3f870d.json"}}, {"family": "Morales", "given": "Rodrigo A", "initials": "RA", "orcid": "0000-0003-4382-5777", "researcher": {"href": "https://publications.scilifelab.se/researcher/61802da2579446d5b2a73c4f06b9969e.json"}}, {"family": "Luo", "given": "Xinxin", "initials": "X"}, {"family": "Monasterio", "given": "Gustavo", "initials": "G"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Gagliani", "given": "Nicola", "initials": "N", "orcid": "0000-0001-8514-1395", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cc11473c8944eebc0974780d1c6919.json"}}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J", "orcid": "0000-0002-8552-8976", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce0043f77cad4f6e8ab9641d7f42c420.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}], "type": "journal article", "published": "2022-02-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "828"}, "abstract": "The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.", "doi": "10.1038/s41467-022-28497-0", "pmid": "35149721", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-28497-0"}, {"db": "pmc", "key": "PMC8837647"}], "notes": [], "created": "2022-03-29T13:47:22.254Z", "modified": "2022-08-19T09:06:40.669Z"}, {"entity": "publication", "iuid": "7feac7b384bd4538b6116d30a4f37f9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7feac7b384bd4538b6116d30a4f37f9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7feac7b384bd4538b6116d30a4f37f9d"}}, "title": "CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations.", "authors": [{"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "\u00d6stlund", "given": "Rebecka", "initials": "R", "orcid": "0000-0003-4460-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/03b1d5938f74406ebffb5b49ba5b182c.json"}}, {"family": "van Schendel", "given": "Robin", "initials": "R", "orcid": "0000-0001-7068-0679", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aa5a36e5b534bab8a04b4c8f040abb4.json"}}, {"family": "Bozorgpana", "given": "Selma", "initials": "S"}, {"family": "Tijsterman", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8465-9002", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1e816845f6048e2a2c7dc29e9a13cdf.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}], "type": "journal article", "published": "2022-02-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "627"}, "abstract": "CRISPR-Cas9 genome editing has potential to cure diseases without current treatments, but therapies must be safe. Here we show that CRISPR-Cas9 editing can introduce unintended mutations in vivo, which are passed on to the next generation. By editing fertilized zebrafish eggs using four guide RNAs selected for off-target activity in vitro, followed by long-read sequencing of DNA from >1100 larvae, juvenile and adult fish across two generations, we find that structural variants (SVs), i.e., insertions and deletions \u226550 bp, represent 6% of editing outcomes in founder larvae. These SVs occur both at on-target and off-target sites. Our results also illustrate that adult founder zebrafish are mosaic in their germ cells, and that 26% of their offspring carries an off-target mutation and 9% an SV. Hence, pre-testing for off-target activity and SVs using patient material is advisable in clinical applications, to reduce the risk of unanticipated effects with potentially large implications.", "doi": "10.1038/s41467-022-28244-5", "pmid": "35110541", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "NGI Long read": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8810904"}, {"db": "pii", "key": "10.1038/s41467-022-28244-5"}], "notes": [], "created": "2022-02-17T14:45:40.515Z", "modified": "2024-01-16T13:48:37.595Z"}, {"entity": "publication", "iuid": "2d7285d7608b49a98338258da32469f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d7285d7608b49a98338258da32469f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d7285d7608b49a98338258da32469f3"}}, "title": "PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides.", "authors": [{"family": "Rush", "given": "Jeffrey S", "initials": "JS"}, {"family": "Parajuli", "given": "Prakash", "initials": "P", "orcid": "0000-0002-3384-2680", "researcher": {"href": "https://publications.scilifelab.se/researcher/483ec8c7dba8472b8fc66d974d5c3648.json"}}, {"family": "Ruda", "given": "Alessandro", "initials": "A", "orcid": "0000-0002-5918-5797", "researcher": {"href": "https://publications.scilifelab.se/researcher/491c22d9414644c3879229f234a2af82.json"}}, {"family": "Li", "given": "Jian", "initials": "J"}, {"family": "Pohane", "given": "Amol Arunrao", "initials": "AA", "orcid": "0000-0003-2574-0366", "researcher": {"href": "https://publications.scilifelab.se/researcher/59ba615ff67f4f73af75dd062bde3f5e.json"}}, {"family": "Zamakhaeva", "given": "Svetlana", "initials": "S"}, {"family": "Rahman", "given": "Mohammad M", "initials": "MM"}, {"family": "Chang", "given": "Jennifer C", "initials": "JC", "orcid": "0000-0002-6175-1284", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea1854b9dba3422f87a8e06f099d5644.json"}}, {"family": "Gogos", "given": "Artemis", "initials": "A", "orcid": "0000-0002-0555-3814", "researcher": {"href": "https://publications.scilifelab.se/researcher/209e056549b1461eac736cfc51613c63.json"}}, {"family": "Kenner", "given": "Cameron W", "initials": "CW"}, {"family": "Lambeau", "given": "G\u00e9rard", "initials": "G", "orcid": "0000-0002-9239-518X", "researcher": {"href": "https://publications.scilifelab.se/researcher/789c0112eb174b61a857e14209c35186.json"}}, {"family": "Federle", "given": "Michael J", "initials": "MJ", "orcid": "0000-0002-4554-543X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e629c6088df240c5ba8c7f4eca583643.json"}}, {"family": "Korotkov", "given": "Konstantin V", "initials": "KV", "orcid": "0000-0002-2182-6843", "researcher": {"href": "https://publications.scilifelab.se/researcher/614c5ba571b84b128e8dfd8fb9d7bdf8.json"}}, {"family": "Widmalm", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-8303-4481", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eb393e8ba544f67b39fd6571b4e6efc.json"}}, {"family": "Korotkova", "given": "Natalia", "initials": "N", "orcid": "0000-0002-8696-4892", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1749c871102451e9206156c010db606.json"}}], "type": "journal article", "published": "2022-02-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "590", "issn-l": "2041-1723"}, "abstract": "The cell wall of the human bacterial pathogen Group A Streptococcus (GAS) consists of peptidoglycan decorated with the Lancefield group A carbohydrate (GAC). GAC is a promising target for the development of GAS vaccines. In this study, employing chemical, compositional, and NMR methods, we show that GAC is attached to peptidoglycan via glucosamine 1-phosphate. This structural feature makes the GAC-peptidoglycan linkage highly sensitive to cleavage by nitrous acid and resistant to mild acid conditions. Using this characteristic of the GAS cell wall, we identify PplD as a protein required for deacetylation of linkage N-acetylglucosamine (GlcNAc). X-ray structural analysis indicates that PplD performs catalysis via a modified acid/base mechanism. Genetic surveys in silico together with functional analysis indicate that PplD homologs deacetylate the polysaccharide linkage in many streptococcal species. We further demonstrate that introduction of positive charges to the cell wall by GlcNAc deacetylation protects GAS against host cationic antimicrobial proteins.", "doi": "10.1038/s41467-022-28257-0", "pmid": "35105886", "labels": {"Swedish NMR Centre": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-28257-0"}, {"db": "pmc", "key": "PMC8807736"}], "notes": [], "created": "2022-04-25T12:22:44.683Z", "modified": "2025-10-17T13:03:55.082Z"}, {"entity": "publication", "iuid": "92f07130682a4fa283e3b89d3d9a1249", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92f07130682a4fa283e3b89d3d9a1249.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92f07130682a4fa283e3b89d3d9a1249"}}, "title": "The formation of avian montane diversity across barriers and along elevational gradients.", "authors": [{"family": "Pujolar", "given": "Jos\u00e9 Mart\u00edn", "initials": "JM"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH"}, {"family": "Kennedy", "given": "Jonathan D", "initials": "JD", "orcid": "0000-0002-2843-122X", "researcher": {"href": "https://publications.scilifelab.se/researcher/efdccdbf3f5a44b39a66d7ece5f174f7.json"}}, {"family": "Marki", "given": "Petter Zahl", "initials": "PZ"}, {"family": "Korneliussen", "given": "Thorfinn S", "initials": "TS"}, {"family": "Freeman", "given": "Benjamin G", "initials": "BG", "orcid": "0000-0001-6131-6832", "researcher": {"href": "https://publications.scilifelab.se/researcher/e05aaf37772b4f50a12b20db5d2db3c8.json"}}, {"family": "Sam", "given": "Katerina", "initials": "K"}, {"family": "Linck", "given": "Ethan", "initials": "E"}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Iova", "given": "Bulisa", "initials": "B"}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Paul", "given": "Luda", "initials": "L"}, {"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": "2022-01-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "268"}, "abstract": "Tropical mountains harbor exceptional concentrations of Earth's biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species' altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.", "doi": "10.1038/s41467-021-27858-5", "pmid": "35022441", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27858-5"}, {"db": "pmc", "key": "PMC8755808"}], "notes": [], "created": "2022-03-29T13:48:03.888Z", "modified": "2024-01-16T13:48:37.739Z"}, {"entity": "publication", "iuid": "818045cf427e448a88ca0016ae161e99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/818045cf427e448a88ca0016ae161e99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/818045cf427e448a88ca0016ae161e99"}}, "title": "Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.", "authors": [{"family": "Chachoua", "given": "Ilyas", "initials": "I"}, {"family": "Tzelepis", "given": "Ilias", "initials": "I", "orcid": "0000-0001-5777-6334", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d93209d4bd4173bebec63d50462fe5.json"}}, {"family": "Dai", "given": "Hao", "initials": "H"}, {"family": "Lim", "given": "Jia Pei", "initials": "JP"}, {"family": "Lewandowska-Ronnegren", "given": "Anna", "initials": "A"}, {"family": "Casagrande", "given": "Felipe Beccaria", "initials": "FB", "orcid": "0000-0003-1117-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec52e8f2c91840858ed9c496481bc97b.json"}}, {"family": "Wu", "given": "Shuangyang", "initials": "S"}, {"family": "Vestlund", "given": "Johanna", "initials": "J", "orcid": "0000-0001-7158-905X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1589ce6268784aa6b599b3fd07caeb9d.json"}}, {"family": "Mallet de Lima", "given": "Carolina Diettrich", "initials": "CD"}, {"family": "Bhartiya", "given": "Deeksha", "initials": "D"}, {"family": "Scholz", "given": "Barbara A", "initials": "BA"}, {"family": "Martino", "given": "Mirco", "initials": "M", "orcid": "0000-0002-0954-0359", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d73809cbf204985a5d90befd9f65766.json"}}, {"family": "Mehmood", "given": "Rashid", "initials": "R", "orcid": "0000-0002-3488-9413", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e41df49c1e8470a9851829de9cf6a08.json"}}, {"family": "G\u00f6nd\u00f6r", "given": "Anita", "initials": "A", "orcid": "0000-0002-1523-4411", "researcher": {"href": "https://publications.scilifelab.se/researcher/611abc86936c400e91670eaee7a91fec.json"}}], "type": "journal article", "published": "2022-01-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "204"}, "abstract": "Abnormal WNT signaling increases MYC expression in colon cancer cells in part via oncogenic super-enhancer-(OSE)-mediated gating of the active MYC to the nuclear pore in a poorly understood process. We show here that the principal tenet of the WNT-regulated MYC gating, facilitating nuclear export of the MYC mRNA, is regulated by a CTCF binding site (CTCFBS) within the OSE to confer growth advantage in HCT-116 cells. To achieve this, the CTCFBS directs the WNT-dependent trafficking of the OSE to the nuclear pore from intra-nucleoplasmic positions in a stepwise manner. Once the OSE reaches a peripheral position, which is triggered by a CTCFBS-mediated CCAT1 eRNA activation, its final stretch (\u22640.7 \u03bcm) to the nuclear pore requires the recruitment of AHCTF1, a key nucleoporin, to the CTCFBS. Thus, a WNT/\u00df-catenin-AHCTF1-CTCF-eRNA circuit enables the OSE to promote pathological cell growth by coordinating the trafficking of the active MYC gene within the 3D nuclear architecture.", "doi": "10.1038/s41467-021-27868-3", "pmid": "35017527", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27868-3"}, {"db": "pmc", "key": "PMC8752836"}], "notes": [], "created": "2022-03-29T13:48:00.967Z", "modified": "2024-01-16T13:48:37.783Z"}, {"entity": "publication", "iuid": "08350a98d5d042829c1d154c715361d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08350a98d5d042829c1d154c715361d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08350a98d5d042829c1d154c715361d9"}}, "title": "Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus.", "authors": [{"family": "Tin", "given": "Adrienne", "initials": "A", "orcid": "0000-0002-4207-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c33ed3b64348be904a14698402445e.json"}}, {"family": "Schlosser", "given": "Pascal", "initials": "P", "orcid": "0000-0002-8460-0462", "researcher": {"href": "https://publications.scilifelab.se/researcher/b69be66d160c4cdc8030a07ebcb8f150.json"}}, {"family": "Matias-Garcia", "given": "Pamela R", "initials": "PR"}, {"family": "Thio", "given": "Chris H L", "initials": "CHL", "orcid": "0000-0003-2623-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/47fba5312ce6449fb9cfc45f6e1717e1.json"}}, {"family": "Joehanes", "given": "Roby", "initials": "R"}, {"family": "Liu", "given": "Hongbo", "initials": "H", "orcid": "0000-0002-0733-8616", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed1bef0b625f42249a5f5364e3759e71.json"}}, {"family": "Yu", "given": "Zhi", "initials": "Z", "orcid": "0000-0003-4810-3474", "researcher": {"href": "https://publications.scilifelab.se/researcher/df8600142a4249b6860fd0cbfa3bda5c.json"}}, {"family": "Weihs", "given": "Antoine", "initials": "A", "orcid": "0000-0002-7113-0027", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1328f6e263640e99a047d68e82a2db3.json"}}, {"family": "Hoppmann", "given": "Anselm", "initials": "A"}, {"family": "Grundner-Culemann", "given": "Franziska", "initials": "F", "orcid": "0000-0001-9649-281X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e201128d0a6348dcbbfd0e8f3c71f828.json"}}, {"family": "Min", "given": "Josine L", "initials": "JL", "orcid": "0000-0003-4456-9824", "researcher": {"href": "https://publications.scilifelab.se/researcher/5896cbc0cb8d427a954b194839adda52.json"}}, {"family": "Kuhns", "given": "Victoria L Halperin", "initials": "VLH", "orcid": "0000-0002-6348-7931", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c86603afad64be0981d383221806781.json"}}, {"family": "Adeyemo", "given": "Adebowale A", "initials": "AA", "orcid": "0000-0002-3105-3231", "researcher": {"href": "https://publications.scilifelab.se/researcher/762f3602e6324dfc991b1d90e21d9ade.json"}}, {"family": "Agyemang", "given": "Charles", "initials": "C", "orcid": "0000-0002-3882-7295", "researcher": {"href": "https://publications.scilifelab.se/researcher/0731c8e87d0f44c3895f01d44cfacaeb.json"}}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Aziz", "given": "Nasir A", "initials": "NA", "orcid": "0000-0001-6184-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1753010c5124e1f85318f62d70611e2.json"}}, {"family": "Baccarelli", "given": "Andrea", "initials": "A", "orcid": "0000-0002-3436-0640", "researcher": {"href": 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"initials": "AB", "orcid": "0000-0001-6099-7066", "researcher": {"href": "https://publications.scilifelab.se/researcher/d12ffb30f50d4c45adf31b328ce4d8fd.json"}}, {"family": "Endlich", "given": "Karlhans", "initials": "K", "orcid": "0000-0001-6052-6061", "researcher": {"href": "https://publications.scilifelab.se/researcher/da4d7341c495488f82994b45756c8de7.json"}}, {"family": "Floyd", "given": "James S", "initials": "JS"}, {"family": "Fraszczyk", "given": "Eliza", "initials": "E"}, {"family": "Gao", "given": "Xu", "initials": "X", "orcid": "0000-0001-6506-6084", "researcher": {"href": "https://publications.scilifelab.se/researcher/82092a375cb8470c97ea5bcfeb15eb47.json"}}, {"family": "G\u00e0o", "given": "X\u012bn", "initials": "X", "orcid": "0000-0003-0108-6961", "researcher": {"href": "https://publications.scilifelab.se/researcher/5eb7f388567b4514a237f2303077a46a.json"}}, {"family": "Gelber", "given": "Allan C", "initials": "AC", "orcid": "0000-0001-8463-311X", "researcher": {"href": 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"D"}, {"family": "Lloyd-Jones", "given": "Donald M", "initials": "DM"}, {"family": "Lorkowski", "given": "Stefan", "initials": "S", "orcid": "0000-0002-9649-840X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc3086dcbba64c65a859bb1fef0010ed.json"}}, {"family": "Lu", "given": "Ake T", "initials": "AT", "orcid": "0000-0002-2866-7961", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ae6f5269a1a4aac9bfa61128a802c6e.json"}}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McCartney", "given": "Daniel L", "initials": "DL", "orcid": "0000-0003-3242-0360", "researcher": {"href": "https://publications.scilifelab.se/researcher/e324cff97e2c49599c0474948c3a1470.json"}}, {"family": "Meeks", "given": "Karlijn A C", "initials": "KAC", "orcid": "0000-0003-3032-405X", "researcher": {"href": 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"initials": "D", "orcid": "0000-0003-1843-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/86bfd3e65ead428c93dc1a461004adab.json"}}, {"family": "Akilesh", "given": "Shreeram", "initials": "S", "orcid": "0000-0003-3152-7991", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cb143e90633471486dbad753d06e3fe.json"}}, {"family": "Woodward", "given": "Owen M", "initials": "OM", "orcid": "0000-0001-9514-2180", "researcher": {"href": "https://publications.scilifelab.se/researcher/669278c697764d249d6668a7d59269a6.json"}}, {"family": "Susztak", "given": "Katalin", "initials": "K", "orcid": "0000-0002-1005-3726", "researcher": {"href": "https://publications.scilifelab.se/researcher/1382eacb5f28444396132254487e3ed9.json"}}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A", "orcid": "0000-0002-4671-3714", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4cb85a14da4db6bc932a8bc4148efb.json"}}], "type": "journal article", "published": "2021-12-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "7173", "issn-l": "2041-1723"}, "abstract": "Elevated serum urate levels, a complex trait and major risk factor for incident gout, are correlated with cardiometabolic traits via incompletely understood mechanisms. DNA methylation in whole blood captures genetic and environmental influences and is assessed in transethnic meta-analysis of epigenome-wide association studies (EWAS) of serum urate (discovery, n = 12,474, replication, n = 5522). The 100 replicated, epigenome-wide significant (p < 1.1E-7) CpGs explain 11.6% of the serum urate variance. At SLC2A9, the serum urate locus with the largest effect in genome-wide association studies (GWAS), five CpGs are associated with SLC2A9 gene expression. Four CpGs at SLC2A9 have significant causal effects on serum urate levels and/or gout, and two of these partly mediate the effects of urate-associated GWAS variants. In other genes, including SLC7A11 and PHGDH, 17 urate-associated CpGs are associated with conditions defining metabolic syndrome, suggesting that these CpGs may represent a blood DNA methylation signature of cardiometabolic risk factors. This study demonstrates that EWAS can provide new insights into GWAS loci and the correlation of serum urate with other complex traits.", "doi": "10.1038/s41467-021-27198-4", "pmid": "34887389", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27198-4"}], "notes": [], "created": "2021-12-22T19:39:57.979Z", "modified": "2021-12-22T19:39:58.563Z"}, {"entity": "publication", "iuid": "c6fcde1c149146be8ea0b5308f8ec628", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6fcde1c149146be8ea0b5308f8ec628.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6fcde1c149146be8ea0b5308f8ec628"}}, "title": "Meta-analyses identify DNA methylation associated with kidney function and damage.", "authors": [{"family": "Schlosser", "given": "Pascal", "initials": "P", "orcid": "0000-0002-8460-0462", "researcher": {"href": 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{"href": "https://publications.scilifelab.se/researcher/f8be03e2acc84b07b342725a768a1f53.json"}}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Prokisch", "given": "Holger", "initials": "H", "orcid": "0000-0003-2379-6286", "researcher": {"href": "https://publications.scilifelab.se/researcher/48fcadf9621143d78b89116929aceb79.json"}}, {"family": "Psaty", "given": "Bruce M", "initials": "BM", "orcid": "0000-0002-7278-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/b18d7cad2e604bcbbb41b8e5d206c22c.json"}}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Ratliff", "given": "Scott M", "initials": "SM"}, {"family": "Reiner", "given": "Alex P", "initials": "AP", "orcid": "0000-0002-1427-4470", "researcher": {"href": "https://publications.scilifelab.se/researcher/931fcf4444904ec398a450a9ec4f4389.json"}}, {"family": "Rosas", "given": "Sylvia E", "initials": "SE"}, {"family": "Sch\u00f6ttker", "given": "Ben", "initials": "B", "orcid": "0000-0002-1217-4521", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfbda7c479a54690a046ef88ebbd5be8.json"}}, {"family": "Schwartz", "given": "Joel", "initials": "J"}, {"family": "Sedaghat", "given": "Sanaz", "initials": "S"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0002-3575-5468", "researcher": {"href": "https://publications.scilifelab.se/researcher/311c7381092b4143bcd2e4ef93250526.json"}}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Stocker", "given": "Hannah R", "initials": "HR", "orcid": "0000-0001-5281-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b29536e37004e708b1c75abc369d1f2.json"}}, {"family": "Stringhini", "given": "Silvia", "initials": "S", "orcid": "0000-0002-4387-8943", "researcher": {"href": "https://publications.scilifelab.se/researcher/e670989692024cc581612a876237d6a7.json"}}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "Swenson", "given": "Brenton R", "initials": "BR"}, {"family": "Tellez-Plaza", "given": "Maria", "initials": "M", "orcid": "0000-0002-3850-1228", "researcher": {"href": "https://publications.scilifelab.se/researcher/e564f740813246958db98ddd1a2a0b58.json"}}, {"family": "van Meurs", "given": "Joyce B J", "initials": "JBJ"}, {"family": "van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV", "orcid": "0000-0002-7943-3153", "researcher": {"href": "https://publications.scilifelab.se/researcher/babcbf8d8f124eceaf0a06dffd39b5cb.json"}}, {"family": "Venema", "given": "Andrea", "initials": "A"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Walker", "given": "Rosie M", "initials": "RM", "orcid": "0000-0002-1060-4479", "researcher": {"href": "https://publications.scilifelab.se/researcher/79a65025d1a64ed2b383e69c803df0a4.json"}}, {"family": "Wielscher", "given": "Matthias", "initials": "M", "orcid": "0000-0003-4138-1383", "researcher": {"href": "https://publications.scilifelab.se/researcher/18bdf16f6b9f4272ae4b03579dc46e00.json"}}, {"family": "Winkelmann", "given": "Juliane", "initials": "J"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BHR", "orcid": "0000-0001-9262-6921", "researcher": {"href": "https://publications.scilifelab.se/researcher/705d5bb109c443289feef937e695dc7d.json"}}, {"family": "Zhao", "given": "Wei", "initials": "W", "orcid": "0000-0001-7388-0692", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0c2246e69494086bab7ead8e6f1f717.json"}}, {"family": "Zheng", "given": "Yinan", "initials": "Y", "orcid": "0000-0002-2006-7320", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8f1e7f80ee4aa8b853ef31295f5709.json"}}, {"family": "Estonian Biobank Research Team", "given": "", "initials": ""}, {"family": "Genetics of DNA Methylation Consortium", "given": "", "initials": ""}, {"family": "Loh", "given": "Marie", "initials": "M", "orcid": "0000-0003-3626-8466", "researcher": {"href": "https://publications.scilifelab.se/researcher/70e1d986dce444f889fda8d47e9cb355.json"}}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "Levy", "given": "Daniel", "initials": "D", "orcid": "0000-0003-1843-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/86bfd3e65ead428c93dc1a461004adab.json"}}, {"family": "Waldenberger", "given": "Melanie", "initials": "M", "orcid": "0000-0003-0583-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8de22214f2448c6a7f86fc1040d0104.json"}}, {"family": "Susztak", "given": "Katalin", "initials": "K", "orcid": "0000-0002-1005-3726", "researcher": {"href": "https://publications.scilifelab.se/researcher/1382eacb5f28444396132254487e3ed9.json"}}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A", "orcid": "0000-0002-4671-3714", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4cb85a14da4db6bc932a8bc4148efb.json"}}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}], "type": "journal article", "published": "2021-12-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "7174", "issn-l": "2041-1723"}, "abstract": "Chronic kidney disease is a major public health burden. Elevated urinary albumin-to-creatinine ratio is a measure of kidney damage, and used to diagnose and stage chronic kidney disease. To extend the knowledge on regulatory mechanisms related to kidney function and disease, we conducted a blood-based epigenome-wide association study for estimated glomerular filtration rate (n = 33,605) and urinary albumin-to-creatinine ratio (n = 15,068) and detected 69 and seven CpG sites where DNA methylation was associated with the respective trait. The majority of these findings showed directionally consistent associations with the respective clinical outcomes chronic kidney disease and moderately increased albuminuria. Associations of DNA methylation with kidney function, such as CpGs at JAZF1, PELI1 and CHD2 were validated in kidney tissue. Methylation at PHRF1, LDB2, CSRNP1 and IRF5 indicated causal effects on kidney function. Enrichment analyses revealed pathways related to hemostasis and blood cell migration for estimated glomerular filtration rate, and immune cell activation and response for urinary albumin-to-creatinineratio-associated CpGs.", "doi": "10.1038/s41467-021-27234-3", "pmid": "34887417", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27234-3"}], "notes": [], "created": "2021-12-22T19:39:46.207Z", "modified": "2021-12-22T19:39:47.563Z"}, {"entity": "publication", "iuid": "0acc2048f2074e63bddc5c1c8e0bc768", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0acc2048f2074e63bddc5c1c8e0bc768.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0acc2048f2074e63bddc5c1c8e0bc768"}}, "title": "Structural basis for transthyretin amyloid formation in vitreous body of the eye.", "authors": [{"family": "Iakovleva", "given": "Irina", "initials": "I", "orcid": "0000-0002-9500-5917", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5fd05e56e164227b137bac9a879af58.json"}}, {"family": "Hall", "given": "Michael", "initials": "M", "orcid": "0000-0003-0864-9798", "researcher": {"href": "https://publications.scilifelab.se/researcher/7489a92a241f4d0d9f8ef6eb4fcb3858.json"}}, {"family": "Oelker", "given": "Melanie", "initials": "M", "orcid": "0000-0001-7301-8445", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d4b43ce3822421e998c7ecead0f2e1a.json"}}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Anan", "given": "Intissar", "initials": "I", "orcid": "0000-0003-2874-7643", "researcher": {"href": "https://publications.scilifelab.se/researcher/923515859dae4f16ae6f4cee53515f98.json"}}, {"family": "Sauer-Eriksson", "given": "A Elisabeth", "initials": "AE", "orcid": "0000-0003-0124-0199", "researcher": {"href": "https://publications.scilifelab.se/researcher/9435049fbe2745b59e04558cc5201f95.json"}}], "type": "journal article", "published": "2021-12-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "7141", "issn-l": "2041-1723"}, "abstract": "Amyloid transthyretin (ATTR) amyloidosis is characterized by the abnormal accumulation of ATTR fibrils in multiple organs. However, the structure of ATTR fibrils from the eye is poorly understood. Here, we used cryo-EM to structurally characterize vitreous body ATTR fibrils. These structures were distinct from previously characterized heart fibrils, even though both have the same mutation and type A pathology. Differences were observed at several structural levels: in both the number and arrangement of protofilaments, and the conformation of the protein fibril in each layer of protofilaments. Thus, our results show that ATTR protein structure and its assembly into protofilaments in the type A fibrils can vary between patients carrying the same mutation. By analyzing and matching the interfaces between the amino acids in the ATTR fibril with those in the natively folded TTR, we are able to propose a mechanism for the structural conversion of TTR into a fibrillar form.", "doi": "10.1038/s41467-021-27481-4", "pmid": "34880242", "labels": {"Cryo-EM": "Collaborative", "Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27481-4"}, {"db": "pmc", "key": "PMC8654999"}], "notes": [], "created": "2021-12-09T13:57:20.280Z", "modified": "2022-01-03T10:03:27.020Z"}, {"entity": "publication", "iuid": "8cbacd9195c24dc99bee025eebec1ab8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cbacd9195c24dc99bee025eebec1ab8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cbacd9195c24dc99bee025eebec1ab8"}}, "title": "Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver.", "authors": [{"family": "Hildebrandt", "given": "Franziska", "initials": "F", "orcid": "0000-0002-2673-1704", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c69d2d421d64a11a719a6fd55c1977a.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Van Hul", "given": "No\u00e9mi", "initials": "N", "orcid": "0000-0003-1410-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce1f79e0359b45c9991d14649ad4bc2b.json"}}, {"family": "Kanatani", "given": "Sachie", "initials": "S"}, {"family": "Masek", "given": "Jan", "initials": "J", "orcid": "0000-0003-2904-3808", "researcher": {"href": "https://publications.scilifelab.se/researcher/23cbd5352a924afcb2fa82185b237cbd.json"}}, {"family": "Ellis", "given": "Ewa", "initials": "E", "orcid": "0000-0002-3057-5337", "researcher": {"href": "https://publications.scilifelab.se/researcher/82ef7cf7903140cfbb7ff8d6f4961dde.json"}}, {"family": "Barragan", "given": "Antonio", "initials": "A", "orcid": "0000-0001-7746-9964", "researcher": {"href": "https://publications.scilifelab.se/researcher/4eefb95f00db42e3891769f384269c6c.json"}}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Andersson", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8608-625X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7313cdcd5f41d4a567a6c315aac3a1.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2021-12-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "7046", "issn-l": "2041-1723"}, "abstract": "Reconstruction of heterogeneity through single cell transcriptional profiling has greatly advanced our understanding of the spatial liver transcriptome in recent years. However, global transcriptional differences across lobular units remain elusive in physical space. Here, we apply Spatial Transcriptomics to perform transcriptomic analysis across sectioned liver tissue. We confirm that the heterogeneity in this complex tissue is predominantly determined by lobular zonation. By introducing novel computational approaches, we enable transcriptional gradient measurements between tissue structures, including several lobules in a variety of orientations. Further, our data suggests the presence of previously transcriptionally uncharacterized structures within liver tissue, contributing to the overall spatial heterogeneity of the organ. This study demonstrates how comprehensive spatial transcriptomic technologies can be used to delineate extensive spatial gene expression patterns in the liver, indicating its future impact for studies of liver function, development and regeneration as well as its potential in pre-clinical and clinical pathology.", "doi": "10.1038/s41467-021-27354-w", "pmid": "34857782", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27354-w"}, {"db": "pmc", "key": "PMC8640072"}], "notes": [], "created": "2022-11-09T15:54:10.121Z", "modified": "2024-01-16T13:48:38.011Z"}, {"entity": "publication", "iuid": "b14a78e083fb49f881706b1722679139", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b14a78e083fb49f881706b1722679139.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b14a78e083fb49f881706b1722679139"}}, "title": "ATR inhibition enables complete tumour regression in ALK-driven NB mouse models.", "authors": [{"family": "Szydzik", "given": "Joanna", "initials": "J", "orcid": "0000-0002-4346-8821", "researcher": {"href": "https://publications.scilifelab.se/researcher/2116e33e7fdd48b8af1664265f02636a.json"}}, {"family": "Lind", "given": "Dan E", "initials": "DE", "orcid": "0000-0002-8299-5659", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ba0b43eeb64fc28393a871fb507ca2.json"}}, {"family": "Arefin", "given": "Badrul", "initials": "B", "orcid": "0000-0003-1117-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/043830a43c6a448cb6e8e3349f2aaa3c.json"}}, {"family": "Kurhe", "given": "Yeshwant", "initials": "Y"}, {"family": "Umapathy", "given": "Ganesh", "initials": "G"}, {"family": "Siaw", "given": "Joachim Tetteh", "initials": "JT", "orcid": "0000-0002-1286-4485", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a4ce00b5a4b4ebb9ee746de59e2e943.json"}}, {"family": "Claeys", "given": "Arne", "initials": "A", "orcid": "0000-0001-6990-1569", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3e7d3acc40b47bd8c5bc8313499dd61.json"}}, {"family": "Gabre", "given": "Jonatan L", "initials": "JL"}, {"family": "Van den Eynden", "given": "Jimmy", "initials": "J", "orcid": "0000-0003-0002-5614", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b20f02703024987bc9791df1dc80e51.json"}}, {"family": "Hallberg", "given": "Bengt", "initials": "B", "orcid": "0000-0003-2032-2616", "researcher": {"href": "https://publications.scilifelab.se/researcher/e34241a23a824d558865ac54d8d07fa7.json"}}, {"family": "Palmer", "given": "Ruth H", "initials": "RH", "orcid": "0000-0002-2735-8470", "researcher": {"href": "https://publications.scilifelab.se/researcher/808281ecc2634b66a274895e58a122bd.json"}}], "type": "journal article", "published": "2021-11-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "6813", "issn-l": "2041-1723"}, "abstract": "High-risk neuroblastoma (NB) often involves MYCN amplification as well as mutations in ALK. Currently, high-risk NB presents significant clinical challenges, and additional therapeutic options are needed. Oncogenes like MYCN and ALK result in increased replication stress in cancer cells, offering therapeutically exploitable options. We have pursued phosphoproteomic analyses highlighting ATR activity in ALK-driven NB cells, identifying the BAY1895344 ATR inhibitor as a potent inhibitor of NB cell growth and proliferation. Using RNA-Seq, proteomics and phosphoproteomics we characterize NB cell and tumour responses to ATR inhibition, identifying key components of the DNA damage response as ATR targets in NB cells. ATR inhibition also produces robust responses in mouse models. Remarkably, a 2-week combined ATR/ALK inhibition protocol leads to complete tumor regression in two independent genetically modified mouse NB models. These results suggest that NB patients, particularly in high-risk groups with oncogene-induced replication stress, may benefit from ATR inhibition as therapeutic intervention.", "doi": "10.1038/s41467-021-27057-2", "pmid": "34819497", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8613282"}, {"db": "pii", "key": "10.1038/s41467-021-27057-2"}], "notes": [], "created": "2023-03-07T14:34:52.316Z", "modified": "2024-01-16T13:46:29.870Z"}, {"entity": "publication", "iuid": "0c150c7610fb4d7ab0600f04c6610e36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c150c7610fb4d7ab0600f04c6610e36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c150c7610fb4d7ab0600f04c6610e36"}}, "title": "Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae.", "authors": [{"family": "Sch\u00f6n", "given": "Max E", "initials": "ME", "orcid": "0000-0002-4453-4173", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac8236efee89497bacf5fa9ada6ee8a5.json"}}, {"family": "Zlatogursky", "given": "Vasily V", "initials": "VV", "orcid": "0000-0002-2688-3900", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd1807f8bc0b4990bb1d4a4037ae4566.json"}}, {"family": "Singh", "given": "Rohan P", "initials": "RP"}, {"family": "Poirier", "given": "Camille", "initials": "C"}, {"family": "Wilken", "given": "Susanne", "initials": "S"}, {"family": "Mathur", "given": "Varsha", "initials": "V"}, {"family": "Strassert", "given": "J\u00fcrgen F H", "initials": "JFH", "orcid": "0000-0001-6786-7563", "researcher": {"href": "https://publications.scilifelab.se/researcher/079bf03f0b2c438ab4e01346eb0be1af.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Worden", "given": "Alexandra Z", "initials": "AZ", "orcid": "0000-0002-9888-9324", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5c3bd7ac29e4564a25fcd334fd4c24a.json"}}, {"family": "Keeling", "given": "Patrick J", "initials": "PJ", "orcid": "0000-0002-7644-0745", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f5e2df178884dd6bc124ebcde2e1483.json"}}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG", "orcid": "0000-0002-6898-6377", "researcher": {"href": "https://publications.scilifelab.se/researcher/42fc4acc111f4c488b23fa41341705e2.json"}}, {"family": "Wideman", "given": "Jeremy G", "initials": "JG", "orcid": "0000-0002-4426-9533", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3403a41c09c480d982a8c1ec018aede.json"}}, {"family": "Burki", "given": "Fabien", "initials": "F", "orcid": "0000-0002-8248-8462", "researcher": {"href": "https://publications.scilifelab.se/researcher/c386a8e440344f25bea35d570450b09b.json"}}], "type": "journal article", "published": "2021-11-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "6651"}, "abstract": "The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we use single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.", "doi": "10.1038/s41467-021-26918-0", "pmid": "34789758", "labels": {"Microbial Single Cell Genomics": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-26918-0"}, {"db": "pmc", "key": "PMC8599508"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5388176"}], "notes": [], "created": "2021-11-17T12:35:08.815Z", "modified": "2024-01-16T13:48:38.070Z"}, {"entity": "publication", "iuid": "a16477100ca44690afdb66e882fc52d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a16477100ca44690afdb66e882fc52d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a16477100ca44690afdb66e882fc52d2"}}, "title": "Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.", "authors": [{"family": "Grosche", "given": "Sarah", "initials": "S"}, {"family": "Marenholz", "given": "Ingo", "initials": "I"}, {"family": "Esparza-Gordillo", "given": "Jorge", "initials": "J"}, {"family": "Arnau-Soler", "given": "Aleix", "initials": "A"}, {"family": "Pairo-Castineira", "given": "Erola", "initials": "E", "orcid": "0000-0002-2423-3090", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8cc869b85f64312b03d353912f1fba4.json"}}, {"family": "R\u00fcschendorf", "given": "Franz", "initials": "F", "orcid": "0000-0001-5640-810X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e02ac817ef224343ba9d9a9ac7cdc43e.json"}}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS", "orcid": "0000-0002-7464-3354", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fde142189574b44a72155785763a327.json"}}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Arnold", "given": "Andreas", "initials": "A"}, {"family": "Australian Asthma Genetics Consortium (AAGC)", "given": "", "initials": ""}, {"family": "Baurecht", "given": "Hansj\u00f6rg", "initials": "H", "orcid": "0000-0002-9265-5594", "researcher": {"href": "https://publications.scilifelab.se/researcher/65098dade92d4b87a691906582cc4fa9.json"}}, {"family": "Bisgaard", "given": "Hans", "initials": "H", "orcid": "0000-0003-4131-7592", "researcher": {"href": "https://publications.scilifelab.se/researcher/5179e5b6e16e482c9d2a9d8250bfc44d.json"}}, {"family": "B\u00f8nnelykke", "given": "Klaus", "initials": "K", "orcid": "0000-0003-2003-1018", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e0992f23e69443c8bf08589711cb9b9.json"}}, {"family": "Brown", "given": "Sara J", "initials": "SJ", "orcid": "0000-0002-3232-5251", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3d24ef4a0034f3fbe0bdf273ffc25fc.json"}}, {"family": "Bustamante", "given": "Mariona", "initials": "M", "orcid": "0000-0003-0127-2860", "researcher": {"href": "https://publications.scilifelab.se/researcher/7283551b36ce4d99851d8eb166af3bf9.json"}}, {"family": "Curtin", "given": "John A", "initials": "JA"}, {"family": "Custovic", "given": "Adnan", "initials": "A", "orcid": "0000-0001-5218-7071", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c2bf8fc54ae68fec26ea7d6bc158.json"}}, {"family": "Dharmage", "given": "Shyamali C", "initials": "SC"}, {"family": "Esplugues", "given": "Ana", "initials": "A"}, {"family": "Falchi", "given": "Mario", "initials": "M", "orcid": "0000-0002-5646-1004", "researcher": {"href": "https://publications.scilifelab.se/researcher/74b676eb136243318749e1a4e265d71e.json"}}, {"family": "Fernandez-Orth", "given": "Dietmar", "initials": "D", "orcid": "0000-0002-1237-3192", "researcher": {"href": "https://publications.scilifelab.se/researcher/119682064dc44f92ba9dffdcc9652e46.json"}}, {"family": "Ferreira", "given": "Manuel A R", "initials": "MAR"}, {"family": "Franke", "given": "Andre", "initials": "A", "orcid": "0000-0003-1530-5811", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fffe3df068c4283a8b8b583717e6bb6.json"}}, {"family": "Gerdes", "given": "Sascha", "initials": "S"}, {"family": "Gieger", "given": "Christian", "initials": "C", "orcid": "0000-0001-6986-9554", "researcher": {"href": "https://publications.scilifelab.se/researcher/86f44e76061c403fadd97b768e2a7e62.json"}}, {"family": "Hakonarson", "given": "Hakon", "initials": "H", "orcid": "0000-0003-2814-7461", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd650cc09eb84d669c55c3f0ef690955.json"}}, {"family": "Holt", "given": "Patrick G", "initials": "PG", "orcid": "0000-0003-1193-0935", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e746298fc4143a3bf5d8a6250d88254.json"}}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Hubner", "given": "Norbert", "initials": "N", "orcid": "0000-0002-1218-6223", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d84f34739c743838cea107286522e42.json"}}, {"family": "Hysi", "given": "Pirro G", "initials": "PG", "orcid": "0000-0001-5752-2510", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d756a9f3294490fa137e2308ccb353e.json"}}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH", "orcid": "0000-0001-8567-3252", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd7e0158050a4ab3860e288c4eb9ae87.json"}}, {"family": "Lau", "given": "Susanne", "initials": "S"}, {"family": "Lutz", "given": "Manuel", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Marks", "given": "Guy B", "initials": "GB"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M", "orcid": "0000-0003-3793-5910", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d21299bb41343f88142255e64a9da57.json"}}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM", "orcid": "0000-0002-8770-2464", "researcher": {"href": "https://publications.scilifelab.se/researcher/903aa25b88bc48adbe60be2a7179929b.json"}}, {"family": "Paternoster", "given": "Lavinia", "initials": "L", "orcid": "0000-0003-2514-0889", "researcher": {"href": "https://publications.scilifelab.se/researcher/826f9852c56d4922ab255ab83d26faa8.json"}}, {"family": "Pennell", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-0937-6165", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e35a98141ce4350b6775593f87e40a5.json"}}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Rawlik", "given": "Konrad", "initials": "K", "orcid": "0000-0002-0010-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c46ce845e5a43b98ba496c13ca987cd.json"}}, {"family": "Robertson", "given": "Colin F", "initials": "CF"}, {"family": "Rodriguez", "given": "Elke", "initials": "E", "orcid": "0000-0003-3692-3950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e8669678dc94c32bda1a12b81a22743.json"}}, {"family": "Sebert", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-6681-6983", "researcher": {"href": "https://publications.scilifelab.se/researcher/c007e85f69d4421bb6cf76dc52a01eb8.json"}}, {"family": "Simpson", "given": "Angela", "initials": "A"}, {"family": "Sleiman", "given": "Patrick M A", "initials": "PMA"}, {"family": "Standl", "given": "Marie", "initials": "M"}, {"family": "St\u00f6lzl", "given": "Dora", "initials": "D"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Szwajda", "given": "Agnieszka", "initials": "A"}, {"family": "Tenesa", "given": "Albert", "initials": "A", "orcid": "0000-0003-4884-4475", "researcher": {"href": "https://publications.scilifelab.se/researcher/99ef99f1a6d5469facdbc8faa2b0ef39.json"}}, {"family": "Thompson", "given": "Philip J", "initials": "PJ"}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V"}, {"family": "Visconti", "given": "Alessia", "initials": "A", "orcid": "0000-0003-4144-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6b388c130a94f66819774f44a4c6e38.json"}}, {"family": "Vonk", "given": "Judith M", "initials": "JM", "orcid": "0000-0001-7531-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/e57100a0e5bc48c59590c043897a8bbd.json"}}, {"family": "Wang", "given": "Carol A", "initials": "CA", "orcid": "0000-0002-4301-3974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf99a43c27034a68976e978b104a91d7.json"}}, {"family": "Weidinger", "given": "Stephan", "initials": "S"}, {"family": "Wielscher", "given": "Matthias", "initials": "M"}, {"family": "Worth", "given": "Catherine L", "initials": "CL", "orcid": "0000-0002-1796-9606", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a8a93c773b54b288809d04813441600.json"}}, {"family": "Xu", "given": "Chen-Jian", "initials": "C"}, {"family": "Lee", "given": "Young-Ae", "initials": "Y"}], "type": "journal article", "published": "2021-11-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "6618"}, "abstract": "Previous genome-wide association studies revealed multiple common variants involved in eczema but the role of rare variants remains to be elucidated. Here, we investigate the role of rare variants in eczema susceptibility. We meta-analyze 21 study populations including 20,016 eczema cases and 380,433 controls. Rare variants are imputed with high accuracy using large population-based reference panels. We identify rare exonic variants in DUSP1, NOTCH4, and SLC9A4 to be associated with eczema. In DUSP1 and NOTCH4 missense variants are predicted to impact conserved functional domains. In addition, five novel common variants at SATB1-AS1/KCNH8, TRIB1/LINC00861, ZBTB1, TBX21/OSBPL7, and CSF2RB are discovered. While genes prioritized based on rare variants are significantly up-regulated in the skin, common variants point to immune cell function. Over 20% of the single nucleotide variant-based heritability is attributable to rare and low-frequency variants. The identified rare/low-frequency variants located in functional protein domains point to promising targets for novel therapeutic approaches to eczema.", "doi": "10.1038/s41467-021-26783-x", "pmid": "34785669", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-26783-x"}, {"db": "pmc", "key": "PMC8595373"}], "notes": [], "created": "2021-11-26T16:27:57.327Z", "modified": "2021-12-07T06:56:28.734Z"}, {"entity": "publication", "iuid": "f150e8e23a9a403d8ed0d635081a5292", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f150e8e23a9a403d8ed0d635081a5292.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f150e8e23a9a403d8ed0d635081a5292"}}, "title": "An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.", "authors": [{"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a75556311084e2b827ab1f646d7a16c.json"}}, {"family": "Beusch", "given": "Christian M", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/278e50b11a3c4ef69b6e2708f99b5f3e.json"}}, {"family": "Saei", "given": "Amir A", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Aoun", "given": "Mike", "initials": "M"}, {"family": "Moruzzi", "given": "Noah", "initials": "N"}, {"family": "Coelho", "given": "Ana", "initials": "A"}, {"family": "Leijten", "given": "Niels", "initials": "N", "orcid": "0000-0002-7305-7249", "researcher": {"href": "https://publications.scilifelab.se/researcher/52533fb586904f1598abab4fe93c8b8f.json"}}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Maltseva", "given": "Diana", "initials": "D", "orcid": "0000-0002-4960-5348", "researcher": {"href": "https://publications.scilifelab.se/researcher/4091fbe97bf84c76b279377cb71f61e9.json"}}, {"family": "Tonevitsky", "given": "Alexander G", "initials": "AG"}, {"family": "Millischer", "given": "Vincent", "initials": "V"}, {"family": "Carlos Villaescusa", "given": "J", "initials": "J"}, {"family": "Kadekar", "given": "Sandeep", "initials": "S"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Altynbekova", "given": "Kamilya", "initials": "K"}, {"family": "Kel", "given": "Alexander", "initials": "A"}, {"family": "Berggren", "given": "Per-Olof", "initials": "P"}, {"family": "Simonson", "given": "Oscar", "initials": "O"}, {"family": "Grinnemo", "given": "Karl-Henrik", "initials": "K"}, {"family": "Holmdahl", "given": "Rikard", "initials": "R", "orcid": "0000-0002-4969-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/49e60d22dd1a4dd1a4ca5a50d9fc4fc7.json"}}, {"family": "Rodin", "given": "Sergey", "initials": "S", "orcid": "0000-0002-6954-1986", "researcher": {"href": "https://publications.scilifelab.se/researcher/2371c1f6b98c46c495530ac860a2beb8.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": "2021-11-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "6558"}, "abstract": "Detailed characterization of cell type transitions is essential for cell biology in general and particularly for the development of stem cell-based therapies in regenerative medicine. To systematically study such transitions, we introduce a method that simultaneously measures protein expression and thermal stability changes in cells and provide the web-based visualization tool ProteoTracker. We apply our method to study differences between human pluripotent stem cells and several cell types including their parental cell line and differentiated progeny. We detect alterations of protein properties in numerous cellular pathways and components including ribosome biogenesis and demonstrate that modulation of ribosome maturation through SBDS protein can be helpful for manipulating cell stemness in vitro. Using our integrative proteomics approach and the web-based tool, we uncover a molecular basis for the uncoupling of robust transcription from parsimonious translation in stem cells and propose a method for maintaining pluripotency in vitro.", "doi": "10.1038/s41467-021-26879-4", "pmid": "34772928", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-26879-4"}, {"db": "pmc", "key": "PMC8590018"}], "notes": [], "created": "2021-11-29T17:23:45.777Z", "modified": "2024-01-18T23:36:09.097Z"}, {"entity": "publication", "iuid": "5f2612f8d9264d70a7d29ec71ee25fab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f2612f8d9264d70a7d29ec71ee25fab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f2612f8d9264d70a7d29ec71ee25fab"}}, "title": "Elevated circulating follistatin associates with an increased risk of type 2 diabetes.", "authors": [{"family": "Wu", "given": "Chuanyan", "initials": "C"}, {"family": "Born\u00e9", "given": "Yan", "initials": "Y"}, {"family": "Gao", "given": "Rui", "initials": "R"}, {"family": "L\u00f3pez Rodriguez", "given": "Maykel", "initials": "M"}, {"family": "Roell", "given": "William C", "initials": "WC"}, {"family": "Wilson", "given": "Jonathan M", "initials": "JM", "orcid": "0000-0002-8648-600X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b464a1eff43a4429b917dc6e7da97774.json"}}, {"family": "Regmi", "given": "Ajit", "initials": "A"}, {"family": "Luan", "given": "Cheng", "initials": "C"}, {"family": "Aly", "given": "Dina Mansour", "initials": "DM"}, {"family": "Peter", "given": "Andreas", "initials": "A"}, {"family": "Machann", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0002-4458-5886", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78304d13a374b049b3422387bf613f1.json"}}, {"family": "Staiger", "given": "Harald", "initials": "H"}, {"family": "Fritsche", "given": "Andreas", "initials": "A"}, {"family": "Birkenfeld", "given": "Andreas L", "initials": "AL", "orcid": "0000-0003-1407-9023", "researcher": {"href": "https://publications.scilifelab.se/researcher/0beaba6737ca4626ab1fbad1d0c2f848.json"}}, {"family": "Tao", "given": "Rongya", "initials": "R"}, {"family": "Wagner", "given": "Robert", "initials": "R", "orcid": "0000-0002-6120-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/26361c8c7fc24433832ae95bb52c55ff.json"}}, {"family": "Canouil", "given": "Micka\u00ebl", "initials": "M", "orcid": "0000-0002-3396-4549", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2bc5739e8e84ae08577977a71dd9b20.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d66c199ece143a6ab15222d8b55e3ea.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ahlqvist", "given": "Emma", "initials": "E", "orcid": "0000-0002-6513-2384", "researcher": {"href": "https://publications.scilifelab.se/researcher/415b737a7da04f13ab0fd104c375b097.json"}}, {"family": "Kaikkonen", "given": "Minna U", "initials": "MU", "orcid": "0000-0001-6294-0979", "researcher": {"href": "https://publications.scilifelab.se/researcher/58a9647f7f374ad0a8d7e3a38cc8e2bb.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-5652-8459", "researcher": {"href": "https://publications.scilifelab.se/researcher/f23c2a10ac2a4d73a8f62b94855635f1.json"}}, {"family": "Shore", "given": "Angela C", "initials": "AC", "orcid": "0000-0003-3039-308X", "researcher": {"href": "https://publications.scilifelab.se/researcher/308929b0ba56442480676e86383c6a4a.json"}}, {"family": "Khan", "given": "Faisel", "initials": "F"}, {"family": "Natali", "given": "Andrea", "initials": "A"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Nilsson", "given": "Jan", "initials": "J", "orcid": "0000-0002-9752-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8777140448bc47f0a7984db3c15c0e23.json"}}, {"family": "H\u00e4ring", "given": "Hans-Ulrich", "initials": "HU"}, {"family": "Renstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Wollheim", "given": "Claes B", "initials": "CB"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Weng", "given": "Jianping", "initials": "J"}, {"family": "Pearson", "given": "Ewan R", "initials": "ER"}, {"family": "Franks", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-0520-7604", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebbf40c0f7e49dd8c75a2b6cbf27276.json"}}, {"family": "White", "given": "Morris F", "initials": "MF"}, {"family": "Duffin", "given": "Kevin L", "initials": "KL"}, {"family": "Vaag", "given": "Allan Arthur", "initials": "AA"}, {"family": "Laakso", "given": "Markku", "initials": "M", "orcid": "0000-0002-3394-7749", "researcher": {"href": "https://publications.scilifelab.se/researcher/13d8518be25141a296d7f2df5cccb4ee.json"}}, {"family": "Stefan", "given": "Norbert", "initials": "N", "orcid": "0000-0002-2186-9595", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7759dc1e26a48e28115a96fe4400de0.json"}}, {"family": "Groop", "given": "Leif", "initials": "L", "orcid": "0000-0002-0187-3263", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1c35ae04cd4e9e9525fbc844d15e14.json"}}, {"family": "De Marinis", "given": "Yang", "initials": "Y", "orcid": "0000-0002-8081-2142", "researcher": {"href": "https://publications.scilifelab.se/researcher/29fe2d7158a44c74b5eee49095ac2d2a.json"}}], "type": "journal article", "published": "2021-11-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "6486", "issn-l": "2041-1723"}, "abstract": "The hepatokine follistatin is elevated in patients with type 2 diabetes (T2D) and promotes hyperglycemia in mice. Here we explore the relationship of plasma follistatin levels with incident T2D and mechanisms involved. Adjusted hazard ratio (HR) per standard deviation (SD) increase in follistatin levels for T2D is 1.24 (CI: 1.04-1.47, p < 0.05) during 19-year follow-up (n = 4060, Sweden); and 1.31 (CI: 1.09-1.58, p < 0.01) during 4-year follow-up (n = 883, Finland). High circulating follistatin associates with adipose tissue insulin resistance and non-alcoholic fatty liver disease (n = 210, Germany). In human adipocytes, follistatin dose-dependently increases free fatty acid release. In genome-wide association study (GWAS), variation in the glucokinase regulatory protein gene (GCKR) associates with plasma follistatin levels (n = 4239, Sweden; n = 885, UK, Italy and Sweden) and GCKR regulates follistatin secretion in hepatocytes in vitro. Our findings suggest that GCKR regulates follistatin secretion and that elevated circulating follistatin associates with an increased risk of T2D by inducing adipose tissue insulin resistance.", "doi": "10.1038/s41467-021-26536-w", "pmid": "34759311", "labels": {"Affinity Proteomics Stockholm": "Collaborative", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8580990"}, {"db": "pii", "key": "10.1038/s41467-021-26536-w"}], "notes": [], "created": "2021-11-17T08:01:36.938Z", "modified": "2023-06-19T13:16:08.485Z"}, {"entity": "publication", "iuid": "2ca50a5a074448858fb0caf8335821a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ca50a5a074448858fb0caf8335821a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ca50a5a074448858fb0caf8335821a6"}}, "title": "De novo biosynthesis of bioactive isoflavonoids by engineered yeast cell factories.", "authors": [{"family": "Liu", "given": "Quanli", "initials": "Q"}, {"family": "Liu", "given": "Yi", "initials": "Y"}, {"family": "Li", "given": "Gang", "initials": "G"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Chen", "given": "Yun", "initials": "Y", "orcid": "0000-0002-2146-6008", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8a0c4c96b7e491496aa0991c7e9a460.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2021-10-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "6085"}, "abstract": "Isoflavonoids comprise a class of plant natural products with great nutraceutical, pharmaceutical and agricultural significance. Their low abundance in nature and structural complexity however hampers access to these phytochemicals through traditional crop-based manufacturing or chemical synthesis. Microbial bioproduction therefore represents an attractive alternative. Here, we engineer the metabolism of Saccharomyces cerevisiae to become a platform for efficient production of daidzein, a core chemical scaffold for isoflavonoid biosynthesis, and demonstrate its application towards producing bioactive glucosides from glucose, following the screening-reconstruction-application engineering framework. First, we rebuild daidzein biosynthesis in yeast and its production is then improved by 94-fold through screening biosynthetic enzymes, identifying rate-limiting steps, implementing dynamic control, engineering substrate trafficking and fine-tuning competing metabolic processes. The optimized strain produces up to 85.4 mg L-1 of daidzein and introducing plant glycosyltransferases in this strain results in production of bioactive puerarin (72.8 mg L-1) and daidzin (73.2 mg L-1). Our work provides a promising step towards developing synthetic yeast cell factories for de novo biosynthesis of value-added isoflavonoids and the multi-phased framework may be extended to engineer pathways of complex natural products in other microbial hosts.", "doi": "10.1038/s41467-021-26361-1", "pmid": "34667183", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-26361-1"}, {"db": "pmc", "key": "PMC8526750"}], "notes": [], "created": "2022-06-30T09:13:48.158Z", "modified": "2023-04-13T09:05:58.031Z"}, {"entity": "publication", "iuid": "06cb8c44cb724e169b03c31f68350a39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06cb8c44cb724e169b03c31f68350a39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06cb8c44cb724e169b03c31f68350a39"}}, "title": "Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.", "authors": [{"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Stenbeck", "given": "Linnea", "initials": "L", "orcid": "0000-0002-0210-7886", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4393e30947441519e7ab28fccb9bc3a.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Ehinger", "given": "Anna", "initials": "A", "orcid": "0000-0001-9225-7396", "researcher": {"href": "https://publications.scilifelab.se/researcher/f500d5e3ba094e208ea53b4c42e44ce8.json"}}, {"family": "Wu", "given": "Sunny Z", "initials": "SZ", "orcid": "0000-0002-6153-0449", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3b354bd9c024e0d9fae3b77b5f7ca3a.json"}}, {"family": "Al-Eryani", "given": "Ghamdan", "initials": "G", "orcid": "0000-0002-1137-1726", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d06a9f413f04f7490b1724c375537c0.json"}}, {"family": "Roden", "given": "Daniel", "initials": "D", "orcid": "0000-0003-2393-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ee5b95b08b243e49af7a837ab9f9d39.json"}}, {"family": "Swarbrick", "given": "Alex", "initials": "A", "orcid": "0000-0002-3051-5676", "researcher": {"href": "https://publications.scilifelab.se/researcher/25d712c54077427abf4a5ac7cbe2b5a6.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.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": "2021-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "6012", "issn-l": "2041-1723"}, "abstract": "In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases.", "doi": "10.1038/s41467-021-26271-2", "pmid": "34650042", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8516894"}, {"db": "pii", "key": "10.1038/s41467-021-26271-2"}], "notes": [], "created": "2021-12-06T13:49:12.030Z", "modified": "2024-01-16T13:48:38.238Z"}, {"entity": "publication", "iuid": "d0afbf6a0f22480dacd378fbb39437db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d0afbf6a0f22480dacd378fbb39437db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d0afbf6a0f22480dacd378fbb39437db"}}, "title": "Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors.", "authors": [{"family": "Bedoya-Reina", "given": "O C", "initials": "OC"}, {"family": "Li", "given": "W", "initials": "W"}, {"family": "Arceo", "given": "M", "initials": "M"}, {"family": "Plescher", "given": "M", "initials": "M"}, {"family": "Bullova", "given": "P", "initials": "P", "orcid": "0000-0002-5411-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c9fa1a447d749f09e98b2d7b39ce499.json"}}, {"family": "Pui", "given": "H", "initials": "H"}, {"family": "Kaucka", "given": "M", "initials": "M"}, {"family": "Kharchenko", "given": "P", "initials": "P", "orcid": "0000-0002-6036-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/a67002dec1264bf2865da0017405ee9b.json"}}, {"family": "Martinsson", "given": "T", "initials": "T", "orcid": "0000-0002-9403-3123", "researcher": {"href": "https://publications.scilifelab.se/researcher/90deb3f5dd5446e5853da797411dfd5d.json"}}, {"family": "Holmberg", "given": "J", "initials": "J"}, {"family": "Adameyko", "given": "I", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Deng", "given": "Q", "initials": "Q", "orcid": "0000-0001-5934-7816", "researcher": {"href": "https://publications.scilifelab.se/researcher/b74efaba0fab49acb7164a45beca5cd9.json"}}, {"family": "Larsson", "given": "C", "initials": "C"}, {"family": "Juhlin", "given": "C C", "initials": "CC", "orcid": "0000-0002-5945-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb660e24421749d4acaaf6e9a90042f8.json"}}, {"family": "Kogner", "given": "P", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications.scilifelab.se/researcher/e963274b921a4a2c8263f509334d4e22.json"}}, {"family": "Schlisio", "given": "S", "initials": "S", "orcid": "0000-0002-2605-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa8c1128e0d54cfe80758282ef94809b.json"}}], "type": "journal article", "published": "2021-09-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "5309"}, "abstract": "Childhood neuroblastoma has a remarkable variability in outcome. Age at diagnosis is one of the most important prognostic factors, with children less than 1 year old having favorable outcomes. Here we study single-cell and single-nuclei transcriptomes of neuroblastoma with different clinical risk groups and stages, including healthy adrenal gland. We compare tumor cell populations with embryonic mouse sympatho-adrenal derivatives, and post-natal human adrenal gland. We provide evidence that low and high-risk neuroblastoma have different cell identities, representing two disease entities. Low-risk neuroblastoma presents a transcriptome that resembles sympatho- and chromaffin cells, whereas malignant cells enriched in high-risk neuroblastoma resembles a subtype of TRKB+ cholinergic progenitor population identified in human post-natal gland. Analyses of these populations reveal different gene expression programs for worst and better survival in correlation with age at diagnosis. Our findings reveal two cellular identities and a composition of human neuroblastoma tumors reflecting clinical heterogeneity and outcome.", "doi": "10.1038/s41467-021-24870-7", "pmid": "34493726", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24870-7"}, {"db": "pmc", "key": "PMC8423786"}], "notes": [], "created": "2021-09-08T09:33:10.810Z", "modified": "2024-01-16T13:48:38.541Z"}, {"entity": "publication", "iuid": "9efcb16d38144c20934369e886656d99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9efcb16d38144c20934369e886656d99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9efcb16d38144c20934369e886656d99"}}, "title": "Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion.", "authors": [{"family": "\u0160kerlov\u00e1", "given": "Jana", "initials": "J", "orcid": "0000-0002-9579-4047", "researcher": {"href": "https://publications.scilifelab.se/researcher/cde5c1c6ccb94ca3be0b092771e67524.json"}}, {"family": "Berndtsson", "given": "Jens", "initials": "J", "orcid": "0000-0001-6627-8134", "researcher": {"href": "https://publications.scilifelab.se/researcher/7620a5c7c0f245a28771d57d7179abbd.json"}}, {"family": "Nolte", "given": "Hendrik", "initials": "H"}, {"family": "Ott", "given": "Martin", "initials": "M", "orcid": "0000-0001-6367-3091", "researcher": {"href": "https://publications.scilifelab.se/researcher/b27b582dbd2a47bcbb0fb3194277902a.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": "2021-09-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "5277", "issn-l": "2041-1723"}, "abstract": "The pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle by converting pyruvate into acetyl-coenzyme A. PDHc encompasses three enzymatically active subunits, namely pyruvate dehydrogenase, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Dihydrolipoyl transacetylase is a multidomain protein comprising a varying number of lipoyl domains, a peripheral subunit-binding domain, and a catalytic domain. It forms the structural core of the complex, provides binding sites for the other enzymes, and shuffles reaction intermediates between the active sites through covalently bound lipoyl domains. The molecular mechanism by which this shuttling occurs has remained elusive. Here, we report a cryo-EM reconstruction of the native E. coli dihydrolipoyl transacetylase core in a resting state. This structure provides molecular details of the assembly of the core and reveals how the lipoyl domains interact with the core at the active site.", "doi": "10.1038/s41467-021-25570-y", "pmid": "34489474", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-25570-y"}, {"db": "pmc", "key": "PMC8421416"}], "notes": [], "created": "2021-09-07T14:15:11.241Z", "modified": "2021-11-10T12:22:09.547Z"}, {"entity": "publication", "iuid": "d113d0c37b074a75b7a8dfb5c565524f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d113d0c37b074a75b7a8dfb5c565524f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d113d0c37b074a75b7a8dfb5c565524f"}}, "title": "Amnion signals are essential for mesoderm formation in primates.", "authors": [{"family": "Yang", "given": "Ran", "initials": "R"}, {"family": "Goedel", "given": "Alexander", "initials": "A", "orcid": "0000-0002-5980-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/866e8580c3d8462da0f3ee3b8909ea6f.json"}}, {"family": "Kang", "given": "Yu", "initials": "Y"}, {"family": "Si", "given": "Chenyang", "initials": "C"}, {"family": "Chu", "given": "Chu", "initials": "C"}, {"family": "Zheng", "given": "Yi", "initials": "Y"}, {"family": "Chen", "given": "Zhenzhen", "initials": "Z"}, {"family": "Gruber", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-7356-905X", "researcher": {"href": "https://publications.scilifelab.se/researcher/623bc96d071d410c8199b178a1e31808.json"}}, {"family": "Xiao", "given": "Yao", "initials": "Y"}, {"family": "Zhou", "given": "Chikai", "initials": "C", "orcid": "0000-0001-9653-3466", "researcher": {"href": "https://publications.scilifelab.se/researcher/05559fcfc7724eb1bf06305a907b58d4.json"}}, {"family": "Witman", "given": "Nevin", "initials": "N"}, {"family": "Eroglu", "given": "Elif", "initials": "E"}, {"family": "Leung", "given": "Chuen-Yan", "initials": "CY"}, {"family": "Chen", "given": "Yongchang", "initials": "Y"}, {"family": "Fu", "given": "Jianping", "initials": "J", "orcid": "0000-0001-9629-6739", "researcher": {"href": "https://publications.scilifelab.se/researcher/127bba88c5534146ae9ba1b10929bb4b.json"}}, {"family": "Ji", "given": "Weizhi", "initials": "W", "orcid": "0000-0003-2550-4224", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e1228641df34f3fa2f8b961d414233b.json"}}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}, {"family": "Niu", "given": "Yuyu", "initials": "Y"}, {"family": "Chien", "given": "Kenneth R", "initials": "KR", "orcid": "0000-0002-2759-8378", "researcher": {"href": "https://publications.scilifelab.se/researcher/971382878b474966bbe58acaa1585999.json"}}], "type": "journal article", "published": "2021-08-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "5126", "issn-l": "2041-1723"}, "abstract": "Embryonic development is largely conserved among mammals. However, certain genes show divergent functions. By generating a transcriptional atlas containing >30,000 cells from post-implantation non-human primate embryos, we uncover that ISL1, a gene with a well-established role in cardiogenesis, controls a gene regulatory network in primate amnion. CRISPR/Cas9-targeting of ISL1 results in non-human primate embryos which do not yield viable offspring, demonstrating that ISL1 is critically required in primate embryogenesis. On a cellular level, mutant ISL1 embryos display a failure in mesoderm formation due to reduced BMP4 signaling from the amnion. Via loss of function and rescue studies in human embryonic stem cells we confirm a similar role of ISL1 in human in vitro derived amnion. This study highlights the importance of the amnion as a signaling center during primate mesoderm formation and demonstrates the potential of in vitro primate model systems to dissect the genetics of early human embryonic development.", "doi": "10.1038/s41467-021-25186-2", "pmid": "34446705", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8390679"}, {"db": "pii", "key": "10.1038/s41467-021-25186-2"}], "notes": [], "created": "2021-08-30T07:44:40.804Z", "modified": "2024-01-16T13:48:38.655Z"}, {"entity": "publication", "iuid": "6c9beebec3bf4e008aa3f11261cfa6e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c9beebec3bf4e008aa3f11261cfa6e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c9beebec3bf4e008aa3f11261cfa6e6"}}, "title": "A simple pressure-assisted method for MicroED specimen preparation.", "authors": [{"family": "Zhao", "given": "Jingjing", "initials": "J", "orcid": "0000-0001-8444-6883", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fbe7f2ca29941ce98c38ca6bf78c534.json"}}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Lebrette", "given": "Hugo", "initials": "H", "orcid": "0000-0002-8081-181X", "researcher": {"href": "https://publications.scilifelab.se/researcher/17ace145c59b4e8695a5c9b95fe81b92.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Taberman", "given": "Helena", "initials": "H"}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M", "orcid": "0000-0001-5574-9383", "researcher": {"href": "https://publications.scilifelab.se/researcher/d968fcccace74b689185bb9fa2d33bf8.json"}}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}], "type": "journal article", "published": "2021-08-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "5036", "issn-l": "2041-1723"}, "abstract": "Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate carbon hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal concentrations. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.", "doi": "10.1038/s41467-021-25335-7", "pmid": "34413316", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-25335-7"}, {"db": "pmc", "key": "PMC8377027"}], "notes": [], "created": "2021-12-14T12:47:04.167Z", "modified": "2023-12-04T10:18:11.258Z"}, {"entity": "publication", "iuid": "d3750af0071a4ba1ad310809381e3fe7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3750af0071a4ba1ad310809381e3fe7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3750af0071a4ba1ad310809381e3fe7"}}, "title": "Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.", "authors": [{"family": "Mehrshad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M", "orcid": "0000-0003-3588-6676", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c5d5c765980461997541605f7512623.json"}}, {"family": "Sundh", "given": "John", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Bell", "given": "Emma", "initials": "E", "orcid": "0000-0002-2064-6496", "researcher": {"href": "https://publications.scilifelab.se/researcher/d81b7088d61947dd823b9a6faff49f31.json"}}, {"family": "Simone", "given": "Domenico", "initials": "D", "orcid": "0000-0003-2858-9809", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cd65b63aec74d7b9375568306d26dce.json"}}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Bernier-Latmani", "given": "Rizlan", "initials": "R", "orcid": "0000-0001-6547-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fba86cb9b29a426fa98fb70ad2c634e5.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2021-07-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "4253", "issn-l": "2041-1723"}, "abstract": "While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.", "doi": "10.1038/s41467-021-24549-z", "pmid": "34253732", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24549-z"}, {"db": "pmc", "key": "PMC8275790"}], "notes": [], "created": "2021-08-09T12:22:57.037Z", "modified": "2024-01-16T13:48:39.118Z"}, {"entity": "publication", "iuid": "0f41cddd0a724aad8eebbd2eee4e75e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f41cddd0a724aad8eebbd2eee4e75e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f41cddd0a724aad8eebbd2eee4e75e2"}}, "title": "A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids.", "authors": [{"family": "Jhun", "given": "Min-A", "initials": "M"}, {"family": "Mendelson", "given": "Michael", "initials": "M", "orcid": "0000-0001-7590-3958", "researcher": {"href": "https://publications.scilifelab.se/researcher/d30230bbef094ca6831089c8e4afc846.json"}}, {"family": "Wilson", "given": "Rory", "initials": "R", "orcid": "0000-0001-6135-3764", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c107a0ec79f4672b6ec73ff4273c338.json"}}, {"family": "Gondalia", "given": "Rahul", "initials": "R"}, {"family": "Joehanes", "given": "Roby", "initials": "R", "orcid": "0000-0001-5549-9054", "researcher": {"href": "https://publications.scilifelab.se/researcher/28dc0f841c0148c59291a83c4ffe1a78.json"}}, {"family": "Salfati", "given": "Elias", "initials": "E"}, {"family": "Zhao", "given": "Xiaoping", "initials": "X"}, {"family": "Braun", "given": "Kim Valeska Emilie", "initials": "KVE", "orcid": "0000-0001-8738-4139", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0966cb600ed4c749be09388bb798d8d.json"}}, {"family": "Do", "given": "Anh Nguyet", "initials": "AN"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0001-5413-204X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b9eaa6a5dfc4ecf8bf82ece793cd457.json"}}, {"family": "Zhang", "given": "Tao", "initials": "T"}, {"family": "Carnero-Montoro", "given": "Elena", "initials": "E", "orcid": "0000-0002-1947-9627", "researcher": {"href": "https://publications.scilifelab.se/researcher/87403846db104d3c9e4283dd00065da3.json"}}, {"family": "Shen", "given": "Jincheng", "initials": "J"}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0001-8509-148X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e137fc0192e4fa295a88589d57e3498.json"}}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "O'Connell", "given": "Jeff R", "initials": "JR"}, {"family": "Yao", "given": "Chen", "initials": "C", "orcid": "0000-0002-3944-7788", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d1a3603e21e4d52a4648eef4b86d3f8.json"}}, {"family": "Xia", "given": "Rui", "initials": "R"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Grove", "given": "Megan", "initials": "M"}, {"family": "Guan", "given": "Weihua", "initials": "W"}, {"family": "Liliane", "given": "Pfeiffer", "initials": "P"}, {"family": "Singmann", "given": "Paula", "initials": "P", "orcid": "0000-0003-2109-9970", "researcher": {"href": "https://publications.scilifelab.se/researcher/db716a10b55f4e57af04c01c5e8007d7.json"}}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M", "orcid": "0000-0003-3793-5910", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d21299bb41343f88142255e64a9da57.json"}}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Zhao", "given": "Wei", "initials": "W", "orcid": "0000-0001-7388-0692", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0c2246e69494086bab7ead8e6f1f717.json"}}, {"family": "Ware", "given": "Erin B", "initials": "EB", "orcid": "0000-0003-4731-8158", "researcher": {"href": "https://publications.scilifelab.se/researcher/675e10a2b27a4f4b9de0ee766c4907dc.json"}}, {"family": "Smith", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0002-3575-5468", "researcher": {"href": "https://publications.scilifelab.se/researcher/311c7381092b4143bcd2e4ef93250526.json"}}, {"family": "Dhana", "given": "Klodian", "initials": "K"}, {"family": "van Meurs", "given": "Joyce", "initials": "J"}, {"family": "Uitterlinden", "given": "Andre", "initials": "A", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "Ikram", "given": "Mohammad Arfan", "initials": "MA", "orcid": "0000-0003-0372-8585", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec81571f4a94af682b4e23526f87385.json"}}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M", "orcid": "0000-0002-9476-7143", "researcher": {"href": "https://publications.scilifelab.se/researcher/52ef9606de1144c994e0e854c5a85569.json"}}, {"family": "Zhi", "given": "Deugi", "initials": "D"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5894-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a0552f8a6514baa9bdb6809148aaddc.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Li", "given": "Shengxu", "initials": "S"}, {"family": "Sun", "given": "Dianjianyi", "initials": "D"}, {"family": "Spector", "given": "Tim D", "initials": "TD", "orcid": "0000-0002-9795-0365", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3b149961364ccbb448a8cc3cdd6687.json"}}, {"family": "Chen", "given": "Yii-der Ida", "initials": "YI"}, {"family": "Damcott", "given": "Coleen", "initials": "C", "orcid": "0000-0001-6233-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/234acf5657cd4ede95641ee045cb23cd.json"}}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Absher", "given": "Devin M", "initials": "DM"}, {"family": "Horvath", "given": "Steve", "initials": "S", "orcid": "0000-0002-4110-3589", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9fd917cfb8e43329e4dadb4e14e32ef.json"}}, {"family": "Tsao", "given": "Philip S", "initials": "PS", "orcid": "0000-0001-7274-9318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1520706d352e454688b0a737b5d590ef.json"}}, {"family": "Kardia", "given": "Sharon", "initials": "S"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Bell", "given": "Jordana T", "initials": "JT", "orcid": "0000-0002-3858-5986", "researcher": {"href": "https://publications.scilifelab.se/researcher/078c46640d7946ed9ed4e08e9f9a71fa.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Chen", "given": "Wei", "initials": "W", "orcid": "0000-0003-1566-7943", "researcher": {"href": "https://publications.scilifelab.se/researcher/905609ccc3704af9afccd0b9ab0553bf.json"}}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Arnett", "given": "Donna K", "initials": "DK", "orcid": "0000-0003-2219-657X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d283344e5c4e7daf4ff1a3709ba492.json"}}, {"family": "Waldenberger", "given": "Melanie", "initials": "M", "orcid": "0000-0003-0583-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8de22214f2448c6a7f86fc1040d0104.json"}}, {"family": "Hou", "given": "Lifang", "initials": "L"}, {"family": "Whitsel", "given": "Eric A", "initials": "EA"}, {"family": "Baccarelli", "given": "Andrea", "initials": "A"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Fornage", "given": "Myriam", "initials": "M", "orcid": "0000-0003-0677-8158", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5de431c325e40f4adfe13c06cf1e0b9.json"}}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL", "orcid": "0000-0003-2349-0009", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e155ca3dd01486580be888d1ded405c.json"}}], "type": "journal article", "published": "2021-06-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "3987"}, "abstract": "Here we examine the association between DNA methylation in circulating leukocytes and blood lipids in a multi-ethnic sample of 16,265 subjects. We identify 148, 35, and 4 novel associations among Europeans, African Americans, and Hispanics, respectively, and an additional 186 novel associations through a trans-ethnic meta-analysis. We observe a high concordance in the direction of effects across racial/ethnic groups, a high correlation of effect sizes between high-density lipoprotein and triglycerides, a modest overlap of associations with epigenome-wide association studies of other cardio-metabolic traits, and a largely non-overlap with lipid loci identified to date through genome-wide association studies. Thirty CpGs reached significance in at least 2 racial/ethnic groups including 7 that showed association with the expression of an annotated gene. CpGs annotated to CPT1A showed evidence of being influenced by triglycerides levels. DNA methylation levels of circulating leukocytes show robust and consistent association with blood lipid levels across multiple racial/ethnic groups.", "doi": "10.1038/s41467-021-23899-y", "pmid": "34183656", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23899-y"}, {"db": "pmc", "key": "PMC8238961"}, {"db": "Dryad", "key": "10.5061/dryad.qfttdz0d8"}], "notes": [], "created": "2021-08-19T13:41:35.464Z", "modified": "2021-12-07T13:25:44.149Z"}, {"entity": "publication", "iuid": "bf0b169843cf4d09860c2c0ff145774a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf0b169843cf4d09860c2c0ff145774a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf0b169843cf4d09860c2c0ff145774a"}}, "title": "Structure and transport mechanism of P5B-ATPases.", "authors": [{"family": "Li", "given": "Ping", "initials": "P", "orcid": "0000-0002-7364-3301", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cc17e1d61cb498b88038a9f5dfa6aff.json"}}, {"family": "Wang", "given": "Kaituo", "initials": "K", "orcid": "0000-0002-5922-7109", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d8ad9a00c1c47fdbf1cadc149914823.json"}}, {"family": "Salustros", "given": "Nina", "initials": "N"}, {"family": "Gr\u00f8nberg", "given": "Christina", "initials": "C"}, {"family": "Gourdon", "given": "Pontus", "initials": "P", "orcid": "0000-0002-8631-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dc6cdbbcab048fab7a65df6cb796aab.json"}}], "type": "journal article", "published": "2021-06-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "3973"}, "abstract": "In human cells, P5B-ATPases execute the active export of physiologically important polyamines such as spermine from lysosomes to the cytosol, a function linked to a palette of disorders. Yet, the overall shape of P5B-ATPases and the mechanisms of polyamine recognition, uptake and transport remain elusive. Here we describe a series of cryo-electron microscopy structures of a yeast homolog of human ATP13A2-5, Ypk9, determined at resolutions reaching 3.4 \u00c5, and depicting three separate transport cycle intermediates, including spermine-bound conformations. Surprisingly, in the absence of cargo, Ypk9 rests in a phosphorylated conformation auto-inhibited by the N-terminus. Spermine uptake is accomplished through an electronegative cleft lined by transmembrane segments 2, 4 and 6. Despite the dramatically different nature of the transported cargo, these findings pinpoint shared principles of transport and regulation among the evolutionary related P4-, P5A- and P5B-ATPases. The data also provide a framework for analysis of associated maladies, such as Parkinson's disease.", "doi": "10.1038/s41467-021-24148-y", "pmid": "34172751", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24148-y"}, {"db": "pmc", "key": "PMC8233418"}], "notes": [], "created": "2021-07-15T15:18:02.436Z", "modified": "2024-11-07T08:45:18.745Z"}, {"entity": "publication", "iuid": "e18b31942e41465999c590cac3365408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408"}}, "title": "COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.", "authors": [{"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Milia", "given": "Maria Grazia", "initials": "MG"}, {"family": "Brossa", "given": "Silvia", "initials": "S"}, {"family": "Huong Nguyen", "given": "Thi Thu", "initials": "TT", "orcid": "0000-0002-9089-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/57451410c8ac4547a4b09111a020e396.json"}}, {"family": "Cerutti", "given": "Francesco", "initials": "F", "orcid": "0000-0003-0480-8296", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a243dc846624a8a8292dde5416fa402.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E"}, {"family": "Sapino", "given": "Anna", "initials": "A"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Sottile", "given": "Antonino", "initials": "A"}, {"family": "Ghisetti", "given": "Valeria", "initials": "V", "orcid": "0000-0002-4698-598X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75237266d0b1496f909cb0c53ff87920.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2021-06-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3903", "issn-l": "2041-1723"}, "abstract": "While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.", "doi": "10.1038/s41467-021-24078-9", "pmid": "34162869", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24078-9"}, {"db": "pmc", "key": "PMC8222401"}], "notes": [], "created": "2021-10-01T09:02:30.491Z", "modified": "2024-01-16T13:48:39.472Z"}, {"entity": "publication", "iuid": "48993691f2c64543b650f3b600450b73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48993691f2c64543b650f3b600450b73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48993691f2c64543b650f3b600450b73"}}, "title": "Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2.", "authors": [{"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Hanke", "given": "Leo", "initials": "L", "orcid": "0000-0001-5514-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece050a286f946f6807170cffc9320e7.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Christian", "given": "Murray", "initials": "M"}, {"family": "Meineke", "given": "Birthe", "initials": "B"}, {"family": "Els\u00e4sser", "given": "Simon", "initials": "S", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Andr\u00e9ll", "given": "Juni", "initials": "J"}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-1345-6491", "researcher": {"href": "https://publications.scilifelab.se/researcher/130fb6ef6b774613a767e98f9f9b2eb4.json"}}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Dillner", "given": "Joakim", "initials": "J", "orcid": "0000-0001-8588-6506", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b5c258635ad412f9e79994dcee4e323.json"}}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Thomas", "given": "Cecilia E", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1156f987764218af202efbd76c31fd.json"}}, {"family": "McInerney", "given": "Gerald", "initials": "G", "orcid": "0000-0003-2257-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac2f68095fe4426b97ec070865e5091.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2021-06-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "3695"}, "abstract": "Serological testing is essential to curb the consequences of the COVID-19 pandemic. However, most assays are still limited to single analytes and samples collected within healthcare. Thus, we establish a multianalyte and multiplexed approach to reliably profile IgG and IgM levels against several versions of SARS-CoV-2 proteins (S, RBD, N) in home-sampled dried blood spots (DBS). We analyse DBS collected during spring of 2020 from 878 random and undiagnosed individuals from the population in Stockholm, Sweden, and use classification approaches to estimate an accumulated seroprevalence of 12.5% (95% CI: 10.3%-14.7%). This includes 5.4% of the samples being IgG+IgM+ against several SARS-CoV-2 proteins, as well as 2.1% being IgG-IgM+ and 5.0% being IgG+IgM- for the virus' S protein. Subjects classified as IgG+ for several SARS-CoV-2 proteins report influenza-like symptoms more frequently than those being IgG+ for only the S protein (OR = 6.1; p < 0.001). Among all seropositive cases, 30% are asymptomatic. Our strategy enables an accurate individual-level and multiplexed assessment of antibodies in home-sampled blood, assisting our understanding about the undiagnosed seroprevalence and diversity of the immune response against the coronavirus.", "doi": "10.1038/s41467-021-23893-4", "pmid": "34140485", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23893-4"}, {"db": "pmc", "key": "PMC8211676"}], "notes": [], "created": "2021-10-05T16:26:34.397Z", "modified": "2021-12-06T07:43:55.459Z"}, {"entity": "publication", "iuid": "9db452ca3ba2471fadd10ad1333ec980", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9db452ca3ba2471fadd10ad1333ec980.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9db452ca3ba2471fadd10ad1333ec980"}}, "title": "Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens.", "authors": [{"family": "Crowe-McAuliffe", "given": "Caillan", "initials": "C"}, {"family": "Murina", "given": "Victoriia", "initials": "V", "orcid": "0000-0003-1523-1816", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb97467a29cb494baa858f2a9c5287c8.json"}}, {"family": "Turnbull", "given": "Kathryn Jane", "initials": "KJ"}, {"family": "Kasari", "given": "Marje", "initials": "M"}, {"family": "Mohamad", "given": "Merianne", "initials": "M"}, {"family": "Polte", "given": "Christine", "initials": "C"}, {"family": "Takada", "given": "Hiraku", "initials": "H", "orcid": "0000-0003-2034-5666", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d9dfa63a3004266bc782f77263dcc9e.json"}}, {"family": "Vaitkevicius", "given": "Karolis", "initials": "K"}, {"family": "Johansson", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Ignatova", "given": "Zoya", "initials": "Z"}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications.scilifelab.se/researcher/d810a2d001a74ccda5b376198896cbf6.json"}}, {"family": "O'Neill", "given": "Alex J", "initials": "AJ"}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications.scilifelab.se/researcher/17ea83b1d20f43f9872edbf89b275e5d.json"}}, {"family": "Wilson", "given": "Daniel N", "initials": "DN", "orcid": "0000-0003-3816-3828", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd50ba35f7c74d7e9d4f42fbc49739f2.json"}}], "type": "journal article", "published": "2021-06-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3577", "issn-l": "2041-1723"}, "abstract": "Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaALC and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms.", "doi": "10.1038/s41467-021-23753-1", "pmid": "34117249", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23753-1"}, {"db": "pmc", "key": "PMC8196190"}], "notes": [], "created": "2021-12-14T12:35:33.249Z", "modified": "2021-12-14T12:35:33.401Z"}, {"entity": "publication", "iuid": "ad3b96b9f1e04610964e663761b2ac63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad3b96b9f1e04610964e663761b2ac63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad3b96b9f1e04610964e663761b2ac63"}}, "title": "Reinforcing one-carbon metabolism via folic acid/Folr1 promotes \u03b2-cell differentiation.", "authors": [{"family": "Karampelias", "given": "Christos", "initials": "C", "orcid": "0000-0002-9990-5760", "researcher": {"href": "https://publications.scilifelab.se/researcher/509894ee3f0e41eeaf57eb2febc18c70.json"}}, {"family": "Rezanejad", "given": "Habib", "initials": "H", "orcid": "0000-0003-3067-6602", "researcher": {"href": "https://publications.scilifelab.se/researcher/8759a9d7c6654216b6336f9fb3d0fb92.json"}}, {"family": "Rosko", "given": "Mandy", "initials": "M"}, {"family": "Duan", "given": "Likun", "initials": "L", "orcid": "0000-0003-3293-6682", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ab937d463cc4fc29a5d31eb9e75ac54.json"}}, {"family": "Lu", "given": "Jing", "initials": "J"}, {"family": "Pazzagli", "given": "Laura", "initials": "L", "orcid": "0000-0002-1908-6073", "researcher": {"href": "https://publications.scilifelab.se/researcher/06de06fae02a4de28dbda5456129fc18.json"}}, {"family": "Bertolino", "given": "Philippe", "initials": "P", "orcid": "0000-0001-8064-8269", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fddf1c144e04b80893cdf2c00a7e85b.json"}}, {"family": "Cesta", "given": "Carolyn E", "initials": "CE", "orcid": "0000-0001-5759-9366", "researcher": {"href": "https://publications.scilifelab.se/researcher/804a85a43f0e42e9ba01f7b77a0e02fb.json"}}, {"family": "Liu", "given": "Xiaojing", "initials": "X", "orcid": "0000-0002-4231-6017", "researcher": {"href": "https://publications.scilifelab.se/researcher/550389a9d42447f6a93b0eb67c9ab119.json"}}, {"family": "Korbutt", "given": "Gregory S", "initials": "GS"}, {"family": "Andersson", "given": "Olov", "initials": "O", "orcid": "0000-0001-6715-781X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f796ff515c95491e9cd47018e02220c0.json"}}], "type": "journal article", "published": "2021-06-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3362", "issn-l": "2041-1723"}, "abstract": "Diabetes can be caused by an insufficiency in \u03b2-cell mass. Here, we performed a genetic screen in a zebrafish model of \u03b2-cell loss to identify pathways promoting \u03b2-cell regeneration. We found that both folate receptor 1 (folr1) overexpression and treatment with folinic acid, stimulated \u03b2-cell differentiation in zebrafish. Treatment with folinic acid also stimulated \u03b2-cell differentiation in cultures of neonatal pig islets, showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets, the increased \u03b2-cell differentiation originated from ductal cells. Mechanistically, comparative metabolomic analysis of zebrafish with/without \u03b2-cell ablation and with/without folinic acid treatment indicated \u03b2-cell regeneration could be attributed to changes in the pyrimidine, carnitine, and serine pathways. Overall, our results suggest evolutionarily conserved and previously unknown roles for folic acid and one-carbon metabolism in the generation of \u03b2-cells.", "doi": "10.1038/s41467-021-23673-0", "pmid": "34099692", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23673-0"}, {"db": "pmc", "key": "PMC8184927"}], "notes": [], "created": "2021-10-01T09:01:03.656Z", "modified": "2024-01-16T13:48:39.535Z"}, {"entity": "publication", "iuid": "b70be864396f40b68d30939cc4e01962", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b70be864396f40b68d30939cc4e01962.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b70be864396f40b68d30939cc4e01962"}}, "title": "Common variants in Alzheimer's disease and risk stratification by polygenic risk scores.", "authors": [{"family": "de Rojas", "given": "Itziar", "initials": "I", "orcid": "0000-0002-2148-381X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4452ee79e504a9fb358068cfa6abbde.json"}}, {"family": "Moreno-Grau", "given": "Sonia", "initials": "S"}, {"family": "Tesi", "given": "Niccolo", "initials": "N"}, {"family": "Grenier-Boley", "given": "Benjamin", "initials": "B"}, {"family": "Andrade", "given": "Victor", "initials": "V"}, {"family": "Jansen", "given": "Iris E", "initials": "IE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Stringa", "given": "Najada", "initials": "N", "orcid": "0000-0001-6350-452X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d286e52366c942c4a9f0eec9e07a7596.json"}}, {"family": "Zettergren", "given": "Anna", "initials": "A", "orcid": "0000-0002-7182-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/238188e1165e4de88918f024e3b1289e.json"}}, {"family": "Hern\u00e1ndez", "given": "Isabel", "initials": "I"}, {"family": "Montrreal", "given": "Laura", "initials": "L"}, {"family": "Ant\u00fanez", "given": "Carmen", "initials": "C"}, {"family": "Antonell", "given": "Anna", "initials": "A"}, {"family": "Tankard", "given": "Rick M", "initials": "RM", "orcid": "0000-0002-8847-9401", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c109642be2b44aabfd7d210a47f6c27.json"}}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Sims", "given": "Rebecca", "initials": "R", "orcid": "0000-0002-3885-1199", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e10b941ee2a4aa19711c68f582f00a5.json"}}, {"family": "Bellenguez", "given": "C\u00e9line", "initials": "C", "orcid": "0000-0002-1240-7874", "researcher": {"href": 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{"family": "Engelborghs", "given": "Sebastiaan", "initials": "S"}, {"family": "Helisalmi", "given": "Seppo", "initials": "S"}, {"family": "Botne Sando", "given": "Sigrid", "initials": "S"}, {"family": "Kern", "given": "Silke", "initials": "S"}, {"family": "Archetti", "given": "Silvana", "initials": "S"}, {"family": "Boschi", "given": "Silvia", "initials": "S"}, {"family": "Fostinelli", "given": "Silvia", "initials": "S"}, {"family": "Gil", "given": "Silvia", "initials": "S"}, {"family": "Mendoza", "given": "Silvia", "initials": "S"}, {"family": "Mead", "given": "Simon", "initials": "S"}, {"family": "Ciccone", "given": "Simona", "initials": "S"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S", "orcid": "0000-0002-8140-8061", "researcher": {"href": "https://publications.scilifelab.se/researcher/906538321c8e4f38b6bb4a7b0bc18fa3.json"}}, {"family": "Heilmann-Heimbach", "given": "Stefanie", "initials": "S"}, {"family": "Riedel-Heller", "given": "Steffi", "initials": "S"}, {"family": "Kuulasmaa", "given": "Teemu", "initials": "T"}, {"family": "Del Ser", "given": "Teodoro", "initials": "T"}, {"family": "Lebouvier", "given": "Thibaud", "initials": "T"}, {"family": "Polak", "given": "Thomas", "initials": "T"}, {"family": "Ngandu", "given": "Tiia", "initials": "T"}, {"family": "Grimmer", "given": "Timo", "initials": "T"}, {"family": "Bessi", "given": "Valentina", "initials": "V", "orcid": "0000-0002-6176-3584", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd0d447f40d244b7a0900c8e13403ddc.json"}}, {"family": "Escott-Price", "given": "Valentina", "initials": "V", "orcid": "0000-0003-1784-5483", "researcher": {"href": "https://publications.scilifelab.se/researcher/22774376fbbe402f899fe94a87e90075.json"}}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V", "orcid": "0000-0003-3423-2021", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c95879213664e00b66aeee2e8ece975.json"}}, {"family": "Deramecourt", "given": "Vincent", "initials": "V"}, {"family": "Maier", "given": "Wolfgang", "initials": "W"}, {"family": "Jian", "given": "Xueqiu", "initials": "X", "orcid": "0000-0002-0313-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cecd3acd6c944feb3c86a18a3839143.json"}}, {"family": "Pijnenburg", "given": "Yolande A L", "initials": "YAL"}, {"family": "EADB contributors", "given": "", "initials": ""}, {"family": "GR@ACE study group", "given": "", "initials": ""}, {"family": "DEGESCO consortium", "given": "", "initials": ""}, {"family": "IGAP (ADGC, CHARGE, EADI, GERAD)", "given": "", "initials": ""}, {"family": "PGC-ALZ consortia", "given": "", "initials": ""}, {"family": "Kehoe", "given": "Patrick Gavin", "initials": "PG", "orcid": "0000-0002-7542-1139", "researcher": {"href": "https://publications.scilifelab.se/researcher/282347b455b74f54aba6e1f1ee20b3b6.json"}}, {"family": "Garcia-Ribas", "given": "Guillermo", "initials": "G"}, {"family": "S\u00e1nchez-Juan", "given": "Pascual", "initials": "P", "orcid": "0000-0002-6081-8037", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7b9cea5b3c845c890c41d8664b6acef.json"}}, {"family": "Pastor", "given": "Pau", "initials": "P", "orcid": "0000-0002-7493-8777", "researcher": {"href": "https://publications.scilifelab.se/researcher/8147a32883a84ca1ba13164506968a93.json"}}, {"family": "P\u00e9rez-Tur", "given": "Jordi", "initials": "J", "orcid": "0000-0002-9111-1712", "researcher": {"href": "https://publications.scilifelab.se/researcher/1da995c21885400787fbe1275bcba156.json"}}, {"family": "Pi\u00f1ol-Ripoll", "given": "Gerard", "initials": "G"}, {"family": "Lopez de Munain", "given": "Adolfo", "initials": "A", "orcid": "0000-0002-9509-4032", "researcher": {"href": "https://publications.scilifelab.se/researcher/e390c82cf4cb4075a20c2f2858912ec6.json"}}, {"family": "Garc\u00eda-Alberca", "given": "Jose Mar\u00eda", "initials": "JM", "orcid": "0000-0003-2951-6644", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee94f765be9142b1a405878dfc8d5fb0.json"}}, {"family": "Bullido", "given": "Mar\u00eda J", "initials": "MJ", "orcid": "0000-0002-6477-1117", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b16229b634f4ed38b8825c3bdf30a4b.json"}}, {"family": "\u00c1lvarez", "given": "Victoria", "initials": "V"}, {"family": "Lle\u00f3", "given": "Alberto", "initials": "A", "orcid": "0000-0002-2568-5478", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f93b0e1f2b0458ea41339b0935e892b.json"}}, {"family": "Real", "given": "Luis M", "initials": "LM", "orcid": "0000-0003-4932-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/7566022edb8d47309631222dcf07bd01.json"}}, {"family": "Mir", "given": "Pablo", "initials": "P"}, {"family": "Medina", "given": "Miguel", "initials": "M", "orcid": "0000-0002-7016-5340", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8bdf4999e6c495fa1e101fdf479701a.json"}}, {"family": "Scheltens", "given": "Philip", "initials": "P"}, {"family": "Holstege", "given": "Henne", "initials": "H", "orcid": "0000-0002-7688-3087", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbb3fd35354e428eb2596e9806db5b9e.json"}}, {"family": "Marqui\u00e9", "given": "Marta", "initials": "M"}, {"family": "S\u00e1ez", "given": "Mar\u00eda Eugenia", "initials": "ME", "orcid": "0000-0001-9299-2534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2d2767678914111968cfecaff39ed01.json"}}, {"family": "Carracedo", "given": "\u00c1ngel", "initials": "\u00c1"}, {"family": "Amouyel", "given": "Philippe", "initials": "P", "orcid": "0000-0001-9088-234X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d82379a59334fcb8cdbc74a04c56765.json"}}, {"family": "Schellenberg", "given": "Gerard D", "initials": "GD"}, {"family": "Williams", "given": "Julie", "initials": "J", "orcid": "0000-0002-4069-0259", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f566fcdd8bd453eb1f3a6953e29451c.json"}}, {"family": "Seshadri", "given": "Sudha", "initials": "S", "orcid": "0000-0001-6135-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/429e370668ec47ce9945bc5262dccbb3.json"}}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM", "orcid": "0000-0002-2374-9204", "researcher": {"href": "https://publications.scilifelab.se/researcher/354ccf94e95f40da96e61c89a0a60adb.json"}}, {"family": "Mather", "given": "Karen A", "initials": "KA", "orcid": "0000-0003-4143-8941", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec0c7f15235d4be4848b56025d5ff4f0.json"}}, {"family": "S\u00e1nchez-Valle", "given": "Raquel", "initials": "R"}, {"family": "Serrano-R\u00edos", "given": "Manuel", "initials": "M"}, {"family": "Orellana", "given": "Adelina", "initials": "A"}, {"family": "T\u00e1rraga", "given": "Llu\u00eds", "initials": "L"}, {"family": "Blennow", "given": "Kaj", "initials": "K", "orcid": "0000-0002-1890-4193", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e646be026ce42ecbfd4d62eca3f9bce.json"}}, {"family": "Huisman", "given": "Martijn", "initials": "M"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA", "orcid": "0000-0002-4461-3568", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f384e8e2fd4a7383c7b26e88a828b2.json"}}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}, {"family": "Clarim\u00f3n", "given": "Jordi", "initials": "J"}, {"family": "Boada", "given": "Merc\u00e8", "initials": "M", "orcid": "0000-0003-2617-3009", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8d00c33569e41b481cf5cdc99cd96e9.json"}}, {"family": "van der Flier", "given": "Wiesje M", "initials": "WM", "orcid": "0000-0001-8766-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b32776a9e524f299765506b6dbe9768.json"}}, {"family": "Ramirez", "given": "Alfredo", "initials": "A", "orcid": "0000-0003-4991-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8995a57e82f4f479ab8251175aeb8d6.json"}}, {"family": "Lambert", "given": "Jean-Charles", "initials": "JC", "orcid": "0000-0003-0829-7817", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0ec452344144906b7e8be95eb8c62d6.json"}}, {"family": "van der Lee", "given": "Sven J", "initials": "SJ", "orcid": "0000-0003-1606-8643", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a34a1b7b98b4360b48dafe3f0d5dcb2.json"}}, {"family": "Ruiz", "given": "Agust\u00edn", "initials": "A", "orcid": "0000-0003-2633-2495", "researcher": {"href": "https://publications.scilifelab.se/researcher/33a263bd6bd24ca897c988d4fcbcaca1.json"}}], "type": "journal article", "published": "2021-06-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "3417"}, "abstract": "Genetic discoveries of Alzheimer's disease are the drivers of our understanding, and together with polygenetic risk stratification can contribute towards planning of feasible and efficient preventive and curative clinical trials. We first perform a large genetic association study by merging all available case-control datasets and by-proxy study results (discovery n = 409,435 and validation size n = 58,190). Here, we add six variants associated with Alzheimer's disease risk (near APP, CHRNE, PRKD3/NDUFAF7, PLCG2 and two exonic variants in the SHARPIN gene). Assessment of the polygenic risk score and stratifying by APOE reveal a 4 to 5.5 years difference in median age at onset of Alzheimer's disease patients in APOE \u025b4 carriers. Because of this study, the underlying mechanisms of APP can be studied to refine the amyloid cascade and the polygenic risk score provides a tool to select individuals at high risk of Alzheimer's disease.", "doi": "10.1038/s41467-021-22491-8", "pmid": "34099642", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8184987"}, {"db": "pii", "key": "10.1038/s41467-021-22491-8"}], "notes": [], "created": "2021-08-19T13:41:32.762Z", "modified": "2023-06-20T15:56:47.699Z"}, {"entity": "publication", "iuid": "4d45ed3127e14888bfb30d089ff84763", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d45ed3127e14888bfb30d089ff84763.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d45ed3127e14888bfb30d089ff84763"}}, "title": "RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection.", "authors": [{"family": "Avican", "given": "Kemal", "initials": "K", "orcid": "0000-0003-0707-2050", "researcher": {"href": "https://publications.scilifelab.se/researcher/84631a1299084ea695653c961e906ff3.json"}}, {"family": "Aldahdooh", "given": "Jehad", "initials": "J"}, {"family": "Togninalli", "given": "Matteo", "initials": "M"}, {"family": "Mahmud", "given": "A K M Firoj", "initials": "AKMF", "orcid": "0000-0002-6541-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6eb0bf023f343359be1914cb9100c0e.json"}}, {"family": "Tang", "given": "Jing", "initials": "J", "orcid": "0000-0001-7480-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1219a45cf6a428c87b6d99369e5f726.json"}}, {"family": "Borgwardt", "given": "Karsten M", "initials": "KM"}, {"family": "Rhen", "given": "Mikael", "initials": "M"}, {"family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "researcher": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}}], "type": "comparative study", "published": "2021-06-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3282", "issn-l": "2041-1723"}, "abstract": "Bacterial processes necessary for adaption to stressful host environments are potential targets for new antimicrobials. Here, we report large-scale transcriptomic analyses of 32 human bacterial pathogens grown under 11 stress conditions mimicking human host environments. The potential relevance of the in vitro stress conditions and responses is supported by comparisons with available in vivo transcriptomes of clinically important pathogens. Calculation of a probability score enables comparative cross-microbial analyses of the stress responses, revealing common and unique regulatory responses to different stresses, as well as overlapping processes participating in different stress responses. We identify conserved and species-specific 'universal stress responders', that is, genes showing altered expression in multiple stress conditions. Non-coding RNAs are involved in a substantial proportion of the responses. The data are collected in a freely available, interactive online resource (PATHOgenex).", "doi": "10.1038/s41467-021-23588-w", "pmid": "34078900", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23588-w"}, {"db": "pmc", "key": "PMC8172932"}], "notes": [], "created": "2021-10-01T09:00:20.445Z", "modified": "2021-12-06T13:46:14.370Z"}, {"entity": "publication", "iuid": "0e37ae638f8a41589a54a60d69ead29f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e37ae638f8a41589a54a60d69ead29f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e37ae638f8a41589a54a60d69ead29f"}}, "title": "Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe.", "authors": [{"family": "Salm\u00f3n", "given": "Pablo", "initials": "P", "orcid": "0000-0001-9718-6611", "researcher": {"href": "https://publications.scilifelab.se/researcher/b60bfa8b60174680a1546f283c2ccbc1.json"}}, {"family": "Jacobs", "given": "Arne", "initials": "A", "orcid": "0000-0001-7635-5447", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c375694c76e48279bdc6e7dcc2808a6.json"}}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Biard", "given": "Clotilde", "initials": "C", "orcid": "0000-0001-7474-5345", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f2845cc669e41f38f4abc7be2d749c2.json"}}, {"family": "Dingemanse", "given": "Niels J", "initials": "NJ", "orcid": "0000-0003-3320-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/364e2f2173244470bc7f9c1feff13bc9.json"}}, {"family": "Dominoni", "given": "Davide M", "initials": "DM", "orcid": "0000-0003-2063-9955", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5c5e5b23a174cecb550e7a68cd0b0d7.json"}}, {"family": "Helm", "given": "Barbara", "initials": "B", "orcid": "0000-0002-6648-1463", "researcher": {"href": "https://publications.scilifelab.se/researcher/54eeba33656a4e44a2a8281b9a1d9c6d.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Senar", "given": "Juan Carlos", "initials": "JC", "orcid": "0000-0001-9955-3892", "researcher": {"href": "https://publications.scilifelab.se/researcher/9acb6c1702bf4ce88d24eb8a35b39ae3.json"}}, {"family": "Sprau", "given": "Philipp", "initials": "P"}, {"family": "Visser", "given": "Marcel E", "initials": "ME", "orcid": "0000-0002-1456-1939", "researcher": {"href": "https://publications.scilifelab.se/researcher/87e0c4d6e845447ab627a26c7d12d989.json"}}, {"family": "Isaksson", "given": "Caroline", "initials": "C", "orcid": "0000-0002-6889-1386", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ddbca044f64cb1b1feef58baf539ba.json"}}], "type": "journal article", "published": "2021-05-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2983", "issn-l": "2041-1723"}, "abstract": "Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.", "doi": "10.1038/s41467-021-23027-w", "pmid": "34016968", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23027-w"}, {"db": "pmc", "key": "PMC8137928"}], "notes": [], "created": "2021-12-10T09:50:47.664Z", "modified": "2021-12-10T09:50:47.897Z"}, {"entity": "publication", "iuid": "735c9b9d0c6245a788a78a937efb44eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/735c9b9d0c6245a788a78a937efb44eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/735c9b9d0c6245a788a78a937efb44eb"}}, "title": "Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.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": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Steiner", "given": "Cynthia C", "initials": "CC", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}, {"family": "Nathan", "given": "Senthilvel K S S", "initials": "SKSS"}, {"family": "Brace", "given": "Selina", "initials": "S", "orcid": "0000-0003-2126-6732", "researcher": {"href": "https://publications.scilifelab.se/researcher/476fbd04aaaf453f943f5eea976c3cff.json"}}, {"family": "Chan", "given": "Yvonne L", "initials": "YL"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Goossens", "given": "Benoit", "initials": "B"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "historical article", "published": "2021-04-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2393", "issn-l": "2041-1723"}, "abstract": "Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.", "doi": "10.1038/s41467-021-22386-8", "pmid": "33896938", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-22386-8"}, {"db": "pmc", "key": "PMC8071806"}], "notes": [], "created": "2021-04-30T07:55:37.656Z", "modified": "2024-01-16T13:48:39.991Z"}, {"entity": "publication", "iuid": "57298ccceabf42caaff99aaa28def71d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57298ccceabf42caaff99aaa28def71d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57298ccceabf42caaff99aaa28def71d"}}, "title": "Phenological shifts in lake stratification under climate change.", "authors": [{"family": "Woolway", "given": "R Iestyn", "initials": "RI", "orcid": "0000-0003-0498-7968", "researcher": {"href": "https://publications.scilifelab.se/researcher/17c3db86f7b145769cf04f5c485eecb1.json"}}, {"family": "Sharma", "given": "Sapna", "initials": "S", "orcid": "0000-0003-4571-2768", "researcher": {"href": "https://publications.scilifelab.se/researcher/7209e01cface421b9fea8ee9b3022454.json"}}, {"family": "Weyhenmeyer", "given": "Gesa A", "initials": "GA", "orcid": "0000-0002-4013-2281", "researcher": {"href": "https://publications.scilifelab.se/researcher/77867fdf5d184f93b2df8e8b7620e9f3.json"}}, {"family": "Debolskiy", "given": "Andrey", "initials": "A"}, {"family": "Golub", "given": "Malgorzata", "initials": "M"}, {"family": "Mercado-Bett\u00edn", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4572-3029", "researcher": {"href": "https://publications.scilifelab.se/researcher/92bafd44336d4620bfc5beb192c3244b.json"}}, {"family": "Perroud", "given": "Marjorie", "initials": "M"}, {"family": "Stepanenko", "given": "Victor", "initials": "V"}, {"family": "Tan", "given": "Zeli", "initials": "Z", "orcid": "0000-0001-5958-2584", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd87015d70fb4f71a9c5c40a22b84d4e.json"}}, {"family": "Grant", "given": "Luke", "initials": "L"}, {"family": "Ladwig", "given": "Robert", "initials": "R", "orcid": "0000-0001-8443-1999", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3f54a6733df4b8d860d559067fbd534.json"}}, {"family": "Mesman", "given": "Jorrit", "initials": "J", "orcid": "0000-0002-4319-260X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1cac2fbbeb74007b1393b21bb6e5722.json"}}, {"family": "Moore", "given": "Tadhg N", "initials": "TN", "orcid": "0000-0002-3834-8868", "researcher": {"href": "https://publications.scilifelab.se/researcher/37ed154cb4e04b74820d2028e0ce09bb.json"}}, {"family": "Shatwell", "given": "Tom", "initials": "T", "orcid": "0000-0002-4520-7916", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ec771efaebd4d0ea12675bf7d59aa91.json"}}, {"family": "Vanderkelen", "given": "Inne", "initials": "I", "orcid": "0000-0002-8673-1933", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d8b0ee04bdd43ee91c1ed564215dc5e.json"}}, {"family": "Austin", "given": "Jay A", "initials": "JA", "orcid": "0000-0002-3580-1794", "researcher": {"href": "https://publications.scilifelab.se/researcher/aee3634fdbff47a09f08d730cdba5557.json"}}, {"family": "DeGasperi", "given": "Curtis L", "initials": "CL", "orcid": "0000-0002-2520-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/a757e7e5b3af43d9ab917b505c201a1c.json"}}, {"family": "Dokulil", "given": "Martin", "initials": "M"}, {"family": "La Fuente", "given": "Sofia", "initials": "S", "orcid": "0000-0002-9665-672X", "researcher": {"href": "https://publications.scilifelab.se/researcher/44ff463a12e94ff88b5e5608452a012d.json"}}, {"family": "Mackay", "given": "Eleanor B", "initials": "EB"}, {"family": "Schladow", "given": "S Geoffrey", "initials": "SG"}, {"family": "Watanabe", "given": "Shohei", "initials": "S"}, {"family": "Marc\u00e9", "given": "Rafael", "initials": "R", "orcid": "0000-0002-7416-4652", "researcher": {"href": "https://publications.scilifelab.se/researcher/25a4cebca664467c87a69ead73741cf4.json"}}, {"family": "Pierson", "given": "Don C", "initials": "DC", "orcid": "0000-0001-6230-0146", "researcher": {"href": "https://publications.scilifelab.se/researcher/416bb47c326d446e9ee434dc252d0240.json"}}, {"family": "Thiery", "given": "Wim", "initials": "W", "orcid": "0000-0002-5183-6145", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0e6d334c3844b2a97855edb7161fa0c.json"}}, {"family": "Jennings", "given": "Eleanor", "initials": "E", "orcid": "0000-0002-9344-2056", "researcher": {"href": "https://publications.scilifelab.se/researcher/53462dc861db4486bc465126071dab1f.json"}}], "type": "journal article", "published": "2021-04-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2318", "issn-l": "2041-1723"}, "abstract": "One of the most important physical characteristics driving lifecycle events in lakes is stratification. Already subtle variations in the timing of stratification onset and break-up (phenology) are known to have major ecological effects, mainly by determining the availability of light, nutrients, carbon and oxygen to organisms. Despite its ecological importance, historic and future global changes in stratification phenology are unknown. Here, we used a lake-climate model ensemble and long-term observational data, to investigate changes in lake stratification phenology across the Northern Hemisphere from 1901 to 2099. Under the high-greenhouse-gas-emission scenario, stratification will begin 22.0 \u00b1 7.0 days earlier and end 11.3 \u00b1 4.7 days later by the end of this century. It is very likely that this 33.3 \u00b1 11.7 day prolongation in stratification will accelerate lake deoxygenation with subsequent effects on nutrient mineralization and phosphorus release from lake sediments. Further misalignment of lifecycle events, with possible irreversible changes for lake ecosystems, is also likely.", "doi": "10.1038/s41467-021-22657-4", "pmid": "33875656", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-22657-4"}, {"db": "pmc", "key": "PMC8055693"}], "notes": [], "created": "2022-11-09T15:58:17.424Z", "modified": "2024-01-16T13:48:40.058Z"}, {"entity": "publication", "iuid": "bd0dbc1ef7b541dc8015a9fde247bd6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd0dbc1ef7b541dc8015a9fde247bd6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd0dbc1ef7b541dc8015a9fde247bd6c"}}, "title": "A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids.", "authors": [{"family": "Strassert", "given": "J\u00fcrgen F H", "initials": "JFH", "orcid": "0000-0001-6786-7563", "researcher": {"href": "https://publications.scilifelab.se/researcher/079bf03f0b2c438ab4e01346eb0be1af.json"}}, {"family": "Irisarri", "given": "Iker", "initials": "I", "orcid": "0000-0002-3628-1137", "researcher": {"href": "https://publications.scilifelab.se/researcher/08dbfdf186164fbb858a89606a309945.json"}}, {"family": "Williams", "given": "Tom A", "initials": "TA", "orcid": "0000-0003-1072-0223", "researcher": {"href": "https://publications.scilifelab.se/researcher/fddfbaaba1d04e59a110a69394a93d6f.json"}}, {"family": "Burki", "given": "Fabien", "initials": "F", "orcid": "0000-0002-8248-8462", "researcher": {"href": "https://publications.scilifelab.se/researcher/c386a8e440344f25bea35d570450b09b.json"}}], "type": "journal article", "published": "2021-03-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1879", "issn-l": "2041-1723"}, "abstract": "In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth.", "doi": "10.1038/s41467-021-22044-z", "pmid": "33767194", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-22044-z"}, {"db": "pmc", "key": "PMC7994803"}, {"db": "figshare", "key": "10.6084/m9.figshare.12417881.v2"}], "notes": [], "created": "2022-11-09T15:43:52.908Z", "modified": "2024-01-16T13:48:40.410Z"}, {"entity": "publication", "iuid": "634a4941b9a3488cb12cafd4aab1d5e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/634a4941b9a3488cb12cafd4aab1d5e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/634a4941b9a3488cb12cafd4aab1d5e2"}}, "title": "Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.", "authors": [{"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"}, {"family": "Parisien", "given": "Marc", "initials": "M", "orcid": "0000-0003-2924-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/046deabca7484670a0c9f7378580d7f5.json"}}, {"family": "Lou", "given": "Daohua", "initials": "D"}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Fatt", "given": "Michael", "initials": "M"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Sp\u00e5ngberg", "given": "Mats", "initials": "M"}, {"family": "Eriksson", "given": "Bengt", "initials": "B"}, {"family": "Barkas", "given": "Nikolaos", "initials": "N", "orcid": "0000-0002-4675-0718", "researcher": {"href": "https://publications.scilifelab.se/researcher/969cdbac84bb434d865b99c3d21be988.json"}}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K", "orcid": "0000-0001-7679-9494", "researcher": {"href": "https://publications.scilifelab.se/researcher/737245a5bc2144bd90be71487cbb3192.json"}}, {"family": "Khoury", "given": "Samar", "initials": "S"}, {"family": "Diatchenko", "given": "Luda", "initials": "L", "orcid": "0000-0002-1350-6727", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ff8b8cc7d444732a4dfcb0c9e3d8507.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": "2021-03-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1510", "issn-l": "2041-1723"}, "abstract": "Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.", "doi": "10.1038/s41467-021-21725-z", "pmid": "33686078", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21725-z"}, {"db": "pmc", "key": "PMC7940623"}], "notes": [], "created": "2021-06-09T12:16:22.425Z", "modified": "2024-01-16T13:48:40.539Z"}, {"entity": "publication", "iuid": "34c177a6bf874180a7803c15a79588ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34c177a6bf874180a7803c15a79588ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34c177a6bf874180a7803c15a79588ae"}}, "title": "System-wide identification and prioritization of enzyme substrates by thermal analysis.", "authors": [{"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Beusch", "given": "Christian M", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/278e50b11a3c4ef69b6e2708f99b5f3e.json"}}, {"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a75556311084e2b827ab1f646d7a16c.json"}}, {"family": "Wells", "given": "Juan Astorga", "initials": "JA", "orcid": "0000-0003-1017-8841", "researcher": {"href": "https://publications.scilifelab.se/researcher/14530d9aa03747858976b4889e959fe5.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85179acfa7e4916ad40ae478d6dcc0a.json"}}, {"family": "Meng", "given": "Zhaowei", "initials": "Z"}, {"family": "Chernobrovkin", "given": "Alexey", "initials": "A", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications.scilifelab.se/researcher/d36b29dc4fd44785b36b9baa9e291757.json"}}, {"family": "Rodin", "given": "Sergey", "initials": "S"}, {"family": "N\u00e4reoja", "given": "Katja", "initials": "K"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "A"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Cheng", "given": "Qing", "initials": "Q"}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Arn\u00e9r", "given": "Elias S J", "initials": "ESJ", "orcid": "0000-0002-4807-6114", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a545effced47da8a5192a7472ceb8f.json"}}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H", "orcid": "0000-0003-4059-3501", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49b25ddfc934f3ca41020c3f38c6bfc.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": "2021-02-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "1296"}, "abstract": "Despite the immense importance of enzyme-substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.", "doi": "10.1038/s41467-021-21540-6", "pmid": "33637753", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21540-6"}, {"db": "pmc", "key": "PMC7910609"}], "notes": [], "created": "2020-01-23T10:41:17.194Z", "modified": "2021-12-09T09:37:12.987Z"}, {"entity": "publication", "iuid": "1c85f5be6d2f425c80709c7f147a6997", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c85f5be6d2f425c80709c7f147a6997.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c85f5be6d2f425c80709c7f147a6997"}}, "title": "Biological and therapeutic implications of a unique subtype of NPM1 mutated AML.", "authors": [{"family": "Mer", "given": "Arvind Singh", "initials": "AS", "orcid": "0000-0001-8510-7963", "researcher": {"href": "https://publications.scilifelab.se/researcher/9095c89e14324176b5143a2a06d4bfa4.json"}}, {"family": "Heath", "given": "Emily M", "initials": "EM"}, {"family": "Madani Tonekaboni", "given": "Seyed Ali", "initials": "SA"}, {"family": "Dogan-Artun", "given": "Nergiz", "initials": "N"}, {"family": "Nair", "given": "Sisira Kadambat", "initials": "SK"}, {"family": "Murison", "given": "Alex", "initials": "A"}, {"family": "Garcia-Prat", "given": "Laura", "initials": "L"}, {"family": "Shlush", "given": "Liran", "initials": "L", "orcid": "0000-0002-3700-270X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e1d7041e5ca4403bb29380b819748f6.json"}}, {"family": "Hurren", "given": "Rose", "initials": "R"}, {"family": "Voisin", "given": "Veronique", "initials": "V"}, {"family": "Bader", "given": "Gary D", "initials": "GD", "orcid": "0000-0003-0185-8861", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d74ad4af0ca460597907e2c71e99d26.json"}}, {"family": "Nislow", "given": "Corey", "initials": "C", "orcid": "0000-0002-4016-8874", "researcher": {"href": "https://publications.scilifelab.se/researcher/6291f40bac3a4231bf291887f4d3992b.json"}}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehmann", "given": "Soren", "initials": "S"}, {"family": "Gower", "given": "Mark", "initials": "M"}, {"family": "Guidos", "given": "Cynthia J", "initials": "CJ", "orcid": "0000-0002-7674-2612", "researcher": {"href": "https://publications.scilifelab.se/researcher/4379fdc3e4134880a2acfbb79bc49f2c.json"}}, {"family": "Lupien", "given": "Mathieu", "initials": "M"}, {"family": "Dick", "given": "John E", "initials": "JE", "orcid": "0000-0002-9527-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/26503cff387441dc962a2453d77379e0.json"}}, {"family": "Minden", "given": "Mark D", "initials": "MD"}, {"family": "Schimmer", "given": "Aaron D", "initials": "AD", "orcid": "0000-0003-4023-3899", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d62741272684ec8993b9540c09bbbad.json"}}, {"family": "Haibe-Kains", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-7684-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/f62c5da881ac4cb7a3d64e99800cfb25.json"}}], "type": "journal article", "published": "2021-02-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1054", "issn-l": "2041-1723"}, "abstract": "In acute myeloid leukemia (AML), molecular heterogeneity across patients constitutes a major challenge for prognosis and therapy. AML with NPM1 mutation is a distinct genetic entity in the revised World Health Organization classification. However, differing patterns of co-mutation and response to therapy within this group necessitate further stratification. Here we report two distinct subtypes within NPM1 mutated AML patients, which we label as primitive and committed based on the respective presence or absence of a stem cell signature. Using gene expression (RNA-seq), epigenomic (ATAC-seq) and immunophenotyping (CyToF) analysis, we associate each subtype with specific molecular characteristics, disease differentiation state and patient survival. Using ex vivo drug sensitivity profiling, we show a differential drug response of the subtypes to specific kinase inhibitors, irrespective of the FLT3-ITD status. Differential drug responses of the primitive and committed subtype are validated in an independent AML cohort. Our results highlight heterogeneity among NPM1 mutated AML patient samples based on stemness and suggest that the addition of kinase inhibitors to the treatment of cases with the primitive signature, lacking FLT3-ITD, could have therapeutic benefit.", "doi": "10.1038/s41467-021-21233-0", "pmid": "33594052", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7886883"}, {"db": "pii", "key": "10.1038/s41467-021-21233-0"}], "notes": [], "created": "2023-11-27T21:46:59.397Z", "modified": "2024-01-16T13:48:40.672Z"}, {"entity": "publication", "iuid": "1ca0729f557a4cd3b8cb790b4a9d5961", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ca0729f557a4cd3b8cb790b4a9d5961.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ca0729f557a4cd3b8cb790b4a9d5961"}}, "title": "Asymmetric introgression reveals the genetic architecture of a plumage trait.", "authors": [{"family": "Semenov", "given": "Georgy A", "initials": "GA", "orcid": "0000-0002-7218-7885", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bb787f3be449299a263dcab28021b9.json"}}, {"family": "Linck", "given": "Ethan", "initials": "E"}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Harris", "given": "Rebecca B", "initials": "RB"}, {"family": "Khaydarov", "given": "David R", "initials": "DR"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Taylor", "given": "Scott A", "initials": "SA", "orcid": "0000-0001-9580-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/36c6baa1b23242e0bfd586d7e42c0cb9.json"}}], "type": "journal article", "published": "2021-02-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1019", "issn-l": "2041-1723"}, "abstract": "Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.", "doi": "10.1038/s41467-021-21340-y", "pmid": "33589637", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21340-y"}, {"db": "pmc", "key": "PMC7884433"}, {"db": "Dryad", "key": "10.5061/dryad.dv41ns1wv"}], "notes": [], "created": "2021-06-09T12:16:14.581Z", "modified": "2024-01-16T13:48:40.705Z"}, {"entity": "publication", "iuid": "a4bbbc6af47c4ff399e4ce88b4e2f840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4bbbc6af47c4ff399e4ce88b4e2f840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4bbbc6af47c4ff399e4ce88b4e2f840"}}, "title": "Distinct subtypes of proprioceptive dorsal root ganglion neurons regulate adaptive proprioception in mice.", "authors": [{"family": "Wu", "given": "Haohao", "initials": "H", "orcid": "0000-0002-5511-7084", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bc2f62b53ce4aabb4db2508e7901228.json"}}, {"family": "Petitpr\u00e9", "given": "Charles", "initials": "C"}, {"family": "Fontanet", "given": "Paula", "initials": "P", "orcid": "0000-0002-5324-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe102480cb7458a941fc70fe7f5cb9b.json"}}, {"family": "Sharma", "given": "Anil", "initials": "A", "orcid": "0000-0002-7442-8494", "researcher": {"href": "https://publications.scilifelab.se/researcher/53eab132449648df8998ae6de526c99f.json"}}, {"family": "Bellardita", "given": "Carmelo", "initials": "C"}, {"family": "Quadros", "given": "Rolen M", "initials": "RM"}, {"family": "Jannig", "given": "Paulo R", "initials": "PR"}, {"family": "Wang", "given": "Yiqiao", "initials": "Y"}, {"family": "Heimel", "given": "J Alexander", "initials": "JA", "orcid": "0000-0002-5291-4184", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc34eb2a27f43c680a9198426041468.json"}}, {"family": "Cheung", "given": "Kylie K Y", "initials": "KKY"}, {"family": "Wanderoy", "given": "Simone", "initials": "S"}, {"family": "Xuan", "given": "Yang", "initials": "Y"}, {"family": "Meletis", "given": "Konstantinos", "initials": "K", "orcid": "0000-0001-5665-4781", "researcher": {"href": "https://publications.scilifelab.se/researcher/56822ffe0341444297c820580f52dfd0.json"}}, {"family": "Ruas", "given": "Jorge", "initials": "J", "orcid": "0000-0002-1110-2606", "researcher": {"href": "https://publications.scilifelab.se/researcher/b91c3fde15f7415aa1f6c9263ff913ff.json"}}, {"family": "Gurumurthy", "given": "Channabasavaiah B", "initials": "CB", "orcid": "0000-0002-8022-4033", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f30aa6db34f4d34b3bdb24ecb2069b4.json"}}, {"family": "Kiehn", "given": "Ole", "initials": "O"}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}, {"family": "Lallemend", "given": "Fran\u00e7ois", "initials": "F", "orcid": "0000-0001-5484-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9494a8ea444facbf3b564670930ab5.json"}}], "type": "journal article", "published": "2021-02-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1026", "issn-l": "2041-1723"}, "abstract": "Proprioceptive neurons (PNs) are essential for the proper execution of all our movements by providing muscle sensory feedback to the central motor network. Here, using deep single cell RNAseq of adult PNs coupled with virus and genetic tracings, we molecularly identify three main types of PNs (Ia, Ib and II) and find that they segregate into eight distinct subgroups. Our data unveil a highly sophisticated organization of PNs into discrete sensory input channels with distinct spatial distribution, innervation patterns and molecular profiles. Altogether, these features contribute to finely regulate proprioception during complex motor behavior. Moreover, while Ib- and II-PN subtypes are specified around birth, Ia-PN subtypes diversify later in life along with increased motor activity. We also show Ia-PNs plasticity following exercise training, suggesting Ia-PNs are important players in adaptive proprioceptive function in adult mice.", "doi": "10.1038/s41467-021-21173-9", "pmid": "33589589", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21173-9"}, {"db": "pmc", "key": "PMC7884389"}], "notes": [], "created": "2021-06-09T12:14:37.963Z", "modified": "2024-01-16T13:48:40.686Z"}, {"entity": "publication", "iuid": "4f215604012947b6b889fbcd7ced04a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f215604012947b6b889fbcd7ced04a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f215604012947b6b889fbcd7ced04a3"}}, "title": "GWAS for autoimmune Addison's disease identifies multiple risk loci and highlights AIRE in disease susceptibility.", "authors": [{"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "R\u00f8yrvik", "given": "Ellen Christine", "initials": "EC", "orcid": "0000-0002-8979-1704", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd868b2b958946959cb0e7e7b5af9da7.json"}}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M", "orcid": "0000-0003-0050-704X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65dc88b917274bc595daed855b63abab.json"}}, {"family": "Berger", "given": "Amund Holte", "initials": "AH", "orcid": "0000-0001-6973-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/af8b1a7f74804ed19a47492d9ae516ef.json"}}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Artaza", "given": "Haydee", "initials": "H", "orcid": "0000-0002-1585-5488", "researcher": {"href": "https://publications.scilifelab.se/researcher/25707fcf0fa84ca78541e70e4ff1eca2.json"}}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Grytaas", "given": "Marianne Aardal", "initials": "MA", "orcid": "0000-0001-9016-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6b1dce0512245619e56be4ecd5de8eb.json"}}, {"family": "Str\u00f6m", "given": "Sara", "initials": "S"}, {"family": "Bratland", "given": "Eirik", "initials": "E"}, {"family": "Botusan", "given": "Ileana Ruxandra", "initials": "IR"}, {"family": "Oftedal", "given": "Bergithe Eikeland", "initials": "BE"}, {"family": "Breivik", "given": "Lars", "initials": "L", "orcid": "0000-0003-2889-7342", "researcher": {"href": "https://publications.scilifelab.se/researcher/8098f538b89d4073b79a3e60eae48b7c.json"}}, {"family": "Vaudel", "given": "Marc", "initials": "M", "orcid": "0000-0003-1179-9578", "researcher": {"href": "https://publications.scilifelab.se/researcher/920056fb632147559a0d9e3f49c6bdbd.json"}}, {"family": "Helgeland", "given": "\u00d8yvind", "initials": "\u00d8", "orcid": "0000-0002-5612-2985", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f27653f5bc6491a88d4336f1b442d3a.json"}}, {"family": "Falorni", "given": "Alberto", "initials": "A"}, {"family": "J\u00f8rgensen", "given": "Anders Palmstr\u00f8m", "initials": "AP", "orcid": "0000-0002-1246-9194", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6e34e97e0e4400f939e3662b19a4075.json"}}, {"family": "Hulting", "given": "Anna-Lena", "initials": "AL"}, {"family": "Svartberg", "given": "Johan", "initials": "J"}, {"family": "Ekwall", "given": "Olov", "initials": "O", "orcid": "0000-0002-4506-9955", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d7af11d7d30410d8fe5f3b5fbd0ba1d.json"}}, {"family": "Fougner", "given": "Kristian Johan", "initials": "KJ"}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J"}, {"family": "Nedreb\u00f8", "given": "Bj\u00f8rn Gunnar", "initials": "BG"}, {"family": "Dahlqvist", "given": "Per", "initials": "P", "orcid": "0000-0002-6471-9503", "researcher": {"href": "https://publications.scilifelab.se/researcher/3577b15f446643499c52143174a5e15b.json"}}, {"family": "Norwegian Addison Registry Study Group", "given": "", "initials": ""}, {"family": "Swedish Addison Registry Study Group", "given": "", "initials": ""}, {"family": "Knappskog", "given": "Per Morten", "initials": "PM"}, {"family": "Wolff", "given": "Anette Susanne B\u00f8e", "initials": "ASB"}, {"family": "Bensing", "given": "Sophie", "initials": "S", "orcid": "0000-0002-9193-2860", "researcher": {"href": "https://publications.scilifelab.se/researcher/acae2ad8ca844588b2b850c863034b7b.json"}}, {"family": "Johansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-2298-7008", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b957ea589b342fb9def8ce13ef3bd7e.json"}}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}, {"family": "Husebye", "given": "Eystein Sverre", "initials": "ES", "orcid": "0000-0002-7886-2976", "researcher": {"href": "https://publications.scilifelab.se/researcher/370273203e0e4734ac49a209ae066ac2.json"}}], "type": "journal article", "published": "2021-02-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "959", "issn-l": "2041-1723"}, "abstract": "Autoimmune Addison's disease (AAD) is characterized by the autoimmune destruction of the adrenal cortex. Low prevalence and complex inheritance have long hindered successful genetic studies. We here report the first genome-wide association study on AAD, which identifies nine independent risk loci (P < 5 \u00d7 10-8). In addition to loci implicated in lymphocyte function and development shared with other autoimmune diseases such as HLA, BACH2, PTPN22 and CTLA4, we associate two protein-coding alterations in Autoimmune Regulator (AIRE) with AAD. The strongest, p.R471C (rs74203920, OR = 3.4 (2.7-4.3), P = 9.0 \u00d7 10-25) introduces an additional cysteine residue in the zinc-finger motif of the second PHD domain of the AIRE protein. This unbiased elucidation of the genetic contribution to development of AAD points to the importance of central immunological tolerance, and explains 35-41% of heritability (h2).", "doi": "10.1038/s41467-021-21015-8", "pmid": "33574239", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21015-8"}, {"db": "pmc", "key": "PMC7878795"}], "notes": [], "created": "2022-11-09T15:43:58.467Z", "modified": "2024-01-16T13:48:40.734Z"}, {"entity": "publication", "iuid": "c5cf7c75465a480c8ba26778bac156d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5cf7c75465a480c8ba26778bac156d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5cf7c75465a480c8ba26778bac156d6"}}, "title": "Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation.", "authors": [{"family": "Norin", "given": "Ulrika", "initials": "U", "orcid": "0000-0003-1063-6339", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb0cc296604c46d0895f150b1905144c.json"}}, {"family": "Rintisch", "given": "Carola", "initials": "C"}, {"family": "Meng", "given": "Liesu", "initials": "L", "orcid": "0000-0003-1985-050X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9715869252ac4fdd913f94e044904c1a.json"}}, {"family": "Forster", "given": "Florian", "initials": "F"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Tuncel", "given": "Jonatan", "initials": "J"}, {"family": "Klocke", "given": "Katrin", "initials": "K"}, {"family": "B\u00e4cklund", "given": "Johan", "initials": "J"}, {"family": "Yang", "given": "Min", "initials": "M"}, {"family": "Bonner", "given": "Michael Y", "initials": "MY"}, {"family": "Lahore", "given": "Gonzalo Fernandez", "initials": "GF"}, {"family": "James", "given": "Jaime", "initials": "J"}, {"family": "Shchetynsky", "given": "Klementy", "initials": "K"}, {"family": "Bergquist", "given": "Maria", "initials": "M"}, {"family": "Gjertsson", "given": "Inger", "initials": "I"}, {"family": "Hubner", "given": "Norbert", "initials": "N", "orcid": "0000-0002-1218-6223", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d84f34739c743838cea107286522e42.json"}}, {"family": "B\u00e4ckdahl", "given": "Liselotte", "initials": "L"}, {"family": "Holmdahl", "given": "Rikard", "initials": "R", "orcid": "0000-0002-4969-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/49e60d22dd1a4dd1a4ca5a50d9fc4fc7.json"}}], "type": "journal article", "published": "2021-01-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "610"}, "abstract": "The introduction of the CTLA-4 recombinant fusion protein has demonstrated therapeutic effects by selectively modulating T-cell activation in rheumatoid arthritis. Here we show, using a forward genetic approach, that a mutation in the SH3gl1 gene encoding the endocytic protein Endophilin A2 is associated with the development of arthritis in rodents. Defective expression of SH3gl1 affects T cell effector functions and alters the activation threshold of autoreactive T cells, thereby leading to complete protection from chronic autoimmune inflammatory disease in both mice and rats. We further show that SH3GL1 regulates human T cell signaling and T cell receptor internalization, and its expression is upregulated in rheumatoid arthritis patients. Collectively our data identify SH3GL1 as a key regulator of T cell activation, and as a potential target for treatment of autoimmune diseases.", "doi": "10.1038/s41467-020-20586-2", "pmid": "33504785", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics (NBIS)": "Collaborative", "Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-20586-2"}, {"db": "pmc", "key": "PMC7840939"}], "notes": [], "created": "2021-01-28T14:33:53.228Z", "modified": "2025-10-17T13:04:28.145Z"}, {"entity": "publication", "iuid": "7d5a739243ab4db79f3121bb6574361e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d5a739243ab4db79f3121bb6574361e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d5a739243ab4db79f3121bb6574361e"}}, "title": "Structure of a full-length bacterial polysaccharide co-polymerase.", "authors": [{"family": "Wiseman", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-2994-5839", "researcher": {"href": "https://publications.scilifelab.se/researcher/2098646fa9de4dbc8f7cca8aeabad319.json"}}, {"family": "Nitharwal", "given": "Ram Gopal", "initials": "RG"}, {"family": "Widmalm", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-8303-4481", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eb393e8ba544f67b39fd6571b4e6efc.json"}}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M", "orcid": "0000-0001-5574-9383", "researcher": {"href": "https://publications.scilifelab.se/researcher/d968fcccace74b689185bb9fa2d33bf8.json"}}], "type": "journal article", "published": "2021-01-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "369"}, "abstract": "Lipopolysaccharides are important components of the bacterial cell envelope that among other things act as a protective barrier against the environment and toxic molecules such as antibiotics. One of the most widely disseminated pathways of polysaccharide biosynthesis is the inner membrane bound Wzy-dependent pathway. Here we present the 3.0 \u00c5 structure of the co-polymerase component of this pathway, WzzB from E. coli solved by single-particle cryo-electron microscopy. The overall architecture is octameric and resembles a box jellyfish containing a large bell-shaped periplasmic domain with the 2-helix transmembrane domain from each protomer, positioned 32 \u00c5 apart, encircling a large empty transmembrane chamber. This structure also reveals the architecture of the transmembrane domain, including the location of key residues for the Wzz-family of proteins and the Wzy-dependent pathway present in many Gram-negative bacteria, explaining several of the previous biochemical and mutational studies and lays the foundation for future investigations.", "doi": "10.1038/s41467-020-20579-1", "pmid": "33446644", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-20579-1"}, {"db": "pmc", "key": "PMC7809406"}], "notes": [], "created": "2021-01-14T16:30:43.331Z", "modified": "2021-12-14T12:33:30.787Z"}, {"entity": "publication", "iuid": "87993d07a2d8462196987caea3385277", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87993d07a2d8462196987caea3385277.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87993d07a2d8462196987caea3385277"}}, "title": "Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 \u00c5 resolution.", "authors": [{"family": "Cunha", "given": "Eva S", "initials": "ES", "orcid": "0000-0003-4491-9054", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d1cbc6873554640bdda883b3b8debc1.json"}}, {"family": "Chen", "given": "Xiaorui", "initials": "X", "orcid": "0000-0002-4492-0883", "researcher": {"href": "https://publications.scilifelab.se/researcher/993b54c4bab2426983f98543fb778d24.json"}}, {"family": "Sanz-Gaitero", "given": "Marta", "initials": "M", "orcid": "0000-0002-9027-8625", "researcher": {"href": "https://publications.scilifelab.se/researcher/17fd78aefbee4044ad3a79e6ce8f645f.json"}}, {"family": "Mills", "given": "Deryck J", "initials": "DJ"}, {"family": "Luecke", "given": "Hartmut", "initials": "H", "orcid": "0000-0002-4938-0775", "researcher": {"href": "https://publications.scilifelab.se/researcher/804c330e80324ff99a778c2d1b0ee236.json"}}], "type": "journal article", "published": "2021-01-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "230"}, "abstract": "Infection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of the world population will continue to be infected with this gastric pathogen. Current eradication, called triple therapy, entails a proton-pump inhibitor and two broadband antibiotics, however resistance to either clarithromycin or metronidazole is greater than 25% and rising. Therefore, there is an urgent need for a targeted, high-specificity eradication drug. Gastric infection by H. pylori depends on the expression of a nickel-dependent urease in the cytoplasm of the bacteria. Here, we report the 2.0 \u00c5 resolution structure of the 1.1 MDa urease in complex with an inhibitor by cryo-electron microscopy and compare it to a \u03b2-mercaptoethanol-inhibited structure at 2.5 \u00c5 resolution. The structural information is of sufficient detail to aid in the development of inhibitors with high specificity and affinity.", "doi": "10.1038/s41467-020-20485-6", "pmid": "33431861", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-20485-6"}, {"db": "pmc", "key": "PMC7801526"}], "notes": [], "created": "2021-01-12T10:03:17.421Z", "modified": "2021-12-09T07:48:47.145Z"}, {"entity": "publication", "iuid": "48f74c2afc0b4af8befb22016e4d7b0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48f74c2afc0b4af8befb22016e4d7b0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48f74c2afc0b4af8befb22016e4d7b0c"}}, "title": "Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability.", "authors": [{"family": "Lagou", "given": "Vasiliki", "initials": "V"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Hottenga", "given": "Jouke- Jan", "initials": "JJ", "orcid": "0000-0002-5668-2368", "researcher": {"href": "https://publications.scilifelab.se/researcher/75553b594b1f4255833de730f7f7d170.json"}}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N", "orcid": "0000-0001-5424-2134", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4f7af2cb2b7464abddf05692a292fc3.json"}}, {"family": "Marullo", "given": "Letizia", "initials": "L"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Jansen", "given": "Rick", "initials": "R", "orcid": "0000-0002-3333-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd392c9b9784ebe8c8730e05463377a.json"}}, {"family": "Min", "given": "Josine L", "initials": "JL", "orcid": "0000-0003-4456-9824", "researcher": {"href": "https://publications.scilifelab.se/researcher/5896cbc0cb8d427a954b194839adda52.json"}}, {"family": "Dimas", "given": "Antigone S", "initials": "AS"}, {"family": "Ulrich", "given": "Anna", "initials": "A"}, {"family": "Zudina", "given": "Liudmila", "initials": "L"}, {"family": "G\u00e5din", "given": "Jesper R", "initials": "JR"}, {"family": "Jiang", "given": "Longda", "initials": "L"}, {"family": "Faggian", "given": "Alessia", "initials": "A", "orcid": "0000-0002-3799-9722", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4f320f96474406c82fef88f1f78dd23.json"}}, {"family": "Bonnefond", "given": "Am\u00e9lie", "initials": "A", "orcid": "0000-0001-9976-3005", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea1984308c1544ba969d4df73971de69.json"}}, {"family": "Fadista", "given": "Joao", "initials": "J"}, {"family": "Stathopoulou", "given": "Maria G", "initials": "MG"}, {"family": "Isaacs", "given": "Aaron", "initials": "A", "orcid": "0000-0001-5037-4834", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ebe49e62404f48bcb979d9671883e7.json"}}, {"family": "Willems", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-6803-3007", "researcher": {"href": "https://publications.scilifelab.se/researcher/307c8a9b3ab54ab586c7b000c110e76b.json"}}, {"family": "Navarro", "given": "Pau", "initials": "P", "orcid": "0000-0001-5576-8584", "researcher": {"href": "https://publications.scilifelab.se/researcher/9420946aedec4a7b8925cc05c0a9abeb.json"}}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Jackson", "given": "Anne U", "initials": "AU", "orcid": "0000-0002-9672-2547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8230afabb0b4dcda8dc58ead349aea0.json"}}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "O'Connell", "given": "Jeff R", "initials": "JR"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF", "orcid": "0000-0002-3443-8030", "researcher": {"href": 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"https://publications.scilifelab.se/researcher/a7d00b649d284101b0501e2024fb651a.json"}}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications.scilifelab.se/researcher/679465193fba4887a68e2aec34ccfd8e.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Dermitzakis", "given": "Emmanouil T", "initials": "ET", "orcid": "0000-0002-9302-6490", "researcher": {"href": "https://publications.scilifelab.se/researcher/3560d19929e94af1bb858a54e29a10cc.json"}}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM", "orcid": "0000-0002-4903-9374", "researcher": {"href": "https://publications.scilifelab.se/researcher/822d2f2a99814a7498f19976ed6381ef.json"}}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Froguel", "given": "Philippe", "initials": "P", "orcid": "0000-0003-2972-0784", "researcher": {"href": "https://publications.scilifelab.se/researcher/34edc6a0f1b343bb8a2abd439c2ee77f.json"}}, {"family": "Kaakinen", "given": "Marika A", "initials": "MA", "orcid": "0000-0002-9228-0462", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9f40717fdd4ce29b148bc569134451.json"}}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM", "orcid": "0000-0003-1015-0531", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4336f8845ac40dfb77ef0ea1a97bbd6.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-2256-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/689bc741ea6547d18de7080c84d0193e.json"}}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J", "orcid": "0000-0003-2871-3603", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9edfafda7364890866115f5343a9583.json"}}, {"family": "Barroso", "given": "In\u00eas", "initials": "I", "orcid": "0000-0001-5800-4520", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2dc6be9aa194bdc9a161e551d5e6747.json"}}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC)", "given": "", "initials": ""}], "type": "journal article", "published": "2021-01-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "24", "issn-l": "2041-1723"}, "abstract": "Differences between sexes contribute to variation in the levels of fasting glucose and insulin. Epidemiological studies established a higher prevalence of impaired fasting glucose in men and impaired glucose tolerance in women, however, the genetic component underlying this phenomenon is not established. We assess sex-dimorphic (73,089/50,404 women and 67,506/47,806 men) and sex-combined (151,188/105,056 individuals) fasting glucose/fasting insulin genetic effects via genome-wide association study meta-analyses in individuals of European descent without diabetes. Here we report sex dimorphism in allelic effects on fasting insulin at IRS1 and ZNF12 loci, the latter showing higher RNA expression in whole blood in women compared to men. We also observe sex-homogeneous effects on fasting glucose at seven novel loci. Fasting insulin in women shows stronger genetic correlations than in men with waist-to-hip ratio and anorexia nervosa. Furthermore, waist-to-hip ratio is causally related to insulin resistance in women, but not in men. These results position dissection of metabolic and glycemic health sex dimorphism as a steppingstone for understanding differences in genetic effects between women and men in related phenotypes.", "doi": "10.1038/s41467-020-19366-9", "pmid": "33402679", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-19366-9"}, {"db": "pmc", "key": "PMC7785747"}], "notes": [], "created": "2021-01-08T16:30:26.062Z", "modified": "2021-11-10T12:27:48.827Z"}, {"entity": "publication", "iuid": "2a6a88ecb8924b3cb97256b268e8c722", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a6a88ecb8924b3cb97256b268e8c722.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a6a88ecb8924b3cb97256b268e8c722"}}, "title": "Direct energy transfer from photosystem II to photosystem I confers winter sustainability in Scots Pine.", "authors": [{"family": "Bag", "given": "Pushan", "initials": "P", "orcid": "0000-0003-3858-4606", "researcher": {"href": "https://publications.scilifelab.se/researcher/033b97dc712047a294d3e801ba750787.json"}}, {"family": "Chukhutsina", "given": "Volha", "initials": "V"}, {"family": "Zhang", "given": "Zishan", "initials": "Z"}, {"family": "Paul", "given": "Suman", "initials": "S"}, {"family": "Ivanov", "given": "Alexander G", "initials": "AG", "orcid": "0000-0001-7910-5494", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cc5e19a40374d67a3ae74182c5dae6f.json"}}, {"family": "Shutova", "given": "Tatyana", "initials": "T", "orcid": "0000-0002-4095-9609", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec5a10e3ad274526b819f24961ab015e.json"}}, {"family": "Croce", "given": "Roberta", "initials": "R", "orcid": "0000-0003-3469-834X", "researcher": {"href": "https://publications.scilifelab.se/researcher/119277ddfe3b4e9ab4e9afc972f5e763.json"}}, {"family": "Holzwarth", "given": "Alfred R", "initials": "AR", "orcid": "0000-0002-9562-4873", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ce08a698124e0f888d3db0a0644162.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}], "type": "journal article", "published": "2020-12-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "6388"}, "abstract": "Evergreen conifers in boreal forests can survive extremely cold (freezing) temperatures during long dark winter and fully recover during summer. A phenomenon called \"sustained quenching\" putatively provides photoprotection and enables their survival, but its precise molecular and physiological mechanisms are not understood. To unveil them, here we have analyzed seasonal adjustment of the photosynthetic machinery of Scots pine (Pinus sylvestris) trees by monitoring multi-year changes in weather, chlorophyll fluorescence, chloroplast ultrastructure, and changes in pigment-protein composition. Analysis of Photosystem II and Photosystem I performance parameters indicate that highly dynamic structural and functional seasonal rearrangements of the photosynthetic apparatus occur. Although several mechanisms might contribute to 'sustained quenching' of winter/early spring pine needles, time-resolved fluorescence analysis shows that extreme down-regulation of photosystem II activity along with direct energy transfer from photosystem II to photosystem I play a major role. This mechanism is enabled by extensive thylakoid destacking allowing for the mixing of PSII with PSI complexes. These two linked phenomena play crucial roles in winter acclimation and protection.", "doi": "10.1038/s41467-020-20137-9", "pmid": "33319777", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7738668"}, {"db": "pii", "key": "10.1038/s41467-020-20137-9"}], "notes": [], "created": "2022-04-01T15:00:18.942Z", "modified": "2023-06-19T12:41:41.017Z"}, {"entity": "publication", "iuid": "5c901b5af4f94bdf82bd969d255f0767", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c901b5af4f94bdf82bd969d255f0767.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c901b5af4f94bdf82bd969d255f0767"}}, "title": "Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury", "authors": [{"family": "Floriddia", "given": "Elisa M", "initials": "EM", "orcid": "0000-0003-2304-8114", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea55e5ce2b74a799fbcce59b53e62ac.json"}}, {"family": "Louren\u00e7o", "given": "T\u00e2nia", "initials": "T"}, {"family": "Zhang", "given": "Shupei", "initials": "S"}, {"family": "van Bruggen", "given": "David", "initials": "D", "orcid": "0000-0001-6794-7731", "researcher": {"href": "https://publications.scilifelab.se/researcher/d613135b6ba740c59062e3e7e4fd8174.json"}}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Kukanja", "given": "Petra", "initials": "P", "orcid": "0000-0003-1228-5923", "researcher": {"href": "https://publications.scilifelab.se/researcher/082ef6e681214c14b8ca36cd0188722b.json"}}, {"family": "Gon\u00e7alves dos Santos", "given": "Jo\u00e3o P", "initials": "JP"}, {"family": "Alt\u0131nk\u00f6k", "given": "M\u00fcge", "initials": "M"}, {"family": "Yokota", "given": "Chika", "initials": "C"}, {"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "researcher": {"href": "https://publications.scilifelab.se/researcher/3144601c466246cfa70acbe8c7ee00ee.json"}}, {"family": "Mulinyawe", "given": "Sara B", "initials": "SB"}, {"family": "Gr\u00e3os", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-2707-1488", "researcher": {"href": "https://publications.scilifelab.se/researcher/86454440d6754732b4d8f813d399a9ed.json"}}, {"family": "Sun", "given": "Lu O", "initials": "LO", "orcid": "0000-0002-9293-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bfd19d5fc054ae1a0e6c0c6f286daca.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.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": "2020-11-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "5860"}, "abstract": "Mature oligodendrocytes (MOLs) show transcriptional heterogeneity, the functional consequences of which are unclear. MOL heterogeneity might correlate with the local environment or their interactions with different neuron types. Here, we show that distinct MOL populations have spatial preference in the mammalian central nervous system (CNS). We found that MOL type 2 (MOL2) is enriched in the spinal cord when compared to the brain, while MOL types 5 and 6 (MOL5/6) increase their contribution to the OL lineage with age in all analyzed regions. MOL2 and MOL5/6 also have distinct spatial preference in the spinal cord regions where motor and sensory tracts run. OL progenitor cells (OPCs) are not specified into distinct MOL populations during development, excluding a major contribution of OPC intrinsic mechanisms determining MOL heterogeneity. In disease, MOL2 and MOL5/6 present different susceptibility during the chronic phase following traumatic spinal cord injury. Our results demonstrate that the distinct MOL populations have different spatial preference and different responses to disease.", "doi": "10.1038/s41467-020-19453-x", "pmid": "33203872", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7673029"}, {"db": "pii", "key": "10.1038/s41467-020-19453-x"}], "notes": [], "created": "2020-12-07T16:36:40.432Z", "modified": "2025-10-17T13:02:18.056Z"}, {"entity": "publication", "iuid": "7799f6442abe4a21905074224e018909", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7799f6442abe4a21905074224e018909.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7799f6442abe4a21905074224e018909"}}, "title": "Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.", "authors": [{"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications.scilifelab.se/researcher/662e96c24ee6442898ec2caab1eec25d.json"}}, {"family": "Mackowiak", "given": "Sebastian D", "initials": "SD"}, {"family": "Frade", "given": "Jo\u00e3o", "initials": "J", "orcid": "0000-0003-3961-7641", "researcher": {"href": "https://publications.scilifelab.se/researcher/92f0e07be91a4e858100b84a287e133a.json"}}, {"family": "Catuara-Solarz", "given": "Silvina", "initials": "S"}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Gelali", "given": "Eleni", "initials": "E", "orcid": "0000-0003-0067-5473", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1a4d90932dd45509d71a672ec5a12af.json"}}, {"family": "Men\u00e9ndez", "given": "Diego B\u00e1rcena", "initials": "DB"}, {"family": "Zapata", "given": "Luis", "initials": "L", "orcid": "0000-0002-1386-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1e6b01d1d074ce78a9cf40a9560e7fc.json"}}, {"family": "Ossowski", "given": "Stephan", "initials": "S"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}], "type": "journal article", "published": "2020-10-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "5445"}, "abstract": "Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex formation. Our results lend support to the concept of post-transcriptional RNA operons, but we further present evidence that nuclear proximity of genes may provide substantial functional regulation in mammalian single cells.", "doi": "10.1038/s41467-020-19011-5", "pmid": "33116115", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-19011-5"}, {"db": "pmc", "key": "PMC7595044"}], "notes": [], "created": "2021-01-11T11:38:53.729Z", "modified": "2024-01-16T13:48:41.524Z"}, {"entity": "publication", "iuid": "13b50e6dabb34ef58cf5cc56f7fc51d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13b50e6dabb34ef58cf5cc56f7fc51d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13b50e6dabb34ef58cf5cc56f7fc51d3"}}, "title": "Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.", "authors": [{"family": "Flygaard", "given": "Rasmus Kock", "initials": "RK", "orcid": "0000-0002-4918-6438", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a5982a29fb44d6b96d84834275b5bd0.json"}}, {"family": "M\u00fchleip", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1877-2282", "researcher": {"href": "https://publications.scilifelab.se/researcher/921b5acb5b7c402fa06c8c148cbd5340.json"}}, {"family": "Tobiasson", "given": "Victor", "initials": "V", "orcid": "0000-0001-8920-017X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5208789057a94d0d9575476bf9c88d5a.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal article", "published": "2020-10-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5342", "issn-l": "2041-1723"}, "abstract": "Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF1. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 \u00c5 resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.", "doi": "10.1038/s41467-020-18993-6", "pmid": "33093501", "labels": {"Cryo-EM": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18993-6"}, {"db": "pmc", "key": "PMC7583250"}], "notes": [], "created": "2020-10-26T14:40:56.262Z", "modified": "2023-12-04T10:09:34.900Z"}, {"entity": "publication", "iuid": "3b8d1f21730c444f9488bdde02b7966a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b8d1f21730c444f9488bdde02b7966a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b8d1f21730c444f9488bdde02b7966a"}}, "title": "A high-stringency blueprint of the human proteome.", "authors": [{"family": "Adhikari", "given": "Subash", "initials": "S"}, {"family": "Nice", "given": "Edouard C", "initials": "EC"}, {"family": "Deutsch", "given": "Eric W", "initials": "EW"}, {"family": "Lane", "given": "Lydie", "initials": "L", "orcid": "0000-0002-9818-3030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0992244993b4f0799f58c63f39a5c5e.json"}}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications.scilifelab.se/researcher/c434ae7226ff49e8b00a33c37a46dd60.json"}}, {"family": "Pennington", "given": "Stephen R", "initials": "SR"}, {"family": "Paik", "given": "Young-Ki", "initials": "YK"}, {"family": "Overall", "given": "Christopher M", "initials": "CM", "orcid": "0000-0001-5844-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f770b082f2447fd96e1daab1b1bc4f1.json"}}, {"family": "Corrales", "given": "Fernando J", "initials": "FJ"}, {"family": "Cristea", "given": "Ileana M", "initials": "IM"}, {"family": "Van Eyk", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0001-9050-148X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e860403a0224d588958a9c588688ff6.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Chan", "given": "Daniel W", "initials": "DW"}, {"family": "Bairoch", "given": "Amos", "initials": "A"}, {"family": "Waddington", "given": "James C", "initials": "JC"}, {"family": "Justice", "given": "Joshua L", "initials": "JL"}, {"family": "LaBaer", "given": "Joshua", "initials": "J"}, {"family": "Rodriguez", "given": "Henry", "initials": "H"}, {"family": "He", "given": "Fuchu", "initials": "F"}, {"family": "Kostrzewa", "given": "Markus", "initials": "M"}, {"family": "Ping", "given": "Peipei", "initials": "P"}, {"family": "Gundry", "given": "Rebekah L", "initials": "RL", "orcid": "0000-0002-9263-833X", "researcher": {"href": "https://publications.scilifelab.se/researcher/60163f86086644e9a74a7793d886dd3e.json"}}, {"family": "Stewart", "given": "Peter", "initials": "P"}, {"family": "Srivastava", "given": "Sanjeeva", "initials": "S"}, {"family": "Srivastava", "given": "Sudhir", "initials": "S"}, {"family": "Nogueira", "given": "Fabio C S", "initials": "FCS"}, {"family": "Domont", "given": "Gilberto B", "initials": "GB"}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y", "orcid": "0000-0002-1292-373X", "researcher": {"href": "https://publications.scilifelab.se/researcher/16eb301087cd46c5b12bdb276fdf561b.json"}}, {"family": "Lam", "given": "Maggie P Y", "initials": "MPY"}, {"family": "Wennersten", "given": "Sara", "initials": "S"}, {"family": "Vizcaino", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df36c9559504428a42edba7ba33ec08.json"}}, {"family": "Wilkins", "given": "Marc", "initials": "M", "orcid": "0000-0002-5700-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/98c5bc0757d145d692312da866ebf51a.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Bandeira", "given": "Nuno", "initials": "N", "orcid": "0000-0001-8385-3655", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6377e04591748fc9450eaff4d41acff.json"}}, {"family": "Marko-Varga", "given": "Gyorgy", "initials": "G"}, {"family": "Weintraub", "given": "Susan T", "initials": "ST"}, {"family": "Pineau", "given": "Charles", "initials": "C"}, {"family": "Kusebauch", "given": "Ulrike", "initials": "U", "orcid": "0000-0001-6162-7577", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b4bcdb047c4b1fa84e513ea0eddd5e.json"}}, {"family": "Moritz", "given": "Robert L", "initials": "RL", "orcid": "0000-0002-3216-9447", "researcher": {"href": "https://publications.scilifelab.se/researcher/2aaa7d54f7de41cf915b47e8037c15cf.json"}}, {"family": "Ahn", "given": "Seong Beom", "initials": "SB"}, {"family": "Palmblad", "given": "Magnus", "initials": "M"}, {"family": "Snyder", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2594af48f3d45e68983030873c06cf5.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications.scilifelab.se/researcher/9222eeba13464c618695f91ea8764abb.json"}}, {"family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4620f71cdce4e6e91264f96b74c6d84.json"}}], "type": "journal article", "published": "2020-10-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5301", "issn-l": "2041-1723"}, "abstract": "The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.", "doi": "10.1038/s41467-020-19045-9", "pmid": "33067450", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-19045-9"}, {"db": "pmc", "key": "PMC7568584"}], "notes": [], "created": "2020-12-10T19:07:09.284Z", "modified": "2021-11-10T12:46:20.338Z"}, {"entity": "publication", "iuid": "f870d06d8746421ebbb308e2a749cf8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f870d06d8746421ebbb308e2a749cf8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f870d06d8746421ebbb308e2a749cf8e"}}, "title": "Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins.", "authors": [{"family": "Nowak", "given": "Kathrin", "initials": "K"}, {"family": "Rosenthal", "given": "Florian", "initials": "F"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "B\u00fctepage", "given": "Mareike", "initials": "M"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "AG"}, {"family": "Dreier", "given": "Birgit", "initials": "B"}, {"family": "Grossmann", "given": "Jonas", "initials": "J"}, {"family": "Sobek", "given": "Jens", "initials": "J"}, {"family": "Imhof", "given": "Ralph", "initials": "R"}, {"family": "L\u00fcscher", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9622-8709", "researcher": {"href": "https://publications.scilifelab.se/researcher/b777138c7e7740c5926a5385997dec9c.json"}}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H", "orcid": "0000-0003-4059-3501", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49b25ddfc934f3ca41020c3f38c6bfc.json"}}, {"family": "Pl\u00fcckthun", "given": "Andreas", "initials": "A", "orcid": "0000-0003-4191-5306", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f67a65bf469443a89665bd244bfd0f7.json"}}, {"family": "Leslie Pedrioli", "given": "Deena M", "initials": "DM", "orcid": "0000-0003-2342-8010", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d2182b2344f4758abdf6fb8a05a39eb.json"}}, {"family": "Hottiger", "given": "Michael O", "initials": "MO", "orcid": "0000-0002-7323-2270", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cc0bd6ccac3417fb8c04e02a5833efd.json"}}], "type": "journal article", "published": "2020-10-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5199", "issn-l": "2041-1723"}, "abstract": "Protein ADP-ribosylation is a reversible post-translational modification that regulates important cellular functions. The identification of modified proteins has proven challenging and has mainly been achieved via enrichment methodologies. Random mutagenesis was used here to develop an engineered Af1521 ADP-ribose binding macro domain protein with 1000-fold increased affinity towards ADP-ribose. The crystal structure reveals that two point mutations K35E and Y145R form a salt bridge within the ADP-ribose binding domain. This forces the proximal ribose to rotate within the binding pocket and, as a consequence, improves engineered Af1521 ADPr-binding affinity. Its use in our proteomic ADP-ribosylome workflow increases the ADP-ribosylated protein identification rates and yields greater ADP-ribosylome coverage. Furthermore, generation of an engineered Af1521 Fc fusion protein confirms the improved detection of cellular ADP-ribosylation by immunoblot and immunofluorescence. Thus, this engineered isoform of Af1521 can also serve as a valuable tool for the analysis of cellular ADP-ribosylation under in vivo conditions.", "doi": "10.1038/s41467-020-18981-w", "pmid": "33060572", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7566600"}, {"db": "pii", "key": "10.1038/s41467-020-18981-w"}], "notes": [], "created": "2024-04-03T14:24:02.267Z", "modified": "2024-04-03T14:24:02.738Z"}, {"entity": "publication", "iuid": "c66db214519348c0863eeb3e089bbccc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c66db214519348c0863eeb3e089bbccc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c66db214519348c0863eeb3e089bbccc"}}, "title": "Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.", "authors": [{"family": "Itoh", "given": "Yuzuru", "initials": "Y", "orcid": "0000-0001-7802-5572", "researcher": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582.json"}}, {"family": "Naschberger", "given": "Andreas", "initials": "A"}, {"family": "Mortezaei", "given": "Narges", "initials": "N"}, {"family": "Herrmann", "given": "Johannes M", "initials": "JM", "orcid": "0000-0003-2081-4506", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d45f53a0781428291e45ebb9ac8a372.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal article", "published": "2020-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5187", "issn-l": "2041-1723"}, "abstract": "Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF1) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation.", "doi": "10.1038/s41467-020-18830-w", "pmid": "33056988", "labels": {"Cryo-EM": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18830-w"}, {"db": "pmc", "key": "PMC7560712"}], "notes": [], "created": "2020-10-14T14:19:09.292Z", "modified": "2021-11-10T12:44:48.768Z"}, {"entity": "publication", "iuid": "e980f00b87dd45d3ab9ceb6c3c4cca0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e980f00b87dd45d3ab9ceb6c3c4cca0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e980f00b87dd45d3ab9ceb6c3c4cca0c"}}, "title": "An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility.", "authors": [{"family": "Navarro", "given": "Carmen", "initials": "C", "orcid": "0000-0001-5438-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}}, {"family": "Lyu", "given": "Jing", "initials": "J", "orcid": "0000-0001-9529-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbe28157081c49debba23f0b9ebd9c74.json"}}, {"family": "Katsori", "given": "Anna-Maria", "initials": "AM", "orcid": "0000-0002-5975-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a338e7f888b4e7fa663fdd87d667713.json"}}, {"family": "Caridha", "given": "Rozina", "initials": "R"}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}], "type": "journal article", "published": "2020-10-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5095", "issn-l": "2041-1723"}, "abstract": "Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. Nucleosome turnover is known to be universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently at intracisternal A-particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28-KAP1/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. Further, we find that Smarcad1 chromatin remodeler evicts nucleosomes generating accessible DNA. Free DNA is repackaged via DAXX-mediated nucleosome assembly with histone variant H3.3 in this dynamic heterochromatin state. Loss of H3.3 in mouse embryonic stem cells elicits a highly specific opening of interstitial heterochromatin with minimal effects on other silent or active regions of the genome.", "doi": "10.1038/s41467-020-18863-1", "pmid": "33037201", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7547087"}, {"db": "pii", "key": "10.1038/s41467-020-18863-1"}], "notes": [], "created": "2024-04-03T14:21:34.373Z", "modified": "2024-04-03T14:22:37.597Z"}, {"entity": "publication", "iuid": "db71f369517e425cac0b1c66d3c937e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db71f369517e425cac0b1c66d3c937e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db71f369517e425cac0b1c66d3c937e0"}}, "title": "SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden.", "authors": [{"family": "Rudberg", "given": "Ann-Sofie", "initials": "AS", "orcid": "0000-0003-3616-9943", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e81215bbec8467388ec0592d4110169.json"}}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d155273b5b54e61b773f263e4f2ce9b.json"}}, {"family": "Jernbom Falk", "given": "August", "initials": "A", "orcid": "0000-0002-7773-1851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe6400bde68b46899515cef5bea05fca.json"}}, {"family": "Aguilera", "given": "Katherina", "initials": "K"}, {"family": "Ng", "given": "Henry", "initials": "H", "orcid": "0000-0003-2873-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcb12c664a64724b5cd42a1267a5bea.json"}}, {"family": "Gabrielsson", "given": "Lena", "initials": "L"}, {"family": "Salomonsson", "given": "Ann-Christin", "initials": "AC"}, {"family": "Hanke", "given": "Leo", "initials": "L", "orcid": "0000-0001-5514-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece050a286f946f6807170cffc9320e7.json"}}, {"family": "Murrell", "given": "Ben", "initials": "B"}, {"family": "McInerney", "given": "Gerald", "initials": "G", "orcid": "0000-0003-2257-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac2f68095fe4426b97ec070865e5091.json"}}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Andersson", "given": "Eni", "initials": "E", "orcid": "0000-0002-5115-0637", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef94cf857c3746088cd01cee49242f24.json"}}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Bayati", "given": "Shaghayegh", "initials": "S"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Phillipson", "given": "Mia", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-1345-6491", "researcher": {"href": "https://publications.scilifelab.se/researcher/130fb6ef6b774613a767e98f9f9b2eb4.json"}}], "type": "journal article", "published": "2020-10-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5064", "issn-l": "2041-1723"}, "abstract": "SARS-CoV-2 may pose an occupational health risk to healthcare workers. Here, we report the seroprevalence of SARS-CoV-2 antibodies, self-reported symptoms and occupational exposure to SARS-CoV-2 among healthcare workers at a large acute care hospital in Sweden. The seroprevalence of IgG antibodies against SARS-CoV-2 was 19.1% among the 2149 healthcare workers recruited between April 14th and May 8th 2020, which was higher than the reported regional seroprevalence during the same time period. Symptoms associated with seroprevalence were anosmia (odds ratio (OR) 28.4, 95% CI 20.6-39.5) and ageusia (OR 19.2, 95% CI 14.3-26.1). Seroprevalence was also associated with patient contact (OR 2.9, 95% CI 1.9-4.5) and covid-19 patient contact (OR 3.3, 95% CI 2.2-5.3). These findings imply an occupational risk for SARS-CoV-2 infection among healthcare workers. Continued measures are warranted to assure healthcare workers safety and reduce transmission from healthcare workers to patients and to the community.", "doi": "10.1038/s41467-020-18848-0", "pmid": "33033249", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18848-0"}, {"db": "pmc", "key": "PMC7544689"}], "notes": [], "created": "2020-10-10T20:52:35.390Z", "modified": "2021-11-10T12:46:29.669Z"}, {"entity": "publication", "iuid": "c4ca7ddb792e49aab70137c27e6970f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4ca7ddb792e49aab70137c27e6970f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4ca7ddb792e49aab70137c27e6970f3"}}, "title": "Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders.", "authors": [{"family": "Wang", "given": "Tianyun", "initials": "T", "orcid": "0000-0002-5179-087X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f8343adbdf84296a4bf04c6890d49d2.json"}}, {"family": "Hoekzema", "given": "Kendra", "initials": "K"}, {"family": "Vecchio", "given": "Davide", "initials": "D", "orcid": "0000-0003-2907-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7d64eefa6a041caad3a8c860e76d84e.json"}}, {"family": "Wu", "given": "Huidan", "initials": "H"}, {"family": "Sulovari", "given": "Arvis", "initials": "A", "orcid": "0000-0003-4354-9020", "researcher": {"href": "https://publications.scilifelab.se/researcher/85f6043d9c7c4ca49ced9ed1c0f97340.json"}}, {"family": "Coe", "given": "Bradley P", "initials": "BP"}, {"family": "Gillentine", "given": "Madelyn A", "initials": "MA", "orcid": "0000-0002-8989-2214", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e5086e94ffb4bc7a8367b15d17b876e.json"}}, {"family": "Wilfert", "given": "Amy B", "initials": "AB"}, {"family": "Perez-Jurado", "given": "Luis A", "initials": "LA"}, {"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Sleyp", "given": "Yoeri", "initials": "Y"}, {"family": "Earl", "given": "Rachel K", "initials": "RK"}, {"family": "Rosenfeld", "given": "Jill A", "initials": "JA", "orcid": "0000-0001-5664-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/1826b4a473304149a22a9646d6f76a3e.json"}}, {"family": "Geisheker", "given": "Madeleine R", "initials": "MR", "orcid": "0000-0002-4166-3236", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3494f8f657c4d0fbbd886ac89ac9cfa.json"}}, {"family": "Han", "given": "Lin", "initials": "L"}, {"family": "Du", "given": "Bing", "initials": "B"}, {"family": "Barnett", "given": "Chris", "initials": "C"}, {"family": "Thompson", "given": "Elizabeth", "initials": "E"}, {"family": "Shaw", "given": "Marie", "initials": "M"}, {"family": "Carroll", "given": "Renee", "initials": "R"}, {"family": "Friend", "given": "Kathryn", "initials": "K"}, {"family": "Catford", "given": "Rachael", "initials": "R"}, {"family": "Palmer", "given": "Elizabeth E", "initials": "EE"}, {"family": "Zou", "given": "Xiaobing", "initials": "X"}, {"family": "Ou", "given": "Jianjun", "initials": "J"}, {"family": "Li", "given": "Honghui", "initials": "H"}, {"family": "Guo", "given": "Hui", "initials": "H", "orcid": "0000-0002-1570-2545", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b7e6c55e24449fd9b53f6ed08003742.json"}}, {"family": "Gerdts", "given": "Jennifer", "initials": "J"}, {"family": "Avola", "given": "Emanuela", "initials": "E"}, {"family": "Calabrese", "given": "Giuseppe", "initials": "G"}, {"family": "Elia", "given": "Maurizio", "initials": "M"}, {"family": "Greco", "given": "Donatella", "initials": "D"}, {"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", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Vandeweyer", "given": "Geert", "initials": "G"}, {"family": "Van Dijck", "given": "Anke", "initials": "A", "orcid": "0000-0002-6713-2943", "researcher": {"href": "https://publications.scilifelab.se/researcher/b190da43c29e4245b71b37ab7cdb81db.json"}}, {"family": "Van der Aa", "given": "Nathalie", "initials": "N"}, {"family": "McKenna", "given": "Brooke", "initials": "B"}, {"family": "Hancarova", "given": "Miroslava", "initials": "M"}, {"family": "Bendova", "given": "Sarka", "initials": "S"}, {"family": "Havlovicova", "given": "Marketa", "initials": "M"}, {"family": "Malerba", "given": "Giovanni", "initials": "G"}, {"family": "Bernardina", "given": "Bernardo Dalla", "initials": "BD"}, {"family": "Muglia", "given": "Pierandrea", "initials": "P"}, {"family": "van Haeringen", "given": "Arie", "initials": "A"}, {"family": "Hoffer", "given": "Mariette J V", "initials": "MJV", "orcid": "0000-0002-1812-7670", "researcher": {"href": "https://publications.scilifelab.se/researcher/04747e9661474d43a1f4a7ed51eb7207.json"}}, {"family": "Franke", "given": "Barbara", "initials": "B", "orcid": "0000-0003-4375-6572", "researcher": {"href": "https://publications.scilifelab.se/researcher/105f0131cfc34a668ed840e622e4f902.json"}}, {"family": "Cappuccio", "given": "Gerarda", "initials": "G"}, {"family": "Delatycki", "given": "Martin", "initials": "M"}, {"family": "Lockhart", "given": "Paul J", "initials": "PJ", "orcid": "0000-0003-2531-8413", "researcher": {"href": "https://publications.scilifelab.se/researcher/af606d21d6524fbdbd65f044fddbd00b.json"}}, {"family": "Manning", "given": "Melanie A", "initials": "MA"}, {"family": "Liu", "given": "Pengfei", "initials": "P", "orcid": "0000-0002-4177-709X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bda9fff7cc042eaa054b5257799c1f4.json"}}, {"family": "Scheffer", "given": "Ingrid E", "initials": "IE"}, {"family": "Brunetti-Pierri", "given": "Nicola", "initials": "N", "orcid": "0000-0002-6895-8819", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9785f9985d645259283e808cdcd77a9.json"}}, {"family": "Rommelse", "given": "Nanda", "initials": "N"}, {"family": "Amaral", "given": "David G", "initials": "DG"}, {"family": "Santen", "given": "Gijs W E", "initials": "GWE"}, {"family": "Trabetti", "given": "Elisabetta", "initials": "E"}, {"family": "Sedl\u00e1\u010dek", "given": "Zden\u011bk", "initials": "Z"}, {"family": "Michaelson", "given": "Jacob J", "initials": "JJ", "orcid": "0000-0001-9713-0992", "researcher": {"href": "https://publications.scilifelab.se/researcher/13cd0bf6a3c3437485c0c8c6a32839dc.json"}}, {"family": "Pierce", "given": "Karen", "initials": "K"}, {"family": "Courchesne", "given": "Eric", "initials": "E", "orcid": "0000-0002-3772-5799", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae6305c8ed044e1ca6b637f982d181c4.json"}}, {"family": "Kooy", "given": "R Frank", "initials": "RF", "orcid": "0000-0003-2024-0485", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0e9d246a6ac47029258886b9537a0e5.json"}}, {"family": "SPARK Consortium", "given": "", "initials": ""}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Romano", "given": "Corrado", "initials": "C", "orcid": "0000-0003-1049-0683", "researcher": {"href": "https://publications.scilifelab.se/researcher/634b98b512e84042af68e05eff055978.json"}}, {"family": "Peeters", "given": "Hilde", "initials": "H"}, {"family": "Bernier", "given": "Raphael A", "initials": "RA"}, {"family": "Gecz", "given": "Jozef", "initials": "J", "orcid": "0000-0002-7884-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfa0d2adb36840858e1f9f8e407269b0.json"}}, {"family": "Xia", "given": "Kun", "initials": "K", "orcid": "0000-0001-8090-6002", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbfe349e05c740a7894d1bab511a3768.json"}}, {"family": "Eichler", "given": "Evan E", "initials": "EE", "orcid": "0000-0002-8246-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/43901cc9fc3b4f5c9a18260e36558eb9.json"}}], "type": "journal article", "published": "2020-10-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4932", "issn-l": "2041-1723"}, "abstract": "Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case-control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF < 0.01%) gene-disruptive mutations (FDR 5%), six of which reach family-wise error rate (FWER) significance (p < 1.25E-06). Among these 125 targeted genes, we also reevaluate DNM excess in 17,426 NDD trios with 6,499 new autism trios. We identify 90 genes enriched for DNMs (FDR 5%; e.g., GABRG2 and UIMC1); of which, 61 reach FWER significance (p < 3.64E-07; e.g., CASZ1). In addition to doubling the number of patients for many NDD risk genes, we present phenotype-genotype correlations for seven risk genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN, and LEO1) based on this large-scale targeted sequencing effort.", "doi": "10.1038/s41467-020-18723-y", "pmid": "33004838", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18723-y"}, {"db": "pmc", "key": "PMC7530681"}], "notes": [], "created": "2021-11-20T12:18:30.540Z", "modified": "2021-11-20T12:18:31.111Z"}, {"entity": "publication", "iuid": "a3077264f8cc4b788b7506ddb9b5546f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3077264f8cc4b788b7506ddb9b5546f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3077264f8cc4b788b7506ddb9b5546f"}}, "title": "Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth.", "authors": [{"family": "Krivanek", "given": "Jan", "initials": "J", "orcid": "0000-0002-7590-187X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e716ca0e1b464dd9850687d8f5aa6758.json"}}, {"family": "Soldatov", "given": "Ruslan A", "initials": "RA"}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME"}, {"family": "Chontorotzea", "given": "Tatiana", "initials": "T"}, {"family": "Herdina", "given": "Anna Nele", "initials": "AN"}, {"family": "Petersen", "given": "Julian", "initials": "J", "orcid": "0000-0002-7444-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/74d20bbfd5a540a58aac82ada8d80b0d.json"}}, {"family": "Szarowska", "given": "Bara", "initials": "B"}, {"family": "Landova", "given": "Marie", "initials": "M"}, {"family": "Matejova", "given": "Veronika Kovar", "initials": "VK"}, {"family": "Holla", "given": "Lydie Izakovicova", "initials": "LI", "orcid": "0000-0002-7610-8929", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c239a2405d04c14ad3d1a08759d1457.json"}}, {"family": "Kuchler", "given": "Ulrike", "initials": "U"}, {"family": "Zdrilic", "given": "Ivana Vidovic", "initials": "IV"}, {"family": "Vijaykumar", "given": "Anushree", "initials": "A", "orcid": "0000-0002-9311-8715", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e151e4b5e2d49ab925969f0b425ed58.json"}}, {"family": "Balic", "given": "Anamaria", "initials": "A", "orcid": "0000-0001-6796-1197", "researcher": {"href": "https://publications.scilifelab.se/researcher/53dc6465cd6b44c38e2e29aeb3f077a7.json"}}, {"family": "Marangoni", "given": "Pauline", "initials": "P"}, {"family": "Klein", "given": "Ophir D", "initials": "OD", "orcid": "0000-0002-6254-7082", "researcher": {"href": "https://publications.scilifelab.se/researcher/aab94ed0b4f549ef941147b2ffbe27c9.json"}}, {"family": "Neves", "given": "Vitor C M", "initials": "VCM"}, {"family": "Yianni", "given": "Val", "initials": "V", "orcid": "0000-0001-9857-7577", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa7601d7378f41319dfb7cc9210ccfea.json"}}, {"family": "Sharpe", "given": "Paul T", "initials": "PT", "orcid": "0000-0003-2116-9561", "researcher": {"href": "https://publications.scilifelab.se/researcher/d32e7381201b4d9e932b44da8f37e3b1.json"}}, {"family": "Harkany", "given": "Tibor", "initials": "T"}, {"family": "Metscher", "given": "Brian D", "initials": "BD", "orcid": "0000-0002-6514-4406", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ab0055dc0374b4bb88f9bfbb2e0313a.json"}}, {"family": "Baj\u00e9noff", "given": "Marc", "initials": "M"}, {"family": "Mina", "given": "Mina", "initials": "M"}, {"family": "Fried", "given": "Kaj", "initials": "K"}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV", "orcid": "0000-0002-6036-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/a67002dec1264bf2865da0017405ee9b.json"}}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}], "type": "journal article", "published": "2020-09-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4816", "issn-l": "2041-1723"}, "abstract": "Understanding cell types and mechanisms of dental growth is essential for reconstruction and engineering of teeth. Therefore, we investigated cellular composition of growing and non-growing mouse and human teeth. As a result, we report an unappreciated cellular complexity of the continuously-growing mouse incisor, which suggests a coherent model of cell dynamics enabling unarrested growth. This model relies on spatially-restricted stem, progenitor and differentiated populations in the epithelial and mesenchymal compartments underlying the coordinated expansion of two major branches of pulpal cells and diverse epithelial subtypes. Further comparisons of human and mouse teeth yield both parallelisms and differences in tissue heterogeneity and highlight the specifics behind growing and non-growing modes. Despite being similar at a coarse level, mouse and human teeth reveal molecular differences and species-specific cell subtypes suggesting possible evolutionary divergence. Overall, here we provide an atlas of human and mouse teeth with a focus on growth and differentiation.", "doi": "10.1038/s41467-020-18512-7", "pmid": "32968047", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18512-7"}, {"db": "pmc", "key": "PMC7511944"}], "notes": [], "created": "2021-12-10T20:15:06.566Z", "modified": "2022-01-03T10:04:22.911Z"}, {"entity": "publication", "iuid": "32d06cd19e9b474391c7e5f6ed354f57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32d06cd19e9b474391c7e5f6ed354f57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32d06cd19e9b474391c7e5f6ed354f57"}}, "title": "Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.", "authors": [{"family": "Bailey", "given": "Matthew H", "initials": "MH", "orcid": "0000-0003-4526-9727", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2acdd4c993a403b825e0509aaae6a46.json"}}, {"family": "Meyerson", "given": "William U", "initials": "WU"}, {"family": "Dursi", "given": "Lewis Jonathan", "initials": "LJ", "orcid": "0000-0002-4697-798X", "researcher": {"href": "https://publications.scilifelab.se/researcher/263b14bd385c42649b4f31a1fee009ce.json"}}, {"family": "Wang", "given": "Liang-Bo", "initials": "LB", "orcid": "0000-0001-6977-9348", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c831d5f02f04d31a89688ba02316aa4.json"}}, {"family": "Dong", "given": "Guanlan", "initials": "G", "orcid": "0000-0002-4747-6036", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad63b4954fc7483bb4eadc4ce7d5938c.json"}}, {"family": "Liang", "given": "Wen-Wei", "initials": "WW"}, {"family": "Weerasinghe", "given": "Amila", "initials": "A", "orcid": "0000-0003-3568-5823", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cb7a3b0bd5641688178c1d84200f9e7.json"}}, {"family": "Li", "given": "Shantao", "initials": "S", "orcid": "0000-0002-5440-2780", "researcher": {"href": "https://publications.scilifelab.se/researcher/9204d1cf2cef4a068c4f0b8bffd4a371.json"}}, {"family": "Li", "given": "Yize", "initials": "Y"}, {"family": "Kelso", "given": "Sean", "initials": "S"}, {"family": "MC3 Working Group", "given": "", "initials": ""}, {"family": "PCAWG novel somatic mutation calling methods working group", "given": "", "initials": ""}, {"family": "Saksena", "given": "Gordon", "initials": "G", "orcid": "0000-0001-6630-7935", "researcher": {"href": "https://publications.scilifelab.se/researcher/9acc7eddfc5047cfb0972de9134e2ad8.json"}}, {"family": "Ellrott", "given": "Kyle", "initials": "K", "orcid": "0000-0002-6573-5900", "researcher": {"href": "https://publications.scilifelab.se/researcher/35d682f015af4da3bff3b13cfd6f3f91.json"}}, {"family": "Wendl", "given": "Michael C", "initials": "MC"}, {"family": "Wheeler", "given": "David A", "initials": "DA", "orcid": "0000-0002-9056-6299", "researcher": {"href": "https://publications.scilifelab.se/researcher/13d586dd710f4452a76af607baeb219f.json"}}, {"family": "Getz", "given": "Gad", "initials": "G", "orcid": "0000-0002-0936-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/974b292190aa40c4a3b0c1d7ab735376.json"}}, {"family": "Simpson", "given": "Jared T", "initials": "JT"}, {"family": "Gerstein", "given": "Mark B", "initials": "MB", "orcid": "0000-0002-9746-3719", "researcher": {"href": "https://publications.scilifelab.se/researcher/345c9cc52dae493595c1d9ce10c0891d.json"}}, {"family": "Ding", "given": "Li", "initials": "L"}, {"family": "PCAWG Consortium", "given": "", "initials": ""}], "type": "comparative study", "published": "2020-09-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4748", "issn-l": "2041-1723"}, "abstract": "The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.", "doi": "10.1038/s41467-020-18151-y", "pmid": "32958763", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18151-y"}, {"db": "pmc", "key": "PMC7505971"}], "notes": [], "created": "2020-12-10T14:46:47.966Z", "modified": "2021-11-10T12:47:09.115Z"}, {"entity": "publication", "iuid": "043ab27fa61944e99a7e279442373b57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/043ab27fa61944e99a7e279442373b57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/043ab27fa61944e99a7e279442373b57"}}, "title": "Integration of molecular profiles in a longitudinal wellness profiling cohort.", "authors": [{"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Koistinen", "given": "Ina Schuppe", "initials": "IS"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Olsson", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-9730-1915", "researcher": {"href": "https://publications.scilifelab.se/researcher/2460963d77ee4eee9409fbd8c257d910.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Stenlund", "given": "Hans", "initials": "H"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Olin", "given": "Axel", "initials": "A", "orcid": "0000-0002-1161-4476", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dfb8efde80a4a508c93714729259aba.json"}}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Jansson", "given": "Per-Anders", "initials": "PA"}, {"family": "Anger\u00e5s", "given": "Oskar", "initials": "O"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Kjellqvist", "given": "Sanela", "initials": "S"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4871-8818", "researcher": {"href": "https://publications.scilifelab.se/researcher/1689878e0c5542d08d3e2d5043a6ce5c.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}], "type": "journal article", "published": "2020-09-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "4487"}, "abstract": "An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.", "doi": "10.1038/s41467-020-18148-7", "pmid": "32900998", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative", "Cellular Immunomonitoring": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18148-7"}, {"db": "pmc", "key": "PMC7479148"}], "notes": [], "created": "2020-09-10T05:17:29.818Z", "modified": "2025-10-17T13:03:16.662Z"}, {"entity": "publication", "iuid": "df0ebcff7ad2473fb0152621838de472", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df0ebcff7ad2473fb0152621838de472.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df0ebcff7ad2473fb0152621838de472"}}, "title": "An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction.", "authors": [{"family": "Hanke", "given": "Leo", "initials": "L", "orcid": "0000-0001-5514-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece050a286f946f6807170cffc9320e7.json"}}, {"family": "Vidakovics Perez", "given": "Laura", "initials": "L", "orcid": "0000-0003-4283-812X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f8d317c1bf74fd5bfb3e63936f5ab5e.json"}}, {"family": "Sheward", "given": "Daniel J", "initials": "DJ"}, {"family": "Das", "given": "Hrishikesh", "initials": "H"}, {"family": "Schulte", "given": "Tim", "initials": "T"}, {"family": "Moliner-Morro", "given": "Ainhoa", "initials": "A"}, {"family": "Corcoran", "given": "Martin", "initials": "M"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB"}, {"family": "H\u00e4llberg", "given": "B Martin", "initials": "BM", "orcid": "0000-0002-6781-0345", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b7e4327d0ac48288afd6061f149156d.json"}}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}, {"family": "McInerney", "given": "Gerald M", "initials": "GM", "orcid": "0000-0003-2257-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac2f68095fe4426b97ec070865e5091.json"}}], "type": "journal article", "published": "2020-09-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4420", "issn-l": "2041-1723"}, "abstract": "SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 \u00c5 resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.", "doi": "10.1038/s41467-020-18174-5", "pmid": "32887876", "labels": {"Protein Science Facility (PSF)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18174-5"}, {"db": "pmc", "key": "PMC7473855"}], "notes": [], "created": "2020-09-08T08:44:04.841Z", "modified": "2024-01-16T13:48:41.765Z"}, {"entity": "publication", "iuid": "bd1a87d416a44b78b1e5b21dd61f2b66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd1a87d416a44b78b1e5b21dd61f2b66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd1a87d416a44b78b1e5b21dd61f2b66"}}, "title": "Sex differences in oncogenic mutational processes.", "authors": [{"family": "Li", "given": "Constance H", "initials": "CH", "orcid": "0000-0002-5487-7225", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1b145ea074a457288ef97554becf7df.json"}}, {"family": "Prokopec", "given": "Stephenie D", "initials": "SD", "orcid": "0000-0001-7936-8577", "researcher": {"href": "https://publications.scilifelab.se/researcher/be46453f056f42fe8a35c0a72201d7e4.json"}}, {"family": "Sun", "given": "Ren X", "initials": "RX"}, {"family": "Yousif", "given": "Fouad", "initials": "F"}, {"family": "Schmitz", "given": "Nathaniel", "initials": "N"}, {"family": "PCAWG Tumour Subtypes and Clinical Translation", "given": "", "initials": ""}, {"family": "Boutros", "given": "Paul C", "initials": "PC", "orcid": "0000-0003-0553-7520", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f627e3789d04a28aa270a5873c5f20b.json"}}, {"family": "PCAWG Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2020-08-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4330", "issn-l": "2041-1723"}, "abstract": "Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.", "doi": "10.1038/s41467-020-17359-2", "pmid": "32859912", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17359-2"}, {"db": "pmc", "key": "PMC7455744"}], "notes": [], "created": "2020-12-10T14:46:49.399Z", "modified": "2021-11-10T12:47:52.388Z"}, {"entity": "publication", "iuid": "acb48c2531964cb4b5a8c73639e2f114", "links": {"self": {"href": "https://publications.scilifelab.se/publication/acb48c2531964cb4b5a8c73639e2f114.json"}, "display": {"href": "https://publications.scilifelab.se/publication/acb48c2531964cb4b5a8c73639e2f114"}}, "title": "Cell-surface receptors enable perception of extracellular cytokinins.", "authors": [{"family": "Antoniadi", "given": "Ioanna", "initials": "I", "orcid": "0000-0001-9053-2788", "researcher": {"href": "https://publications.scilifelab.se/researcher/60bcbb474ded4df08079520c92de49bf.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Gelov\u00e1", "given": "Zuzana", "initials": "Z", "orcid": "0000-0003-4783-1752", "researcher": {"href": "https://publications.scilifelab.se/researcher/afc862721b52467aa092f0ecf9fc7bed.json"}}, {"family": "Johnson", "given": "Alexander", "initials": "A", "orcid": "0000-0002-2739-8843", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9414092144944429b428466733e6567.json"}}, {"family": "Pl\u00edhal", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-0645-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/f42115be2a6b4268a3bf6f9200479f93.json"}}, {"family": "Simersk\u00fd", "given": "Radim", "initials": "R", "orcid": "0000-0002-4481-6680", "researcher": {"href": "https://publications.scilifelab.se/researcher/218c11787cf2467a98ab7d0c826de187.json"}}, {"family": "Mik", "given": "V\u00e1clav", "initials": "V", "orcid": "0000-0002-8515-3035", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f69a95dba24bd793e708f0cdcc2ded.json"}}, {"family": "Vain", "given": "Thomas", "initials": "T"}, {"family": "Mateo-Bonmat\u00ed", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-2364-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1e96edf1a914d2f8ea8eb46c3ebacc4.json"}}, {"family": "Karady", "given": "Michal", "initials": "M"}, {"family": "Pernisov\u00e1", "given": "Mark\u00e9ta", "initials": "M", "orcid": "0000-0002-5803-2879", "researcher": {"href": "https://publications.scilifelab.se/researcher/acc243598b74495999230f9b1b0da0be.json"}}, {"family": "Pla\u010dkov\u00e1", "given": "Lenka", "initials": "L"}, {"family": "Opassathian", "given": "Korawit", "initials": "K"}, {"family": "Hej\u00e1tko", "given": "Jan", "initials": "J"}, {"family": "Robert", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0002-0013-3239", "researcher": {"href": "https://publications.scilifelab.se/researcher/74a96c43520f4c9c91e44be8a7d39e6c.json"}}, {"family": "Friml", "given": "Ji\u0159\u00ed", "initials": "J", "orcid": "0000-0002-8302-7596", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e525fe6afc5490a86223e38be195cee.json"}}, {"family": "Dole\u017eal", "given": "Karel", "initials": "K", "orcid": "0000-0003-4938-0350", "researcher": {"href": "https://publications.scilifelab.se/researcher/f209cf1d8e5d4945b81bd9f01c2b2665.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Turnbull", "given": "Colin", "initials": "C", "orcid": "0000-0001-6635-1418", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd75adef49f4c789b69206cdb7e8cf0.json"}}], "type": "journal article", "published": "2020-08-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4284", "issn-l": "2041-1723"}, "abstract": "Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.", "doi": "10.1038/s41467-020-17700-9", "pmid": "32855409", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17700-9"}, {"db": "pmc", "key": "PMC7453015"}], "notes": [], "created": "2020-12-11T11:56:05.497Z", "modified": "2025-10-17T13:03:16.685Z"}, {"entity": "publication", "iuid": "6f59a84f1afe4e30bd4fb89e91d3311d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f59a84f1afe4e30bd4fb89e91d3311d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f59a84f1afe4e30bd4fb89e91d3311d"}}, "title": "Single cell RNA sequencing identifies early diversity of sensory neurons forming via bi-potential intermediates.", "authors": [{"family": "Faure", "given": "Louis", "initials": "L", "orcid": "0000-0003-4621-586X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbf218e53c854d69a1b474a61480c33f.json"}}, {"family": "Wang", "given": "Yiqiao", "initials": "Y"}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME", "orcid": "0000-0002-0563-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e0722d8c5484a13bb37c3a3b084ff8c.json"}}, {"family": "Fontanet", "given": "Paula", "initials": "P", "orcid": "0000-0002-5324-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe102480cb7458a941fc70fe7f5cb9b.json"}}, {"family": "Cheung", "given": "Kylie K Y", "initials": "KKY"}, {"family": "Petitpr\u00e9", "given": "Charles", "initials": "C"}, {"family": "Wu", "given": "Haohao", "initials": "H"}, {"family": "Sun", "given": "Lynn Linyu", "initials": "LL"}, {"family": "Runge", "given": "Karen", "initials": "K"}, {"family": "Croci", "given": "Laura", "initials": "L", "orcid": "0000-0002-7826-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e08f8646894441297506e2a3eb5fb57.json"}}, {"family": "Landy", "given": "Mark A", "initials": "MA", "orcid": "0000-0002-2789-0774", "researcher": {"href": "https://publications.scilifelab.se/researcher/5334230675f543fc8b870741f103854d.json"}}, {"family": "Lai", "given": "Helen C", "initials": "HC", "orcid": "0000-0003-4334-0243", "researcher": {"href": "https://publications.scilifelab.se/researcher/de71bea36e954743b1e576c7e681f9eb.json"}}, {"family": "Consalez", "given": "Gian Giacomo", "initials": "GG"}, {"family": "de Chevigny", "given": "Antoine", "initials": "A", "orcid": "0000-0002-7413-0591", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a2d23fc97564742905b48e36f4bc585.json"}}, {"family": "Lallemend", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}], "type": "journal article", "published": "2020-08-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4175", "issn-l": "2041-1723"}, "abstract": "Somatic sensation is defined by the existence of a diversity of primary sensory neurons with unique biological features and response profiles to external and internal stimuli. However, there is no coherent picture about how this diversity of cell states is transcriptionally generated. Here, we use deep single cell analysis to resolve fate splits and molecular biasing processes during sensory neurogenesis in mice. Our results identify a complex series of successive and specific transcriptional changes in post-mitotic neurons that delineate hierarchical regulatory states leading to the generation of the main sensory neuron classes. In addition, our analysis identifies previously undetected early gene modules expressed long before fate determination although being clearly associated with defined sensory subtypes. Overall, the early diversity of sensory neurons is generated through successive bi-potential intermediates in which synchronization of relevant gene modules and concurrent repression of competing fate programs precede cell fate stabilization and final commitment.", "doi": "10.1038/s41467-020-17929-4", "pmid": "32826903", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17929-4"}, {"db": "pmc", "key": "PMC7442800"}], "notes": [], "created": "2020-10-06T11:10:56.370Z", "modified": "2024-01-16T13:48:41.901Z"}, {"entity": "publication", "iuid": "ec6422dbc5dc4b039f6c638f56ddcca9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec6422dbc5dc4b039f6c638f56ddcca9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec6422dbc5dc4b039f6c638f56ddcca9"}}, "title": "Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis.", "authors": [{"family": "Carlstr\u00f6m", "given": "Karl E", "initials": "KE"}, {"family": "Zhu", "given": "Keying", "initials": "K", "orcid": "0000-0001-7500-1532", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b85d1ae8136464788be19d62a8863d7.json"}}, {"family": "Ewing", "given": "Ewoud", "initials": "E", "orcid": "0000-0001-8644-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aea9350a4f864d8e8781ab111b4f9273.json"}}, {"family": "Krabbendam", "given": "Inge E", "initials": "IE"}, {"family": "Harris", "given": "Robert A", "initials": "RA", "orcid": "0000-0003-4990-509X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b0733d3c25145139f42cad897d6726b.json"}}, {"family": "Falc\u00e3o", "given": "Ana Mendanha", "initials": "AM"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}], "type": "journal article", "published": "2020-08-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4071", "issn-l": "2041-1723"}, "abstract": "Arrest of oligodendrocyte (OL) differentiation and remyelination following myelin damage in multiple sclerosis (MS) is associated with neurodegeneration and clinical worsening. We show that Glutathione S-transferase 4\u03b1 (Gsta4) is highly expressed during adult OL differentiation and that Gsta4 loss impairs differentiation into myelinating OLs in vitro. In addition, we identify Gsta4 as a target of both dimethyl fumarate, an existing MS therapy, and clemastine fumarate, a candidate remyelinating agent in MS. Overexpression of Gsta4 reduces expression of Fas and activity of the mitochondria-associated Casp8-Bid-axis in adult oligodendrocyte precursor cells, leading to improved OL survival during differentiation. The Gsta4 effect on apoptosis during adult OL differentiation was corroborated in vivo in both lysolecithin-induced demyelination and experimental autoimmune encephalomyelitis models, where Casp8 activity was reduced in Gsta4-overexpressing OLs. Our results identify Gsta4 as an intrinsic regulator of OL differentiation, survival and remyelination, as well as a potential target for future reparative MS therapies.", "doi": "10.1038/s41467-020-17871-5", "pmid": "32792491", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17871-5"}, {"db": "pmc", "key": "PMC7426940"}], "notes": [], "created": "2021-01-08T16:29:42.593Z", "modified": "2024-01-16T13:48:41.933Z"}, {"entity": "publication", "iuid": "c7e200350fda45a291ec77006ecc5bbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7e200350fda45a291ec77006ecc5bbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7e200350fda45a291ec77006ecc5bbb"}}, "title": "Discovery and population genomics of structural variation in a songbird genus.", "authors": [{"family": "Weissensteiner", "given": "Matthias H", "initials": "MH", "orcid": "0000-0001-9302-798X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5550a93e906d4e25985cd7641f8be554.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Catal\u00e1n", "given": "Ana", "initials": "A"}, {"family": "Francoijs", "given": "Kees-Jan", "initials": "KJ"}, {"family": "Knief", "given": "Ulrich", "initials": "U", "orcid": "0000-0001-6959-3033", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d8858c7c7b44a008a172bc637957ce1.json"}}, {"family": "Heim", "given": "Wieland", "initials": "W", "orcid": "0000-0002-3262-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/a88dd35e7b8a46b49c9e2ccc6d712b45.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Pophaly", "given": "Saurabh D", "initials": "SD"}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Warmuth", "given": "Vera M", "initials": "VM"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2020-07-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "3403"}, "abstract": "Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.", "doi": "10.1038/s41467-020-17195-4", "pmid": "32636372", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17195-4"}, {"db": "pmc", "key": "PMC7341801"}, {"db": "Dryad", "key": "10.5061/dryad.ns1rn8ppj"}], "notes": [], "created": "2020-08-25T12:55:18.199Z", "modified": "2024-01-16T13:48:42.202Z"}, {"entity": "publication", "iuid": "91408d68992c46ec9a960d86551d53a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/91408d68992c46ec9a960d86551d53a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/91408d68992c46ec9a960d86551d53a4"}}, "title": "Diamond Blackfan anemia is mediated by hyperactive Nemo-like kinase.", "authors": [{"family": "Wilkes", "given": "M C", "initials": "MC", "orcid": "0000-0002-9600-6831", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca84b03e6bf54c65a2b76fb3e64e0fbf.json"}}, {"family": "Siva", "given": "K", "initials": "K", "orcid": "0000-0001-9480-4496", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1a374557b76413cb2e620349d1de2b0.json"}}, {"family": "Chen", "given": "J", "initials": "J", "orcid": "0000-0001-8516-0975", "researcher": {"href": "https://publications.scilifelab.se/researcher/93cf6eaa8a61475789a772d30f29d2e5.json"}}, {"family": "Varetti", "given": "G", "initials": "G"}, {"family": "Youn", "given": "M Y", "initials": "MY", "orcid": "0000-0002-8112-2346", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0d57655fc0140e98bff8d5a38591a08.json"}}, {"family": "Chae", "given": "H", "initials": "H"}, {"family": "Ek", "given": "F", "initials": "F", "orcid": "0000-0002-5651-8445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad7f4358932945309129f9a6c16bedf3.json"}}, {"family": "Olsson", "given": "R", "initials": "R", "orcid": "0000-0002-7107-3472", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3e5a72515bf44e98f43d4690c6e577e.json"}}, {"family": "Lundb\u00e4ck", "given": "T", "initials": "T"}, {"family": "Dever", "given": "D P", "initials": "DP", "orcid": "0000-0001-5966-4803", "researcher": {"href": "https://publications.scilifelab.se/researcher/26948c8bb03f49e38ac7a3a902e78818.json"}}, {"family": "Nishimura", "given": "T", "initials": "T", "orcid": "0000-0002-5425-1708", "researcher": {"href": "https://publications.scilifelab.se/researcher/2262afd615c94810b338de701266a1e8.json"}}, {"family": "Narla", "given": "A", "initials": "A"}, {"family": "Glader", "given": "B", "initials": "B", "orcid": "0000-0003-2092-6276", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d18e9cf455741ada3a80c925e1bd462.json"}}, {"family": "Nakauchi", "given": "H", "initials": "H", "orcid": "0000-0002-9841-6973", "researcher": {"href": "https://publications.scilifelab.se/researcher/05684f8f727b43109f4d79d5bfec7c33.json"}}, {"family": "Porteus", "given": "M H", "initials": "MH", "orcid": "0000-0002-3850-4648", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b4f9245987d4111b06d16f2afc9bb12.json"}}, {"family": "Repellin", "given": "C E", "initials": "CE", "orcid": "0000-0002-6552-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e36d8ec30b64efba4c0a91752598cd4.json"}}, {"family": "Gazda", "given": "H T", "initials": "HT"}, {"family": "Lin", "given": "S", "initials": "S"}, {"family": "Serrano", "given": "M", "initials": "M", "orcid": "0000-0001-7177-9312", "researcher": {"href": "https://publications.scilifelab.se/researcher/68e6f5d0278d4a7da30286ac0a59b5e0.json"}}, {"family": "Flygare", "given": "J", "initials": "J", "orcid": "0000-0002-1962-5276", "researcher": {"href": "https://publications.scilifelab.se/researcher/0814225ca796418c82b446b1c8c91961.json"}}, {"family": "Sakamoto", "given": "K M", "initials": "KM"}], "type": "journal article", "published": "2020-07-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "3344"}, "abstract": "Diamond Blackfan Anemia (DBA) is a congenital bone marrow failure syndrome associated with ribosomal gene mutations that lead to ribosomal insufficiency. DBA is characterized by anemia, congenital anomalies, and cancer predisposition. Treatment for DBA is associated with significant morbidity. Here, we report the identification of Nemo-like kinase (NLK) as a potential target for DBA therapy. To identify new DBA targets, we screen for small molecules that increase erythroid expansion in mouse models of DBA. This screen identified a compound that inhibits NLK. Chemical and genetic inhibition of NLK increases erythroid expansion in mouse and human progenitors, including bone marrow cells from DBA patients. In DBA models and patient samples, aberrant NLK activation is initiated at the Megakaryocyte/Erythroid Progenitor (MEP) stage of differentiation and is not observed in non-erythroid hematopoietic lineages or healthy erythroblasts. We propose that NLK mediates aberrant erythropoiesis in DBA and is a potential target for therapy.", "doi": "10.1038/s41467-020-17100-z", "pmid": "32620751", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17100-z"}, {"db": "pmc", "key": "PMC7334220"}], "notes": [], "created": "2022-03-24T08:52:06.800Z", "modified": "2025-10-17T13:04:28.288Z"}, {"entity": "publication", "iuid": "bc5dea45b8d148c38c3f0096804469f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc5dea45b8d148c38c3f0096804469f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc5dea45b8d148c38c3f0096804469f7"}}, "title": "A\u03b2(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage.", "authors": [{"family": "Ciudad", "given": "Sonia", "initials": "S", "orcid": "0000-0002-9030-175X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a5cf9b106604a72a8f873df97dab76e.json"}}, {"family": "Puig", "given": "Eduard", "initials": "E"}, {"family": "Botzanowski", "given": "Thomas", "initials": "T"}, {"family": "Meigooni", "given": "Moeen", "initials": "M"}, {"family": "Arango", "given": "Andres S", "initials": "AS"}, {"family": "Do", "given": "Jimmy", "initials": "J"}, {"family": "Mayzel", "given": "Maxim", "initials": "M", "orcid": "0000-0002-7413-0444", "researcher": {"href": "https://publications.scilifelab.se/researcher/467c29017024478692460a363ed9a945.json"}}, {"family": "Bayoumi", "given": "Mariam", "initials": "M"}, {"family": "Chaignepain", "given": "St\u00e9phane", "initials": "S"}, {"family": "Maglia", "given": "Giovanni", "initials": "G", "orcid": "0000-0003-2784-0811", "researcher": {"href": "https://publications.scilifelab.se/researcher/98d18f36cb0644029036fde5c55dff28.json"}}, {"family": "Cianferani", "given": "Sarah", "initials": "S"}, {"family": "Orekhov", "given": "Vladislav", "initials": "V"}, {"family": "Tajkhorshid", "given": "Emad", "initials": "E", "orcid": "0000-0001-8434-1010", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ca6a74c70b14ccbaaa39b96415114b5.json"}}, {"family": "Bardiaux", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-4014-9195", "researcher": {"href": "https://publications.scilifelab.se/researcher/f23e6431b8254c01bddb4279617d78f3.json"}}, {"family": "Carulla", "given": "Nat\u00e0lia", "initials": "N", "orcid": "0000-0002-3787-978X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e44e07561344299d0d29b03011a2ef.json"}}], "type": "journal article", "published": "2020-06-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "3014", "issn-l": "2041-1723"}, "abstract": "Formation of amyloid-beta (A\u03b2) oligomer pores in the membrane of neurons has been proposed to explain neurotoxicity in Alzheimer's disease (AD). Here, we present the three-dimensional structure of an A\u03b2 oligomer formed in a membrane mimicking environment, namely an A\u03b2(1-42) tetramer, which comprises a six stranded \u03b2-sheet core. The two faces of the \u03b2-sheet core are hydrophobic and surrounded by the membrane-mimicking environment while the edges are hydrophilic and solvent-exposed. By increasing the concentration of A\u03b2(1-42) in the sample, A\u03b2(1-42) octamers are also formed, made by two A\u03b2(1-42) tetramers facing each other forming a \u03b2-sandwich structure. Notably, A\u03b2(1-42) tetramers and octamers inserted into lipid bilayers as well-defined pores. To establish oligomer structure-membrane activity relationships, molecular dynamics simulations were carried out. These studies revealed a mechanism of membrane disruption in which water permeation occurred through lipid-stabilized pores mediated by the hydrophilic residues located on the core \u03b2-sheets edges of the oligomers.", "doi": "10.1038/s41467-020-16566-1", "pmid": "32541820", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-16566-1"}, {"db": "pmc", "key": "PMC7296003"}], "notes": [], "created": "2020-12-11T09:17:34.243Z", "modified": "2025-10-17T13:03:56.893Z"}, {"entity": "publication", "iuid": "8e84f5a3ca5548628b22e3d122c5eed6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e84f5a3ca5548628b22e3d122c5eed6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e84f5a3ca5548628b22e3d122c5eed6"}}, "title": "Distinct pre-initiation steps in human mitochondrial translation.", "authors": [{"family": "Khawaja", "given": "Anas", "initials": "A"}, {"family": "Itoh", "given": "Yuzuru", "initials": "Y", "orcid": "0000-0001-7802-5572", "researcher": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582.json"}}, {"family": "Remes", "given": "Cristina", "initials": "C"}, {"family": "Sp\u00e5hr", "given": "Henrik", "initials": "H"}, {"family": "Yukhnovets", "given": "Olessya", "initials": "O"}, {"family": "H\u00f6fig", "given": "Henning", "initials": "H", "orcid": "0000-0003-0506-783X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5d914f8854e4010949124154dfa1539.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}], "type": "journal article", "published": "2020-06-10", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "2932", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two distinct mitochondrial pre-initiation assembly steps involving those factors. Single-particle cryo-EM revealed that in the first step, interactions between mitochondria-specific protein mS37 and mtIF3 keep the small mitoribosomal subunit in a conformation favorable for a subsequent accommodation of mtIF2 in the second step. Combination with fluorescence cross-correlation spectroscopy analyses suggests that mtIF3 promotes complex assembly without mRNA or initiator tRNA binding, where exclusion is achieved by the N-terminal and C-terminal domains of mtIF3. Finally, the association of large mitoribosomal subunit is required for initiator tRNA and leaderless mRNA recruitment to form a stable initiation complex. These data reveal fundamental aspects of mammalian protein synthesis that are specific to mitochondria.", "doi": "10.1038/s41467-020-16503-2", "pmid": "32522994", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-16503-2"}, {"db": "pmc", "key": "PMC7287080"}], "notes": [], "created": "2020-06-20T05:51:40.998Z", "modified": "2021-11-10T12:50:19.697Z"}, {"entity": "publication", "iuid": "2b160d0829af493f9894f3148bb0ad8f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b160d0829af493f9894f3148bb0ad8f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b160d0829af493f9894f3148bb0ad8f"}}, "title": "CYCLIN-B1/2 and -D1 act in opposition to coordinate cortical progenitor self-renewal and lineage commitment.", "authors": [{"family": "Hagey", "given": "Daniel W", "initials": "DW", "orcid": "0000-0001-9246-6235", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9b5df8185a54da58f080ea7a7b956ef.json"}}, {"family": "Topcic", "given": "Danijal", "initials": "D"}, {"family": "Kee", "given": "Nigel", "initials": "N"}, {"family": "Reynaud", "given": "Florie", "initials": "F"}, {"family": "Bergsland", "given": "Maria", "initials": "M"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Muhr", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0704-0788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a665f02acc432e9d80feb5c61f4572.json"}}], "type": "journal article", "published": "2020-06-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "2898", "issn-l": "2041-1723"}, "abstract": "The sequential generation of layer-specific cortical neurons requires radial glia cells (RGCs) to precisely balance self-renewal and lineage commitment. While specific cell-cycle phases have been associated with these decisions, the mechanisms linking the cell-cycle machinery to cell-fate commitment remain obscure. Using single-cell RNA-sequencing, we find that the strongest transcriptional signature defining multipotent RGCs is that of G2/M-phase, and particularly CYCLIN-B1/2, while lineage-committed progenitors are enriched in G1/S-phase genes, including CYCLIN-D1. These data also reveal cell-surface markers that allow us to isolate RGCs and lineage-committed progenitors, and functionally confirm the relationship between cell-cycle phase enrichment and cell fate competence. Finally, we use cortical electroporation to demonstrate that CYCLIN-B1/2 cooperate with CDK1 to maintain uncommitted RGCs by activating the NOTCH pathway, and that CYCLIN-D1 promotes differentiation. Thus, this work establishes that cell-cycle phase-specific regulators act in opposition to coordinate the self-renewal and lineage commitment of RGCs via core stem cell regulatory pathways.", "doi": "10.1038/s41467-020-16597-8", "pmid": "32518258", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-16597-8"}, {"db": "pmc", "key": "PMC7283355"}], "notes": [], "created": "2020-12-07T16:26:58.923Z", "modified": "2024-01-16T13:48:42.396Z"}, {"entity": "publication", "iuid": "d98c58bf1e6e4de9b468b52b6592fa41", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d98c58bf1e6e4de9b468b52b6592fa41.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d98c58bf1e6e4de9b468b52b6592fa41"}}, "title": "Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction.", "authors": [{"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Weng", "given": "Lu-Chen", "initials": "LC", "orcid": "0000-0003-1475-4930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e52c9c21794412bbb3750fda1fecfe0.json"}}, {"family": "Cartwright", "given": "James H", "initials": "JH"}, {"family": "Hall", "given": "Amelia Weber", "initials": "AW", "orcid": "0000-0002-7915-0313", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a151b393a6c434585d4834fd32de6a4.json"}}, {"family": "Sveinbjornsson", "given": "Gardar", "initials": "G"}, {"family": "Tucker", "given": "Nathan R", "initials": "NR", "orcid": "0000-0002-5071-4218", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89b1366ff014dc6a9cc5fe4bd37becf.json"}}, {"family": "Choi", "given": "Seung Hoan", "initials": "SH"}, {"family": "Chaffin", "given": "Mark D", "initials": "MD", "orcid": "0000-0002-1234-5562", "researcher": {"href": "https://publications.scilifelab.se/researcher/c73477de5ca0468ab051fd6eab7bad81.json"}}, {"family": "Roselli", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5267-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dd28aad250f42719d505c21ed76013b.json"}}, {"family": "Barnes", "given": "Michael R", "initials": "MR", "orcid": "0000-0001-9097-7381", "researcher": {"href": "https://publications.scilifelab.se/researcher/bffbcdd5aad340b98d7da297ffc21e6b.json"}}, {"family": "Mifsud", "given": "Borbala", "initials": "B", "orcid": "0000-0003-3429-3094", "researcher": {"href": "https://publications.scilifelab.se/researcher/0105dc446d594b0bb3be38b8eb94a16b.json"}}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Cranley", "given": "James J", "initials": "JJ"}, {"family": "Concas", "given": "Maria Pina", "initials": "MP", "orcid": "0000-0003-3598-2537", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f63075f4ce43cc921c658fb353bd25.json"}}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Boutin", "given": "Thibaud", "initials": "T", "orcid": "0000-0003-4754-1675", "researcher": {"href": "https://publications.scilifelab.se/researcher/d573e6802c4c4702839902830dbbea71.json"}}, {"family": "Kolcic", "given": "Ivana", "initials": "I", "orcid": "0000-0001-7918-6052", "researcher": {"href": "https://publications.scilifelab.se/researcher/891cf7a5a8ae496d99e92e4ef7de7b65.json"}}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Rudan", "given": "Igor", "initials": "I", "orcid": "0000-0001-6993-6884", "researcher": {"href": "https://publications.scilifelab.se/researcher/d50e1ca836e841f8a7a748ae93b59d75.json"}}, {"family": "Araujo", "given": "Nathalia M", "initials": "NM"}, {"family": "Lima-Costa", "given": "Maria Fernanda", "initials": "MF"}, {"family": "Ribeiro", "given": "Antonio Luiz P", "initials": "ALP"}, {"family": "Souza", "given": "Renan P", "initials": "RP", "orcid": "0000-0002-9479-4432", "researcher": {"href": "https://publications.scilifelab.se/researcher/5063e735c93847978a9eba44224a3495.json"}}, {"family": "Tarazona-Santos", "given": "Eduardo", "initials": "E"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V", "orcid": "0000-0003-3423-2021", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c95879213664e00b66aeee2e8ece975.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-2256-6972", "researcher": {"href": 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"type": "journal article", "published": "2020-05-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "2542", "issn-l": "2041-1723"}, "abstract": "The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N = 293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease.", "doi": "10.1038/s41467-020-15706-x", "pmid": "32439900", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15706-x"}, {"db": "pmc", "key": "PMC7242331"}], "notes": [], "created": "2020-05-27T13:29:26.954Z", "modified": "2021-11-10T12:50:53.503Z"}, {"entity": "publication", "iuid": "943e2024538744c492d89c63c743f034", "links": {"self": {"href": "https://publications.scilifelab.se/publication/943e2024538744c492d89c63c743f034.json"}, "display": {"href": "https://publications.scilifelab.se/publication/943e2024538744c492d89c63c743f034"}}, "title": "Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson's disease.", "authors": [{"family": "Tiklov\u00e1", "given": "Katar\u00edna", "initials": "K"}, {"family": "Nolbrant", "given": "Sara", "initials": "S", "orcid": "0000-0003-2184-1741", "researcher": {"href": "https://publications.scilifelab.se/researcher/91ab50f5e5874992a0703470230a8462.json"}}, {"family": "Fiorenzano", "given": "Alessandro", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Sharma", "given": "Yogita", "initials": "Y"}, {"family": "Heuer", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0300-7606", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc2bac2f0e63487792fd5525ee1c2b1e.json"}}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Hoban", "given": "Deirdre B", "initials": "DB"}, {"family": "Cardoso", "given": "Tiago", "initials": "T", "orcid": "0000-0003-2686-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/08d76d0b77f14d39a6c097386e158174.json"}}, {"family": "Adler", "given": "Andrew F", "initials": "AF"}, {"family": "Birtele", "given": "Marcella", "initials": "M"}, {"family": "Lund\u00e9n-Miguel", "given": "Hilda", "initials": "H"}, {"family": "Volakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Kirkeby", "given": "Agnete", "initials": "A"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Parmar", "given": "Malin", "initials": "M", "orcid": "0000-0001-5002-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48b5aaff3bc4832a96fda4f2cf127cb.json"}}], "type": "journal article", "published": "2020-05-15", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "2434", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Cell replacement is a long-standing and realistic goal for the treatment of Parkinson's disease (PD). Cells for transplantation can be obtained from fetal brain tissue or from stem cells. However, after transplantation, dopamine (DA) neurons are seen to be a minor component of grafts, and it has remained difficult to determine the identity of other cell types. Here, we report analysis by single-cell RNA sequencing (scRNA-seq) combined with comprehensive histological analyses to characterize intracerebral grafts from human embryonic stem cells (hESCs) and fetal tissue after functional maturation in a pre-clinical rat PD model. We show that neurons and astrocytes are major components in both fetal and stem cell-derived grafts. Additionally, we identify a cell type closely resembling a class of recently identified perivascular-like cells in stem cell-derived grafts. Thus, this study uncovers previously unknown cellular diversity in a clinically relevant cell replacement PD model.", "doi": "10.1038/s41467-020-16225-5", "pmid": "32415072", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-16225-5"}, {"db": "pmc", "key": "PMC7229159"}], "notes": [], "created": "2020-06-02T07:25:59.289Z", "modified": "2024-01-16T13:48:42.494Z"}, {"entity": "publication", "iuid": "4317205fc07d449db7735d0732d85a4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4317205fc07d449db7735d0732d85a4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4317205fc07d449db7735d0732d85a4c"}}, "title": "Molecular profiling of driver events in metastatic uveal melanoma.", "authors": [{"family": "Karlsson", "given": "Joakim", "initials": "J", "orcid": "0000-0001-6332-4043", "researcher": {"href": "https://publications.scilifelab.se/researcher/6190c1a8a7d54cd6807f120e8748cfcd.json"}}, {"family": "Nilsson", "given": "Lisa M", "initials": "LM"}, {"family": "Mitra", "given": "Suman", "initials": "S"}, {"family": "Als\u00e9n", "given": "Samuel", "initials": "S"}, {"family": "Shelke", "given": "Ganesh Vilas", "initials": "GV", "orcid": "0000-0001-5883-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaee610fe341d79fa92f2f4f9a9683.json"}}, {"family": "Sah", "given": "Vasu R", "initials": "VR"}, {"family": "Forsberg", "given": "Elin M V", "initials": "EMV", "orcid": "0000-0002-4196-3060", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e6342bc14ba426bbf61704b4873377a.json"}}, {"family": "Stierner", "given": "Ulrika", "initials": "U"}, {"family": "All-Eriksson", "given": "Charlotta", "initials": "C"}, {"family": "Einarsdottir", "given": "Berglind", "initials": "B"}, {"family": "Jespersen", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6543-5369", "researcher": {"href": "https://publications.scilifelab.se/researcher/d220a3bcbfea44228722a123b25ec1b2.json"}}, {"family": "Ny", "given": "Lars", "initials": "L"}, {"family": "Lindn\u00e9r", "given": "Per", "initials": "P"}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "Olofsson Bagge", "given": "Roger", "initials": "R", "orcid": "0000-0001-5795-0355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1f8016d5e64418ca71f230e64e415ba.json"}}, {"family": "Nilsson", "given": "Jonas A", "initials": "JA", "orcid": "0000-0003-0346-6837", "researcher": {"href": "https://publications.scilifelab.se/researcher/27f0581f25124e98b0bd0eef8c3f3331.json"}}], "type": "journal article", "published": "2020-04-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "1894", "issn-l": "2041-1723"}, "abstract": "Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma, and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations are overrepresented and found in 29/32 of cases. Reintroducing a functional BAP1 allele into a deficient patient-derived cell line, reveals a broad shift towards a transcriptomic subtype previously associated with better prognosis of the primary disease. One outlier tumor has a high mutational burden associated with UV-damage. CDKN2A deletions also occur, which are rarely present in primaries. A focused knockdown screen is used to investigate overexpressed genes associated withcopy number gains. Tumor-infiltrating lymphocytes are in several cases found tumor-reactive, but expression of the immune checkpoint receptors TIM-3, TIGIT and LAG3 is also abundant. This study represents the largest whole-genome analysis of uveal melanoma to date, and presents an updated view of the metastatic disease.", "doi": "10.1038/s41467-020-15606-0", "pmid": "32313009", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15606-0"}, {"db": "pmc", "key": "PMC7171146"}], "notes": [], "created": "2020-07-08T13:04:38.039Z", "modified": "2024-01-16T13:48:42.590Z"}, {"entity": "publication", "iuid": "0501e4e6d44c4a8c947ef756d0262288", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0501e4e6d44c4a8c947ef756d0262288.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0501e4e6d44c4a8c947ef756d0262288"}}, "title": "Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia.", "authors": [{"family": "Halvorsen", "given": "Matthew", "initials": "M"}, {"family": "Huh", "given": "Ruth", "initials": "R"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Wen", "given": "Jia", "initials": "J", "orcid": "0000-0003-3273-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/872570fb0f94464d988fd5b2d3a8b7e7.json"}}, {"family": "Netotea", "given": "Sergiu", "initials": "S"}, {"family": "Giusti-Rodriguez", "given": "Paola", "initials": "P", "orcid": "0000-0002-1921-1305", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6594f03c6c344d69b08234fd751ab23.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Ancalade", "given": "NaEshia", "initials": "N"}, {"family": "Farrell", "given": "Martilias", "initials": "M", "orcid": "0000-0002-9520-6209", "researcher": {"href": "https://publications.scilifelab.se/researcher/20be04f56c474537ad8fa07cb17241cf.json"}}, {"family": "Crowley", "given": "James J", "initials": "JJ"}, {"family": "Li", "given": "Yun", "initials": "Y"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Szatkiewicz", "given": "Jin P", "initials": "JP", "orcid": "0000-0002-4898-7401", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb39edd3c6c14938a47f1e22ecfea080.json"}}], "type": "journal article", "published": "2020-04-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "1842"}, "abstract": "Despite considerable progress in schizophrenia genetics, most findings have been for large rare structural variants and common variants in well-imputed regions with few genes implicated from exome sequencing. Whole genome sequencing (WGS) can potentially provide a more complete enumeration of etiological genetic variation apart from the exome and regions of high linkage disequilibrium. We analyze high-coverage WGS data from 1162 Swedish schizophrenia cases and 936 ancestry-matched population controls. Our main objective is to evaluate the contribution to schizophrenia etiology from a variety of genetic variants accessible to WGS but not by previous technologies. Our results suggest that ultra-rare structural variants that affect the boundaries of topologically associated domains (TADs) increase risk for schizophrenia. Alterations in TAD boundaries may lead to dysregulation of gene expression. Future mechanistic studies will be needed to determine the precise functional effects of these variants on biology.", "doi": "10.1038/s41467-020-15707-w", "pmid": "32296054", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Systems Biology": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15707-w"}, {"db": "pmc", "key": "PMC7160146"}], "notes": [], "created": "2020-04-20T06:46:04.706Z", "modified": "2024-01-16T13:48:42.613Z"}, {"entity": "publication", "iuid": "35ceb41b656a47a982d5b274b2ccd969", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35ceb41b656a47a982d5b274b2ccd969.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35ceb41b656a47a982d5b274b2ccd969"}}, "title": "Identification of cell surface markers and establishment of monolayer differentiation to retinal pigment epithelial cells.", "authors": [{"family": "Plaza Reyes", "given": "Alvaro", "initials": "A", "orcid": "0000-0003-1167-6316", "researcher": {"href": "https://publications.scilifelab.se/researcher/36f7ddaf16ac45bfad26c96f292f2072.json"}}, {"family": "Petrus-Reurer", "given": "Sandra", "initials": "S", "orcid": "0000-0002-7051-1741", "researcher": {"href": "https://publications.scilifelab.se/researcher/716f74c81a3240e5b612dab55e997267.json"}}, {"family": "Padrell S\u00e1nchez", "given": "Sara", "initials": "S"}, {"family": "Kumar", "given": "Pankaj", "initials": "P", "orcid": "0000-0002-8411-1634", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e9109710e2e45009c332e257c3c498a.json"}}, {"family": "Douagi", "given": "Iyadh", "initials": "I", "orcid": "0000-0002-3221-8667", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a19504ddb2544bca5aeab9abf885b13.json"}}, {"family": "Bartuma", "given": "Hammurabi", "initials": "H"}, {"family": "Aronsson", "given": "Monica", "initials": "M"}, {"family": "Westman", "given": "Sofie", "initials": "S"}, {"family": "Lardner", "given": "Emma", "initials": "E"}, {"family": "Andr\u00e9", "given": "Helder", "initials": "H", "orcid": "0000-0002-2926-2376", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e7098d1d25b4f31a2a45d41ab11da2f.json"}}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Nandrot", "given": "Emeline F", "initials": "EF", "orcid": "0000-0003-3087-078X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed12259fa5b24f04853b930077e50077.json"}}, {"family": "Kvanta", "given": "Anders", "initials": "A"}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}], "type": "journal article", "published": "2020-03-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "1609", "issn-l": "2041-1723"}, "abstract": "In vitro differentiation of human pluripotent stem cells into functional retinal pigment epithelial (RPE) cells provides a potentially unlimited source for cell based reparative therapy of age-related macular degeneration. Although the inherent pigmentation of the RPE cells have been useful to grossly evaluate differentiation efficiency and allowed manual isolation of pigmented structures, accurate quantification and automated isolation has been challenging. To address this issue, here we perform a comprehensive antibody screening and identify cell surface markers for RPE cells. We show that these markers can be used to isolate RPE cells during in vitro differentiation and to track, quantify and improve differentiation efficiency. Finally, these surface markers aided to develop a robust, direct and scalable monolayer differentiation protocol on human recombinant laminin-111 and -521 without the need for manual isolation.", "doi": "10.1038/s41467-020-15326-5", "pmid": "32231223", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15326-5"}, {"db": "pmc", "key": "PMC7105463"}], "notes": [], "created": "2020-10-06T11:08:22.218Z", "modified": "2024-01-16T13:48:42.729Z"}, {"entity": "publication", "iuid": "f4b79cf485ae4ae2b999a8ce542884b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4b79cf485ae4ae2b999a8ce542884b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4b79cf485ae4ae2b999a8ce542884b9"}}, "title": "Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA.", "authors": [{"family": "Madru", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Henneke", "given": "Ghislaine", "initials": "G"}, {"family": "Raia", "given": "Pierre", "initials": "P", "orcid": "0000-0003-3469-1922", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdf3d3b11b384d52ba1bc00e7173b44b.json"}}, {"family": "Hugonneau-Beaufet", "given": "In\u00e8s", "initials": "I"}, {"family": "Pehau-Arnaudet", "given": "G\u00e9rard", "initials": "G"}, {"family": "England", "given": "Patrick", "initials": "P"}, {"family": "Lindahl", "given": "Erik", "initials": "E"}, {"family": "Delarue", "given": "Marc", "initials": "M"}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Sauguet", "given": "Ludovic", "initials": "L"}], "type": "journal article", "published": "2020-03-27", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "1591", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD-PCNA complex from Pyrococcus abyssi at 3.77 \u00c5. Using an integrative structural biology approach - combining cryo-EM, X-ray crystallography, protein-protein interaction measurements, and activity assays - we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA. PolD recruits PCNA via a complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Pol\u03b1 replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation and a processive phase during replication.", "doi": "10.1038/s41467-020-15392-9", "pmid": "32221299", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15392-9"}, {"db": "pmc", "key": "PMC7101311"}], "notes": [], "created": "2020-04-16T10:31:32.697Z", "modified": "2021-11-10T12:52:47.618Z"}, {"entity": "publication", "iuid": "d18a2001ca2a484ea1267aaed4906d19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d18a2001ca2a484ea1267aaed4906d19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d18a2001ca2a484ea1267aaed4906d19"}}, "title": "Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy.", "authors": [{"family": "Rendo", "given": "Veronica", "initials": "V", "orcid": "0000-0002-2983-4020", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f3fe17dd4464af585b16916a88c34b7.json"}}, {"family": "Stoimenov", "given": "Ivaylo", "initials": "I"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-6870-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/d79942eca68f4b2d8c2e72cf258f1213.json"}}, {"family": "Sj\u00f6berg", "given": "Elin", "initials": "E"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Ng", "given": "Adrian", "initials": "A"}, {"family": "O\u02bcBrien", "given": "Casey", "initials": "C", "orcid": "0000-0002-6572-4881", "researcher": {"href": "https://publications.scilifelab.se/researcher/5782c9d8ce674fe8ad55eba0d514da54.json"}}, {"family": "Giannakis", "given": "Marios", "initials": "M"}, {"family": "Artursson", "given": "Per", "initials": "P", "orcid": "0000-0002-3708-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/31575936c2714e1eb2f35c12df9a65a8.json"}}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Cheong", "given": "Ian", "initials": "I"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}], "type": "journal article", "published": "2020-03-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "1308"}, "abstract": "Cancer chemotherapy targeting frequent loss of heterozygosity events is an attractive concept, since tumor cells may lack enzymatic activities present in normal constitutional cells. To find exploitable targets, we map prevalent genetic polymorphisms to protein structures and identify 45 nsSNVs (non-synonymous small nucleotide variations) near the catalytic sites of 17 enzymes frequently lost in cancer. For proof of concept, we select the gastrointestinal drug metabolic enzyme NAT2 at 8p22, which is frequently lost in colorectal cancers and has a common variant with 10-fold reduced activity. Small molecule screening results in a cytotoxic kinase inhibitor that impairs growth of cells with slow NAT2 and decreases the growth of tumors with slow NAT2 by half as compared to those with wild-type NAT2. Most of the patient-derived CRC cells expressing slow NAT2 also show sensitivity to 6-(4-aminophenyl)-N-(3,4,5-trimethoxyphenyl)pyrazin-2-amine (APA) treatment. These findings indicate that the therapeutic index of anti-cancer drugs can be altered by bystander mutations affecting drug metabolic genes.", "doi": "10.1038/s41467-020-15111-4", "pmid": "32161261", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15111-4"}, {"db": "pmc", "key": "PMC7066191"}], "notes": [], "created": "2020-03-17T11:11:47.766Z", "modified": "2025-10-17T13:05:08.058Z"}, {"entity": "publication", "iuid": "a223b2180f754d79971096d57b714ee6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a223b2180f754d79971096d57b714ee6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a223b2180f754d79971096d57b714ee6"}}, "title": "Single-cell analysis of human ovarian cortex identifies distinct cell populations but no oogonial stem cells.", "authors": [{"family": "Wagner", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-6266-1248", "researcher": {"href": "https://publications.scilifelab.se/researcher/124ac27397f845a68732369680da7c5a.json"}}, {"family": "Yoshihara", "given": "Masahito", "initials": "M", "orcid": "0000-0002-8915-9282", "researcher": {"href": "https://publications.scilifelab.se/researcher/4303ab7a18254bb59f8e2386a7f7fb0a.json"}}, {"family": "Douagi", "given": "Iyadh", "initials": "I", "orcid": "0000-0002-3221-8667", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a19504ddb2544bca5aeab9abf885b13.json"}}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Panula", "given": "Sarita", "initials": "S"}, {"family": "Petropoulos", "given": "Sophie", "initials": "S"}, {"family": "Lu", "given": "Haojiang", "initials": "H"}, {"family": "Pettersson", "given": "Karin", "initials": "K"}, {"family": "Palm", "given": "Kerstin", "initials": "K"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Hovatta", "given": "Outi", "initials": "O", "orcid": "0000-0001-5395-3807", "researcher": {"href": "https://publications.scilifelab.se/researcher/f822ca12dfe0462b99c06e57cace4ce0.json"}}, {"family": "Kere", "given": "Juha", "initials": "J", "orcid": "0000-0003-1974-0271", "researcher": {"href": "https://publications.scilifelab.se/researcher/102085fb1c3147ceaf8dcb7651df1303.json"}}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}, {"family": "Damdimopoulou", "given": "Pauliina", "initials": "P", "orcid": "0000-0001-8458-0855", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d258c0f0d9b417ea4608769fc3ebaaf.json"}}], "type": "journal article", "published": "2020-03-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "1147", "issn-l": "2041-1723"}, "abstract": "The human ovary orchestrates sex hormone production and undergoes monthly structural changes to release mature oocytes. The outer lining of the ovary (cortex) has a key role in defining fertility in women as it harbors the ovarian reserve. It has been postulated that putative oogonial stem cells exist in the ovarian cortex and that these can be captured by DDX4 antibody isolation. Here, we report single-cell transcriptomes and cell surface antigen profiles of over 24,000 cells from high quality ovarian cortex samples from 21 patients. Our data identify transcriptional profiles of six main cell types; oocytes, granulosa cells, immune cells, endothelial cells, perivascular cells, and stromal cells. Cells captured by DDX4 antibody are perivascular cells, not oogonial stem cells. Our data do not support the existence of germline stem cells in adult human ovaries, thereby reinforcing the dogma of a limited ovarian reserve.", "doi": "10.1038/s41467-020-14936-3", "pmid": "32123174", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-14936-3"}, {"db": "pmc", "key": "PMC7052271"}], "notes": [], "created": "2020-03-03T10:20:08.878Z", "modified": "2024-01-16T13:48:42.834Z"}, {"entity": "publication", "iuid": "9909cb432f9745cbafcae0c1b08b44fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9909cb432f9745cbafcae0c1b08b44fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9909cb432f9745cbafcae0c1b08b44fd"}}, "title": "Primary cell wall inspired micro containers as a step towards a synthetic plant cell.", "authors": [{"family": "Paulraj", "given": "T", "initials": "T", "orcid": "0000-0001-5098-3525", "researcher": {"href": "https://publications.scilifelab.se/researcher/9be07d632ea8443fa8bfa2aaee6c93af.json"}}, {"family": "Wennmalm", "given": "S", "initials": "S"}, {"family": "Wieland", "given": "D C F", "initials": "DCF"}, {"family": "Riazanova", "given": "A V", "initials": "AV"}, {"family": "D\u0117dinait\u0117", "given": "A", "initials": "A"}, {"family": "G\u00fcnther Pomorski", "given": "T", "initials": "T"}, {"family": "C\u00e1rdenas", "given": "M", "initials": "M"}, {"family": "Svagan", "given": "A J", "initials": "AJ"}], "type": "journal article", "published": "2020-02-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "958", "issn-l": "2041-1723"}, "abstract": "The structural integrity of living plant cells heavily relies on the plant cell wall containing a nanofibrous cellulose skeleton. Hence, if synthetic plant cells consist of such a cell wall, they would allow for manipulation into more complex synthetic plant structures. Herein, we have overcome the fundamental difficulties associated with assembling lipid vesicles with cellulosic nanofibers (CNFs). We prepare plantosomes with an outer shell of CNF and pectin, and beneath this, a thin layer of lipids (oleic acid and phospholipids) that surrounds a water core. By exploiting the phase behavior of the lipids, regulated by pH and Mg2+ ions, we form vesicle-crowded interiors that change the outer dimension of the plantosomes, mimicking the expansion in real plant cells during, e.g., growth. The internal pressure enables growth of lipid tubules through the plantosome cell wall, which paves the way to the development of hierarchical plant structures and advanced synthetic plant cell mimics.", "doi": "10.1038/s41467-020-14718-x", "pmid": "32075974", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-14718-x"}, {"db": "pmc", "key": "PMC7031234"}], "notes": [], "created": "2020-06-29T15:46:04.008Z", "modified": "2021-11-10T12:53:55.840Z"}, {"entity": "publication", "iuid": "7e69f131beb747948a82b285b2993442", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e69f131beb747948a82b285b2993442.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e69f131beb747948a82b285b2993442"}}, "title": "Clonal competition within complex evolutionary hierarchies shapes AML over time.", "authors": [{"family": "Sand\u00e9n", "given": "Carl", "initials": "C", "orcid": "0000-0002-8931-9565", "researcher": {"href": "https://publications.scilifelab.se/researcher/29207805704e4660b20eebc87efe5282.json"}}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H", "orcid": "0000-0001-8703-1173", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a75300e8c346858ce8dd8f64ecae85.json"}}, {"family": "Orsmark Pietras", "given": "Christina", "initials": "C"}, {"family": "Henningsson", "given": "Rasmus", "initials": "R"}, {"family": "Saba", "given": "Karim H", "initials": "KH", "orcid": "0000-0003-4946-6488", "researcher": {"href": "https://publications.scilifelab.se/researcher/42cc0dd26f394abb9117550f4e5a034c.json"}}, {"family": "Landberg", "given": "Niklas", "initials": "N", "orcid": "0000-0001-6752-6507", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ad422be3ea44e419662d514ca40cbbe.json"}}, {"family": "Thorsson", "given": "Hanna", "initials": "H"}, {"family": "von Palffy", "given": "Sofia", "initials": "S", "orcid": "0000-0001-5640-4037", "researcher": {"href": "https://publications.scilifelab.se/researcher/594eb39f228241efb0f055799f5eaa88.json"}}, {"family": "Pe\u00f1a-Martinez", "given": "Pablo", "initials": "P", "orcid": "0000-0002-0789-6431", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d675e892dfc4334bb12051e004a7711.json"}}, {"family": "H\u00f6gberg", "given": "Carl", "initials": "C"}, {"family": "Rissler", "given": "Marianne", "initials": "M"}, {"family": "Gisselsson", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3653582762b14f9a9ad2fe6aba511115.json"}}, {"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": "\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": "2020-02-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "579", "issn-l": "2041-1723"}, "abstract": "Clonal heterogeneity and evolution has major implications for disease progression and relapse in acute myeloid leukemia (AML). To model clonal dynamics in vivo, we serially transplanted 23 AML cases to immunodeficient mice and followed clonal composition for up to 15 months by whole-exome sequencing of 84 xenografts across two generations. We demonstrate vast changes in clonality that both progress and reverse over time, and define five patterns of clonal dynamics: Monoclonal, Stable, Loss, Expansion and Burst. We also show that subclonal expansion in vivo correlates with a more adverse prognosis. Furthermore, clonal expansion enabled detection of very rare clones with AML driver mutations that were undetectable by sequencing at diagnosis, demonstrating that the vast majority of AML cases harbor multiple clones already at diagnosis. Finally, the rise and fall of related clones enabled deconstruction of the complex evolutionary hierarchies of the clones that compete to shape AML over time.", "doi": "10.1038/s41467-019-14106-0", "pmid": "32024830", "labels": {"Clinical Genomics Lund": null, "Clinical Genomics": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-14106-0"}, {"db": "pmc", "key": "PMC7002407"}], "notes": [], "created": "2020-02-24T10:54:40.951Z", "modified": "2021-11-10T12:54:09.856Z"}, {"entity": "publication", "iuid": "2fbb3c01bdfc42fcb76d81c03118c91a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fbb3c01bdfc42fcb76d81c03118c91a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fbb3c01bdfc42fcb76d81c03118c91a"}}, "title": "Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.", "authors": [{"family": "Pillon", "given": "Nicolas J", "initials": "NJ", "orcid": "0000-0003-1107-9490", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b917d3e521149ec9d695c62ac2d1b85.json"}}, {"family": "Gabriel", "given": "Brendan M", "initials": "BM", "orcid": "0000-0001-6878-8779", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fa7198e43f648b5ab2da4d43f71962d.json"}}, {"family": "Dollet", "given": "Lucile", "initials": "L"}, {"family": "Smith", "given": "Jonathon A B", "initials": "JAB", "orcid": "0000-0003-2452-1655", "researcher": {"href": "https://publications.scilifelab.se/researcher/bffd42f562b3485fb50090c02aceeaef.json"}}, {"family": "Sard\u00f3n Puig", "given": "Laura", "initials": "L", "orcid": "0000-0002-0481-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/73c9841603dc43edae07c7e606776225.json"}}, {"family": "Botella", "given": "Javier", "initials": "J", "orcid": "0000-0001-9722-8519", "researcher": {"href": "https://publications.scilifelab.se/researcher/199f6b058cb342b391566273dc4faf78.json"}}, {"family": "Bishop", "given": "David J", "initials": "DJ", "orcid": "0000-0002-6956-9188", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecaa5fe4ab9649c8a90ae1fed84a222e.json"}}, {"family": "Krook", "given": "Anna", "initials": "A", "orcid": "0000-0002-0891-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/f43339bcd571486b845a3b10e241bcc4.json"}}, {"family": "Zierath", "given": "Juleen R", "initials": "JR", "orcid": "0000-0001-6891-7497", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ef2b94ba2d44dd9b41192567a7af53.json"}}], "type": "journal article", "published": "2020-01-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "470"}, "abstract": "The molecular mechanisms underlying the response to exercise and inactivity are not fully understood. We propose an innovative approach to profile the skeletal muscle transcriptome to exercise and inactivity using 66 published datasets. Data collected from human studies of aerobic and resistance exercise, including acute and chronic exercise training, were integrated using meta-analysis methods (www.metamex.eu). Here we use gene ontology and pathway analyses to reveal selective pathways activated by inactivity, aerobic versus resistance and acute versus chronic exercise training. We identify NR4A3 as one of the most exercise- and inactivity-responsive genes, and establish a role for this nuclear receptor in mediating the metabolic responses to exercise-like stimuli in vitro. The meta-analysis (MetaMEx) also highlights the differential response to exercise in individuals with metabolic impairments. MetaMEx provides the most extensive dataset of skeletal muscle transcriptional responses to different modes of exercise and an online interface to readily interrogate the database.", "doi": "10.1038/s41467-019-13869-w", "pmid": "31980607", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13869-w"}, {"db": "pmc", "key": "PMC6981202"}], "notes": [], "created": "2020-01-07T15:03:10.909Z", "modified": "2021-11-10T12:54:37.387Z"}, {"entity": "publication", "iuid": "be7a47db1e114288bbb480454a47fab5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be7a47db1e114288bbb480454a47fab5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be7a47db1e114288bbb480454a47fab5"}}, "title": "The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly.", "authors": [{"family": "Pinese", "given": "Mark", "initials": "M"}, {"family": "Lacaze", "given": "Paul", "initials": "P", "orcid": "0000-0002-0902-6798", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe2ef319274d47af81a415d276772fd2.json"}}, {"family": "Rath", "given": "Emma M", "initials": "EM", "orcid": "0000-0002-8430-5236", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbb64814760845e898ad26b3f5bd3631.json"}}, {"family": "Stone", "given": "Andrew", "initials": "A"}, {"family": "Brion", "given": "Marie-Jo", "initials": "MJ"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Nagpal", "given": "Sini", "initials": "S"}, {"family": "Puttick", "given": "Clare", "initials": "C"}, {"family": "Husson", "given": "Shane", "initials": "S"}, {"family": "Degrave", "given": "Dmitry", "initials": "D"}, {"family": "Cristina", "given": "Tina Navin", "initials": "TN"}, {"family": "Kahl", "given": "Vivian F S", "initials": "VFS"}, {"family": "Statham", "given": "Aaron L", "initials": "AL"}, {"family": "Woods", "given": "Robyn L", "initials": "RL"}, {"family": "McNeil", "given": "John J", "initials": "JJ", "orcid": "0000-0002-1049-5129", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f523d0ed8654c6cad196a4a30273dc1.json"}}, {"family": "Riaz", "given": "Moeen", "initials": "M"}, {"family": "Barr", "given": "Margo", "initials": "M"}, {"family": "Nelson", "given": "Mark R", "initials": "MR"}, {"family": "Reid", "given": "Christopher M", "initials": "CM"}, {"family": "Murray", "given": "Anne M", "initials": "AM"}, {"family": "Shah", "given": "Raj C", "initials": "RC"}, {"family": "Wolfe", "given": "Rory", "initials": "R"}, {"family": "Atkins", "given": "Joshua R", "initials": "JR", "orcid": "0000-0003-0821-1112", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5c3c3b5566f4189893fc6f9b59bd639.json"}}, {"family": "Fitzsimmons", "given": "Chantel", "initials": "C"}, {"family": "Cairns", "given": "Heath M", "initials": "HM"}, {"family": "Green", "given": "Melissa J", "initials": "MJ"}, {"family": "Carr", "given": "Vaughan J", "initials": "VJ"}, {"family": "Cowley", "given": "Mark J", "initials": "MJ"}, {"family": "Pickett", "given": "Hilda A", "initials": "HA"}, {"family": "James", "given": "Paul A", "initials": "PA", "orcid": "0000-0002-4361-4657", "researcher": {"href": "https://publications.scilifelab.se/researcher/441138eb23d04342bca5e835815f5a79.json"}}, {"family": "Powell", "given": "Joseph E", "initials": "JE"}, {"family": "Kaplan", "given": "Warren", "initials": "W"}, {"family": "Gibson", "given": "Greg", "initials": "G", "orcid": "0000-0002-5352-5877", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4cf08629614ba3986edd2971a28848.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Cairns", "given": "Murray J", "initials": "MJ", "orcid": "0000-0003-2490-2538", "researcher": {"href": "https://publications.scilifelab.se/researcher/45db703eb69a49c390ce333c778617fa.json"}}, {"family": "McNamara", "given": "Martin", "initials": "M"}, {"family": "Dinger", "given": "Marcel E", "initials": "ME", "orcid": "0000-0003-4423-934X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5451fbf330bf4a5e9cfe17b9a66d5bd7.json"}}, {"family": "Thomas", "given": "David M", "initials": "DM", "orcid": "0000-0002-2527-5428", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5d3768414324650b161ccbb0de36a00.json"}}], "type": "journal article", "published": "2020-01-23", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "435", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Population health research is increasingly focused on the genetic determinants of healthy ageing, but there is no public resource of whole genome sequences and phenotype data from healthy elderly individuals. Here we describe the first release of the Medical Genome Reference Bank (MGRB), comprising whole genome sequence and phenotype of 2570 elderly Australians depleted for cancer, cardiovascular disease, and dementia. We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitochondrial genomes. MGRB individuals have fewer disease-associated common and rare germline variants, relative to both cancer cases and the gnomAD and UK Biobank cohorts, consistent with risk depletion. Age-related somatic changes are correlated with grip strength in men, suggesting blood-derived whole genomes may also provide a biologic measure of age-related functional deterioration. The MGRB provides a broadly applicable reference cohort for clinical genetics and genomic association studies, and for understanding the genetics of healthy ageing.", "doi": "10.1038/s41467-019-14079-0", "pmid": "31974348", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-14079-0"}, {"db": "pmc", "key": "PMC6978518"}], "notes": [], "created": "2020-02-11T10:08:40.950Z", "modified": "2021-11-10T12:54:41.902Z"}, {"entity": "publication", "iuid": "798d0c199a87482abd2a408a2148a1ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/798d0c199a87482abd2a408a2148a1ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/798d0c199a87482abd2a408a2148a1ac"}}, "title": "A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice.", "authors": [{"family": "Purhonen", "given": "Janne", "initials": "J"}, {"family": "Grigorjev", "given": "Vladislav", "initials": "V"}, {"family": "Ekiert", "given": "Robert", "initials": "R", "orcid": "0000-0002-8879-0646", "researcher": {"href": "https://publications.scilifelab.se/researcher/18f5478e3272434f8e04014a4da545b5.json"}}, {"family": "Aho", "given": "Noora", "initials": "N"}, {"family": "Rajendran", "given": "Jayasimman", "initials": "J", "orcid": "0000-0003-3487-8260", "researcher": {"href": "https://publications.scilifelab.se/researcher/92dfb99f063c475086ad84783ab34716.json"}}, {"family": "Pietras", "given": "Rafa\u0142", "initials": "R", "orcid": "0000-0001-8424-6590", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f9c7e05c9284550ad49f0cc9237ad45.json"}}, {"family": "Truv\u00e9", "given": "Katarina", "initials": "K", "orcid": "0000-0002-2449-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c36d2ff5111435aa23416cdfc359b2d.json"}}, {"family": "Wikstr\u00f6m", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0002-7527-4415", "researcher": {"href": "https://publications.scilifelab.se/researcher/66d471fc1c914756ac37da41bb759da4.json"}}, {"family": "Sharma", "given": "Vivek", "initials": "V"}, {"family": "Osyczka", "given": "Artur", "initials": "A"}, {"family": "Fellman", "given": "Vineta", "initials": "V", "orcid": "0000-0002-1355-5633", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c2179b7025441f688426ab24abd390e.json"}}, {"family": "Kallij\u00e4rvi", "given": "Jukka", "initials": "J", "orcid": "0000-0003-3773-7025", "researcher": {"href": "https://publications.scilifelab.se/researcher/c592c2565d4f42efb54b3e6016968ddf.json"}}], "type": "journal article", "published": "2020-01-16", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "322", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "We previously observed an unexpected fivefold (35 vs. 200 days) difference in the survival of respiratory chain complex III (CIII) deficient Bcs1lp.S78G mice between two congenic backgrounds. Here, we identify a spontaneous homoplasmic mtDNA variant (m.G14904A, mt-Cybp.D254N), affecting the CIII subunit cytochrome b (MT-CYB), in the background with short survival. We utilize maternal inheritance of mtDNA to confirm this as the causative variant and show that it further decreases the low CIII activity in Bcs1lp.S78G tissues to below survival threshold by 35 days of age. Molecular dynamics simulations predict D254N to restrict the flexibility of MT-CYB ef loop, potentially affecting RISP dynamics. In Rhodobacter cytochrome bc1 complex the equivalent substitution causes a kinetics defect with longer occupancy of RISP head domain towards the quinol oxidation site. These findings represent a unique case of spontaneous mitonuclear epistasis and highlight the role of mtDNA variation as modifier of mitochondrial disease phenotypes.", "doi": "10.1038/s41467-019-14201-2", "pmid": "31949167", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-14201-2"}, {"db": "pmc", "key": "PMC6965120"}], "notes": [], "created": "2020-02-03T09:00:33.293Z", "modified": "2021-11-10T12:44:51.374Z"}, {"entity": "publication", "iuid": "7ece5c90f5a84512a7eef65aed76aed2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7ece5c90f5a84512a7eef65aed76aed2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7ece5c90f5a84512a7eef65aed76aed2"}}, "title": "Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure.", "authors": [{"family": "Shah", "given": "Sonia", "initials": "S", "orcid": "0000-0001-5860-4526", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6a8568b3cae476199b27818eeb19e4d.json"}}, {"family": "Henry", "given": "Albert", "initials": "A", "orcid": "0000-0001-7422-2288", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b1557b87fc542eb8e4d7b733e5b79dc.json"}}, {"family": "Roselli", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5267-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dd28aad250f42719d505c21ed76013b.json"}}, {"family": "Lin", "given": "Honghuang", "initials": "H", "orcid": "0000-0003-3043-3942", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bc2f1e6bb1140dfa054376eac685d5e.json"}}, {"family": "Sveinbj\u00f6rnsson", "given": "Gar\u00f0ar", "initials": "G"}, {"family": "Fatemifar", "given": "Ghazaleh", "initials": "G"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Wilk", "given": "Jemma B", "initials": "JB"}, {"family": "Morley", "given": "Michael P", "initials": "MP"}, {"family": "Chaffin", "given": "Mark D", "initials": "MD", "orcid": "0000-0002-1234-5562", "researcher": {"href": "https://publications.scilifelab.se/researcher/c73477de5ca0468ab051fd6eab7bad81.json"}}, {"family": "Helgadottir", "given": "Anna", "initials": "A", "orcid": "0000-0002-1806-2467", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b5de2b760674dbfba05df40af0eb38f.json"}}, {"family": "Verweij", "given": "Niek", "initials": "N", "orcid": "0000-0002-4303-7685", "researcher": {"href": "https://publications.scilifelab.se/researcher/7306319d42a640a483b937de588a17a4.json"}}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Almgren", "given": "Peter", "initials": "P", "orcid": "0000-0002-0473-0241", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1a61189c4846eaa1de74d1fd79c8bb.json"}}, {"family": "Andersson", "given": "Charlotte", "initials": "C"}, {"family": "Aragam", "given": "Krishna G", "initials": "KG"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Backman", "given": "Joshua D", "initials": "JD"}, {"family": "Biggs", "given": "Mary L", "initials": "ML"}, {"family": "Bloom", "given": "Heather L", "initials": "HL"}, {"family": "Brandimarto", "given": "Jeffrey", "initials": "J"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "Buckbinder", "given": "Leonard", "initials": "L"}, {"family": "Carey", "given": "David J", "initials": "DJ"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chen", "given": "Xing", "initials": "X", "orcid": "0000-0002-7299-3238", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d354d5ca83c4059b8151c8e67b99405.json"}}, {"family": "Chen", "given": "Xu", "initials": "X", "orcid": "0000-0002-7299-3238", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d354d5ca83c4059b8151c8e67b99405.json"}}, {"family": "Chung", "given": "Jonathan", "initials": "J"}, {"family": "Chutkow", "given": "William", "initials": "W"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "Denaxas", "given": "Spiros", "initials": "S"}, {"family": "Doney", "given": "Alexander S", "initials": "AS"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Dudley", "given": "Samuel C", "initials": "SC"}, {"family": "Dunn", "given": "Michael E", "initials": "ME"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Finan", "given": "Chris", "initials": "C"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M", "orcid": "0000-0002-9476-7143", "researcher": {"href": "https://publications.scilifelab.se/researcher/52ef9606de1144c994e0e854c5a85569.json"}}, {"family": "Ghasemi", "given": "Sahar", "initials": "S"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V", "orcid": "0000-0003-3423-2021", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c95879213664e00b66aeee2e8ece975.json"}}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Gottdiener", "given": "John S", "initials": "JS"}, {"family": "Gross", "given": "Stefan", "initials": "S", "orcid": "0000-0003-4121-7161", "researcher": {"href": 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"researcher": {"href": "https://publications.scilifelab.se/researcher/0479b794031d4df7bed96340b3470c19.json"}}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME", "orcid": "0000-0003-0663-7275", "researcher": {"href": "https://publications.scilifelab.se/researcher/a51175112cfb4721b8c9fbfdc71c4307.json"}}, {"family": "K\u00f8ber", "given": "Lars", "initials": "L"}, {"family": "Koekemoer", "given": "Andrea", "initials": "A", "orcid": "0000-0001-8222-3547", "researcher": {"href": "https://publications.scilifelab.se/researcher/74525ced82a7490d939b480e07fadfdd.json"}}, {"family": "Langenberg", "given": "Claudia", "initials": "C", "orcid": "0000-0002-5017-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca19370bb4d6437aa9df3905db9d3dd2.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia 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"https://publications.scilifelab.se/researcher/5da07a509b1740648199997ee5ea73a3.json"}}, {"family": "Nelson", "given": "Christopher P", "initials": "CP", "orcid": "0000-0001-8025-2897", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cac4df8cd7241558b51f2abdc1c28eb.json"}}, {"family": "Niessner", "given": "Alexander", "initials": "A"}, {"family": "Niiranen", "given": "Teemu", "initials": "T"}, {"family": "O'Donoghue", "given": "Michelle L", "initials": "ML"}, {"family": "Owens", "given": "Anjali T", "initials": "AT"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA", "orcid": "0000-0002-6415-6560", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a0f019dcb7a453a84480953a5514dd5.json"}}, {"family": "Parry", "given": "Helen M", "initials": "HM"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Portilla-Fernandez", "given": "Eliana", "initials": "E"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Regeneron Genetics Center", "given": "", "initials": ""}, {"family": "Rice", "given": "Kenneth M", "initials": "KM", "orcid": "0000-0002-3071-7278", "researcher": {"href": "https://publications.scilifelab.se/researcher/5affb61f3ef141e8a6e7c7bfd2477ae3.json"}}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Romaine", "given": "Simon P R", "initials": "SPR"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI", "orcid": "0000-0001-7191-1723", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9bdbf58ae94fc8b455bbbcbcaa50ce.json"}}, {"family": "Salo", "given": "Perttu", "initials": "P"}, {"family": "Salomaa", "given": "Veikko", "initials": "V", "orcid": "0000-0001-7563-5324", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2396c578c254e39b66538c3033c9ce9.json"}}, {"family": "van Setten", "given": "Jessica", "initials": "J", "orcid": "0000-0002-4934-7510", "researcher": {"href": "https://publications.scilifelab.se/researcher/4be6dce84e8a4f46bf15f4de178f70ba.json"}}, {"family": "Shalaby", "given": "Alaa A", "initials": "AA"}, {"family": "Smelser", "given": "Diane T", "initials": "DT"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Stender", "given": "Steen", "initials": "S"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Svensson", "given": "Per", "initials": "P", "orcid": "0000-0003-0372-6272", "researcher": {"href": "https://publications.scilifelab.se/researcher/199e569cd05e456488ead34240b91c5b.json"}}, {"family": "Tammesoo", "given": "Mari-Liis", "initials": "ML"}, {"family": "Taylor", "given": "Kent D", "initials": "KD", "orcid": "0000-0002-2756-4370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f5450c63d194100ab6cda3b83250fc7.json"}}, {"family": "Teder-Laving", "given": "Maris", "initials": "M", "orcid": "0000-0002-5872-1850", "researcher": {"href": "https://publications.scilifelab.se/researcher/f27feb6c2c23492bb1e442116d0ba49e.json"}}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Thorgeirsson", "given": "Gu\u00f0mundur", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Torp-Pedersen", "given": "Christian", "initials": "C"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Tyl", "given": "Benoit", "initials": "B", "orcid": "0000-0001-5297-8412", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e192aa671144e20916948eaadc4b738.json"}}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "Veluchamy", "given": "Abirami", "initials": "A"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U", "orcid": "0000-0002-5689-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/e529a40052644d83bdef588a3e4f4e99.json"}}, {"family": "Voors", "given": "Adriaan A", "initials": "AA"}, {"family": "Wang", "given": "Xiaosong", "initials": "X"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Waterworth", "given": "Dawn", "initials": "D"}, {"family": "Weeke", "given": "Peter E", "initials": "PE"}, {"family": "Weiss", "given": "Raul", "initials": "R"}, {"family": "Wiggins", "given": "Kerri L", "initials": "KL", "orcid": "0000-0003-2749-1279", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9d1f9cb10ef4038abb10fb6ee289504.json"}}, {"family": "Xing", "given": "Heming", "initials": "H"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Zannad", "given": "Faiez", "initials": "F"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Hemingway", "given": "Harry", "initials": "H", "orcid": "0000-0003-2279-0624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bc6b343a8ab4b4c9ff6380d8d4aa626.json"}}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "McMurray", "given": "John J V", "initials": "JJV"}, {"family": "Yang", "given": "Jian", "initials": "J", "orcid": "0000-0003-2001-2474", "researcher": {"href": "https://publications.scilifelab.se/researcher/99b6239b59ad42248e8f18583b40777a.json"}}, {"family": "Visscher", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-2143-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdb41d4720b436494304f74e33206ae.json"}}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Malarstig", "given": "Anders", "initials": "A"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA", "orcid": "0000-0002-9599-4866", "researcher": {"href": "https://publications.scilifelab.se/researcher/25bb007311104c92983dbcce80f72260.json"}}, {"family": "Sattar", "given": "Naveed", "initials": "N", "orcid": "0000-0002-1604-2593", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fbc7cdcfc444acb066449f80f87181.json"}}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Cappola", "given": "Thomas P", "initials": "TP", "orcid": "0000-0002-9630-7204", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cc50d241ad14477b91f83e012918181.json"}}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW", "orcid": "0000-0002-1692-8669", "researcher": {"href": "https://publications.scilifelab.se/researcher/7037429ef1304bdaabd837d242b1e6f5.json"}}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Kuchenbaecker", "given": "Karoline", "initials": "K", "orcid": "0000-0001-9726-603X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e142157c79648ce96b258ea78019829.json"}}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd513dc49e0945bc8298f72d1244648d.json"}}, {"family": "Lang", "given": "Chim C", "initials": "CC"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS", "orcid": "0000-0001-7357-5970", "researcher": {"href": "https://publications.scilifelab.se/researcher/50ceef6f00ea4251a5e1e83cd379a506.json"}}, {"family": "Swerdlow", "given": "Daniel I", "initials": "DI"}, {"family": "Lumbers", "given": "R Thomas", "initials": "RT", "orcid": "0000-0002-9077-4741", "researcher": {"href": "https://publications.scilifelab.se/researcher/a53e4d6591db481f881ec6046d54535b.json"}}], "type": "journal article", "published": "2020-01-09", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "163", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies.", "doi": "10.1038/s41467-019-13690-5", "pmid": "31919418", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6952380"}, {"db": "pii", "key": "10.1038/s41467-019-13690-5"}], "notes": [], "created": "2020-01-14T10:04:57.921Z", "modified": "2023-06-19T13:01:57.741Z"}, {"entity": "publication", "iuid": "9b592e44470a4ba18b57b727b2011b71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b592e44470a4ba18b57b727b2011b71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b592e44470a4ba18b57b727b2011b71"}}, "title": "Integrative discovery of treatments for high-risk neuroblastoma.", "authors": [{"family": "Almstedt", "given": "Elin", "initials": "E", "orcid": "0000-0002-1946-9138", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4414ac7f9284bf9bf0b52530ec19ee3.json"}}, {"family": "Elgendy", "given": "Ramy", "initials": "R", "orcid": "0000-0002-2592-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a5ce4db4317446bb1ef113f7c6e8eb5.json"}}, {"family": "Hekmati", "given": "Neda", "initials": "N"}, {"family": "Ros\u00e9n", "given": "Emil", "initials": "E", "orcid": "0000-0002-1664-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/db0751a3a95e488bb849059c09c4fc7d.json"}}, {"family": "W\u00e4rn", "given": "Caroline", "initials": "C"}, {"family": "Olsen", "given": "Thale Kristin", "initials": "TK"}, {"family": "Dyberg", "given": "Cecilia", "initials": "C"}, {"family": "Doroszko", "given": "Milena", "initials": "M"}, {"family": "Larsson", "given": "Ida", "initials": "I", "orcid": "0000-0001-5422-4243", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ac604ca793048e9b6ddaa3459b4e97a.json"}}, {"family": "Sundstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Arsenian Henriksson", "given": "Marie", "initials": "M"}, {"family": "P\u00e5hlman", "given": "Sven", "initials": "S"}, {"family": "Bexell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9426-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda650768a264d93a80f40da6cb8d7e1.json"}}, {"family": "Vanlandewijck", "given": "Michael", "initials": "M", "orcid": "0000-0002-0709-7808", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa2148fbafb44d59bd110e36bd77769c.json"}}, {"family": "Kogner", "given": "Per", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications.scilifelab.se/researcher/e963274b921a4a2c8263f509334d4e22.json"}}, {"family": "J\u00f6rnsten", "given": "Rebecka", "initials": "R"}, {"family": "Krona", "given": "Cecilia", "initials": "C"}, {"family": "Nelander", "given": "Sven", "initials": "S"}], "type": "journal article", "published": "2020-01-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "71"}, "abstract": "Despite advances in the molecular exploration of paediatric cancers, approximately 50% of children with high-risk neuroblastoma lack effective treatment. To identify therapeutic options for this group of high-risk patients, we combine predictive data mining with experimental evaluation in patient-derived xenograft cells. Our proposed algorithm, TargetTranslator, integrates data from tumour biobanks, pharmacological databases, and cellular networks to predict how targeted interventions affect mRNA signatures associated with high patient risk or disease processes. We find more than 80 targets to be associated with neuroblastoma risk and differentiation signatures. Selected targets are evaluated in cell lines derived from high-risk patients to demonstrate reversal of risk signatures and malignant phenotypes. Using neuroblastoma xenograft models, we establish CNR2 and MAPK8 as promising candidates for the treatment of high-risk neuroblastoma. We expect that our method, available as a public tool (targettranslator.org), will enhance and expedite the discovery of risk-associated targets for paediatric and adult cancers.", "doi": "10.1038/s41467-019-13817-8", "pmid": "31900415", "labels": {"Genome Engineering Zebrafish": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13817-8"}, {"db": "pmc", "key": "PMC6941971"}], "notes": [], "created": "2020-01-08T11:24:16.666Z", "modified": "2021-12-09T14:05:49.139Z"}, {"entity": "publication", "iuid": "15fab752b91e4f3889c3ea995c9c69c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15fab752b91e4f3889c3ea995c9c69c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15fab752b91e4f3889c3ea995c9c69c7"}}, "title": "A transposable element insertion is associated with an alternative life history strategy.", "authors": [{"family": "Woronik", "given": "Alyssa", "initials": "A"}, {"family": "Tunstr\u00f6m", "given": "Kalle", "initials": "K"}, {"family": "Perry", "given": "Michael W", "initials": "MW"}, {"family": "Neethiraj", "given": "Ramprasad", "initials": "R"}, {"family": "Stefanescu", "given": "Constanti", "initials": "C"}, {"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "MP"}, {"family": "Brattstr\u00f6m", "given": "Oskar", "initials": "O"}, {"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Lehmann", "given": "Philipp", "initials": "P"}, {"family": "K\u00e4kel\u00e4", "given": "Reijo", "initials": "R"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}], "type": "journal article", "published": "2019-12-17", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "5757", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Tradeoffs affect resource allocation during development and result in fitness consequences that drive the evolution of life history strategies. Yet despite their importance, we know little about the mechanisms underlying life history tradeoffs. Many species of Colias butterflies exhibit an alternative life history strategy (ALHS) where females divert resources from wing pigment synthesis to reproductive and somatic development. Due to this reallocation, a wing color polymorphism is associated with the ALHS: either yellow/orange or white. Here we map the locus associated with this ALHS in Colias crocea to a transposable element insertion located downstream of the Colias homolog of BarH-1, a homeobox transcription factor. Using CRISPR/Cas9 gene editing, antibody staining, and electron microscopy we find white-specific expression of BarH-1 suppresses the formation of pigment granules in wing scales and gives rise to white wing color. Lipid and transcriptome analyses reveal physiological differences associated with the ALHS. Together, these findings characterize a mechanism for a female-limited ALHS.", "doi": "10.1038/s41467-019-13596-2", "pmid": "31848330", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13596-2"}, {"db": "pmc", "key": "PMC6917731"}], "notes": [], "created": "2020-01-08T16:48:54.088Z", "modified": "2020-01-21T13:56:16.533Z"}, {"entity": "publication", "iuid": "dbc92553ebbe4a27bb1181acdc5a493e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbc92553ebbe4a27bb1181acdc5a493e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbc92553ebbe4a27bb1181acdc5a493e"}}, "title": "BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila.", "authors": [{"family": "Uebersch\u00e4r", "given": "Malin", "initials": "M"}, {"family": "Wang", "given": "Huazhen", "initials": "H"}, {"family": "Zhang", "given": "Chun", "initials": "C"}, {"family": "Kondo", "given": "Shu", "initials": "S"}, {"family": "Aoki", "given": "Tsutomu", "initials": "T"}, {"family": "Schedl", "given": "Paul", "initials": "P"}, {"family": "Lai", "given": "Eric C", "initials": "EC"}, {"family": "Wen", "given": "Jiayu", "initials": "J"}, {"family": "Dai", "given": "Qi", "initials": "Q"}], "type": "journal article", "published": "2019-12-13", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "5700", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The Drosophila genome encodes three BEN-solo proteins including Insensitive (Insv), Elba1 and Elba2 that possess activities in transcriptional repression and chromatin insulation. A fourth protein-Elba3-bridges Elba1 and Elba2 to form an ELBA complex. Here, we report comprehensive investigation of these proteins in Drosophila embryos. We assess common and distinct binding sites for Insv and ELBA and their genetic interdependencies. While Elba1 and Elba2 binding generally requires the ELBA complex, Elba3 can associate with chromatin independently of Elba1 and Elba2. We further demonstrate that ELBA collaborates with other insulators to regulate developmental patterning. Finally, we find that adjacent gene pairs separated by an ELBA bound sequence become less differentially expressed in ELBA mutants. Transgenic reporters confirm the insulating activity of ELBA- and Insv-bound sites. These findings define ELBA and Insv as general insulator proteins in Drosophila and demonstrate the functional importance of insulators to partition transcription units.", "doi": "10.1038/s41467-019-13558-8", "pmid": "31836703", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13558-8"}, {"db": "pmc", "key": "PMC6911014"}], "notes": [], "created": "2020-01-08T16:48:51.677Z", "modified": "2020-01-21T13:56:16.511Z"}, {"entity": "publication", "iuid": "0db4269a42a5414c862b6766046b6288", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0db4269a42a5414c862b6766046b6288.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0db4269a42a5414c862b6766046b6288"}}, "title": "ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery", "authors": [{"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Beusch", "given": "Christian Michel", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/278e50b11a3c4ef69b6e2708f99b5f3e.json"}}, {"family": "Chernobrovkin", "given": "Alexey", "initials": "A", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications.scilifelab.se/researcher/d36b29dc4fd44785b36b9baa9e291757.json"}}, {"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a75556311084e2b827ab1f646d7a16c.json"}}, {"family": "Zhang", "given": "Bo", "initials": "B", "orcid": "0000-0001-8890-8416", "researcher": {"href": "https://publications.scilifelab.se/researcher/79097385e3ea4496bb498c981302b344.json"}}, {"family": "Tokat", "given": "\u00dclk\u00fc G\u00fcler", "initials": "\u00dcG"}, {"family": "Stergiou", "given": "Eleni", "initials": "E", "orcid": "0000-0001-9115-4985", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ff5335a69db40848ec6131d4735da18.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.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": "2019-12-00", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "10", "issue": "1", "pages": "5715"}, "abstract": "Deconvolution of targets and action mechanisms of anticancer compounds is fundamental in drug development. Here, we report on ProTargetMiner as a publicly available expandable proteome signature library of anticancer molecules in cancer cell lines. Based on 287 A549 adenocarcinoma proteomes affected by 56 compounds, the main dataset contains 7,328 proteins and 1,307,859 refined protein-drug pairs. These proteomic signatures cluster by compound targets and action mechanisms. The targets and mechanistic proteins are deconvoluted by partial least square modeling, provided through the website http://protargetminer.genexplain.com. For 9 molecules representing the most diverse mechanisms and the common cancer cell lines MCF-7, RKO and A549, deep proteome datasets are obtained. Combining data from the three cell lines highlights common drug targets and cell-specific differences. The database can be easily extended and merged with new compound signatures. ProTargetMiner serves as a chemical proteomics resource for the cancer research community, and can become a valuable tool in drug discovery.", "doi": "10.1038/s41467-019-13582-8", "pmid": "31844049", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13582-8"}, {"db": "pmc", "key": "PMC6915695"}], "notes": [], "created": "2019-01-10T14:09:06.234Z", "modified": "2021-06-21T14:06:27.659Z"}, {"entity": "publication", "iuid": "2022891d3217451b8ae7c76bc9132e3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2022891d3217451b8ae7c76bc9132e3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2022891d3217451b8ae7c76bc9132e3d"}}, "title": "A cell fitness selection model for neuronal survival during development", "authors": [{"family": "Wang", "given": "Yiqiao", "initials": "Y"}, {"family": "Wu", "given": "Haohao", "initials": "H"}, {"family": "Fontanet", "given": "Paula", "initials": "P"}, {"family": "Codeluppi", "given": "Simone", "initials": "S"}, {"family": "Akkuratova", "given": "Natalia", "initials": "N"}, {"family": "Petitpr\u00e9", "given": "Charles", "initials": "C"}, {"family": "Xue-Franz\u00e9n", "given": "Yongtao", "initials": "Y"}, {"family": "Niederreither", "given": "Karen", "initials": "K"}, {"family": "Sharma", "given": "Anil", "initials": "A"}, {"family": "Da Silva", "given": "Fabio", "initials": "F"}, {"family": "Comai", "given": "Glenda", "initials": "G"}, {"family": "Agirman", "given": "Gulistan", "initials": "G"}, {"family": "Palumberi", "given": "Domenico", "initials": "D"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}, {"family": "Moqrich", "given": "Aziz", "initials": "A"}, {"family": "Schedl", "given": "Andreas", "initials": "A"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Hadjab", "given": "Saida", "initials": "S"}, {"family": "Lallemend", "given": "Fran\u00e7ois", "initials": "F"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Developmental cell death plays an important role in the construction of functional neural circuits. In vertebrates, the canonical view proposes a selection of the surviving neurons through stochastic competition for target-derived neurotrophic signals, implying an equal potential for neurons to compete. Here we show an alternative cell fitness selection of neurons that is defined by a specific neuronal heterogeneity code. Proprioceptive sensory neurons that will undergo cell death and those that will survive exhibit different molecular signatures that are regulated by retinoic acid and transcription factors, and are independent of the target and neurotrophins. These molecular features are genetically encoded, representing two distinct subgroups of neurons with contrasted functional maturation states and survival outcome. Thus, in this model, a heterogeneous code of intrinsic cell fitness in neighboring neurons provides differential competitive advantage resulting in the selection of cells with higher capacity to survive and functionally integrate into neural networks.", "doi": "10.1038/s41467-019-12119-3", "pmid": "31515492", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-09-27T09:40:06.695Z", "modified": "2024-01-16T13:48:43.462Z"}, {"entity": "publication", "iuid": "5e8d78fd132842c38fb5e1b379715f70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e8d78fd132842c38fb5e1b379715f70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e8d78fd132842c38fb5e1b379715f70"}}, "title": "iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture", "authors": [{"family": "Gelali", "given": "Eleni", "initials": "E"}, {"family": "Girelli", "given": "Gabriele", "initials": "G"}, {"family": "Matsumoto", "given": "Masahiro", "initials": "M"}, {"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Mota", "given": "Ana", "initials": "A"}, {"family": "Schweitzer", "given": "Maud", "initials": "M"}, {"family": "Ferenc", "given": "Katalin", "initials": "K"}, {"family": "Li", "given": "Xinge", "initials": "X"}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Agostini", "given": "Federico", "initials": "F"}, {"family": "Schell", "given": "John P", "initials": "JP"}, {"family": "Lanner", "given": "Fredrik", "initials": "F"}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Bienko", "given": "Magda", "initials": "M"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.", "doi": "10.1038/s41467-019-09616-w", "pmid": "30967549", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Advanced FISH Technologies": "Technology development", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-07T15:04:55.085Z", "modified": "2020-02-12T15:15:07.277Z"}, {"entity": "publication", "iuid": "f688346e12c14ec4bf96068a3bb2d1e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f688346e12c14ec4bf96068a3bb2d1e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f688346e12c14ec4bf96068a3bb2d1e9"}}, "title": "Towards a standardized bioinformatics infrastructure for N- and O-glycomics", "authors": [{"family": "Rojas-Macias", "given": "Miguel A", "initials": "MA"}, {"family": "Mariethoz", "given": "Julien", "initials": "J"}, {"family": "Andersson", "given": "Peter", "initials": "P"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Venkatakrishnan", "given": "Vignesh", "initials": "V"}, {"family": "Aoki", "given": "Nobuyuki P", "initials": "NP"}, {"family": "Shinmachi", "given": "Daisuke", "initials": "D"}, {"family": "Ashwood", "given": "Christopher", "initials": "C"}, {"family": "Madunic", "given": "Katarina", "initials": "K"}, {"family": "Zhang", "given": "Tao", "initials": "T"}, {"family": "Miller", "given": "Rebecca L", "initials": "RL"}, {"family": "Horlacher", "given": "Oliver", "initials": "O"}, {"family": "Struwe", "given": "Weston B", "initials": "WB"}, {"family": "Watanabe", "given": "Yu", "initials": "Y"}, {"family": "Okuda", "given": "Shujiro", "initials": "S"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Kolarich", "given": "Daniel", "initials": "D"}, {"family": "Rudd", "given": "Pauline M", "initials": "PM"}, {"family": "Wuhrer", "given": "Manfred", "initials": "M"}, {"family": "Kettner", "given": "Carsten", "initials": "C"}, {"family": "Packer", "given": "Nicolle H", "initials": "NH"}, {"family": "Aoki-Kinoshita", "given": "Kiyoko F", "initials": "KF"}, {"family": "Lisacek", "given": "Fr\u00e9d\u00e9rique", "initials": "F"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.", "doi": "10.1038/s41467-019-11131-x", "pmid": "31332201", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Glycoproteomics and MS Proteomics": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-09-16T11:46:23.026Z", "modified": "2024-01-16T13:46:31.254Z"}, {"entity": "publication", "iuid": "2f3fc2505d90467ea15d6d7fd508de68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f3fc2505d90467ea15d6d7fd508de68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f3fc2505d90467ea15d6d7fd508de68"}}, "title": "Programmed DNA elimination of germline development genes in songbirds.", "authors": [{"family": "Kinsella", "given": "Cormac M", "initials": "CM"}, {"family": "Ruiz-Ruano", "given": "Francisco J", "initials": "FJ"}, {"family": "Dion-C\u00f4t\u00e9", "given": "Anne-Marie", "initials": "AM"}, {"family": "Charles", "given": "Alexander J", "initials": "AJ"}, {"family": "Gossmann", "given": "Toni I", "initials": "TI"}, {"family": "Cabrero", "given": "Josefa", "initials": "J"}, {"family": "Kappei", "given": "Dennis", "initials": "D"}, {"family": "Hemmings", "given": "Nicola", "initials": "N"}, {"family": "Simons", "given": "Mirre J P", "initials": "MJP"}, {"family": "Camacho", "given": "Juan Pedro M", "initials": "JPM"}, {"family": "Forstmeier", "given": "Wolfgang", "initials": "W"}, {"family": "Suh", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2019-11-29", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "5468", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "In some eukaryotes, germline and somatic genomes differ dramatically in their composition. Here we characterise a major germline-soma dissimilarity caused by a germline-restricted chromosome (GRC) in songbirds. We show that the zebra finch GRC contains >115 genes paralogous to single-copy genes on 18 autosomes and the Z chromosome, and is enriched in genes involved in female gonad development. Many genes are likely functional, evidenced by expression in testes and ovaries at the RNA and protein level. Using comparative genomics, we show that genes have been added to the GRC over millions of years of evolution, with embryonic development genes bicc1 and trim71 dating to the ancestor of songbirds and dozens of other genes added very recently. The somatic elimination of this evolutionarily dynamic chromosome in songbirds implies a unique mechanism to minimise genetic conflict between germline and soma, relevant to antagonistic pleiotropy, an evolutionary process underlying ageing and sexual traits.", "doi": "10.1038/s41467-019-13427-4", "pmid": "31784533", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13427-4"}, {"db": "pmc", "key": "PMC6884545"}], "notes": [], "created": "2020-01-08T16:48:20.466Z", "modified": "2020-01-21T13:56:16.488Z"}, {"entity": "publication", "iuid": "89c87476555544e39ef6bf6717603f84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89c87476555544e39ef6bf6717603f84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89c87476555544e39ef6bf6717603f84"}}, "title": "Associations of autozygosity with a broad range of human phenotypes.", "authors": [{"family": "Clark", "given": "David W", "initials": "DW", "orcid": "0000-0002-1025-9185", "researcher": {"href": "https://publications.scilifelab.se/researcher/a71ee9badf4f458d9b04ebf89f5f16c9.json"}}, {"family": "Okada", "given": "Yukinori", "initials": "Y", "orcid": "0000-0002-0311-8472", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b13860bfef41959c29be2de853b456.json"}}, {"family": "Moore", "given": "Kristjan H S", "initials": "KHS", "orcid": "0000-0002-9579-4362", "researcher": {"href": "https://publications.scilifelab.se/researcher/38a8eaf6f23c4dd9a90cda85b0a998b5.json"}}, {"family": "Mason", "given": "Dan", "initials": "D", "orcid": "0000-0002-0026-9216", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e9d969adc0849ab83d0080430bb6758.json"}}, {"family": "Pirastu", "given": "Nicola", "initials": "N", "orcid": "0000-0002-5363-3886", "researcher": {"href": "https://publications.scilifelab.se/researcher/badf4678d37546ce993bccb3880d4f12.json"}}, {"family": "Gandin", "given": "Ilaria", "initials": "I", "orcid": "0000-0003-3196-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee19a08d128d40cf8bffcff35e37481d.json"}}, {"family": "Mattsson", "given": "Hannele", "initials": "H"}, {"family": "Barnes", "given": "Catriona L K", "initials": "CLK"}, {"family": "Lin", "given": "Kuang", "initials": "K"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Deelen", "given": "Patrick", "initials": "P", "orcid": "0000-0002-5654-3966", "researcher": {"href": "https://publications.scilifelab.se/researcher/29b4f65a7b6e454d92315f99841f0e70.json"}}, {"family": "Rohde", "given": "Rebecca", "initials": "R"}, {"family": "Schurmann", "given": "Claudia", "initials": "C", "orcid": "0000-0003-4158-9192", "researcher": {"href": "https://publications.scilifelab.se/researcher/357aae1711d34a0e993b10c93c73cfb4.json"}}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C", "orcid": "0000-0001-7999-5538", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1f97914d1c34f1f8190738c2d2e27b0.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Bao", "given": "Yanchun", "initials": "Y", "orcid": "0000-0002-6102-5098", "researcher": {"href": "https://publications.scilifelab.se/researcher/edd80af47df24a508164d6b550093563.json"}}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Baumbach", "given": "Clemens", "initials": "C"}, {"family": "Biino", "given": "Ginevra", "initials": "G", "orcid": "0000-0002-9936-946X", "researcher": {"href": "https://publications.scilifelab.se/researcher/791ca64b8e7c4930a8727ea9a52a5c15.json"}}, {"family": "Bixley", "given": "Matthew J", "initials": "MJ"}, {"family": "Brumat", "given": "Marco", "initials": "M", "orcid": "0000-0003-3268-039X", "researcher": {"href": "https://publications.scilifelab.se/researcher/422e5540e38047cfaa64708b0b118760.json"}}, {"family": "Chai", "given": "Jin-Fang", "initials": "JF", "orcid": "0000-0003-3770-1137", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cac060e59cd405b94a588203b5955ca.json"}}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Cousminer", "given": "Diana L", "initials": "DL"}, {"family": "Dekker", "given": "Annelot M", "initials": "AM"}, {"family": "Eccles", "given": "David A", "initials": "DA", "orcid": "0000-0003-4634-4995", "researcher": {"href": "https://publications.scilifelab.se/researcher/94670fee34be4f47ab7cf5c46a054fa4.json"}}, {"family": "van Eijk", "given": "Kristel R", "initials": "KR"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Gao", "given": "He", "initials": "H"}, {"family": "Germain", "given": "Marine", "initials": "M"}, {"family": "Gordon", "given": "Scott D", "initials": "SD", "orcid": "0000-0001-7623-328X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8815739662214e75b60f71f0b1ca58a6.json"}}, {"family": "de Haan", "given": "Hugoline G", "initials": "HG"}, {"family": "Harris", "given": "Sarah E", "initials": "SE", "orcid": "0000-0002-4941-5106", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bbd06383e594035ab80af3bcdb29f91.json"}}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Huerta-Chagoya", "given": "Alicia", "initials": "A"}, {"family": "Igartua", "given": "Catherine", "initials": "C"}, {"family": "Jansen", "given": "Iris E", "initials": "IE"}, {"family": "Jia", "given": "Yucheng", "initials": "Y"}, {"family": "Kacprowski", "given": "Tim", "initials": "T", "orcid": "0000-0002-5393-2413", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5e640df1f184777a3066805d02a67c7.json"}}, {"family": "Karlsson", "given": "Torgny", "initials": "T", "orcid": "0000-0001-8095-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/691d6823b8e04c5abf1613513da32b08.json"}}, {"family": "Kleber", "given": "Marcus E", "initials": "ME", "orcid": "0000-0003-0663-7275", "researcher": {"href": "https://publications.scilifelab.se/researcher/a51175112cfb4721b8c9fbfdc71c4307.json"}}, {"family": "Li", "given": "Shengchao Alfred", "initials": "SA"}, {"family": "Li-Gao", "given": "Ruifang", "initials": "R"}, {"family": "Mahajan", "given": "Anubha", "initials": "A", "orcid": "0000-0001-5585-3420", "researcher": {"href": "https://publications.scilifelab.se/researcher/194be8a851164e2ea4d004dd2febc9be.json"}}, {"family": "Matsuda", "given": "Koichi", "initials": "K", "orcid": "0000-0001-7292-2686", "researcher": {"href": "https://publications.scilifelab.se/researcher/016c48eb6c8341b7b593c4b1c9e39266.json"}}, {"family": "Meidtner", "given": "Karina", "initials": "K"}, {"family": "Meng", "given": "Weihua", "initials": "W", "orcid": "0000-0001-5388-8494", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb05cc4a7554f4d8fdc57ec60b542d2.json"}}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ", "orcid": "0000-0001-8450-3518", "researcher": {"href": "https://publications.scilifelab.se/researcher/17cd11842111490ba5460f3093a366f3.json"}}, {"family": "Munz", "given": "Matthias", "initials": "M", "orcid": "0000-0002-4728-3357", "researcher": {"href": "https://publications.scilifelab.se/researcher/715a85c9e5794eac8d55860014a3e407.json"}}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Palviainen", "given": "Teemu", "initials": "T", "orcid": 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"given": "Walter", "initials": "W"}, {"family": "Palmer", "given": "Colin", "initials": "C", "orcid": "0000-0002-6415-6560", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a0f019dcb7a453a84480953a5514dd5.json"}}, {"family": "Pasterkamp", "given": "Gerard G", "initials": "GG"}, {"family": "Patin", "given": "Etienne", "initials": "E"}, {"family": "Pennell", "given": "Craig E", "initials": "CE"}, {"family": "Perusse", "given": "Louis", "initials": "L", "orcid": "0000-0001-6440-9698", "researcher": {"href": "https://publications.scilifelab.se/researcher/28a47f0e72074741a12430ffd7555a0a.json"}}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Pirastu", "given": "Mario", "initials": "M"}, {"family": "Polderman", "given": "Tinca J C", "initials": "TJC", "orcid": "0000-0001-5564-301X", "researcher": {"href": "https://publications.scilifelab.se/researcher/80068e29fa614ba4a9bc0b070723ff75.json"}}, {"family": "Porteous", "given": "David J", "initials": "DJ", "orcid": "0000-0003-1249-6106", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6e3ae11c02e4cb89e638e1e5ae0f50a.json"}}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rioux", "given": "John D", "initials": "JD", "orcid": "0000-0001-7560-8326", "researcher": {"href": "https://publications.scilifelab.se/researcher/93bdd54d4d5d402481de2c66601100df.json"}}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F", "orcid": "0000-0001-9435-9441", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8894904d3cf4671a2e563169829322a.json"}}, {"family": "Rotimi", "given": "Charles", "initials": "C", "orcid": "0000-0001-5759-053X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fa2951fdebf4fddaad296d49b8f3f2b.json"}}, {"family": "Rotter", "given": "Jerome I", "initials": "JI", "orcid": "0000-0001-7191-1723", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9bdbf58ae94fc8b455bbbcbcaa50ce.json"}}, {"family": "Rudan", "given": "Igor", "initials": "I", "orcid": "0000-0001-6993-6884", "researcher": {"href": "https://publications.scilifelab.se/researcher/d50e1ca836e841f8a7a748ae93b59d75.json"}}, {"family": "Den Ruijter", "given": "Hester M", "initials": "HM"}, {"family": "Sanghera", "given": "Dharambir K", "initials": "DK"}, {"family": "Sattar", "given": "Naveed", "initials": "N", "orcid": "0000-0002-1604-2593", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fbc7cdcfc444acb066449f80f87181.json"}}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Sim", "given": "Xueling", "initials": "X", "orcid": "0000-0002-1233-7642", "researcher": {"href": "https://publications.scilifelab.se/researcher/3216a8d2a7264a1390a886fa09d5d648.json"}}, {"family": "Small", "given": "Neil", "initials": "N"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0002-3575-5468", "researcher": {"href": "https://publications.scilifelab.se/researcher/311c7381092b4143bcd2e4ef93250526.json"}}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Tai", "given": "E-Shyong", "initials": "ES"}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0002-7141-9189", "researcher": {"href": "https://publications.scilifelab.se/researcher/764ab7a82db24557a5de0fad97bf53f3.json"}}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Tregouet", "given": "David-Alexandre", "initials": "DA"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T", "orcid": "0000-0002-8306-6202", "researcher": {"href": "https://publications.scilifelab.se/researcher/19f5ce9936ca454c85f0af966acac5c0.json"}}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wang", "given": "Carol A", "initials": "CA", "orcid": "0000-0002-4301-3974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf99a43c27034a68976e978b104a91d7.json"}}, {"family": "Weir", "given": "David R", "initials": "DR", "orcid": "0000-0002-1661-2402", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90b7cfe829845fb8cbea9558a5c82a7.json"}}, {"family": "Whitfield", "given": "John B", "initials": "JB", "orcid": "0000-0002-1103-0876", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0f61a914f9748ee9047301da8026bd7.json"}}, {"family": "Wijmenga", "given": "Cisca", "initials": "C"}, {"family": "Wong", "given": "Tien-Yin", "initials": "TY"}, {"family": "Wright", "given": "John", "initials": "J"}, {"family": "Yang", "given": "Jingyun", "initials": "J"}, {"family": "Yu", "given": "Lei", "initials": "L"}, {"family": "Zemel", "given": "Babette S", "initials": "BS"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF", "orcid": "0000-0002-8532-5087", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5b6c24c302d42828806076ded81afe1.json"}}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Franke", "given": "Lude", "initials": "L", "orcid": "0000-0002-5159-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee63161f78274a53b615c05555b81a10.json"}}, {"family": "Haley", "given": "Chris S", "initials": "CS", "orcid": "0000-0002-9811-0210", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4fee769cfe84186abbc285881e0529c.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Walters", "given": "Robin G", "initials": "RG", "orcid": "0000-0002-9179-0321", "researcher": {"href": "https://publications.scilifelab.se/researcher/f36254611faa44b782b76da870e89bd3.json"}}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Esko", "given": "T\u014dnu", "initials": "T"}, {"family": "Helgason", "given": "Agnar", "initials": "A"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Joshi", "given": "Peter K", "initials": "PK", "orcid": "0000-0002-6361-5059", "researcher": {"href": "https://publications.scilifelab.se/researcher/46050ddec8f64054b3bab46c5016aebf.json"}}, {"family": "Kubo", "given": "Michiaki", "initials": "M"}, {"family": "Wilson", "given": "James F", "initials": "JF", "orcid": "0000-0001-5751-9178", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39e6e0f7210494cb4f80be0f7413b6f.json"}}], "type": "journal article", "published": "2019-10-31", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "4957", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44-66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding.", "doi": "10.1038/s41467-019-12283-6", "pmid": "31673082", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6823371"}, {"db": "pii", "key": "10.1038/s41467-019-12283-6"}], "notes": [], "created": "2019-11-28T07:41:34.797Z", "modified": "2023-06-19T13:09:10.356Z"}, {"entity": "publication", "iuid": "f8ad8e9980a54d9caeff5a105bd9b6a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8ad8e9980a54d9caeff5a105bd9b6a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8ad8e9980a54d9caeff5a105bd9b6a2"}}, "title": "Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.", "authors": [{"family": "Saremi", "given": "Nedda F", "initials": "NF"}, {"family": "Supple", "given": "Megan A", "initials": "MA"}, {"family": "Byrne", "given": "Ashley", "initials": "A"}, {"family": "Cahill", "given": "James A", "initials": "JA"}, {"family": "Coutinho", "given": "Luiz Lehmann", "initials": "LL"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Figueir\u00f3", "given": "Henrique V", "initials": "HV"}, {"family": "Johnson", "given": "Warren E", "initials": "WE"}, {"family": "Milne", "given": "Heather J", "initials": "HJ"}, {"family": "O'Brien", "given": "Stephen J", "initials": "SJ"}, {"family": "O'Connell", "given": "Brendan", "initials": "B"}, {"family": "Onorato", "given": "David P", "initials": "DP"}, {"family": "Riley", "given": "Seth P D", "initials": "SPD"}, {"family": "Sikich", "given": "Jeff A", "initials": "JA"}, {"family": "Stahler", "given": "Daniel R", "initials": "DR"}, {"family": "Villela", "given": "Priscilla Marqui Schmidt", "initials": "PMS"}, {"family": "Vollmers", "given": "Christopher", "initials": "C"}, {"family": "Wayne", "given": "Robert K", "initials": "RK"}, {"family": "Eizirik", "given": "Eduardo", "initials": "E"}, {"family": "Corbett-Detig", "given": "Russell B", "initials": "RB"}, {"family": "Green", "given": "Richard E", "initials": "RE"}, {"family": "Wilmers", "given": "Christopher C", "initials": "CC"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}], "type": "journal article", "published": "2019-10-18", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "4769", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.", "doi": "10.1038/s41467-019-12741-1", "pmid": "31628318", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-12741-1"}, {"db": "pmc", "key": "PMC6800433"}], "notes": [], "created": "2019-12-02T16:53:08.735Z", "modified": "2021-07-07T20:31:10.946Z"}, {"entity": "publication", "iuid": "f8f7e1aa81ab4c7ab893a61f6c326981", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8f7e1aa81ab4c7ab893a61f6c326981.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8f7e1aa81ab4c7ab893a61f6c326981"}}, "title": "Microbe-host interplay in atopic dermatitis and psoriasis.", "authors": [{"family": "Fyhrquist", "given": "Nanna", "initials": "N"}, {"family": "Muirhead", "given": "Gareth", "initials": "G"}, {"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S"}, {"family": "Jeanmougin", "given": "Marine", "initials": "M"}, {"family": "Olah", "given": "Peter", "initials": "P"}, {"family": "Skoog", "given": "Tiina", "initials": "T"}, {"family": "Jules-Clement", "given": "Gerome", "initials": "G"}, {"family": "Feld", "given": "Micha", "initials": "M"}, {"family": "Barrientos-Somarribas", "given": "Mauricio", "initials": "M"}, {"family": "Sinkko", "given": "Hanna", "initials": "H"}, {"family": "van den Bogaard", "given": "Ellen H", "initials": "EH"}, {"family": "Zeeuwen", "given": "Patrick L J M", "initials": "PLJM"}, {"family": "Rikken", "given": "Gijs", "initials": "G"}, {"family": "Schalkwijk", "given": "Joost", "initials": "J"}, {"family": "Niehues", "given": "Hanna", "initials": "H"}, {"family": "D\u00e4ubener", "given": "Walter", "initials": "W"}, {"family": "Eller", "given": "Silvia Kathrin", "initials": "SK"}, {"family": "Alexander", "given": "Helen", "initials": "H"}, {"family": "Pennino", "given": "Davide", "initials": "D"}, {"family": "Suomela", "given": "Sari", "initials": "S"}, {"family": "Tessas", "given": "Ioannis", "initials": "I"}, {"family": "Lybeck", "given": "Emilia", "initials": "E"}, {"family": "Baran", "given": "Anna M", "initials": "AM"}, {"family": "Darban", "given": "Hamid", "initials": "H"}, {"family": "Gangwar", "given": "Roopesh Singh", "initials": "RS"}, {"family": "Gerstel", "given": "Ulrich", "initials": "U"}, {"family": "Jahn", "given": "Katharina", "initials": "K"}, {"family": "Karisola", "given": "Piia", "initials": "P"}, {"family": "Yan", "given": "Lee", "initials": "L"}, {"family": "Hansmann", "given": "Britta", "initials": "B"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Meller", "given": "Stephan", "initials": "S"}, {"family": "Bylesj\u00f6", "given": "Max", "initials": "M"}, {"family": "Hup\u00e9", "given": "Philippe", "initials": "P"}, {"family": "Levi-Schaffer", "given": "Francesca", "initials": "F"}, {"family": "Greco", "given": "Dario", "initials": "D"}, {"family": "Ranki", "given": "Annamari", "initials": "A"}, {"family": "Schr\u00f6der", "given": "Jens M", "initials": "JM"}, {"family": "Barker", "given": "Jonathan", "initials": "J"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Tsoka", "given": "Sophia", "initials": "S"}, {"family": "Lauerma", "given": "Antti", "initials": "A"}, {"family": "Soumelis", "given": "Vassili", "initials": "V"}, {"family": "Nestle", "given": "Frank O", "initials": "FO"}, {"family": "Homey", "given": "Bernhard", "initials": "B"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Alenius", "given": "Harri", "initials": "H"}], "type": "journal article", "published": "2019-10-16", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "4703", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Despite recent advances in understanding microbial diversity in skin homeostasis, the relevance of microbial dysbiosis in inflammatory disease is poorly understood. Here we perform a comparative analysis of skin microbial communities coupled to global patterns of cutaneous gene expression in patients with atopic dermatitis or psoriasis. The skin microbiota is analysed by 16S amplicon or whole genome sequencing and the skin transcriptome by microarrays, followed by integration of the data layers. We find that atopic dermatitis and psoriasis can be classified by distinct microbes, which differ from healthy volunteers microbiome composition. Atopic dermatitis is dominated by a single microbe (Staphylococcus aureus), and associated with a disease relevant host transcriptomic signature enriched for skin barrier function, tryptophan metabolism and immune activation. In contrast, psoriasis is characterized by co-occurring communities of microbes with weak associations with disease related gene expression. Our work provides a basis for biomarker discovery and targeted therapies in skin dysbiosis.", "doi": "10.1038/s41467-019-12253-y", "pmid": "31619666", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-12253-y"}, {"db": "pmc", "key": "PMC6795799"}], "notes": [], "created": "2019-12-02T16:50:28.663Z", "modified": "2024-01-16T13:48:43.676Z"}, {"entity": "publication", "iuid": "177f8de8154a4af7973a67c59e5500d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/177f8de8154a4af7973a67c59e5500d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/177f8de8154a4af7973a67c59e5500d0"}}, "title": "Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria.", "authors": [{"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Li", "given": "Yong", "initials": "Y"}, {"family": "Ghasemi", "given": "Sahar", "initials": "S"}, {"family": "Prins", "given": "Bram P", "initials": "BP"}, {"family": "Wuttke", "given": "Matthias", "initials": "M"}, {"family": "Hermle", "given": "Tobias", "initials": "T"}, {"family": "Giri", "given": "Ayush", "initials": "A"}, {"family": "Sieber", "given": "Karsten B", "initials": "KB"}, {"family": "Qiu", "given": "Chengxiang", "initials": "C"}, {"family": "Kirsten", "given": "Holger", "initials": "H"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Bansal", "given": "Nisha", "initials": "N"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Wang", "given": "Lihua", "initials": "L"}, {"family": "Chai", "given": "Jin-Fang", "initials": "JF"}, {"family": "Cocca", "given": "Massimiliano", "initials": "M"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Hoppmann", "given": "Anselm", "initials": "A"}, {"family": "Horn", "given": "Katrin", "initials": "K"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Noce", "given": "Damia", "initials": "D"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Sedaghat", "given": "Sanaz", "initials": "S"}, {"family": "Sveinbjornsson", "given": "Gardar", "initials": "G"}, {"family": "Tayo", "given": "Bamidele O", "initials": "BO"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Xu", "given": "Yizhe", "initials": "Y"}, {"family": "Yu", "given": "Zhi", "initials": "Z"}, {"family": "Gerstner", "given": "Lea", "initials": "L"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL"}, {"family": "Baptista", "given": "Daniela", "initials": "D"}, {"family": "Biggs", "given": "Mary L", "initials": "ML"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Burkhardt", "given": "Ralph", "initials": "R"}, {"family": "Carroll", "given": "Robert J", "initials": "RJ"}, {"family": "Chee", "given": "Miao-Li", "initials": "ML"}, {"family": "Chee", "given": "Miao-Ling", "initials": "ML"}, {"family": "Chen", "given": "Mengmeng", "initials": "M"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "Coresh", "given": "Josef", "initials": "J"}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "de Borst", "given": "Martin H", "initials": "MH"}, {"family": "De Grandi", "given": "Alessandro", "initials": "A"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "de Vries", "given": "Aiko P J", "initials": "APJ"}, {"family": "Degenhardt", "given": "Frauke", "initials": "F"}, {"family": "Dittrich", "given": "Katalin", "initials": "K"}, {"family": "Divers", "given": "Jasmin", "initials": "J"}, {"family": "Eckardt", "given": "Kai-Uwe", "initials": "KU"}, {"family": "Ehret", "given": "Georg", "initials": "G"}, {"family": "Endlich", "given": "Karlhans", "initials": "K"}, {"family": "Felix", "given": "Janine F", "initials": "JF"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Freedman", "given": "Barry I", "initials": "BI"}, {"family": "Freitag-Wolf", "given": "Sandra", "initials": "S"}, {"family": "Gansevoort", "given": "Ron T", "initials": "RT"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "G\u00f6gele", "given": "Martin", "initials": "M"}, {"family": "Grundner-Culemann", "given": "Franziska", "initials": "F"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hamet", "given": "Pavel", "initials": "P"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Foo", "given": "Valencia Hui Xian", "initials": "VHX"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Jaddoe", "given": "Vincent W V", "initials": "VWV"}, {"family": "Jakobsdottir", "given": "Johanna", "initials": "J"}, {"family": "Josyula", "given": "Navya Shilpa", "initials": "NS"}, {"family": "Jung", "given": "Bettina", "initials": "B"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Khor", "given": "Chiea-Chuen", "initials": "CC"}, {"family": "Kiess", "given": "Wieland", "initials": "W"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "K\u00f6rner", "given": "Antje", "initials": "A"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Kramer", "given": "Holly", "initials": "H"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Lee", "given": "Jeannette Jen-Mai", "initials": "JJ"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lieb", "given": "Wolfgang", "initials": "W"}, {"family": "Lim", "given": "Su-Chi", "initials": "SC"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Loeffler", "given": "Markus", "initials": "M"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Maranville", "given": "Joseph C", "initials": "JC"}, {"family": "Mascalzoni", "given": "Deborah", "initials": "D"}, {"family": "McMullen", "given": "Barbara", "initials": "B"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Miliku", "given": "Kozeta", "initials": "K"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Mychaleckyj", "given": "Josyf C", "initials": "JC"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Ning", "given": "Boting", "initials": "B"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Connell", "given": "Jeffrey O'", "initials": "JO"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Palmer", "given": "Nicholette D", "initials": "ND"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Podgornaia", "given": "Anna I", "initials": "AI"}, {"family": "Ponte", "given": "Belen", "initials": "B"}, {"family": "Poulain", "given": "Tanja", "initials": "T"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Rabelink", "given": "Ton J", "initials": "TJ"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Reilly", "given": "Dermot F", "initials": "DF"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "Rheinberger", "given": "Myriam", "initials": "M"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Runz", "given": "Heiko", "initials": "H"}, {"family": "Ryan", "given": "Kathleen A", "initials": "KA"}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C"}, {"family": "Saum", "given": "Kai-Uwe", "initials": "KU"}, {"family": "Sch\u00f6ttker", "given": "Ben", "initials": "B"}, {"family": "Shaffer", "given": "Christian M", "initials": "CM"}, {"family": "Shi", "given": "Yuan", "initials": "Y"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Sun", "given": "Benjamin B", "initials": "BB"}, {"family": "Szymczak", "given": "Silke", "initials": "S"}, {"family": "Tai", "given": "E-Shyong", "initials": "ES"}, {"family": "Tan", "given": "Nicholas Y Q", "initials": "NYQ"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teren", "given": "Andrej", "initials": "A"}, {"family": "Tham", "given": "Yih-Chung", "initials": "YC"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "Thio", "given": "Chris H L", "initials": "CHL"}, {"family": "Thomsen", "given": "Hauke", "initials": "H"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Tremblay", "given": "Johanne", "initials": "J"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Vogelezang", "given": "Suzanne", "initials": "S"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wang", "given": "Chaolong", "initials": "C"}, {"family": "Wilson", "given": "Otis D", "initials": "OD"}, {"family": "Wong", "given": "Charlene", "initials": "C"}, {"family": "Wong", "given": "Tien-Yin", "initials": "TY"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Yasuda", "given": "Masayuki", "initials": "M"}, {"family": "Akilesh", "given": "Shreeram", "initials": "S"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Devuyst", "given": "Olivier", "initials": "O"}, {"family": "Edwards", "given": "Todd L", "initials": "TL"}, {"family": "Ho", "given": "Kevin", "initials": "K"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "Pendergrass", "given": "Sarah A", "initials": "SA"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Susztak", "given": "Katalin", "initials": "K"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Hung", "given": "Adriana M", "initials": "AM"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-09-11", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "4130", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Increased levels of the urinary albumin-to-creatinine ratio (UACR) are associated with higher risk of kidney disease progression and cardiovascular events, but underlying mechanisms are incompletely understood. Here, we conduct trans-ethnic (n\u2009=\u2009564,257) and European-ancestry specific meta-analyses of genome-wide association studies of UACR, including ancestry- and diabetes-specific analyses, and identify 68 UACR-associated loci. Genetic correlation analyses and risk score associations in an independent electronic medical records database (n\u2009=\u2009192,868) reveal connections with proteinuria, hyperlipidemia, gout, and hypertension. Fine-mapping and trans-Omics analyses with gene expression in 47 tissues and plasma protein levels implicate genes potentially operating through differential expression in kidney (including TGFB1, MUC1, PRKCI, and OAF), and allow coupling of UACR associations to altered plasma OAF concentrations. Knockdown of OAF and PRKCI orthologs in Drosophila nephrocytes reduces albumin endocytosis. Silencing fly PRKCI further impairs slit diaphragm formation. These results generate a priority list of genes and pathways for translational research to reduce albuminuria.", "doi": "10.1038/s41467-019-11576-0", "pmid": "31511532", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11576-0"}, {"db": "pmc", "key": "PMC6739370"}], "notes": [], "created": "2019-09-16T11:35:17.679Z", "modified": "2020-01-21T13:56:14.381Z"}, {"entity": "publication", "iuid": "5d06d21f8ba04e248e5c41f2d8650052", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d06d21f8ba04e248e5c41f2d8650052.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d06d21f8ba04e248e5c41f2d8650052"}}, "title": "Protein prenylation restrains innate immunity by inhibiting Rac1 effector interactions.", "authors": [{"family": "Akula", "given": "Murali K", "initials": "MK"}, {"family": "Ibrahim", "given": "Mohamed X", "initials": "MX"}, {"family": "Ivarsson", "given": "Emil G", "initials": "EG"}, {"family": "Khan", "given": "Omar M", "initials": "OM"}, {"family": "Kumar", "given": "Israiel T", "initials": "IT"}, {"family": "Erlandsson", "given": "Malin", "initials": "M"}, {"family": "Karlsson", "given": "Christin", "initials": "C"}, {"family": "Xu", "given": "Xiufeng", "initials": "X"}, {"family": "Brisslert", "given": "Mikael", "initials": "M"}, {"family": "Brakebusch", "given": "Cord", "initials": "C"}, {"family": "Wang", "given": "Donghai", "initials": "D"}, {"family": "Bokarewa", "given": "Maria", "initials": "M"}, {"family": "Sayin", "given": "Volkan I", "initials": "VI"}, {"family": "Bergo", "given": "Martin O", "initials": "MO"}], "type": "journal article", "published": "2019-09-04", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3975", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Rho family proteins are prenylated by geranylgeranyltransferase type I (GGTase-I), which normally target proteins to membranes for GTP-loading. However, conditional deletion of GGTase-I in mouse macrophages increases GTP-loading of Rho proteins, leading to enhanced inflammatory responses and severe rheumatoid arthritis. Here we show that heterozygous deletion of the Rho family gene Rac1, but not Rhoa and Cdc42, reverses inflammation and arthritis in GGTase-I-deficient mice. Non-prenylated Rac1 has a high affinity for the adaptor protein Ras GTPase-activating-like protein 1 (Iqgap1), which facilitates both GTP exchange and ubiquitination-mediated degradation of Rac1. Consistently, inactivating Iqgap1 normalizes Rac1 GTP-loading, and reduces inflammation and arthritis in GGTase-I-deficient mice, as well as prevents statins from increasing Rac1 GTP-loading and cytokine production in macrophages. We conclude that blocking prenylation stimulates Rac1 effector interactions and unleashes proinflammatory signaling. Our results thus suggest that prenylation normally restrains innate immune responses by preventing Rac1 effector interactions.", "doi": "10.1038/s41467-019-11606-x", "pmid": "31484924", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11606-x"}, {"db": "pmc", "key": "PMC6726657"}], "notes": [], "created": "2020-01-27T22:51:33.003Z", "modified": "2024-01-16T13:46:31.619Z"}, {"entity": "publication", "iuid": "03e1d400d72c4ecdb3a49ed132d7ef7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03e1d400d72c4ecdb3a49ed132d7ef7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03e1d400d72c4ecdb3a49ed132d7ef7a"}}, "title": "Unique transcriptional and protein-expression signature in human lung tissue-resident NK cells.", "authors": [{"family": "Marquardt", "given": "Nicole", "initials": "N"}, {"family": "Kek\u00e4l\u00e4inen", "given": "Eliisa", "initials": "E"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Lourda", "given": "Magda", "initials": "M"}, {"family": "Wilson", "given": "Jennifer N", "initials": "JN"}, {"family": "Scharenberg", "given": "Marlena", "initials": "M"}, {"family": "Bergman", "given": "Per", "initials": "P"}, {"family": "Al-Ameri", "given": "Mamdoh", "initials": "M"}, {"family": "H\u00e5rd", "given": "Joanna", "initials": "J"}, {"family": "Mold", "given": "Jeffrey E", "initials": "JE"}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG"}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}], "type": "journal article", "published": "2019-08-26", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3841", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Human lung tissue-resident NK cells (trNK cells) are likely to play an important role in host responses towards viral infections, inflammatory conditions and cancer. However, detailed insights into these cells are still largely lacking. Here we show, using RNA sequencing and flow cytometry-based analyses, that subsets of human lung CD69 +CD16- NK cells display hallmarks of tissue-residency, including high expression of CD49a, CD103, and ZNF683, and reduced expression of SELL, S1PR5, and KLF2/3. CD49a+CD16- NK cells are functionally competent, and produce IFN-\u03b3, TNF, MIP-1\u03b2, and GM-CSF. After stimulation with IL-15, they upregulate perforin, granzyme B, and Ki67 to a similar degree as CD49a-CD16- NK cells. Comparing datasets from trNK cells in human lung and bone marrow with tissue-resident memory CD8+ T cells identifies core genes co-regulated either by tissue-residency, cell-type or location. Together, our data indicate that human lung trNK cells have distinct features, likely regulating their function in barrier immunity.", "doi": "10.1038/s41467-019-11632-9", "pmid": "31451696", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11632-9"}, {"db": "pmc", "key": "PMC6710242"}], "notes": [], "created": "2019-12-02T16:52:30.576Z", "modified": "2020-01-21T13:56:15.499Z"}, {"entity": "publication", "iuid": "666d3b0626004dd0978b871abd17db71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/666d3b0626004dd0978b871abd17db71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/666d3b0626004dd0978b871abd17db71"}}, "title": "Profiling surface proteins on individual exosomes using a proximity barcoding assay.", "authors": [{"family": "Wu", "given": "Di", "initials": "D", "orcid": "0000-0003-0293-9057", "researcher": {"href": "https://publications.scilifelab.se/researcher/2664b0c2ac7245508b02bbd8f78998ae.json"}}, {"family": "Yan", "given": "Junhong", "initials": "J"}, {"family": "Shen", "given": "Xia", "initials": "X", "orcid": "0000-0003-4390-1979", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40d1f7f07ed482b9c95f56c61f0a836.json"}}, {"family": "Sun", "given": "Yu", "initials": "Y", "orcid": "0000-0003-4799-0745", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba9de321f10248a8b81c73daa05c5d48.json"}}, {"family": "Thulin", "given": "M\u00e5ns", "initials": "M", "orcid": "0000-0002-2756-3933", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae987ebb24a423392fd51b3ba0166e9.json"}}, {"family": "Cai", "given": "Yanling", "initials": "Y"}, {"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Shen", "given": "Qiujin", "initials": "Q"}, {"family": "Oelrich", "given": "Johan", "initials": "J", "orcid": "0000-0002-8591-7728", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e97acea3e040adb1b8ee20cba7cdc0.json"}}, {"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3.json"}}, {"family": "Dubois", "given": "K Louise", "initials": "KL"}, {"family": "Ronquist", "given": "K G\u00f6ran", "initials": "KG", "orcid": "0000-0001-5885-8067", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1cdc49a4467457a894cd62c3051306a.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U", "orcid": "0000-0002-7820-1000", "researcher": {"href": "https://publications.scilifelab.se/researcher/87392e51288f4ef9a38fe3989d10d180.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2019-08-26", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3854", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Exosomes have been implicated in numerous biological processes, and they may serve as important disease markers. Surface proteins on exosomes carry information about their tissues of origin. Because of the heterogeneity of exosomes it is desirable to investigate them individually, but this has so far remained impractical. Here, we demonstrate a proximity-dependent barcoding assay to profile surface proteins of individual exosomes using antibody-DNA conjugates and next-generation sequencing. We first validate the method using artificial streptavidin-oligonucleotide complexes, followed by analysis of the variable composition of surface proteins on individual exosomes, derived from human body fluids or cell culture media. Exosomes from different sources are characterized by the presence of specific combinations of surface proteins and their abundance, allowing exosomes to be separately quantified in mixed samples to serve as markers for tissue-specific engagement in disease.", "doi": "10.1038/s41467-019-11486-1", "pmid": "31451692", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11486-1"}, {"db": "pmc", "key": "PMC6710248"}], "notes": [], "created": "2020-01-07T15:00:02.216Z", "modified": "2024-01-16T13:48:43.995Z"}, {"entity": "publication", "iuid": "eaa21c61aecb4f6091ceca70d6dd7175", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eaa21c61aecb4f6091ceca70d6dd7175.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eaa21c61aecb4f6091ceca70d6dd7175"}}, "title": "Genome-wide systematic identification of methyltransferase recognition and modification patterns.", "authors": [{"family": "Jensen", "given": "Torbj\u00f8rn \u00d8lsh\u00f8j", "initials": "T\u00d8"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Redl", "given": "Stephanie", "initials": "S"}, {"family": "Maury", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Jacobsen", "given": "Simo Abdessamad Baallal", "initials": "SAB"}, {"family": "Pedersen", "given": "Lasse Ebdrup", "initials": "LE"}, {"family": "Nielsen", "given": "Alex Toftgaard", "initials": "AT"}], "type": "journal article", "published": "2019-08-19", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3311", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Genome-wide analysis of DNA methylation patterns using single molecule real-time DNA sequencing has boosted the number of publicly available methylomes. However, there is a lack of tools coupling methylation patterns and the corresponding methyltransferase genes. Here we demonstrate a high-throughput method for coupling methyltransferases with their respective motifs, using automated cloning and analysing the methyltransferases in vectors carrying a strain-specific cassette containing all potential target sites. To validate the method, we analyse the genomes of the thermophile Moorella thermoacetica and the mesophile Acetobacterium woodii, two acetogenic bacteria having substantially modified genomes with 12 methylation motifs and a total of 23 methyltransferase genes. Using our method, we characterize the 23 methyltransferases, assign motifs to the respective enzymes and verify activity for 11 of the 12 motifs.", "doi": "10.1038/s41467-019-11179-9", "pmid": "31427571", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11179-9"}, {"db": "pmc", "key": "PMC6700114"}], "notes": [], "created": "2019-08-26T14:05:31.867Z", "modified": "2020-01-21T13:56:14.326Z"}, {"entity": "publication", "iuid": "4c24079e980f4d5a92a0cefe7b18f5ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c24079e980f4d5a92a0cefe7b18f5ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c24079e980f4d5a92a0cefe7b18f5ef"}}, "title": "PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer.", "authors": [{"family": "Costa", "given": "T\u00e2nia D F", "initials": "TDF"}, {"family": "Zhuang", "given": "Ting", "initials": "T"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Turco", "given": "Emilia", "initials": "E"}, {"family": "Olofsson", "given": "Helene", "initials": "H"}, {"family": "Masia-Balague", "given": "Miriam", "initials": "M"}, {"family": "Zhao", "given": "Miao", "initials": "M"}, {"family": "Rabieifar", "given": "Parisa", "initials": "P"}, {"family": "Robertson", "given": "Neil", "initials": "N"}, {"family": "Kuiper", "given": "Raoul", "initials": "R"}, {"family": "Sj\u00f6lund", "given": "Jonas", "initials": "J"}, {"family": "Spiess", "given": "Matthias", "initials": "M"}, {"family": "Hern\u00e1ndez-Varas", "given": "Pablo", "initials": "P"}, {"family": "Rabenhorst", "given": "Uta", "initials": "U"}, {"family": "Roswall", "given": "Pernilla", "initials": "P"}, {"family": "Ma", "given": "Ran", "initials": "R"}, {"family": "Gong", "given": "Xiaowei", "initials": "X"}, {"family": "Hartman", "given": "Johan", "initials": "J"}, {"family": "Pietras", "given": "Kristian", "initials": "K"}, {"family": "Adams", "given": "Peter D", "initials": "PD"}, {"family": "Defilippi", "given": "Paola", "initials": "P"}, {"family": "Str\u00f6mblad", "given": "Staffan", "initials": "S"}], "type": "journal article", "published": "2019-08-09", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3589", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Overcoming cellular growth restriction, including the evasion of cellular senescence, is a hallmark of cancer. We report that PAK4 is overexpressed in all human breast cancer subtypes and associated with poor patient outcome. In mice, MMTV-PAK4 overexpression promotes spontaneous mammary cancer, while PAK4 gene depletion delays MMTV-PyMT driven tumors. Importantly, PAK4 prevents senescence-like growth arrest in breast cancer cells in vitro, in vivo and ex vivo, but is not needed in non-immortalized cells, while PAK4 overexpression in untransformed human mammary epithelial cells abrogates H-RAS-V12-induced senescence. Mechanistically, a PAK4 - RELB - C/EBP\u03b2 axis controls the senescence-like growth arrest and a PAK4 phosphorylation residue (RELB-Ser151) is critical for RELB-DNA interaction, transcriptional activity and expression of the senescence regulator C/EBP\u03b2. These findings establish PAK4 as a promoter of breast cancer that can overcome oncogene-induced senescence and reveal a selective vulnerability of cancer to PAK4 inhibition.", "doi": "10.1038/s41467-019-11510-4", "pmid": "31399573", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11510-4"}, {"db": "pmc", "key": "PMC6689091"}], "notes": [], "created": "2019-12-02T16:53:04.441Z", "modified": "2020-01-21T13:56:15.526Z"}, {"entity": "publication", "iuid": "12fa8cdef0e741259e14edbd8e9cb2df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12fa8cdef0e741259e14edbd8e9cb2df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12fa8cdef0e741259e14edbd8e9cb2df"}}, "title": "Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC.", "authors": [{"family": "Nirwan", "given": "Neha", "initials": "N"}, {"family": "Itoh", "given": "Yuzuru", "initials": "Y", "orcid": "0000-0001-7802-5572", "researcher": {"href": "https://publications.scilifelab.se/researcher/12516bf2aeb44f9ba7e380b7be1bf582.json"}}, {"family": "Singh", "given": "Pratima", "initials": "P"}, {"family": "Bandyopadhyay", "given": "Sutirtha", "initials": "S"}, {"family": "Vinothkumar", "given": "Kutti R", "initials": "KR", "orcid": "0000-0002-6746-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bad216089a24c7f950de5a7f05939dc.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Saikrishnan", "given": "Kayarat", "initials": "K", "orcid": "0000-0003-4177-8508", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc61783f167447e2bd214c8ceb1e5074.json"}}], "type": "journal article", "published": "2019-07-11", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3058", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The AAA+ GTPase McrB powers DNA cleavage by the endonuclease McrC. The GTPase itself is activated by McrC. The architecture of the GTPase and nuclease complex, and the mechanism of their activation remained unknown. Here, we report a 3.6 \u00c5 structure of a GTPase-active and DNA-binding deficient construct of McrBC. Two hexameric rings of McrB are bridged by McrC dimer. McrC interacts asymmetrically with McrB protomers and inserts a stalk into the pore of the ring, reminiscent of the \u03b3 subunit complexed to \u03b1 3\u03b23 of F1-ATPase. Activation of the GTPase involves conformational changes of residues essential for hydrolysis. Three consecutive nucleotide-binding pockets are occupied by the GTP analogue 5'-guanylyl imidodiphosphate and the next three by GDP, which is suggestive of sequential GTP hydrolysis.", "doi": "10.1038/s41467-019-11084-1", "pmid": "31296862", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11084-1"}, {"db": "pmc", "key": "PMC6624300"}], "notes": "Cryo-EM maps and models are deposited in the Electron Microscopy and Protein Data Banks: EMD-0310 and 6HZ4. Maps and coordinates of five major classes are deposited \u2014 EMD-0311 and 6HZ5; EMD-0312 and 6HZ6; EMD-0313 and 6HZ7; EMD-0314 and 6HZ8; EMD-0315 and 6HZ9. Other data are available from the corresponding authors upon reasonable request.", "created": "2019-08-21T10:53:27.809Z", "modified": "2021-06-16T16:13:49.944Z"}, {"entity": "publication", "iuid": "cb37677921194ab3a4e0306fa262a79c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb37677921194ab3a4e0306fa262a79c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb37677921194ab3a4e0306fa262a79c"}}, "title": "Genome-wide analysis of dental caries and periodontitis combining clinical and self-reported data.", "authors": [{"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Haworth", "given": "Simon", "initials": "S", "orcid": "0000-0001-7793-7326", "researcher": {"href": "https://publications.scilifelab.se/researcher/43fa9fb331c849b58d4ac4b14f04fbda.json"}}, {"family": "Divaris", "given": "Kimon", "initials": "K", "orcid": "0000-0003-1290-7251", "researcher": {"href": "https://publications.scilifelab.se/researcher/faf6f5fd1c224f8e8733c944a62c6821.json"}}, {"family": "Agler", "given": "Cary S", "initials": "CS"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y", "orcid": "0000-0001-8748-5597", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf00b09991c4b40bd77a4f2c5bfad97.json"}}, {"family": "Keun Lee", "given": "Myoung", "initials": "M"}, {"family": "Grinde", "given": "Kelsey", "initials": "K"}, {"family": "Hindy", "given": "George", "initials": "G"}, {"family": "Alaraudanjoki", "given": "Viivi", "initials": "V"}, {"family": "Pesonen", "given": "Paula", "initials": "P"}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Holtfreter", "given": "Birte", "initials": "B"}, {"family": "Sakaue", "given": "Saori", "initials": "S", "orcid": "0000-0003-3618-9717", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b766fd8b9f54da4aee3275bc5864bc5.json"}}, {"family": "Hirata", "given": "Jun", "initials": "J"}, {"family": "Yu", "given": "Yau-Hua", "initials": "YH", "orcid": "0000-0002-4723-5064", "researcher": {"href": "https://publications.scilifelab.se/researcher/1721a03cdef84fbc848c40757d4d33cf.json"}}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Sudo", "given": "Takeaki", "initials": "T"}, {"family": "Okada", "given": "Yukinori", "initials": "Y", "orcid": "0000-0002-0311-8472", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b13860bfef41959c29be2de853b456.json"}}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U", "orcid": "0000-0002-5689-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/e529a40052644d83bdef588a3e4f4e99.json"}}, {"family": "Kocher", "given": "Thomas", "initials": "T", "orcid": "0000-0001-9605-2822", "researcher": {"href": "https://publications.scilifelab.se/researcher/eda3d0e849684448992e43011860b1ed.json"}}, {"family": "Anttonen", "given": "Vuokko", "initials": "V"}, {"family": "Laitala", "given": "Marja-Liisa", "initials": "ML", "orcid": "0000-0001-7323-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5a4749f0323465faa3ac823fc057f22.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Sofer", "given": "Tamar", "initials": "T", "orcid": "0000-0001-8520-8860", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a07473be2d0489a83ba0180d19eef95.json"}}, {"family": "Shaffer", "given": "John R", "initials": "JR", "orcid": "0000-0003-1897-1131", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bcd086471fe49d49534518327f66a50.json"}}, {"family": "Vieira", "given": "Alexandre", "initials": "A"}, {"family": "Marazita", "given": "Mary L", "initials": "ML"}, {"family": "Kubo", "given": "Michiaki", "initials": "M"}, {"family": "Furuichi", "given": "Yasushi", "initials": "Y"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Offenbacher", "given": "Steve", "initials": "S"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0002-7141-9189", "researcher": {"href": "https://publications.scilifelab.se/researcher/764ab7a82db24557a5de0fad97bf53f3.json"}}, {"family": "Johansson", "given": "Ingegerd", "initials": "I"}], "type": "journal article", "published": "2019-06-24", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "2773", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Dental caries and periodontitis account for a vast burden of morbidity and healthcare spending, yet their genetic basis remains largely uncharacterized. Here, we identify self-reported dental disease proxies which have similar underlying genetic contributions to clinical disease measures and then combine these in a genome-wide association study meta-analysis, identifying 47 novel and conditionally-independent risk loci for dental caries. We show that the heritability of dental caries is enriched for conserved genomic regions and partially overlapping with a range of complex traits including smoking, education, personality traits and metabolic measures. Using cardio-metabolic traits as an example in Mendelian randomization analysis, we estimate causal relationships and provide evidence suggesting that the processes contributing to dental caries may have undesirable downstream effects on health.", "doi": "10.1038/s41467-019-10630-1", "pmid": "31235808", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6591304"}, {"db": "pii", "key": "10.1038/s41467-019-10630-1"}], "notes": [], "created": "2019-07-05T12:56:39.673Z", "modified": "2023-06-19T13:23:39.048Z"}, {"entity": "publication", "iuid": "fdf49b77eedc47dabba348f1b59c5e54", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdf49b77eedc47dabba348f1b59c5e54.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdf49b77eedc47dabba348f1b59c5e54"}}, "title": "A quantitative Streptococcus pyogenes-human protein-protein interaction map reveals localization of opsonizing antibodies.", "authors": [{"family": "Happonen", "given": "Lotta", "initials": "L"}, {"family": "Hauri", "given": "Simon", "initials": "S"}, {"family": "Svensson Birkedal", "given": "Gabriel", "initials": "G"}, {"family": "Karlsson", "given": "Christofer", "initials": "C"}, {"family": "de Neergaard", "given": "Therese", "initials": "T"}, {"family": "Khakzad", "given": "Hamed", "initials": "H"}, {"family": "Nordenfelt", "given": "Pontus", "initials": "P"}, {"family": "Wikstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Wisniewska", "given": "Magdalena", "initials": "M"}, {"family": "Bj\u00f6rck", "given": "Lars", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2019-06-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "10", "issue": "1", "pages": "2727", "issn-l": "2041-1723"}, "abstract": "A fundamental challenge in medical microbiology is to characterize the dynamic protein-protein interaction networks formed at the host-pathogen interface. Here, we generate a quantitative interaction map between the significant human pathogen, Streptococcus pyogenes, and proteins from human saliva and plasma obtained via complementary affinity-purification and bacterial-surface centered enrichment strategies and quantitative mass spectrometry. Perturbation of the network using immunoglobulin protease cleavage, mixtures of different concentrations of saliva and plasma, and different S. pyogenes serotypes and their isogenic mutants, reveals how changing microenvironments alter the interconnectivity of the interaction map. The importance of host immunoglobulins for the interaction with human complement proteins is demonstrated and potential protective epitopes of importance for phagocytosis of S. pyogenes cells are localized. The interaction map confirms several previously described protein-protein interactions; however, it also reveals a multitude of additional interactions, with possible implications for host-pathogen interactions involving other bacterial species.", "doi": "10.1038/s41467-019-10583-5", "pmid": "31227708", "labels": {"Structural Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-10583-5"}, {"db": "pmc", "key": "PMC6588558"}], "notes": [], "created": "2020-01-27T10:12:37.634Z", "modified": "2021-05-24T15:39:50.429Z"}, {"entity": "publication", "iuid": "aa033e622fbc43ffb6090c29ba97d1a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa033e622fbc43ffb6090c29ba97d1a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa033e622fbc43ffb6090c29ba97d1a8"}}, "title": "The viral protein corona directs viral pathogenesis and amyloid aggregation.", "authors": [{"family": "Ezzat", "given": "Kariem", "initials": "K", "orcid": "0000-0003-4186-0675", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f2f1d3d8a5d467c8fc3b95388e4c606.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}, {"family": "P\u00e5lsson", "given": "Sandra", "initials": "S"}, {"family": "Roberts", "given": "Thomas C", "initials": "TC"}, {"family": "J\u00e4rver", "given": "Peter", "initials": "P"}, {"family": "Dondalska", "given": "Aleksandra", "initials": "A"}, {"family": "Bestas", "given": "Burcu", "initials": "B"}, {"family": "Sobkowiak", "given": "Michal J", "initials": "MJ"}, {"family": "Lev\u00e4nen", "given": "Bettina", "initials": "B"}, {"family": "Sk\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Thompson", "given": "Elizabeth A", "initials": "EA"}, {"family": "Saher", "given": "Osama", "initials": "O"}, {"family": "Kari", "given": "Otto K", "initials": "OK"}, {"family": "Lajunen", "given": "Tatu", "initials": "T", "orcid": "0000-0001-6234-9193", "researcher": {"href": "https://publications.scilifelab.se/researcher/55d9cb27b0734ca496514762ed1627f0.json"}}, {"family": "Sverremark Ekstr\u00f6m", "given": "Eva", "initials": "E", "orcid": "0000-0001-6271-8681", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7519ea4bf1f43dcab124c3d62b489db.json"}}, {"family": "Nilsson", "given": "Caroline", "initials": "C"}, {"family": "Ishchenko", "given": "Yevheniia", "initials": "Y"}, {"family": "Malm", "given": "Tarja", "initials": "T"}, {"family": "Wood", "given": "Matthew J A", "initials": "MJA"}, {"family": "Power", "given": "Ultan F", "initials": "UF", "orcid": "0000-0003-3246-3774", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0d135555da74520a0d4b7733cd6ddd7.json"}}, {"family": "Masich", "given": "Sergej", "initials": "S"}, {"family": "Lind\u00e9n", "given": "Anders", "initials": "A"}, {"family": "Sandberg", "given": "Johan K", "initials": "JK", "orcid": "0000-0002-6275-0750", "researcher": {"href": "https://publications.scilifelab.se/researcher/7468c415a46645a3a4c3d28badcff954.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Spetz", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-3964-9512", "researcher": {"href": "https://publications.scilifelab.se/researcher/70270e32d48d486799cc9dd61e36a4f1.json"}}, {"family": "El Andaloussi", "given": "Samir", "initials": "S"}], "type": "journal article", "published": "2019-05-27", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "2331", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Artificial nanoparticles accumulate a protein corona layer in biological fluids, which significantly influences their bioactivity. As nanosized obligate intracellular parasites, viruses share many biophysical properties with artificial nanoparticles in extracellular environments and here we show that respiratory syncytial virus (RSV) and herpes simplex virus type 1 (HSV-1) accumulate a rich and distinctive protein corona in different biological fluids. Moreover, we show that corona pre-coating differentially affects viral infectivity and immune cell activation. In addition, we demonstrate that viruses bind amyloidogenic peptides in their corona and catalyze amyloid formation via surface-assisted heterogeneous nucleation. Importantly, we show that HSV-1 catalyzes the aggregation of the amyloid \u03b2-peptide (A\u03b242), a major constituent of amyloid plaques in Alzheimer's disease, in vitro and in animal models. Our results highlight the viral protein corona as an acquired structural layer that is critical for viral-host interactions and illustrate a mechanistic convergence between viral and amyloid pathologies.", "doi": "10.1038/s41467-019-10192-2", "pmid": "31133680", "labels": {"Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-10192-2"}, {"db": "pmc", "key": "PMC6536551"}], "notes": [], "created": "2020-01-07T12:31:23.818Z", "modified": "2024-01-16T13:48:44.332Z"}, {"entity": "publication", "iuid": "c712089f45ee420497574a4fbdf3867b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c712089f45ee420497574a4fbdf3867b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c712089f45ee420497574a4fbdf3867b"}}, "title": "Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma.", "authors": [{"family": "Carow", "given": "Berit", "initials": "B", "orcid": "0000-0002-8760-6253", "researcher": {"href": "https://publications.scilifelab.se/researcher/f434d654fb5842708da79b3481017852.json"}}, {"family": "Hauling", "given": "Thomas", "initials": "T"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3.json"}}, {"family": "Kramnik", "given": "Igor", "initials": "I"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Rottenberg", "given": "Martin E", "initials": "ME"}], "type": "journal article", "published": "2019-04-23", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "1823", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Granulomas are the pathological hallmark of tuberculosis (TB) and the niche where bacilli can grow and disseminate or the immunological microenvironment in which host cells interact to prevent bacterial dissemination. Here we show 34 immune transcripts align to the morphology of lung sections from Mycobacterium tuberculosis-infected mice at cellular resolution. Colocalizing transcript networks at <10 \u03bcm in C57BL/6 mouse granulomas increase complexity with time after infection. B-cell clusters develop late after infection. Transcripts from activated macrophages are enriched at subcellular distances from M. tuberculosis. Encapsulated C3HeB/FeJ granulomas show necrotic centers with transcripts associated with immunosuppression (Foxp3, Il10), whereas those in the granuloma rims associate with activated T cells and macrophages. We see highly diverse networks with common interactors in similar lesions. Different immune landscapes of M. tuberculosis granulomas depending on the time after infection, the histopathological features of the lesion, and the proximity to bacteria are here defined.", "doi": "10.1038/s41467-019-09816-4", "pmid": "31015452", "labels": {"In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-09816-4"}, {"db": "pmc", "key": "PMC6479067"}], "notes": [], "created": "2020-01-10T04:54:56.986Z", "modified": "2025-10-17T13:02:18.396Z"}, {"entity": "publication", "iuid": "a07bf03ce5af4d6591890d439e270911", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a07bf03ce5af4d6591890d439e270911.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a07bf03ce5af4d6591890d439e270911"}}, "title": "Neutrophil extracellular traps in the central nervous system hinder bacterial clearance during pneumococcal meningitis.", "authors": [{"family": "Mohanty", "given": "Tirthankar", "initials": "T"}, {"family": "Fisher", "given": "Jane", "initials": "J"}, {"family": "Bakochi", "given": "Anahita", "initials": "A"}, {"family": "Neumann", "given": "Ariane", "initials": "A"}, {"family": "Cardoso", "given": "Jos\u00e9 Francisco Pereira", "initials": "JFP"}, {"family": "Karlsson", "given": "Christofer A Q", "initials": "CAQ"}, {"family": "Pavan", "given": "Chiara", "initials": "C"}, {"family": "Lundgaard", "given": "Iben", "initials": "I"}, {"family": "Nilson", "given": "Bo", "initials": "B"}, {"family": "Reinstrup", "given": "Peter", "initials": "P"}, {"family": "Bonnevier", "given": "Johan", "initials": "J"}, {"family": "Cederberg", "given": "David", "initials": "D"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Bentzer", "given": "Peter", "initials": "P"}, {"family": "Linder", "given": "Adam", "initials": "A"}], "type": "journal article", "published": "2019-04-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "10", "issue": "1", "pages": "1667", "issn-l": "2041-1723"}, "abstract": "Neutrophils are crucial mediators of host defense that are recruited to the central nervous system (CNS) in large numbers during acute bacterial meningitis caused by Streptococcus pneumoniae. Neutrophils release neutrophil extracellular traps (NETs) during infections to trap and kill bacteria. Intact NETs are fibrous structures composed of decondensed DNA and neutrophil-derived antimicrobial proteins. Here we show NETs in the cerebrospinal fluid (CSF) of patients with pneumococcal meningitis, and their absence in other forms of meningitis with neutrophil influx into the CSF caused by viruses, Borrelia and subarachnoid hemorrhage. In a rat model of meningitis, a clinical strain of pneumococci induced NET formation in the CSF. Disrupting NETs using DNase I significantly reduces bacterial load, demonstrating that NETs contribute to pneumococcal meningitis pathogenesis in vivo. We conclude that NETs in the CNS reduce bacterial clearance and degrading NETs using DNase I may have significant therapeutic implications.", "doi": "10.1038/s41467-019-09040-0", "pmid": "30971685", "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-09040-0"}, {"db": "pmc", "key": "PMC6458182"}], "notes": [], "created": "2020-01-27T10:13:11.503Z", "modified": "2021-05-24T15:39:50.336Z"}, {"entity": "publication", "iuid": "e7f90faca0e64cfe9379be8900367d06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7f90faca0e64cfe9379be8900367d06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7f90faca0e64cfe9379be8900367d06"}}, "title": "Breast cancer quantitative proteome and proteogenomic landscape.", "authors": [{"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Socciarelli", "given": "Fabio", "initials": "F"}, {"family": "Vacanti", "given": "Nathaniel M", "initials": "NM"}, {"family": "Haugen", "given": "Mads H", "initials": "MH"}, {"family": "Zhu", "given": "Yafeng", "initials": "Y"}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Fernandez-Woodbridge", "given": "Alejandro", "initials": "A"}, {"family": "Aure", "given": "Miriam R", "initials": "MR"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Branca", "given": "Rui M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a.json"}}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Beraki", "given": "Elsa", "initials": "E"}, {"family": "Garred", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Boekel", "given": "Jorrit", "initials": "J"}, {"family": "Sauer", "given": "Torill", "initials": "T"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Nord", "given": "Silje", "initials": "S"}, {"family": "H\u00f6glander", "given": "Elen K", "initials": "EK"}, {"family": "Jans", "given": "Daniel C", "initials": "DC"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Haukaas", "given": "Tonje H", "initials": "TH"}, {"family": "Bathen", "given": "Tone F", "initials": "TF"}, {"family": "Schlichting", "given": "Ellen", "initials": "E"}, {"family": "Naume", "given": "Bj\u00f8rn", "initials": "B"}, {"family": "Consortia Oslo Breast Cancer Research Consortium (OSBREAC)", "given": "", "initials": ""}, {"family": "Luders", "given": "Torben", "initials": "T"}, {"family": "Borgen", "given": "Elin", "initials": "E"}, {"family": "Kristensen", "given": "Vessela N", "initials": "VN"}, {"family": "Russnes", "given": "Hege G", "initials": "HG"}, {"family": "Lingj\u00e6rde", "given": "Ole Christian", "initials": "OC", "orcid": "0000-0003-3565-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/759346ec4321470f96ca42af68ed760c.json"}}, {"family": "Mills", "given": "Gordon B", "initials": "GB"}, {"family": "Sahlberg", "given": "Kristine K", "initials": "KK"}, {"family": "B\u00f8rresen-Dale", "given": "Anne-Lise", "initials": "AL"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2019-04-08", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "1600", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.", "doi": "10.1038/s41467-019-09018-y", "pmid": "30962452", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Global Proteomics and Proteogenomics": "Technology development", "Integrated Microscopy Technologies Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-09018-y"}, {"db": "pmc", "key": "PMC6453966"}], "notes": [], "created": "2019-04-12T07:18:25.320Z", "modified": "2024-01-16T13:48:44.506Z"}, {"entity": "publication", "iuid": "779091cd62cc4a6c9e742911d1a1d949", "links": {"self": {"href": "https://publications.scilifelab.se/publication/779091cd62cc4a6c9e742911d1a1d949.json"}, "display": {"href": "https://publications.scilifelab.se/publication/779091cd62cc4a6c9e742911d1a1d949"}}, "title": "A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.", "authors": [{"family": "Wang", "given": "Kun", "initials": "K"}, {"family": "Sybers", "given": "David", "initials": "D"}, {"family": "Maklad", "given": "Hassan Ramadan", "initials": "HR"}, {"family": "Lemmens", "given": "Liesbeth", "initials": "L"}, {"family": "Lewyllie", "given": "Charlotte", "initials": "C"}, {"family": "Zhou", "given": "Xiaoxiao", "initials": "X"}, {"family": "Schult", "given": "Frank", "initials": "F"}, {"family": "Br\u00e4sen", "given": "Christopher", "initials": "C"}, {"family": "Siebers", "given": "Bettina", "initials": "B"}, {"family": "Valeg\u00e5rd", "given": "Karin", "initials": "K"}, {"family": "Lind\u00e5s", "given": "Ann-Christin", "initials": "AC"}, {"family": "Peeters", "given": "Eveline", "initials": "E"}], "type": "journal article", "published": "2019-04-04", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "1542", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Fatty acid metabolism and its regulation are known to play important roles in bacteria and eukaryotes. By contrast, although certain archaea appear to metabolize fatty acids, the regulation of the underlying pathways in these organisms remains unclear. Here, we show that a TetR-family transcriptional regulator (FadR Sa) is involved in regulation of fatty acid metabolism in the crenarchaeon Sulfolobus acidocaldarius. Functional and structural analyses show that FadRSa binds to DNA at semi-palindromic recognition sites in two distinct stoichiometric binding modes depending on the operator sequence. Genome-wide transcriptomic and chromatin immunoprecipitation analyses demonstrate that the protein binds to only four genomic sites, acting as a repressor of a 30-kb gene cluster comprising 23 open reading frames encoding lipases and \u03b2-oxidation enzymes. Fatty acyl-CoA molecules cause dissociation of FadRSa binding by inducing conformational changes in the protein. Our results indicate that, despite its similarity in overall structure to bacterial TetR-family FadR regulators, FadRSa displays a different acyl-CoA binding mode and a distinct regulatory mechanism.", "doi": "10.1038/s41467-019-09479-1", "pmid": "30948713", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-09479-1"}, {"db": "pmc", "key": "PMC6449355"}], "notes": [], "created": "2019-12-02T17:20:02.213Z", "modified": "2020-01-21T13:56:15.630Z"}, {"entity": "publication", "iuid": "18fd999856294d44be3211726b2f3dc5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18fd999856294d44be3211726b2f3dc5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18fd999856294d44be3211726b2f3dc5"}}, "title": "Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.", "authors": [{"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Moura-Castro", "given": "Larissa H", "initials": "LH"}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/481b2a2329634f9086cf52fb808edea5.json"}}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H", "orcid": "0000-0001-8703-1173", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a75300e8c346858ce8dd8f64ecae85.json"}}, {"family": "Odom", "given": "Duncan T", "initials": "DT", "orcid": "0000-0001-6201-5599", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82aabbc9a42473a985e49eb1b184b6a.json"}}, {"family": "Olsson", "given": "Linda", "initials": "L"}, {"family": "Ravi", "given": "Naveen", "initials": "N"}, {"family": "Woodward", "given": "Eleanor L", "initials": "EL"}, {"family": "Harewood", "given": "Louise", "initials": "L"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Paulsson", "given": "Kajsa", "initials": "K", "orcid": "0000-0001-7950-222X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2033b23811f1432c90ad860dd993e7a8.json"}}], "type": "journal article", "published": "2019-04-03", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "1519", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Hyperdiploidy, i.e. gain of whole chromosomes, is one of the most common genetic features of childhood acute lymphoblastic leukemia (ALL), but its pathogenetic impact is poorly understood. Here, we report a proteogenomic analysis on matched datasets from genomic profiling, RNA-sequencing, and mass spectrometry-based analysis of >8,000 genes and proteins as well as Hi-C of primary patient samples from hyperdiploid and ETV6/RUNX1-positive pediatric ALL. We show that CTCF and cohesin, which are master regulators of chromatin architecture, display low expression in hyperdiploid ALL. In line with this, a general genome-wide dysregulation of gene expression in relation to topologically associating domain (TAD) borders were seen in the hyperdiploid group. Furthermore, Hi-C of a limited number of hyperdiploid childhood ALL cases revealed that 2/4 cases displayed a clear loss of TAD boundary strength and 3/4 showed reduced insulation at TAD borders, with putative leukemogenic effects.", "doi": "10.1038/s41467-019-09469-3", "pmid": "30944321", "labels": {"Clinical Genomics Lund": "Service", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-09469-3"}, {"db": "pmc", "key": "PMC6447538"}], "notes": [], "created": "2019-12-13T15:04:45.801Z", "modified": "2024-01-16T13:48:44.549Z"}, {"entity": "publication", "iuid": "7f23deeee8024f17a9c8e7ac127d2e9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f23deeee8024f17a9c8e7ac127d2e9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f23deeee8024f17a9c8e7ac127d2e9c"}}, "title": "Polymer gels with tunable ionic Seebeck coefficient for ultra-sensitive printed thermopiles.", "authors": [{"family": "Zhao", "given": "Dan", "initials": "D"}, {"family": "Martinelli", "given": "Anna", "initials": "A"}, {"family": "Willfahrt", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2321-0986", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf03a4255d3b4279ae689517fba5637c.json"}}, {"family": "Fischer", "given": "Thomas", "initials": "T"}, {"family": "Bernin", "given": "Diana", "initials": "D"}, {"family": "Khan", "given": "Zia Ullah", "initials": "ZU"}, {"family": "Shahi", "given": "Maryam", "initials": "M"}, {"family": "Brill", "given": "Joseph", "initials": "J", "orcid": "0000-0003-2358-8006", "researcher": {"href": "https://publications.scilifelab.se/researcher/618b4ef8b0e6412aa4b9e12b556587ef.json"}}, {"family": "Jonsson", "given": "Magnus P", "initials": "MP", "orcid": "0000-0002-3002-3639", "researcher": {"href": "https://publications.scilifelab.se/researcher/524b110bf1064aee9e5f2a0b4315ff4d.json"}}, {"family": "Fabiano", "given": "Simone", "initials": "S", "orcid": "0000-0001-7016-6514", "researcher": {"href": "https://publications.scilifelab.se/researcher/c562adbdd38f4f41843165f66af9042d.json"}}, {"family": "Crispin", "given": "Xavier", "initials": "X", "orcid": "0000-0001-8845-6296", "researcher": {"href": "https://publications.scilifelab.se/researcher/342b764a135348c4b91448f182c4bca8.json"}}], "type": "journal article", "published": "2019-03-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "10", "issue": "1", "pages": "1093", "issn-l": "2041-1723"}, "abstract": "Measuring temperature and heat flux is important for regulating any physical, chemical, and biological processes. Traditional thermopiles can provide accurate and stable temperature reading but they are based on brittle inorganic materials with low Seebeck coefficient, and are difficult to manufacture over large areas. Recently, polymer electrolytes have been proposed for thermoelectric applications because of their giant ionic Seebeck coefficient, high flexibility and ease of manufacturing. However, the materials reported to date have positive Seebeck coefficients, hampering the design of ultra-sensitive ionic thermopiles. Here we report an \"ambipolar\" ionic polymer gel with giant negative ionic Seebeck coefficient. The latter can be tuned from negative to positive by adjusting the gel composition. We show that the ion-polymer matrix interaction is crucial to control the sign and magnitude of the ionic Seebeck coefficient. The ambipolar gel can be easily screen printed, enabling large-area device manufacturing at low cost.", "doi": "10.1038/s41467-019-08930-7", "pmid": "30842422", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-08930-7"}, {"db": "pmc", "key": "PMC6403253"}], "notes": [], "created": "2020-01-07T11:45:27.476Z", "modified": "2025-10-17T13:03:58.151Z"}, {"entity": "publication", "iuid": "faac1a8ff3494e0f94ca37d79798c71c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/faac1a8ff3494e0f94ca37d79798c71c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/faac1a8ff3494e0f94ca37d79798c71c"}}, "title": "Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development", "authors": [{"family": "Tiklov\u00e1", "given": "Katar\u00edna", "initials": "K"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Lahti", "given": "Laura", "initials": "L"}, {"family": "Fiorenzano", "given": "Alessandro", "initials": "A"}, {"family": "Nolbrant", "given": "Sara", "initials": "S"}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Volakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Yokota", "given": "Chika", "initials": "C"}, {"family": "Hilscher", "given": "Markus M", "initials": "MM"}, {"family": "Hauling", "given": "Thomas", "initials": "T"}, {"family": "Holmstr\u00f6m", "given": "Fredrik", "initials": "F"}, {"family": "Joodmardi", "given": "Eliza", "initials": "E"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Parmar", "given": "Malin", "initials": "M", "orcid": "0000-0001-5002-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48b5aaff3bc4832a96fda4f2cf127cb.json"}}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}], "type": "journal-article", "published": "2019-02-04", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "581", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Midbrain dopamine (mDA) neurons constitute a heterogenous group of cells that have been intensely studied, not least because their degeneration causes major symptoms in Parkinson's disease. Understanding the diversity of mDA neurons - previously well characterized anatomically - requires a systematic molecular classification at the genome-wide gene expression level. Here, we use single cell RNA sequencing of isolated mouse neurons expressing the transcription factor Pitx3, a marker for mDA neurons. Analyses include cells isolated during development up until adulthood and the results are validated by histological characterization of newly identified markers. This identifies seven neuron subgroups divided in two major branches of developing Pitx3-expressing neurons. Five of them express dopaminergic markers, while two express glutamatergic and GABAergic markers, respectively. Analysis also indicate evolutionary conservation of diversity in humans. This comprehensive molecular characterization will provide a valuable resource for elucidating mDA neuron subgroup development and function in the mammalian brain.", "doi": "10.1038/s41467-019-08453-1", "pmid": "30718509", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6362095"}, {"db": "pii", "key": "10.1038/s41467-019-08453-1"}], "notes": [], "created": "2019-02-07T09:21:49.701Z", "modified": "2025-10-17T13:02:18.544Z"}, {"entity": "publication", "iuid": "d827751fe5bd40ffb8ceda3c1052fc64", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d827751fe5bd40ffb8ceda3c1052fc64.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d827751fe5bd40ffb8ceda3c1052fc64"}}, "title": "Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity.", "authors": [{"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Bentley", "given": "Amy R", "initials": "AR"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Sung", "given": "Yun Ju", "initials": "YJ"}, {"family": "Schwander", "given": "Karen", "initials": "K"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Jakupovi\u0107", "given": "Hermina", "initials": "H"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Manning", "given": "Alisa", "initials": "A"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Aschard", "given": "Hugues", "initials": "H"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "de Las Fuentes", "given": "Lisa", "initials": "L"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Vojinovic", "given": "Dina", "initials": "D"}, {"family": "Aslibekyan", "given": "Stella", "initials": "S"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Kho", "given": "Minjung", "initials": "M"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Richard", "given": "Melissa", "initials": "M"}, {"family": "Wang", "given": "Heming", "initials": "H"}, {"family": "Wang", "given": "Zhe", "initials": "Z"}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Dorajoo", "given": "Rajkumar", "initials": "R"}, {"family": "Fisher", "given": "Virginia", "initials": "V"}, {"family": "Hartwig", "given": "Fernando P", "initials": "FP"}, {"family": "Horimoto", "given": "Andrea R V R", "initials": "ARVR"}, {"family": "Li", "given": "Changwei", "initials": "C"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Tajuddin", "given": "Salman M", "initials": "SM"}, {"family": "Alver", "given": "Maris", "initials": "M"}, {"family": "Amini", "given": "Marzyeh", "initials": "M"}, {"family": "Boissel", "given": "Mathilde", "initials": "M"}, {"family": "Chai", "given": "Jin Fang", "initials": "JF"}, {"family": "Chen", "given": "Xu", "initials": "X"}, {"family": "Divers", "given": "Jasmin", "initials": "J"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Gao", "given": "Chuan", "initials": "C"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "He", "given": "Meian", "initials": "M"}, {"family": "Hsu", "given": "Fang-Chi", "initials": "FC"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Laguzzi", "given": "Federica", "initials": "F"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Riaz", "given": "Muhammad", "initials": "M"}, {"family": "Robino", "given": "Antonietta", "initials": "A"}, {"family": "Rueedi", "given": "Rico", "initials": "R"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Takeuchi", "given": "Fumihiko", "initials": "F"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Ware", "given": "Erin B", "initials": "EB"}, {"family": "Wen", "given": "Wanqing", "initials": "W"}, {"family": "Li", "given": "Xiaoyin", "initials": "X"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Brumat", "given": "Marco", "initials": "M"}, {"family": "Cade", "given": "Brian", "initials": "B"}, {"family": "Canouil", "given": "Micka\u00ebl", "initials": "M"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Concas", "given": "Maria Pina", "initials": "MP"}, {"family": "Connell", "given": "John", "initials": "J"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "de Silva", "given": "H Janaka", "initials": "HJ"}, {"family": "de Vries", "given": "Paul S", "initials": "PS"}, {"family": "Demirkan", "given": "Ay\u015fe", "initials": "A"}, {"family": "Ding", "given": "Jingzhong", "initials": "J"}, {"family": "Eaton", "given": "Charles B", "initials": "CB"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Friedlander", "given": "Yechiel", "initials": "Y"}, {"family": "Gabriel", "given": "Kelley P", "initials": "KP"}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Gu", "given": "Chi Charles", "initials": "CC"}, {"family": "Gu", "given": "Dongfeng", "initials": "D"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "He", "given": "Jiang", "initials": "J"}, {"family": "Heikkinen", "given": "Sami", "initials": "S"}, {"family": "Heng", "given": "Chew-Kiat", "initials": "CK"}, {"family": "Hunt", "given": "Steven C", "initials": "SC"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Jonas", "given": "Jost B", "initials": "JB"}, {"family": "Koh", "given": "Woon-Puay", "initials": "WP"}, {"family": "Komulainen", "given": "Pirjo", "initials": "P"}, {"family": "Krieger", "given": "Jose E", "initials": "JE"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Lemaitre", "given": "Rozenn N", "initials": "RN"}, {"family": "Lewis", "given": "Cora E", "initials": "CE"}, {"family": "Liang", "given": "Jingjing", "initials": "J"}, {"family": "Lifelines Cohort Study", "given": "", "initials": ""}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Mosley", "given": "Thomas H", "initials": "TH"}, {"family": "Murray", "given": "Alison D", "initials": "AD"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Nang", "given": "Ei-Ei Khaing", "initials": "EK"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Nona", "given": "Sotoodehnia", "initials": "S"}, {"family": "Norris", "given": "Jill M", "initials": "JM"}, {"family": "Nwuba", "given": "Chiamaka Vivian", "initials": "CV"}, {"family": "O'Connell", "given": "Jeff", "initials": "J"}, {"family": "Palmer", "given": "Nicholette D", "initials": "ND"}, {"family": "Papanicolau", "given": "George J", "initials": "GJ"}, {"family": "Pazoki", "given": "Raha", "initials": "R"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Poveda", "given": "Alaitz", "initials": "A"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Risch", "given": "Neil", "initials": "N"}, {"family": "Robinson", "given": "Jennifer G", "initials": "JG"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Schreiner", "given": "Pamela J", "initials": "PJ"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Sidney", "given": "Stephen S", "initials": "SS"}, {"family": "Sims", "given": "Mario", "initials": "M"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Sofer", "given": "Tamar", "initials": "T"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Sternfeld", "given": "Barbara", "initials": "B"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Tang", "given": "Hua", "initials": "H"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Tsai", "given": "Michael Y", "initials": "MY"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van der Ende", "given": "M Yldau", "initials": "MY"}, {"family": "van Heemst", "given": "Diana", "initials": "D"}, {"family": "Voortman", "given": "Trudy", "initials": "T"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wennberg", "given": "Patrik", "initials": "P"}, {"family": "Wilson", "given": "Gregory", "initials": "G"}, {"family": "Xiang", "given": "Yong-Bing", "initials": "YB"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Yu", "given": "Caizheng", "initials": "C"}, {"family": "Yuan", "given": "Jian-Min", "initials": "JM"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Becker", "given": "Diane M", "initials": "DM"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Freedman", "given": "Barry I", "initials": "BI"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Kato", "given": "Norihiro", "initials": "N"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Shu", "given": "Xiao-Ou", "initials": "XO"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wagenknecht", "given": "Lynne E", "initials": "LE"}, {"family": "Wang", "given": "Ya X", "initials": "YX"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Wu", "given": "Tangchun", "initials": "T"}, {"family": "Zheng", "given": "Wei", "initials": "W"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Horta", "given": "Bernardo L", "initials": "BL"}, {"family": "Kelly", "given": "Tanika N", "initials": "TN"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Pereira", "given": "Alexandre C", "initials": "AC"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Redline", "given": "Susan", "initials": "S"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Kooperberg", "given": "Charles B", "initials": "CB"}, {"family": "Gauderman", "given": "W James", "initials": "WJ"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Rotimi", "given": "Charles N", "initials": "CN"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}], "type": "journal article", "published": "2019-01-22", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "376", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Many genetic loci affect circulating lipid levels, but it remains unknown whether lifestyle factors, such as physical activity, modify these genetic effects. To identify lipid loci interacting with physical activity, we performed genome-wide analyses of circulating HDL cholesterol, LDL cholesterol, and triglyceride levels in up to 120,979 individuals of European, African, Asian, Hispanic, and Brazilian ancestry, with follow-up of suggestive associations in an additional 131,012 individuals. We find four loci, in/near CLASP1, LHX1, SNTA1, and CNTNAP2, that are associated with circulating lipid levels through interaction with physical activity; higher levels of physical activity enhance the HDL cholesterol-increasing effects of the CLASP1, LHX1, and SNTA1 loci and attenuate the LDL cholesterol-increasing effect of the CNTNAP2 locus. The CLASP1, LHX1, and SNTA1 regions harbor genes linked to muscle function and lipid metabolism. Our results elucidate the role of physical activity interactions in the genetic contribution to blood lipid levels.", "doi": "10.1038/s41467-018-08008-w", "pmid": "30670697", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-08008-w"}, {"db": "pmc", "key": "PMC6342931"}], "notes": [], "created": "2019-10-16T15:10:15.717Z", "modified": "2020-01-21T13:56:14.665Z"}, {"entity": "publication", "iuid": "14a95d287a8e44edab977079e94daafe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14a95d287a8e44edab977079e94daafe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14a95d287a8e44edab977079e94daafe"}}, "title": "Rapid determination of quaternary protein structures in complex biological samples.", "authors": [{"family": "Hauri", "given": "Simon", "initials": "S"}, {"family": "Khakzad", "given": "Hamed", "initials": "H"}, {"family": "Happonen", "given": "Lotta", "initials": "L"}, {"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L"}], "type": "evaluation study", "published": "2019-01-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "10", "issue": "1", "pages": "192", "issn-l": "2041-1723"}, "abstract": "The understanding of complex biological systems is still hampered by limited knowledge of biologically relevant quaternary protein structures. Here, we demonstrate quaternary structure determination in biological samples using a combination of chemical cross-linking, high-resolution mass spectrometry and high-accuracy protein structure modeling. This approach, termed targeted cross-linking mass spectrometry (TX-MS), relies on computational structural models to score sets of targeted cross-linked peptide signals acquired using a combination of mass spectrometry acquisition techniques. We demonstrate the utility of TX-MS by creating a high-resolution quaternary model of a 1.8 MDa protein complex composed of a pathogen surface protein and ten human plasma proteins. The model is based on a dense network of cross-link distance constraints obtained directly in a mixture of human plasma and live bacteria. These results demonstrate that TX-MS can increase the applicability of flexible backbone docking algorithms to large protein complexes by providing rich cross-link distance information from complex biological samples.", "doi": "10.1038/s41467-018-07986-1", "pmid": "30643114", "labels": {"Structural Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-07986-1"}, {"db": "pmc", "key": "PMC6331586"}], "notes": [], "created": "2020-01-27T10:13:20.484Z", "modified": "2021-05-24T15:39:50.133Z"}, {"entity": "publication", "iuid": "cae9c2df7b7d47efacb17c8207b6c573", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cae9c2df7b7d47efacb17c8207b6c573.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cae9c2df7b7d47efacb17c8207b6c573"}}, "title": "Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.", "authors": [{"family": "Karkman", "given": "Antti", "initials": "A"}, {"family": "P\u00e4rn\u00e4nen", "given": "Katariina", "initials": "K"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2019-01-08", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "80", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Discharge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. However, it is unclear whether increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments is due to on-site selection pressure by residual antibiotics, or is simply a result of fecal contamination with resistant bacteria. Here we analyze relative resistance gene abundance and accompanying extent of fecal pollution in publicly available metagenomic data, using crAssphage sequences as a marker of human fecal contamination (crAssphage is a bacteriophage that is exceptionally abundant in, and specific to, human feces). We find that the presence of resistance genes can largely be explained by fecal pollution, with no clear signs of selection in the environment, with the exception of environments polluted by very high levels of antibiotics from manufacturing, where selection is evident. Our results demonstrate the necessity to take into account fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance.", "doi": "10.1038/s41467-018-07992-3", "pmid": "30622259", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-07992-3"}, {"db": "pmc", "key": "PMC6325112"}], "notes": [], "created": "2020-01-08T16:47:12.638Z", "modified": "2020-01-21T13:56:16.251Z"}, {"entity": "publication", "iuid": "58d22ea9779545d3bb67e719d15ac7d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58d22ea9779545d3bb67e719d15ac7d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58d22ea9779545d3bb67e719d15ac7d5"}}, "title": "Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies.", "authors": [{"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Le", "given": "Thu H", "initials": "TH"}, {"family": "Wu", "given": "Haojia", "initials": "H"}, {"family": "Akbarov", "given": "Artur", "initials": "A"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Hemani", "given": "Gibran", "initials": "G"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Gaulton", "given": "Kyle J", "initials": "KJ"}, {"family": "Nadkarni", "given": "Girish N", "initials": "GN"}, {"family": "Valladares-Salgado", "given": "Adan", "initials": "A"}, {"family": "Wacher-Rodarte", "given": "Niels", "initials": "N"}, {"family": "Mychaleckyj", "given": "Josyf C", "initials": "JC"}, {"family": "Dueker", "given": "Nicole D", "initials": "ND"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Hai", "given": "Yang", "initials": "Y"}, {"family": "Haessler", "given": "Jeffrey", "initials": "J"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y"}, {"family": "Stilp", "given": "Adrienne M", "initials": "AM"}, {"family": "Zhu", "given": "Gu", "initials": "G"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Blanton", "given": "Susan H", "initials": "SH"}, {"family": "de Borst", "given": "Martin H", "initials": "MH"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Buchanan", "given": "Thomas A", "initials": "TA"}, {"family": "Cechova", "given": "Sylvia", "initials": "S"}, {"family": "Charchar", "given": "Fadi J", "initials": "FJ"}, {"family": "Chu", "given": "Pei-Lun", "initials": "PL"}, {"family": "Damman", "given": "Jeffrey", "initials": "J"}, {"family": "Eales", "given": "James", "initials": "J"}, {"family": "Gharavi", "given": "Ali G", "initials": "AG"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Ipp", "given": "Eli", "initials": "E"}, {"family": "Kiryluk", "given": "Krzysztof", "initials": "K"}, {"family": "Kramer", "given": "Holly J", "initials": "HJ"}, {"family": "Kubo", "given": "Michiaki", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Madden", "given": "Pamela A F", "initials": "PAF"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Papanicolaou", "given": "George J", "initials": "GJ"}, {"family": "Raffel", "given": "Leslie J", "initials": "LJ"}, {"family": "Sacco", "given": "Ralph L", "initials": "RL"}, {"family": "Sanchez", "given": "Elena", "initials": "E"}, {"family": "Stark", "given": "Holger", "initials": "H"}, {"family": "Sundstrom", "given": "Johan", "initials": "J"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Xiang", "given": "Anny H", "initials": "AH"}, {"family": "Zivkovic", "given": "Aleksandra", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Cai", "given": "Jianwen", "initials": "J"}, {"family": "Laurie", "given": "Cathy C", "initials": "CC"}, {"family": "Okada", "given": "Yukinori", "initials": "Y"}, {"family": "Matsuda", "given": "Koichi", "initials": "K"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Rundek", "given": "Tatjana", "initials": "T"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Parra", "given": "Esteban J", "initials": "EJ"}, {"family": "Cruz", "given": "Miguel", "initials": "M"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Tomaszewski", "given": "Maciej", "initials": "M"}, {"family": "Humphreys", "given": "Benjamin D", "initials": "BD"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}], "type": "journal article", "published": "2019-01-03", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "29", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Chronic kidney disease (CKD) affects ~10% of the global population, with considerable ethnic differences in prevalence and aetiology. We assemble genome-wide association studies of estimated glomerular filtration rate (eGFR), a measure of kidney function that defines CKD, in 312,468 individuals of diverse ancestry. We identify 127 distinct association signals with homogeneous effects on eGFR across ancestries and enrichment in genomic annotations including kidney-specific histone modifications. Fine-mapping reveals 40 high-confidence variants driving eGFR associations and highlights putative causal genes with cell-type specific expression in glomerulus, and in\u00a0proximal and distal nephron. Mendelian randomisation supports causal effects of eGFR on overall and cause-specific CKD, kidney stone formation, diastolic blood pressure and hypertension. These results define novel molecular mechanisms and putative causal genes for eGFR, offering insight into clinical outcomes and routes to CKD treatment development.", "doi": "10.1038/s41467-018-07867-7", "pmid": "30604766", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-07867-7"}, {"db": "pmc", "key": "PMC6318312"}], "notes": [], "created": "2019-09-16T14:28:28.864Z", "modified": "2024-01-16T13:48:44.852Z"}, {"entity": "publication", "iuid": "bf80a77c714149e6afd1d0a41d15178d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf80a77c714149e6afd1d0a41d15178d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf80a77c714149e6afd1d0a41d15178d"}}, "title": "Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.", "authors": [{"family": "Bartoschek", "given": "Michael", "initials": "M", "orcid": "0000-0002-1567-795X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4b53427bada4ea58971be691444ea45.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Bocci", "given": "Matteo", "initials": "M", "orcid": "0000-0002-8774-0006", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff52ba58701141f88766777a3d7ef21e.json"}}, {"family": "L\u00f6vrot", "given": "John", "initials": "J", "orcid": "0000-0002-9339-8059", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c71f7e4aa948d99d8dfbb9bf9e5d2e.json"}}, {"family": "Larsson", "given": "Christer", "initials": "C"}, {"family": "Sommarin", "given": "Mikael", "initials": "M"}, {"family": "Madsen", "given": "Chris D", "initials": "CD", "orcid": "0000-0001-6838-2103", "researcher": {"href": "https://publications.scilifelab.se/researcher/466f82bcf9364350a22cd7d3be0833e4.json"}}, {"family": "Lindgren", "given": "David", "initials": "D"}, {"family": "Pekar", "given": "Gyula", "initials": "G"}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M", "orcid": "0000-0001-5469-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0308e6d9c534033b431d2552cfe2af6.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Pietras", "given": "Kristian", "initials": "K", "orcid": "0000-0001-6738-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/5be0a3ec07654822a91df964eab1d6e4.json"}}], "type": "journal article", "published": "2018-12-04", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "5150", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Cancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment, although their origin and roles in shaping disease initiation, progression and treatment response remain unclear due to significant heterogeneity. Here, following a negative selection strategy combined with single-cell RNA sequencing of 768 transcriptomes of mesenchymal cells from a genetically engineered mouse model of breast cancer, we define three distinct subpopulations of CAFs. Validation at the transcriptional and protein level in several experimental models of cancer and human tumors reveal spatial separation of the CAF subclasses attributable to different origins, including the peri-vascular niche, the mammary fat pad and the transformed epithelium. Gene profiles for each CAF subtype correlate to distinctive functional programs and hold independent prognostic capability in clinical cohorts by association to metastatic disease. In conclusion, the improved resolution of the widely defined CAF population opens the possibility for biomarker-driven development of drugs for precision targeting of CAFs.", "doi": "10.1038/s41467-018-07582-3", "pmid": "30514914", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-07582-3"}, {"db": "pmc", "key": "PMC6279758"}], "notes": [], "created": "2018-12-04T14:20:27.020Z", "modified": "2024-01-16T13:48:44.935Z"}, {"entity": "publication", "iuid": "29554dc6aaa44333bfb51775f77c064f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29554dc6aaa44333bfb51775f77c064f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29554dc6aaa44333bfb51775f77c064f"}}, "title": "Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination", "authors": [{"family": "Gustafsson", "given": "Nina M S", "initials": "NMS"}, {"family": "F\u00e4rneg\u00e5rdh", "given": "Katarina", "initials": "K"}, {"family": "Bonagas", "given": "Nadilly", "initials": "N"}, {"family": "Ninou", "given": "Anna Huguet", "initials": "AH"}, {"family": "Groth", "given": "Petra", "initials": "P"}, {"family": "Wiita", "given": "Elisee", "initials": "E"}, {"family": "J\u00f6nsson", "given": "Mattias", "initials": "M"}, {"family": "Hallberg", "given": "Kenth", "initials": "K"}, {"family": "Lehto", "given": "Jemina", "initials": "J"}, {"family": "Pennisi", "given": "Rosa", "initials": "R"}, {"family": "Martinsson", "given": "Jessica", "initials": "J"}, {"family": "Norstr\u00f6m", "given": "Carina", "initials": "C"}, {"family": "Hollers", "given": "Jessica", "initials": "J"}, {"family": "Schultz", "given": "Johan", "initials": "J"}, {"family": "Andersson", "given": "Martin", "initials": "M"}, {"family": "Markova", "given": "Natalia", "initials": "N"}, {"family": "Marttila", "given": "Petra", "initials": "P"}, {"family": "Kim", "given": "Baek", "initials": "B"}, {"family": "Norin", "given": "Martin", "initials": "M"}, {"family": "Olin", "given": "Thomas", "initials": "T"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-018-06287-x", "pmid": "30250201", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Service", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "PDB", "description": "HUMAN PFKFB3 IN COMPLEX WITH KAN0438241", "key": "6ETJ"}], "notes": [], "created": "2018-10-22T13:35:38.490Z", "modified": "2025-10-17T13:05:08.304Z"}, {"entity": "publication", "iuid": "29ec285c10f54847ae79de7575c84980", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29ec285c10f54847ae79de7575c84980.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29ec285c10f54847ae79de7575c84980"}}, "title": "Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements", "authors": [{"family": "Svedberg", "given": "Jesper", "initials": "J"}, {"family": "Hosseini", "given": "Sara", "initials": "S"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Vogan", "given": "Aaron A", "initials": "AA"}, {"family": "Mozgova", "given": "Iva", "initials": "I"}, {"family": "Hennig", "given": "Lars", "initials": "L"}, {"family": "Manitchotpisit", "given": "Pennapa", "initials": "P"}, {"family": "Abusharekh", "given": "Anna", "initials": "A"}, {"family": "Hammond", "given": "Thomas M", "initials": "TM"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.", "doi": "10.1038/s41467-018-06562-x", "pmid": "30315196", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Genomics of spore killing in Neurospora intermedia.", "key": "PRJNA486257"}, {"db": "figshare", "description": "Follow link to download", "key": "https://doi.org/10.6084/m9.figshare.c.4202669.v1"}], "notes": [], "created": "2018-10-22T10:10:47.479Z", "modified": "2024-01-16T13:48:45.117Z"}, {"entity": "publication", "iuid": "791d6a9d1a0548cc8e8c542c88a7269c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/791d6a9d1a0548cc8e8c542c88a7269c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/791d6a9d1a0548cc8e8c542c88a7269c"}}, "title": "Somatic mutagenesis in satellite cells associates with human skeletal muscle aging", "authors": [{"family": "Franco", "given": "Irene", "initials": "I"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Olsson", "given": "Karl", "initials": "K"}, {"family": "Vrta\u010dnik", "given": "Peter", "initials": "P"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Helgadottir", "given": "Hafdis T", "initials": "HT"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Rev\u00eachon", "given": "Gwladys", "initials": "G"}, {"family": "Bosia", "given": "Carla", "initials": "C"}, {"family": "Pagnani", "given": "Andrea", "initials": "A"}, {"family": "Provero", "given": "Paolo", "initials": "P"}, {"family": "Gustafsson", "given": "Thomas", "initials": "T"}, {"family": "Fischer", "given": "Helene", "initials": "H"}, {"family": "Eriksson", "given": "Maria", "initials": "M"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Human aging is associated with a decline in skeletal muscle (SkM) function and a reduction in the number and activity of satellite cells (SCs), the resident stem cells. To study the connection between SC aging and muscle impairment, we analyze the whole genome of single SC clones of the leg muscle vastus lateralis from healthy individuals of different ages (21-78 years). We find an accumulation rate of 13 somatic mutations per genome per year, consistent with proliferation of SCs in the healthy adult muscle. SkM-expressed genes are protected from mutations, but aging results in an increase in mutations in exons and promoters, targeting genes involved in SC activity and muscle function. In agreement with SC mutations affecting the whole tissue, we detect a missense mutation in a SC propagating to the muscle. Our results suggest somatic mutagenesis in SCs as a driving force in the age-related decline of SkM function.", "doi": "10.1038/s41467-018-03244-6", "pmid": "29476074", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-02-26T14:11:01.492Z", "modified": "2024-01-16T13:48:44.998Z"}, {"entity": "publication", "iuid": "84a17b565be4486b99e827275a31a204", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84a17b565be4486b99e827275a31a204.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84a17b565be4486b99e827275a31a204"}}, "title": "GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes", "authors": [{"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": null, "given": "", "initials": ""}, {"family": "Giambartolomei", "given": "Claudia", "initials": "C"}, {"family": "de Vries", "given": "Paul S", "initials": "PS"}, {"family": "Finan", "given": "Chris", "initials": "C"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Huntley", "given": "Rachael P", "initials": "RP"}, {"family": "Lovering", "given": "Ruth C", "initials": "RC"}, {"family": "Tajuddin", "given": "Salman M", "initials": "SM"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Graff", "given": "Misa", "initials": "M"}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "Dale", "given": "Caroline", "initials": "C"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "van Leeuwen", "given": "Elisabeth M", "initials": "EM"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Lu", "given": "Lingyi", "initials": "L"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Sargurupremraj", "given": "Muralidharan", "initials": "M"}, {"family": "Pitk\u00e4nen", "given": "Niina", "initials": "N"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "Hwang", "given": "Shih Jen", "initials": "SJ"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Schminke", "given": "Ulf", "initials": "U"}, {"family": "Palmas", "given": "Walter", "initials": "W"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Cox", "given": "Amanda J", "initials": "AJ"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Newman", "given": "Anne B", "initials": "AB"}, {"family": "Britton", "given": "Annie", "initials": "A"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Hedblad", "given": "Bo", "initials": "B"}, {"family": "Pasaniuc", "given": "Bogdan", "initials": "B"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Wassel", "given": "Christina L", "initials": "CL"}, {"family": "Tzourio", "given": "Christophe", "initials": "C"}, {"family": "Fava", "given": "Cristiano", "initials": "C"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "O\u2019Leary", "given": "Daniel H", "initials": "DH"}, {"family": "Teupser", "given": "Daniel", "initials": "D"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Mannarino", "given": "Elmo", "initials": "E"}, {"family": "Grossi", "given": "Enzo", "initials": "E"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Beutner", "given": "Frank", "initials": "F"}, {"family": "Chauhan", "given": "Ganesh", "initials": "G"}, {"family": "Heiss", "given": "Gerardo", "initials": "G"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Markus", "given": "Hugh S", "initials": "HS"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "de Graaf", "given": "Jacqueline", "initials": "J"}, {"family": "Price", "given": "Jacqueline", "initials": "J"}, {"family": "Pott", "given": "Janne", "initials": "J"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Liang", "given": "Jingjing", "initials": "J"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "Engmann", "given": "Jorgen", "initials": "J"}, {"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Dhana", "given": "Klodian", "initials": "K"}, {"family": "Kiemeney", "given": "Lambertus A L M", "initials": "LALM"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Holdt", "given": "Lesca M", "initials": "LM"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Dichgans", "given": "Martin", "initials": "M"}, {"family": "Traylor", "given": "Matthew", "initials": "M"}, {"family": "Sitzer", "given": "Matthias", "initials": "M"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Rueda-Ochoa", "given": "Oscar L", "initials": "OL"}, {"family": "Roussos", "given": "Panos", "initials": "P"}, {"family": "Whincup", "given": "Peter H", "initials": "PH"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Anugu", "given": "Pramod", "initials": "P"}, {"family": "Wong", "given": "Quenna", "initials": "Q"}, {"family": "Malik", "given": "Rainer", "initials": "R"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Burkhardt", "given": "Ralph", "initials": "R"}, {"family": "Hardy", "given": "Rebecca", "initials": "R"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Morris", "given": "Richard W", "initials": "RW"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Wannamethee", "given": "S Goya", "initials": "SG"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "McLachlan", "given": "Stela", "initials": "S"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Ring", "given": "Susan", "initials": "S"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Galesloot", "given": "Tessel E", "initials": "TE"}, {"family": "Shah", "given": "Tina", "initials": "T"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Plagnol", "given": "Vincent", "initials": "V"}, {"family": "Rosamond", "given": "Wayne D", "initials": "WD"}, {"family": "Post", "given": "Wendy", "initials": "W"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Zhang", "given": "Xiaoling", "initials": "X"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Saba", "given": "Yasaman", "initials": "Y"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Seldenrijk", "given": "Adrie", "initials": "A"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Lawlor", "given": "Deborah A", "initials": "DA"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Wardlaw", "given": "Joanna M", "initials": "JM"}, {"family": "Deanfield", "given": "John", "initials": "J"}, {"family": "Halcox", "given": "Julian", "initials": "J"}, {"family": "Lyytik\u00e4inen", "given": "Leo Pekka", "initials": "LP"}, {"family": "Loeffler", "given": "Markus", "initials": "M"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Debette", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Casas", "given": "Juan P", "initials": "JP"}, {"family": "O\u2019Donnell", "given": "Christopher J", "initials": "CJ"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-018-07340-5", "pmid": "30510157", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-06T16:14:41.258Z", "modified": "2024-01-16T13:48:45.075Z"}, {"entity": "publication", "iuid": "a579ec8927004a0f8b0802cc13cc20e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a579ec8927004a0f8b0802cc13cc20e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a579ec8927004a0f8b0802cc13cc20e2"}}, "title": "Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia", "authors": [{"family": "Shiozawa", "given": "Yusuke", "initials": "Y"}, {"family": "Malcovati", "given": "Luca", "initials": "L"}, {"family": "Gall\u00ec", "given": "Anna", "initials": "A"}, {"family": "Sato-Otsubo", "given": "Aiko", "initials": "A"}, {"family": "Kataoka", "given": "Keisuke", "initials": "K"}, {"family": "Sato", "given": "Yusuke", "initials": "Y"}, {"family": "Watatani", "given": "Yosaku", "initials": "Y"}, {"family": "Suzuki", "given": "Hiromichi", "initials": "H"}, {"family": "Yoshizato", "given": "Tetsuichi", "initials": "T"}, {"family": "Yoshida", "given": "Kenichi", "initials": "K"}, {"family": "Sanada", "given": "Masashi", "initials": "M"}, {"family": "Makishima", "given": "Hideki", "initials": "H"}, {"family": "Shiraishi", "given": "Yuichi", "initials": "Y"}, {"family": "Chiba", "given": "Kenichi", "initials": "K"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Miyano", "given": "Satoru", "initials": "S"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Cazzola", "given": "Mario", "initials": "M"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-018-06063-x", "pmid": "30194306", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "EBI", "description": "https://www.ebi.ac.uk/ega/studies/EGAS00001002346", "key": "EGAS00001002346"}], "notes": [], "created": "2018-10-31T13:06:08.081Z", "modified": "2018-12-10T12:45:39.510Z"}, {"entity": "publication", "iuid": "c148b498822c43108e78e3a56a3112bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c148b498822c43108e78e3a56a3112bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c148b498822c43108e78e3a56a3112bf"}}, "title": "Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage", "authors": [{"family": "Ladds", "given": "Marcus J G W", "initials": "MJGW"}, {"family": "van Leeuwen", "given": "Ingeborg M M", "initials": "IMM"}, {"family": "Drummond", "given": "Catherine J", "initials": "CJ"}, {"family": "Chu", "given": "Su", "initials": "S"}, {"family": "Healy", "given": "Alan R", "initials": "AR"}, {"family": "Popova", "given": "Gergana", "initials": "G"}, {"family": "Pastor Fern\u00e1ndez", "given": "Andr\u00e9s", "initials": "A"}, {"family": "Mollick", "given": "Tanzina", "initials": "T"}, {"family": "Darekar", "given": "Suhas", "initials": "S"}, {"family": "Sedimbi", "given": "Saikiran K", "initials": "SK"}, {"family": "Nekulova", "given": "Marta", "initials": "M"}, {"family": "Sachweh", "given": "Marijke C C", "initials": "MCC"}, {"family": "Campbell", "given": "Johanna", "initials": "J"}, {"family": "Higgins", "given": "Maureen", "initials": "M"}, {"family": "Tuck", "given": "Chloe", "initials": "C"}, {"family": "Popa", "given": "Mihaela", "initials": "M"}, {"family": "Safont", "given": "Mireia Mayoral", "initials": "MM"}, {"family": "Gelebart", "given": "Pascal", "initials": "P"}, {"family": "Fandalyuk", "given": "Zinayida", "initials": "Z"}, {"family": "Thompson", "given": "Alastair M", "initials": "AM"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Gustavsson", "given": "Anna Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "F\u00e4rneg\u00e5rdh", "given": "Katarina", "initials": "K"}, {"family": "Yngve", "given": "Ulrika", "initials": "U"}, {"family": "Saleh", "given": "Aljona", "initials": "A"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "D\u2019Hollander", "given": "Agathe C A", "initials": "ACA"}, {"family": "Franco", "given": "Marcela", "initials": "M"}, {"family": "Zhao", "given": "Yan", "initials": "Y"}, {"family": "H\u00e5kansson", "given": "Maria", "initials": "M"}, {"family": "Walse", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Larsson", "given": "Karin", "initials": "K"}, {"family": "Peat", "given": "Emma M", "initials": "EM"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Lunec", "given": "John", "initials": "J"}, {"family": "Vojtesek", "given": "Borivoj", "initials": "B"}, {"family": "Carmena", "given": "Mar", "initials": "M"}, {"family": "Earnshaw", "given": "William C", "initials": "WC"}, {"family": "McCarthy", "given": "Anna R", "initials": "AR"}, {"family": "Westwood", "given": "Nicholas J", "initials": "NJ"}, {"family": "Arsenian-Henriksson", "given": "Marie", "initials": "M"}, {"family": "Lane", "given": "David P", "initials": "DP"}, {"family": "Bhatia", "given": "Ravi", "initials": "R"}, {"family": "McCormack", "given": "Emmet", "initials": "E"}, {"family": "La\u00edn", "given": "Sonia", "initials": "S"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The original PDF version of this Article listed the authors as \"Marcus J.G.W. Ladds,\" where it should have read \"Marcus J. G. W. Ladds, Ingeborg M. M. van Leeuwen, Catherine J. Drummond et al.\n            #\".Also in the PDF version, it was incorrectly stated that \"Correspondence and requests for materials should be addressed to S. L\u00edn.\", instead of the correct \"Correspondence and requests for materials should be addressed to S. La\u00edn.\"This has been corrected in the PDF version of the Article. The HTML version was correct from the time of publication.", "doi": "10.1038/s41467-018-04198-5", "pmid": "29789663", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Drug Discovery and Development": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-22T13:17:34.442Z", "modified": "2025-10-17T13:05:08.314Z"}, {"entity": "publication", "iuid": "d2a5def06c4c4e11b87c62b594c4363a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2a5def06c4c4e11b87c62b594c4363a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2a5def06c4c4e11b87c62b594c4363a"}}, "title": "A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons", "authors": [{"family": "S\u00f6dersten", "given": "Erik", "initials": "E"}, {"family": "Toskas", "given": "Konstantinos", "initials": "K"}, {"family": "Rraklli", "given": "Vilma", "initials": "V"}, {"family": "Tiklova", "given": "Katarina", "initials": "K"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Holmberg", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The brain is composed of hundreds of different neuronal subtypes, which largely retain their identity throughout the lifespan of the organism. The mechanisms governing this stability are not fully understood, partly due to the diversity and limited size of clinically relevant neuronal populations, which constitute a technical challenge for analysis. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in small neuronal populations in vivo, we present a comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons, and embryonic neural progenitors. Furthermore, we utilize the map generated by our analysis to show that the transcriptional response of midbrain dopaminergic neurons following 6-OHDA or methamphetamine injection is characterized by increased expression of genes with promoters dually marked by H3K4me3/H3K27me3. Our study provides an in vivo genome-wide analysis of permissive/repressive histone modifications coupled to gene expression in these rare neuronal subtypes.", "doi": "10.1038/s41467-018-03538-9", "pmid": "29581424", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "GEO", "description": "RNA-seq, ChIP-seq and TRAP-seq data", "key": "GSE107656"}], "notes": [], "created": "2018-04-25T12:52:16.083Z", "modified": "2024-01-16T13:48:45.162Z"}, {"entity": "publication", "iuid": "d794f36d72b34629b910abcbdfae6a78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d794f36d72b34629b910abcbdfae6a78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d794f36d72b34629b910abcbdfae6a78"}}, "title": "Enhanced validation of antibodies for research applications.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a007c2aea2c40ada113ffe87fc3daf0.json"}}, {"family": "Linderb\u00e4ck", "given": "Klas", "initials": "K"}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Azimi", "given": "Alireza", "initials": "A"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"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"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23dc2e614784017b08cb2d8f6b60ded.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2018-10-08", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "4130", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.", "doi": "10.1038/s41467-018-06642-y", "pmid": "30297845", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-06642-y"}, {"db": "pmc", "key": "PMC6175901"}], "notes": [], "created": "2018-10-31T19:45:59.871Z", "modified": "2024-01-16T13:48:45.378Z"}, {"entity": "publication", "iuid": "e89bae0bea434005ba4ddc7ceb519507", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e89bae0bea434005ba4ddc7ceb519507.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e89bae0bea434005ba4ddc7ceb519507"}}, "title": "14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface.", "authors": [{"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Hornyak", "given": "Peter", "initials": "P"}, {"family": "Pinto", "given": "Ana Filipa", "initials": "AF"}, {"family": "Milanova", "given": "Stefina", "initials": "S"}, {"family": "Ebrahimi", "given": "Mahsa", "initials": "M"}, {"family": "Lindberg", "given": "Mikael", "initials": "M"}, {"family": "P\u00fcllen", "given": "Nikolai", "initials": "N"}, {"family": "Nordstr\u00f6m", "given": "Axel", "initials": "A", "orcid": "0000-0003-2314-3322", "researcher": {"href": "https://publications.scilifelab.se/researcher/718995e4280a4976831170548a64d96f.json"}}, {"family": "L\u00f6verli", "given": "Elinor", "initials": "E"}, {"family": "Caraballo", "given": "R\u00e9mi", "initials": "R"}, {"family": "Wong", "given": "Emily V", "initials": "EV"}, {"family": "N\u00e4reoja", "given": "Katja", "initials": "K"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "AG"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "De La Cruz", "given": "Enrique M", "initials": "EM"}, {"family": "Bj\u00f6rkegren", "given": "Camilla", "initials": "C", "orcid": "0000-0001-7354-9270", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bb62675186e4e13b6eb47c10c307ab8.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": "2018-09-17", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "3785", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Pseudomonas are a common cause of hospital-acquired infections that may be lethal. ADP-ribosyltransferase activities of Pseudomonas exotoxin-S and -T depend on 14-3-3 proteins inside the host cell. By binding in the 14-3-3 phosphopeptide binding groove, an amphipathic C-terminal helix of ExoS and ExoT has been thought to be crucial for their activation. However, crystal structures of the 14-3-3\u03b2:ExoS and -ExoT complexes presented here reveal an extensive hydrophobic interface that is sufficient for complex formation and toxin activation. We show that C-terminally truncated ExoS ADP-ribosyltransferase domain lacking the amphipathic binding motif is active when co-expressed with 14-3-3. Moreover, swapping the amphipathic C-terminus with a fragment from Vibrio Vis toxin creates a 14-3-3 independent toxin that ADP-ribosylates known ExoS targets. Finally, we show that 14-3-3 stabilizes ExoS against thermal aggregation. Together, this indicates that 14-3-3 proteins activate exotoxin ADP-ribosyltransferase domains by chaperoning their hydrophobic surfaces independently of the amphipathic C-terminal segment.", "doi": "10.1038/s41467-018-06194-1", "pmid": "30224724", "labels": {"Protein Science Facility (PSF)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-06194-1"}, {"db": "pmc", "key": "PMC6141617"}], "notes": [], "created": "2018-09-18T08:55:18.810Z", "modified": "2024-01-16T13:48:45.502Z"}, {"entity": "publication", "iuid": "df0a1aaa78164376888bf09b18a0d205", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df0a1aaa78164376888bf09b18a0d205.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df0a1aaa78164376888bf09b18a0d205"}}, "title": "Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.", "authors": [{"family": "Petitpr\u00e9", "given": "Charles", "initials": "C"}, {"family": "Wu", "given": "Haohao", "initials": "H"}, {"family": "Sharma", "given": "Anil", "initials": "A"}, {"family": "Tokarska", "given": "Anna", "initials": "A"}, {"family": "Fontanet", "given": "Paula", "initials": "P"}, {"family": "Wang", "given": "Yiqiao", "initials": "Y"}, {"family": "Helmbacher", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Yackle", "given": "Kevin", "initials": "K"}, {"family": "Silberberg", "given": "Gilad", "initials": "G"}, {"family": "Hadjab", "given": "Saida", "initials": "S"}, {"family": "Lallemend", "given": "Fran\u00e7ois", "initials": "F"}], "type": "journal article", "published": "2018-09-12", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "3691", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Spiral ganglion (SG) neurons of the cochlea convey all auditory inputs to the brain, yet the cellular and molecular complexity necessary to decode the various acoustic features in the SG has remained unresolved. Using single-cell RNA sequencing, we identify four types of SG neurons, including three novel subclasses of type I neurons and the type II neurons, and provide a comprehensive genetic framework that define their potential synaptic communication patterns. The connectivity patterns of the three subclasses of type I neurons with inner hair cells and their electrophysiological profiles suggest that they represent the intensity-coding properties of auditory afferents. Moreover, neuron type specification is already established at birth, indicating a neuronal diversification process independent of neuronal activity. Thus, this work provides a transcriptional catalog of neuron types in the cochlea, which serves as a valuable resource for dissecting cell-type-specific functions of dedicated afferents in auditory perception and in hearing disorders.", "doi": "10.1038/s41467-018-06033-3", "pmid": "30209249", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-06033-3"}, {"db": "pmc", "key": "PMC6135759"}, {"db": "GEO", "description": "Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system", "key": "GSE117055"}], "notes": [], "created": "2018-10-31T13:03:39.950Z", "modified": "2024-01-16T13:48:45.517Z"}, {"entity": "publication", "iuid": "d20710fa0ed14236b32b9fd18ef95c95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d20710fa0ed14236b32b9fd18ef95c95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d20710fa0ed14236b32b9fd18ef95c95"}}, "title": "Contribution of allelic imbalance to colorectal cancer.", "authors": [{"family": "Palin", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-4621-6128", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b279cedd14f4c1eac3b917571a793b6.json"}}, {"family": "Pitk\u00e4nen", "given": "Esa", "initials": "E"}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Sahu", "given": "Biswajyoti", "initials": "B"}, {"family": "Pihlajamaa", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Kivioja", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7732-2177", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c318f57c5ce4f4bb747e19514caa907.json"}}, {"family": "Kaasinen", "given": "Eevi", "initials": "E"}, {"family": "V\u00e4lim\u00e4ki", "given": "Niko", "initials": "N"}, {"family": "H\u00e4nninen", "given": "Ulrika A", "initials": "UA"}, {"family": "Cajuso", "given": "Tatiana", "initials": "T"}, {"family": "Aavikko", "given": "Mervi", "initials": "M"}, {"family": "Tuupanen", "given": "Sari", "initials": "S"}, {"family": "Kilpivaara", "given": "Outi", "initials": "O"}, {"family": "van den Berg", "given": "Linda", "initials": "L"}, {"family": "Kondelin", "given": "Johanna", "initials": "J"}, {"family": "Tanskanen", "given": "Tomas", "initials": "T"}, {"family": "Katainen", "given": "Riku", "initials": "R"}, {"family": "Grau", "given": "Marta", "initials": "M"}, {"family": "Rauanheimo", "given": "Heli", "initials": "H"}, {"family": "Plaketti", "given": "Roosa-Maria", "initials": "RM"}, {"family": "Taira", "given": "Aurora", "initials": "A"}, {"family": "Sulo", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Hartonen", "given": "Tuomo", "initials": "T"}, {"family": "Dave", "given": "Kashyap", "initials": "K"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Botla", "given": "Sandeep", "initials": "S"}, {"family": "Sokolova", "given": "Maria", "initials": "M"}, {"family": "V\u00e4h\u00e4rautio", "given": "Anna", "initials": "A"}, {"family": "Gladysz", "given": "Kornelia", "initials": "K"}, {"family": "Ongen", "given": "Halit", "initials": "H", "orcid": "0000-0002-4197-5790", "researcher": {"href": "https://publications.scilifelab.se/researcher/c32fbd0537b74601b6e8d8ede15acffd.json"}}, {"family": "Dermitzakis", "given": "Emmanouil", "initials": "E", "orcid": "0000-0002-9302-6490", "researcher": {"href": "https://publications.scilifelab.se/researcher/3560d19929e94af1bb858a54e29a10cc.json"}}, {"family": "Bramsen", "given": "Jesper Bertram", "initials": "JB"}, {"family": "\u00d8rntoft", "given": "Torben Falck", "initials": "TF"}, {"family": "Andersen", "given": "Claus Lindbjerg", "initials": "CL"}, {"family": "Ristim\u00e4ki", "given": "Ari", "initials": "A"}, {"family": "Lepist\u00f6", "given": "Anna", "initials": "A"}, {"family": "Renkonen-Sinisalo", "given": "Laura", "initials": "L"}, {"family": "Mecklin", "given": "Jukka-Pekka", "initials": "JP"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}, {"family": "Aaltonen", "given": "Lauri A", "initials": "LA"}], "type": "journal article", "published": "2018-09-10", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "3664", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole-genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge. Unbiased CRISPR-Cas9 knockout and activation screens identified in total 79 genes within AI peaks regulating cell growth. Genetic and functional data implicate loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.", "doi": "10.1038/s41467-018-06132-1", "pmid": "30202008", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "CRISPR Functional Genomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-06132-1"}, {"db": "pmc", "key": "PMC6131244"}], "notes": [], "created": "2018-10-31T19:47:37.243Z", "modified": "2024-01-16T13:48:45.538Z"}, {"entity": "publication", "iuid": "471053d6a2a541b5b8fb4ed85f279f95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/471053d6a2a541b5b8fb4ed85f279f95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/471053d6a2a541b5b8fb4ed85f279f95"}}, "title": "Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides.", "authors": [{"family": "Saravanan", "given": "Rathi", "initials": "R"}, {"family": "Holdbrook", "given": "Daniel A", "initials": "DA"}, {"family": "Petrlova", "given": "Jitka", "initials": "J"}, {"family": "Singh", "given": "Shalini", "initials": "S"}, {"family": "Berglund", "given": "Nils A", "initials": "NA"}, {"family": "Choong", "given": "Yeu Khai", "initials": "YK"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Bond", "given": "Peter J", "initials": "PJ"}, {"family": "Malmsten", "given": "Martin", "initials": "M"}, {"family": "Schmidtchen", "given": "Artur", "initials": "A"}], "type": "journal article", "published": "2018-07-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "9", "issue": "1", "pages": "2762", "issn-l": "2041-1723"}, "abstract": "Thrombin-derived C-terminal peptides (TCPs) of about 2 kDa are present in wounds, where they exert anti-endotoxic functions. Employing a combination of nuclear magnetic resonance spectroscopy (NMR), biophysical, mass spectrometry and cellular studies combined with in silico multiscale modelling, we here determine the bound conformation of HVF18 (HVFRLKKWIQKVIDQFGE), a TCP generated by neutrophil elastase, in complex with bacterial lipopolysaccharide (LPS) and define a previously undisclosed interaction between TCPs and human CD14. Further, we show that TCPs bind to the LPS-binding hydrophobic pocket of CD14 and identify the peptide region crucial for TCP interaction with LPS and CD14. Taken together, our results demonstrate the role of structural transitions in LPS complex formation and CD14 interaction, providing a molecular explanation for the previously observed therapeutic effects of TCPs in experimental models of bacterial sepsis and endotoxin shock.", "doi": "10.1038/s41467-018-05242-0", "pmid": "30018388", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-05242-0"}, {"db": "pmc", "key": "PMC6050251"}], "notes": [], "created": "2020-01-27T10:01:53.611Z", "modified": "2021-05-24T15:39:50.180Z"}, {"entity": "publication", "iuid": "12c76ece8d6343d1beeb7137840accd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12c76ece8d6343d1beeb7137840accd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12c76ece8d6343d1beeb7137840accd9"}}, "title": "Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity", "authors": [{"family": "Berglund", "given": "Emelie", "initials": "E"}, {"family": "Maaskola", "given": "Jonas", "initials": "J"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Friedrich", "given": "Stefanie", "initials": "S"}, {"family": "Marklund", "given": "Maja", "initials": "M"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Tanoglidi", "given": "Anna", "initials": "A"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Salme\u0301n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Ogris", "given": "Christoph", "initials": "C"}, {"family": "Wallenborg", "given": "Karolina", "initials": "K"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "St\u00e5hl", "given": "Patrik", "initials": "P"}, {"family": "Sonnhammer", "given": "Erik", "initials": "E"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.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": "2018-06-20", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "2419", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor microenvironment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies.", "doi": "10.1038/s41467-018-04724-5", "pmid": "29925878", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6010471"}, {"db": "pii", "key": "10.1038/s41467-018-04724-5"}], "notes": [], "created": "2018-10-31T19:44:55.262Z", "modified": "2024-01-16T13:48:46.097Z"}, {"entity": "publication", "iuid": "96bd8b6dcdb74d11b8606d14c56cd047", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96bd8b6dcdb74d11b8606d14c56cd047.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96bd8b6dcdb74d11b8606d14c56cd047"}}, "title": "Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins.", "authors": [{"family": "Sp\u00e5hr", "given": "Henrik", "initials": "H"}, {"family": "Chia", "given": "Tiongsun", "initials": "T", "orcid": "0000-0002-7328-6615", "researcher": {"href": "https://publications.scilifelab.se/researcher/3797d4dcd76f40fcb8b0bbd9026788e7.json"}}, {"family": "Lingford", "given": "James P", "initials": "JP", "orcid": "0000-0003-1980-3949", "researcher": {"href": "https://publications.scilifelab.se/researcher/1024585276d94e16a832870daa25d57f.json"}}, {"family": "Siira", "given": "Stefan J", "initials": "SJ"}, {"family": "Cohen", "given": "Scott B", "initials": "SB"}, {"family": "Filipovska", "given": "Aleksandra", "initials": "A"}, {"family": "Rackham", "given": "Oliver", "initials": "O", "orcid": "0000-0002-5301-9624", "researcher": {"href": "https://publications.scilifelab.se/researcher/bddaa9d94fbc4dd19df3f12cc5d146ff.json"}}], "type": "journal article", "published": "2018-06-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "9", "issue": "1", "pages": "2212", "issn-l": "2041-1723"}, "abstract": "DNA is typically found as a double helix, however it must be separated into single strands during all phases of DNA metabolism; including transcription, replication, recombination and repair. Although recent breakthroughs have enabled the design of modular RNA- and double-stranded DNA-binding proteins, there are currently no tools available to manipulate single-stranded DNA (ssDNA). Here we show that artificial pentatricopeptide repeat (PPR) proteins can be programmed for sequence-specific ssDNA binding. Interactions occur using the same code and specificity as for RNA binding. We solve the structures of DNA-bound and apo proteins revealing the basis for ssDNA binding and how hydrogen bond rearrangements enable the PPR structure to envelope its ssDNA target. Finally, we show that engineered PPRs can be designed to bind telomeric ssDNA and can block telomerase activity. The modular mode of ssDNA binding by PPR proteins provides tools to target ssDNA and to understand its importance in cells.", "doi": "10.1038/s41467-018-04388-1", "pmid": "29880855", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-04388-1"}, {"db": "pmc", "key": "PMC5992170"}], "notes": [], "created": "2019-09-17T08:11:39.667Z", "modified": "2021-06-21T13:57:14.203Z"}, {"entity": "publication", "iuid": "f6c63ebca6b24dbdb0c965a6353ac836", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6c63ebca6b24dbdb0c965a6353ac836.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6c63ebca6b24dbdb0c965a6353ac836"}}, "title": "Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.", "authors": [{"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Lam", "given": "Max", "initials": "M"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Trampush", "given": "Joey W", "initials": "JW"}, {"family": "Luciano", "given": "Michelle", "initials": "M"}, {"family": "Hill", "given": "W David", "initials": "WD"}, {"family": "Hagenaars", "given": "Saskia P", "initials": "SP"}, {"family": "Ritchie", "given": "Stuart J", "initials": "SJ"}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "Fawns-Ritchie", "given": "Chloe", "initials": "C"}, {"family": "Liewald", "given": "David C M", "initials": "DCM"}, {"family": "Okely", "given": "Judith A", "initials": "JA"}, {"family": "Ahola-Olli", "given": "Ari V", "initials": "AV"}, {"family": "Barnes", "given": "Catriona L K", "initials": "CLK"}, {"family": "Bertram", "given": "Lars", "initials": "L"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Burdick", "given": "Katherine E", "initials": "KE"}, {"family": "Christoforou", "given": "Andrea", "initials": "A"}, {"family": "DeRosse", "given": "Pamela", "initials": "P"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Espeseth", "given": "Thomas", "initials": "T"}, {"family": "Giakoumaki", "given": "Stella", "initials": "S"}, {"family": "Giddaluru", "given": "Sudheer", "initials": "S"}, {"family": "Gustavson", "given": "Daniel E", "initials": "DE"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Knowles", "given": "Emma", "initials": "E"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Leber", "given": "Markus", "initials": "M"}, {"family": "Li", "given": "Shuo", "initials": "S"}, {"family": "Mather", "given": "Karen A", "initials": "KA"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Morris", "given": "Derek", "initials": "D"}, {"family": "Oldmeadow", "given": "Christopher", "initials": "C"}, {"family": "Palviainen", "given": "Teemu", "initials": "T"}, {"family": "Payton", "given": "Antony", "initials": "A"}, {"family": "Pazoki", "given": "Raha", "initials": "R"}, {"family": "Petrovic", "given": "Katja", "initials": "K"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Sargurupremraj", "given": "Muralidharan", "initials": "M"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Terzikhan", "given": "Natalie", "initials": "N"}, {"family": "Thalamuthu", "given": "Anbupalam", "initials": "A"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "van der Lee", "given": "Sven J", "initials": "SJ"}, {"family": "Ware", "given": "Erin B", "initials": "EB"}, {"family": "Windham", "given": "B Gwen", "initials": "BG"}, {"family": "Wright", "given": "Margaret J", "initials": "MJ"}, {"family": "Yang", "given": "Jingyun", "initials": "J"}, {"family": "Yu", "given": "Jin", "initials": "J"}, {"family": "Ames", "given": "David", "initials": "D"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Armstrong", "given": "Nicola J", "initials": "NJ"}, {"family": "Assareh", "given": "Amelia A", "initials": "AA"}, {"family": "Attia", "given": "John R", "initials": "JR"}, {"family": "Attix", "given": "Deborah", "initials": "D"}, {"family": "Avramopoulos", "given": "Dimitrios", "initials": "D"}, {"family": "Bennett", "given": "David A", "initials": "DA"}, {"family": "B\u00f6hmer", "given": "Anne C", "initials": "AC"}, {"family": "Boyle", "given": "Patricia A", "initials": "PA"}, {"family": "Brodaty", "given": "Henry", "initials": "H"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Cannon", "given": "Tyrone D", "initials": "TD"}, {"family": "Cirulli", "given": "Elizabeth T", "initials": "ET"}, {"family": "Congdon", "given": "Eliza", "initials": "E"}, {"family": "Conley", "given": "Emily Drabant", "initials": "ED"}, {"family": "Corley", "given": "Janie", "initials": "J"}, {"family": "Cox", "given": "Simon R", "initials": "SR"}, {"family": "Dale", "given": "Anders M", "initials": "AM"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Dick", "given": "Danielle", "initials": "D"}, {"family": "Dickinson", "given": "Dwight", "initials": "D"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Freimer", "given": "Nelson A", "initials": "NA"}, {"family": "Gao", "given": "He", "initials": "H"}, {"family": "Giegling", "given": "Ina", "initials": "I"}, {"family": "Gillespie", "given": "Nathan A", "initials": "NA"}, {"family": "Gordon", "given": "Scott D", "initials": "SD"}, {"family": "Gottesman", "given": "Rebecca F", "initials": "RF"}, {"family": "Griswold", "given": "Michael E", "initials": "ME"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hartmann", "given": "Annette M", "initials": "AM"}, {"family": "Hatzimanolis", "given": "Alex", "initials": "A"}, {"family": "Heiss", "given": "Gerardo", "initials": "G"}, {"family": "Holliday", "given": "Elizabeth G", "initials": "EG"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Karlsson", "given": "Ida", "initials": "I"}, {"family": "Kleineidam", "given": "Luca", "initials": "L"}, {"family": "Knopman", "given": "David S", "initials": "DS"}, {"family": "Kochan", "given": "Nicole A", "initials": "NA"}, {"family": "Konte", "given": "Bettina", "initials": "B"}, {"family": "Kwok", "given": "John B", "initials": "JB"}, {"family": "Le Hellard", "given": "Stephanie", "initials": "S"}, {"family": "Lee", "given": "Teresa", "initials": "T"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Li", "given": "Shu-Chen", "initials": "SC"}, {"family": "Liu", "given": "Tian", "initials": "T"}, {"family": "Koini", "given": "Marisa", "initials": "M"}, {"family": "London", "given": "Edythe", "initials": "E"}, {"family": "Longstreth", "given": "Will T", "initials": "WT"}, {"family": "Lopez", "given": "Oscar L", "initials": "OL"}, {"family": "Loukola", "given": "Anu", "initials": "A"}, {"family": "Luck", "given": "Tobias", "initials": "T"}, {"family": "Lundervold", "given": "Astri J", "initials": "AJ"}, {"family": "Lundquist", "given": "Anders", "initials": "A"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Murray", "given": "Alison D", "initials": "AD"}, {"family": "Need", "given": "Anna C", "initials": "AC"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Nyberg", "given": "Lars", "initials": "L"}, {"family": "Ollier", "given": "William", "initials": "W"}, {"family": "Papenberg", "given": "Goran", "initials": "G"}, {"family": "Pattie", "given": "Alison", "initials": "A"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Poldrack", "given": "Russell A", "initials": "RA"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Reppermund", "given": "Simone", "initials": "S"}, {"family": "Riedel-Heller", "given": "Steffi G", "initials": "SG"}, {"family": "Rose", "given": "Richard J", "initials": "RJ"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Roussos", "given": "Panos", "initials": "P"}, {"family": "Rovio", "given": "Suvi P", "initials": "SP"}, {"family": "Saba", "given": "Yasaman", "initials": "Y"}, {"family": "Sabb", "given": "Fred W", "initials": "FW"}, {"family": "Sachdev", "given": "Perminder S", "initials": "PS"}, {"family": "Satizabal", "given": "Claudia L", "initials": "CL"}, {"family": "Schmid", "given": "Matthias", "initials": "M"}, {"family": "Scott", "given": "Rodney J", "initials": "RJ"}, {"family": "Scult", "given": "Matthew A", "initials": "MA"}, {"family": "Simino", "given": "Jeannette", "initials": "J"}, {"family": "Slagboom", "given": "P Eline", "initials": "PE"}, {"family": "Smyrnis", "given": "Nikolaos", "initials": "N"}, {"family": "Soumar\u00e9", "given": "A\u00efcha", "initials": "A"}, {"family": "Stefanis", "given": "Nikos C", "initials": "NC"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Straub", "given": "Richard E", "initials": "RE"}, {"family": "Sundet", "given": "Kjetil", "initials": "K"}, {"family": "Taylor", "given": "Adele M", "initials": "AM"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Tzoulaki", "given": "Ioanna", "initials": "I"}, {"family": "Tzourio", "given": "Christophe", "initials": "C"}, {"family": "Uitterlinden", "given": "Andr\u00e9", "initials": "A"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Voineskos", "given": "Aristotle N", "initials": "AN"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Wagner", "given": "Michael", "initials": "M"}, {"family": "Wagner", "given": "Holger", "initials": "H"}, {"family": "Weinhold", "given": "Leonie", "initials": "L"}, {"family": "Wen", "given": "K Hoyan", "initials": "KH"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Adams", "given": "Hieab H H", "initials": "HHH"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Bilder", "given": "Robert M", "initials": "RM"}, {"family": "Bitsios", "given": "Panos", "initials": "P"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Chiba-Falek", "given": "Ornit", "initials": "O"}, {"family": "Corvin", "given": "Aiden", "initials": "A"}, {"family": "De Jager", "given": "Philip L", "initials": "PL"}, {"family": "Debette", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Donohoe", "given": "Gary", "initials": "G"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Fitzpatrick", "given": "Annette L", "initials": "AL"}, {"family": "Gill", "given": "Michael", "initials": "M"}, {"family": "Glahn", "given": "David C", "initials": "DC"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Hansell", "given": "Narelle K", "initials": "NK"}, {"family": "Hariri", "given": "Ahmad R", "initials": "AR"}, {"family": "Ikram", "given": "M Kamran", "initials": "MK"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Vuoksimaa", "given": "Eero", "initials": "E"}, {"family": "Keller", "given": "Matthew C", "initials": "MC"}, {"family": "Kremen", "given": "William S", "initials": "WS"}, {"family": "Launer", "given": "Lenore", "initials": "L"}, {"family": "Lindenberger", "given": "Ulman", "initials": "U"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Pendleton", "given": "Neil", "initials": "N"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Ramirez", "given": "Alfredo", "initials": "A"}, {"family": "Reinvang", "given": "Ivar", "initials": "I"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schofield", "given": "Peter W", "initials": "PW"}, {"family": "Schofield", "given": "Peter R", "initials": "PR"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Steen", "given": "Vidar M", "initials": "VM"}, {"family": "Trollor", "given": "Julian N", "initials": "JN"}, {"family": "Turner", "given": "Steven T", "initials": "ST"}, {"family": "Van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Villringer", "given": "Arno", "initials": "A"}, {"family": "Weinberger", "given": "Daniel R", "initials": "DR"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Malhotra", "given": "Anil", "initials": "A"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Gale", "given": "Catharine R", "initials": "CR"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Mosley", "given": "Thomas H", "initials": "TH"}, {"family": "Bressler", "given": "Jan", "initials": "J"}, {"family": "Lencz", "given": "Todd", "initials": "T"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}], "type": "journal article", "published": "2018-05-29", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "2098", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "General cognitive function is a prominent and relatively stable human trait that is associated with many important life outcomes. We combine cognitive and genetic data from the CHARGE and COGENT consortia, and UK Biobank (total N\u2009=\u2009300,486; age 16-102) and find 148 genome-wide significant independent loci (P\u2009<\u20095\u2009\u00d7\u200910", "doi": "10.1038/s41467-018-04362-x", "pmid": "29844566", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-04362-x"}, {"db": "pmc", "key": "PMC5974083"}], "notes": [], "created": "2018-06-15T07:31:31.488Z", "modified": "2024-01-16T13:48:46.281Z"}, {"entity": "publication", "iuid": "13196c56bb9843da951bac3edff3233f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13196c56bb9843da951bac3edff3233f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13196c56bb9843da951bac3edff3233f"}}, "title": "Repeated evolution of self-compatibility for reproductive assurance.", "authors": [{"family": "Nieuwenhuis", "given": "Bart P S", "initials": "BPS"}, {"family": "Tusso", "given": "Sergio", "initials": "S"}, {"family": "Bjerling", "given": "Pernilla", "initials": "P"}, {"family": "St\u00e5ngberg", "given": "Josefine", "initials": "J"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}, {"family": "Immler", "given": "Simone", "initials": "S"}], "type": "journal article", "published": "2018-04-24", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "1639", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Sexual reproduction in eukaryotes requires the fusion of two compatible gametes of opposite sexes or mating types. To meet the challenge of finding a mating partner with compatible gametes, evolutionary mechanisms such as hermaphroditism and self-fertilization have repeatedly evolved. Here, by combining the insights from comparative genomics, computer simulations and experimental evolution in fission yeast, we shed light on the conditions promoting separate mating types or self-compatibility by mating-type switching. Analogous to multiple independent transitions between switchers and non-switchers in natural populations mediated by structural genomic changes, novel switching genotypes readily evolved under selection in the experimental populations. Detailed fitness measurements accompanied by computer simulations show the benefits and costs of switching during sexual and asexual reproduction, governing the occurrence of both strategies in nature. Our findings illuminate the trade-off between the benefits of reproductive assurance and its fitness costs under benign conditions facilitating the evolution of self-compatibility.", "doi": "10.1038/s41467-018-04054-6", "pmid": "29691402", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-04054-6"}, {"db": "pmc", "key": "PMC5915400"}], "notes": [], "created": "2018-06-25T14:03:22.956Z", "modified": "2024-01-16T13:48:46.472Z"}, {"entity": "publication", "iuid": "34020a4f185544d5bb305aa946f19dd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34020a4f185544d5bb305aa946f19dd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34020a4f185544d5bb305aa946f19dd1"}}, "title": "Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate.", "authors": [{"family": "Giri", "given": "Jitender", "initials": "J", "orcid": "0000-0001-6969-5187", "researcher": {"href": "https://publications.scilifelab.se/researcher/b33c00f86f614268ad5c04114d66379d.json"}}, {"family": "Bhosale", "given": "Rahul", "initials": "R", "orcid": "0000-0001-6515-4922", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca14fb832e6e41d6993fd93cf5280200.json"}}, {"family": "Huang", "given": "Guoqiang", "initials": "G", "orcid": "0000-0002-6103-5704", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbbeb650d2a6405cada0e94c406bfae0.json"}}, {"family": "Pandey", "given": "Bipin K", "initials": "BK", "orcid": "0000-0002-9614-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/cde6eb2186ed490e8b7d22a15d4dfce0.json"}}, {"family": "Parker", "given": "Helen", "initials": "H"}, {"family": "Zappala", "given": "Susan", "initials": "S"}, {"family": "Yang", "given": "Jing", "initials": "J", "orcid": "0000-0001-5697-3707", "researcher": {"href": "https://publications.scilifelab.se/researcher/2275548941f643739d6d58218160b08f.json"}}, {"family": "Dievart", "given": "Anne", "initials": "A"}, {"family": "Bureau", "given": "Charlotte", "initials": "C"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Price", "given": "Adam", "initials": "A"}, {"family": "Rose", "given": "Terry", "initials": "T"}, {"family": "Larrieu", "given": "Antoine", "initials": "A", "orcid": "0000-0002-9024-5348", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf2d8e7d8d14ba6a80aabe38d88e2a0.json"}}, {"family": "Mairhofer", "given": "Stefan", "initials": "S"}, {"family": "Sturrock", "given": "Craig J", "initials": "CJ", "orcid": "0000-0002-5333-8502", "researcher": {"href": "https://publications.scilifelab.se/researcher/0222b8d310fc4296ba6d9ceb78cb524b.json"}}, {"family": "White", "given": "Philip", "initials": "P"}, {"family": "Dupuy", "given": "Lionel", "initials": "L"}, {"family": "Hawkesford", "given": "Malcolm", "initials": "M", "orcid": "0000-0001-8759-3969", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc82093d73d94fee9b294567c058623b.json"}}, {"family": "Perin", "given": "Christophe", "initials": "C"}, {"family": "Liang", "given": "Wanqi", "initials": "W"}, {"family": "Peret", "given": "Benjamin", "initials": "B"}, {"family": "Hodgman", "given": "Charlie T", "initials": "CT", "orcid": "0000-0001-5862-8296", "researcher": {"href": "https://publications.scilifelab.se/researcher/95fa6b3a6043457a9f2eded0b5a43e53.json"}}, {"family": "Lynch", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-7265-9790", "researcher": {"href": "https://publications.scilifelab.se/researcher/82842d9b8e064b3686ec640bc6552e8b.json"}}, {"family": "Wissuwa", "given": "Matthias", "initials": "M"}, {"family": "Zhang", "given": "Dabing", "initials": "D", "orcid": "0000-0002-1764-2929", "researcher": {"href": "https://publications.scilifelab.se/researcher/94c346340452487795b97dc569711aa8.json"}}, {"family": "Pridmore", "given": "Tony", "initials": "T"}, {"family": "Mooney", "given": "Sacha J", "initials": "SJ"}, {"family": "Guiderdoni", "given": "Emmanuel", "initials": "E"}, {"family": "Swarup", "given": "Ranjan", "initials": "R"}, {"family": "Bennett", "given": "Malcolm J", "initials": "MJ", "orcid": "0000-0003-0475-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e4df838f034767afdcc563e61ed0b4.json"}}], "type": "journal article", "published": "2018-04-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "9", "issue": "1", "pages": "1408", "issn-l": "2041-1723"}, "abstract": "Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice.", "doi": "10.1038/s41467-018-03850-4", "pmid": "29650967", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-03850-4"}, {"db": "pmc", "key": "PMC5897452"}], "notes": [], "created": "2019-01-10T11:25:40.540Z", "modified": "2025-10-17T13:03:18.246Z"}, {"entity": "publication", "iuid": "edad18053a0d4013a32b354e4b6ddd7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edad18053a0d4013a32b354e4b6ddd7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edad18053a0d4013a32b354e4b6ddd7b"}}, "title": "A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate.", "authors": [{"family": "Bhosale", "given": "Rahul", "initials": "R", "orcid": "0000-0001-6515-4922", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca14fb832e6e41d6993fd93cf5280200.json"}}, {"family": "Giri", "given": "Jitender", "initials": "J", "orcid": "0000-0001-6969-5187", "researcher": {"href": "https://publications.scilifelab.se/researcher/b33c00f86f614268ad5c04114d66379d.json"}}, {"family": "Pandey", "given": "Bipin K", "initials": "BK", "orcid": "0000-0002-9614-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/cde6eb2186ed490e8b7d22a15d4dfce0.json"}}, {"family": "Giehl", "given": "Ricardo F H", "initials": "RFH"}, {"family": "Hartmann", "given": "Anja", "initials": "A"}, {"family": "Traini", "given": "Richard", "initials": "R"}, {"family": "Truskina", "given": "Jekaterina", "initials": "J"}, {"family": "Leftley", "given": "Nicola", "initials": "N"}, {"family": "Hanlon", "given": "Meredith", "initials": "M"}, {"family": "Swarup", "given": "Kamal", "initials": "K"}, {"family": "Rashed", "given": "Afaf", "initials": "A"}, {"family": "Vo\u00df", "given": "Ute", "initials": "U"}, {"family": "Alonso", "given": "Jose", "initials": "J"}, {"family": "Stepanova", "given": "Anna", "initials": "A"}, {"family": "Yun", "given": "Jeonga", "initials": "J"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Brown", "given": "Kathleen M", "initials": "KM", "orcid": "0000-0002-4960-5292", "researcher": {"href": "https://publications.scilifelab.se/researcher/640dd3f9f7754cd18437be93d1374182.json"}}, {"family": "Lynch", "given": "Jonathan P", "initials": "JP", "orcid": "0000-0002-7265-9790", "researcher": {"href": "https://publications.scilifelab.se/researcher/82842d9b8e064b3686ec640bc6552e8b.json"}}, {"family": "Dolan", "given": "Liam", "initials": "L"}, {"family": "Vernoux", "given": "Teva", "initials": "T", "orcid": "0000-0002-8257-4088", "researcher": {"href": "https://publications.scilifelab.se/researcher/c01a5903e379401da311ef3d90e46e16.json"}}, {"family": "Bishopp", "given": "Anthony", "initials": "A"}, {"family": "Wells", "given": "Darren", "initials": "D", "orcid": "0000-0002-4246-4909", "researcher": {"href": "https://publications.scilifelab.se/researcher/00bb3b1089064493853de8524abd75cb.json"}}, {"family": "von Wir\u00e9n", "given": "Nicolaus", "initials": "N", "orcid": "0000-0002-4966-425X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4c7f25ca3954d0fbd0a13c7f46ff001.json"}}, {"family": "Bennett", "given": "Malcolm J", "initials": "MJ", "orcid": "0000-0003-0475-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e4df838f034767afdcc563e61ed0b4.json"}}, {"family": "Swarup", "given": "Ranjan", "initials": "R"}], "type": "journal article", "published": "2018-04-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "9", "issue": "1", "pages": "1409", "issn-l": "2041-1723"}, "abstract": "Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.", "doi": "10.1038/s41467-018-03851-3", "pmid": "29651114", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-03851-3"}, {"db": "pmc", "key": "PMC5897496"}], "notes": [], "created": "2019-01-10T11:26:37.991Z", "modified": "2025-10-17T13:03:18.263Z"}, {"entity": "publication", "iuid": "906aeab4b0d1446586bd69fdcaf47fce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/906aeab4b0d1446586bd69fdcaf47fce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/906aeab4b0d1446586bd69fdcaf47fce"}}, "title": "A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.", "authors": [{"family": "Ladds", "given": "Marcus J G W", "initials": "MJGW"}, {"family": "van Leeuwen", "given": "Ingeborg M M", "initials": "IMM"}, {"family": "Drummond", "given": "Catherine J", "initials": "CJ"}, {"family": "Chu", "given": "Su", "initials": "S"}, {"family": "Healy", "given": "Alan R", "initials": "AR"}, {"family": "Popova", "given": "Gergana", "initials": "G"}, {"family": "Pastor Fern\u00e1ndez", "given": "Andr\u00e9s", "initials": "A"}, {"family": "Mollick", "given": "Tanzina", "initials": "T"}, {"family": "Darekar", "given": "Suhas", "initials": "S"}, {"family": "Sedimbi", "given": "Saikiran K", "initials": "SK"}, {"family": "Nekulova", "given": "Marta", "initials": "M"}, {"family": "Sachweh", "given": "Marijke C C", "initials": "MCC"}, {"family": "Campbell", "given": "Johanna", "initials": "J"}, {"family": "Higgins", "given": "Maureen", "initials": "M"}, {"family": "Tuck", "given": "Chloe", "initials": "C"}, {"family": "Popa", "given": "Mihaela", "initials": "M"}, {"family": "Safont", "given": "Mireia Mayoral", "initials": "MM"}, {"family": "Gelebart", "given": "Pascal", "initials": "P"}, {"family": "Fandalyuk", "given": "Zinayida", "initials": "Z"}, {"family": "Thompson", "given": "Alastair M", "initials": "AM"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "F\u00e4rneg\u00e5rdh", "given": "Katarina", "initials": "K"}, {"family": "Yngve", "given": "Ulrika", "initials": "U"}, {"family": "Saleh", "given": "Aljona", "initials": "A"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "D'Hollander", "given": "Agathe C A", "initials": "ACA"}, {"family": "Franco", "given": "Marcela", "initials": "M"}, {"family": "Zhao", "given": "Yan", "initials": "Y"}, {"family": "H\u00e5kansson", "given": "Maria", "initials": "M"}, {"family": "Walse", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Larsson", "given": "Karin", "initials": "K", "orcid": "0000-0002-6403-2736", "researcher": {"href": "https://publications.scilifelab.se/researcher/c015846a43c54cd1a1a2b52e6caa1740.json"}}, {"family": "Peat", "given": "Emma M", "initials": "EM"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Lunec", "given": "John", "initials": "J"}, {"family": "Vojtesek", "given": "Borivoj", "initials": "B"}, {"family": "Carmena", "given": "Mar", "initials": "M", "orcid": "0000-0002-2352-1066", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd5d0ef8fa3947bfbe59606a74da4eaa.json"}}, {"family": "Earnshaw", "given": "William C", "initials": "WC"}, {"family": "McCarthy", "given": "Anna R", "initials": "AR"}, {"family": "Westwood", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0003-0630-0138", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6d109f545d5477e9686475989c8ef5a.json"}}, {"family": "Arsenian-Henriksson", "given": "Marie", "initials": "M"}, {"family": "Lane", "given": "David P", "initials": "DP"}, {"family": "Bhatia", "given": "Ravi", "initials": "R"}, {"family": "McCormack", "given": "Emmet", "initials": "E"}, {"family": "La\u00edn", "given": "Sonia", "initials": "S"}], "type": "journal article", "published": "2018-03-16", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "1107", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The development of non-genotoxic therapies that activate wild-type p53 in tumors is of great interest since the discovery of p53 as a tumor suppressor. Here we report the identification of over 100 small-molecules activating p53 in cells. We elucidate the mechanism of action of a chiral tetrahydroindazole (HZ00), and through target deconvolution, we deduce that its active enantiomer (R)-HZ00, inhibits dihydroorotate dehydrogenase (DHODH). The chiral specificity of HZ05, a more potent analog, is revealed by the crystal structure of the (R)-HZ05/DHODH complex. Twelve other DHODH inhibitor chemotypes are detailed among the p53 activators, which identifies DHODH as a frequent target for structurally diverse compounds. We observe that HZ compounds accumulate cancer cells in S-phase, increase p53 synthesis, and synergize with an inhibitor of p53 degradation to reduce tumor growth in vivo. We, therefore, propose a strategy to promote cancer cell killing by p53 instead of its reversible cell cycle arresting effect.", "doi": "10.1038/s41467-018-03441-3", "pmid": "29549331", "labels": {"Protein Science Facility (PSF)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-03441-3"}, {"db": "pmc", "key": "PMC5856786"}], "notes": [], "created": "2018-04-09T08:28:05.800Z", "modified": "2025-10-17T13:05:08.481Z"}, {"entity": "publication", "iuid": "45cc3396e39641618b4e80f82db3a99c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45cc3396e39641618b4e80f82db3a99c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45cc3396e39641618b4e80f82db3a99c"}}, "title": "Genome-wide analysis yields new loci associating with aortic valve stenosis.", "authors": [{"family": "Helgadottir", "given": "Anna", "initials": "A"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Gretarsdottir", "given": "Solveig", "initials": "S"}, {"family": "Stefansson", "given": "Olafur A", "initials": "OA"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Thorolfsdottir", "given": "Rosa B", "initials": "RB"}, {"family": "Jonsdottir", "given": "Ingileif", "initials": "I"}, {"family": "Bjornsson", "given": "Thorsteinn", "initials": "T"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Nielsen", "given": "Jonas B", "initials": "JB"}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Martinsson", "given": "Andreas", "initials": "A"}, {"family": "Heydarpour", "given": "Mahyar", "initials": "M"}, {"family": "Prakash", "given": "Siddharth", "initials": "S"}, {"family": "Oskarsson", "given": "Gylfi", "initials": "G"}, {"family": "Gudbjartsson", "given": "Tomas", "initials": "T"}, {"family": "Geirsson", "given": "Arnar", "initials": "A"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Sigurdsson", "given": "Emil L", "initials": "EL"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Fritsche", "given": "Lars", "initials": "L"}, {"family": "Lin", "given": "Maoxuan", "initials": "M"}, {"family": "Yang", "given": "Bo", "initials": "B"}, {"family": "Hornsby", "given": "Whitney", "initials": "W"}, {"family": "Guo", "given": "Dongchuan", "initials": "D"}, {"family": "Brummett", "given": "Chad M", "initials": "CM"}, {"family": "Abecasis", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Mathis", "given": "Michael", "initials": "M"}, {"family": "Milewicz", "given": "Dianna", "initials": "D"}, {"family": "Body", "given": "Simon C", "initials": "SC"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Danielsen", "given": "Ragnar", "initials": "R"}, {"family": "Thorgeirsson", "given": "Gudmundur", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}], "type": "journal article", "published": "2018-03-07", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "987", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Aortic valve stenosis (AS) is the most common valvular heart disease, and valve replacement is the only definitive treatment. Here we report a large genome-wide association (GWA) study of 2,457 Icelandic AS cases and 349,342 controls with a follow-up in up to 4,850 cases and 451,731 controls of European ancestry. We identify two new AS loci, on chromosome 1p21 near PALMD (rs7543130; odds ratio (OR)\u2009=\u20091.20, P\u2009=\u20091.2\u2009\u00d7\u200910\n            -22) and on chromosome 2q22 in TEX41 (rs1830321; OR\u2009=\u20091.15, P\u2009=\u20091.8\u2009\u00d7\u200910-13). Rs7543130 also associates with bicuspid aortic valve (BAV) (OR\u2009=\u20091.28, P\u2009=\u20096.6\u2009\u00d7\u200910-10) and aortic root diameter (P\u2009=\u20091.30\u2009\u00d7\u200910-8), and rs1830321 associates with BAV (OR\u2009=\u20091.12, P\u2009=\u20095.3\u2009\u00d7\u200910-3) and coronary artery disease (OR\u2009=\u20091.05, P\u2009=\u20099.3\u2009\u00d7\u200910-5). The results implicate both cardiac developmental abnormalities and atherosclerosis-like processes in the pathogenesis of AS. We show that several pathways are shared by CAD and AS. Causal analysis suggests that the shared risk factors of Lp(a) and non-high-density lipoprotein cholesterol contribute substantially to the frequent co-occurence of these diseases.", "doi": "10.1038/s41467-018-03252-6", "pmid": "29511194", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-03252-6"}, {"db": "pmc", "key": "PMC5840367"}], "notes": [], "created": "2019-01-09T07:22:21.037Z", "modified": "2020-01-21T13:56:13.753Z"}, {"entity": "publication", "iuid": "5c73c68928714d1ca470927905211c8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c73c68928714d1ca470927905211c8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c73c68928714d1ca470927905211c8e"}}, "title": "Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.", "authors": [{"family": "Zhu", "given": "Yafeng", "initials": "Y"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Boekel", "given": "Jorrit", "initials": "J"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Fernandez-Woodbridge", "given": "Alejandro", "initials": "A"}, {"family": "Branca", "given": "Rui M M", "initials": "RMM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2018-03-02", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "903", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3-10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific.", "doi": "10.1038/s41467-018-03311-y", "pmid": "29500430", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-03311-y"}, {"db": "pmc", "key": "PMC5834625"}], "notes": [], "created": "2018-03-04T17:55:08.112Z", "modified": "2024-01-16T13:48:46.793Z"}, {"entity": "publication", "iuid": "bebd428b1dba4d089a4570a609b57d25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bebd428b1dba4d089a4570a609b57d25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bebd428b1dba4d089a4570a609b57d25"}}, "title": "Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels.", "authors": [{"family": "Jiang", "given": "Xia", "initials": "X"}, {"family": "O'Reilly", "given": "Paul F", "initials": "PF"}, {"family": "Aschard", "given": "Hugues", "initials": "H"}, {"family": "Hsu", "given": "Yi-Hsiang", "initials": "YH"}, {"family": "Richards", "given": "J Brent", "initials": "JB"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Pilz", "given": "Stefan", "initials": "S"}, {"family": "Berry", "given": "Diane", "initials": "D"}, {"family": "Kestenbaum", "given": "Bryan", "initials": "B"}, {"family": "Zheng", "given": "Jusheng", "initials": "J"}, {"family": "Luan", "given": "Jianan", "initials": "J"}, {"family": "Sofianopoulou", "given": "Eleni", "initials": "E"}, {"family": "Streeten", "given": "Elizabeth A", "initials": "EA"}, {"family": "Albanes", "given": "Demetrius", "initials": "D"}, {"family": "Lutsey", "given": "Pamela L", "initials": "PL"}, {"family": "Yao", "given": "Lu", "initials": "L"}, {"family": "Tang", "given": "Weihong", "initials": "W"}, {"family": "Econs", "given": "Michael J", "initials": "MJ"}, {"family": "Wallaschofski", "given": "Henri", "initials": "H"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Zhou", "given": "Ang", "initials": "A"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Michos", "given": "Erin D", "initials": "ED"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Weinstein", "given": "Stephanie J", "initials": "SJ"}, {"family": "Freedman", "given": "Neal D", "initials": "ND"}, {"family": "Huang", "given": "Wen-Yi", "initials": "WY"}, {"family": "Van Schoor", "given": "Natasja M", "initials": "NM"}, {"family": "van der Velde", "given": "Nathalie", "initials": "N"}, {"family": "Groot", "given": "Lisette C P G M de", "initials": "LCPGM"}, {"family": "Enneman", "given": "Anke", "initials": "A"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Booth", "given": "Sarah L", "initials": "SL"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Zhou", "given": "Yanhua", "initials": "Y"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Shea", "given": "M Kyla", "initials": "MK"}, {"family": "Houston", "given": "Denise K", "initials": "DK"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Peacock", "given": "Munro", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Beekman", "given": "Marian", "initials": "M"}, {"family": "Slagboom", "given": "Eline", "initials": "E"}, {"family": "Deelen", "given": "Joris", "initials": "J"}, {"family": "Heemst", "given": "Diana van", "initials": "DV"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "de Boer", "given": "Ian H", "initials": "IH"}, {"family": "Wood", "given": "Alexis C", "initials": "AC"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Robinson-Cohen", "given": "Cassianne", "initials": "C"}, {"family": "den Heijer", "given": "Martin", "initials": "M"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Cavadino", "given": "Alana", "initials": "A"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Zgaga", "given": "Lina", "initials": "L"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Theodoratou", "given": "Evropi", "initials": "E"}, {"family": "Farrington", "given": "Susan M", "initials": "SM"}, {"family": "Timofeeva", "given": "Maria", "initials": "M"}, {"family": "Dunlop", "given": "Malcolm G", "initials": "MG"}, {"family": "Valdes", "given": "Ana M", "initials": "AM"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Mikkil\u00e4", "given": "Vera", "initials": "V"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Gundersen", "given": "Thomas E", "initials": "TE"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Spector", "given": "Timothy", "initials": "T"}, {"family": "Wang", "given": "Thomas J", "initials": "TJ"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}], "type": "journal article", "published": "2018-01-17", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "260", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P\u2009=\u20094.7\u00d710", "doi": "10.1038/s41467-017-02662-2", "pmid": "29343764", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-02662-2"}, {"db": "pmc", "key": "PMC5772647"}], "notes": [], "created": "2018-05-25T13:31:03.142Z", "modified": "2024-01-16T13:48:47.068Z"}, {"entity": "publication", "iuid": "c33bf4e24f0f40d896b8cb6d1284a5f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c33bf4e24f0f40d896b8cb6d1284a5f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c33bf4e24f0f40d896b8cb6d1284a5f8"}}, "title": "Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells.", "authors": [{"family": "Page", "given": "Brent D G", "initials": "BDG"}, {"family": "Valerie", "given": "Nicholas C K", "initials": "NCK", "orcid": "0000-0002-9423-964X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d90c5a1f924c8b97409934dec74b0b.json"}}, {"family": "Wright", "given": "Roni H G", "initials": "RHG"}, {"family": "Wallner", "given": "Olov", "initials": "O"}, {"family": "Isaksson", "given": "Rebecka", "initials": "R"}, {"family": "Carter", "given": "Megan", "initials": "M"}, {"family": "Rudd", "given": "Sean G", "initials": "SG", "orcid": "0000-0002-4368-3855", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1e23d9748e4868a4b5e966e423b1a9.json"}}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "A"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Font-Mateu", "given": "Jofre", "initials": "J"}, {"family": "Llona-Minguez", "given": "Sabin", "initials": "S", "orcid": "0000-0003-3187-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/437b1f98ad21471f884226ed89a3da12.json"}}, {"family": "Baranczewski", "given": "Pawel", "initials": "P"}, {"family": "Jeppsson", "given": "Fredrik", "initials": "F"}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Almqvist", "given": "Helena", "initials": "H"}, {"family": "Axelsson", "given": "Hanna", "initials": "H"}, {"family": "Regmi", "given": "Shruti", "initials": "S"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "A"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Str\u00f6mberg", "given": "Kia", "initials": "K"}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P"}, {"family": "Beato", "given": "Miguel", "initials": "M"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2018-01-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "9", "issue": "1", "pages": "250"}, "abstract": "With a diverse network of substrates, NUDIX hydrolases have emerged as a key family of nucleotide-metabolizing enzymes. NUDT5 (also called NUDIX5) has been implicated in ADP-ribose and 8-oxo-guanine metabolism and was recently identified as a rheostat of hormone-dependent gene regulation and proliferation in breast cancer cells. Here, we further elucidate the physiological relevance of known NUDT5 substrates and underscore the biological requirement for NUDT5 in gene regulation and proliferation of breast cancer cells. We confirm the involvement of NUDT5 in ADP-ribose metabolism and dissociate a relationship to oxidized nucleotide sanitation. Furthermore, we identify potent NUDT5 inhibitors, which are optimized to promote maximal NUDT5 cellular target engagement by CETSA. Lead compound, TH5427, blocks progestin-dependent, PAR-derived nuclear ATP synthesis and subsequent chromatin remodeling, gene regulation and proliferation in breast cancer cells. We herein present TH5427 as a promising, targeted inhibitor that can be used to further study NUDT5 activity and ADP-ribose metabolism.", "doi": "10.1038/s41467-017-02293-7", "pmid": "29343827", "labels": {"Protein Science Facility (PSF)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5772648"}, {"db": "pii", "key": "10.1038/s41467-017-02293-7"}], "notes": [], "created": "2018-01-17T12:31:11.673Z", "modified": "2025-10-17T13:05:08.549Z"}, {"entity": "publication", "iuid": "0d4095789678406cba65e6ce25b7b0a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d4095789678406cba65e6ce25b7b0a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d4095789678406cba65e6ce25b7b0a9"}}, "title": "Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.", "authors": [{"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Wang", "given": "Heng", "initials": "H"}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Joven", "given": "Alberto", "initials": "A"}, {"family": "Brito", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2134-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0196703e4df4518b212ed1f3322e811.json"}}, {"family": "Kumar", "given": "Anoop", "initials": "A"}, {"family": "Hameed", "given": "L Shahul", "initials": "LS"}, {"family": "Penrad-Mobayed", "given": "May", "initials": "M"}, {"family": "Yao", "given": "Zeyu", "initials": "Z"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Abbas", "given": "Yamen", "initials": "Y"}, {"family": "Abdullayev", "given": "Ilgar", "initials": "I"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-4624-0259", "researcher": {"href": "https://publications.scilifelab.se/researcher/d85416dce306436ab0c4cdeea22a1f59.json"}}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A"}], "type": "journal article", "published": "2017-12-22", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "2286", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Salamanders exhibit an extraordinary ability among vertebrates to regenerate complex body parts. However, scarce genomic resources have limited our understanding of regeneration in adult salamanders. Here, we present the ~20 Gb genome and transcriptome of the Iberian ribbed newt Pleurodeles waltl, a tractable species suitable for laboratory research. We find that embryonic stem cell-specific miRNAs mir-93b and mir-427/430/302, as well as Harbinger DNA transposons carrying the Myb-like proto-oncogene have expanded dramatically in the Pleurodeles waltl genome and are co-expressed during limb regeneration. Moreover, we find that a family of salamander methyltransferases is expressed specifically in adult appendages. Using CRISPR/Cas9 technology to perturb transcription factors, we demonstrate that, unlike the axolotl, Pax3 is present and necessary for development and that contrary to mammals, muscle regeneration is normal without functional Pax7 gene. Our data provide a foundation for comparative genomic studies that generate models for the uneven distribution of regenerative capacities among vertebrates.", "doi": "10.1038/s41467-017-01964-9", "pmid": "29273779", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-01964-9"}, {"db": "pmc", "key": "PMC5741667"}], "notes": [], "created": "2018-01-10T09:44:17.789Z", "modified": "2021-07-07T11:44:07.846Z"}, {"entity": "publication", "iuid": "13b158b1f8104b7f8cf82c52e803ff32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13b158b1f8104b7f8cf82c52e803ff32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13b158b1f8104b7f8cf82c52e803ff32"}}, "title": "Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma", "authors": [{"family": "Lauss", "given": "Martin", "initials": "M"}, {"family": "Donia", "given": "Marco", "initials": "M"}, {"family": "Harbst", "given": "Katja", "initials": "K"}, {"family": "Andersen", "given": "Rikke", "initials": "R"}, {"family": "Mitra", "given": "Shamik", "initials": "S"}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Salim", "given": "Maryem", "initials": "M"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J"}, {"family": "T\u00f6rngren", "given": "Therese", "initials": "T"}, {"family": "Kvist", "given": "Anders", "initials": "A"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Svane", "given": "Inge Marie", "initials": "IM"}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-01460-0", "pmid": "29170503", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-24T11:50:36.213Z", "modified": "2020-01-21T13:53:22.045Z"}, {"entity": "publication", "iuid": "36b0ab5dc4b2438a83cf7164999249d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36b0ab5dc4b2438a83cf7164999249d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36b0ab5dc4b2438a83cf7164999249d8"}}, "title": "The dynamic dimer structure of the chaperone Trigger Factor", "authors": [{"family": "Morgado", "given": "Leonor", "initials": "L"}, {"family": "Burmann", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Sharpe", "given": "Timothy", "initials": "T"}, {"family": "Mazur", "given": "Adam", "initials": "A"}, {"family": "Hiller", "given": "Sebastian", "initials": "S"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-02196-7", "pmid": "29222465", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:31:30.436Z", "modified": "2025-10-17T13:03:59.239Z"}, {"entity": "publication", "iuid": "3ed56227ce694d0b8a4fbaabec439db8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ed56227ce694d0b8a4fbaabec439db8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ed56227ce694d0b8a4fbaabec439db8"}}, "title": "Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling", "authors": [{"family": "Petersen", "given": "Julian", "initials": "J"}, {"family": "Wright", "given": "Shane C", "initials": "SC"}, {"family": "Rodr\u00edguez", "given": "David", "initials": "D"}, {"family": "Matricon", "given": "Pierre", "initials": "P"}, {"family": "Lahav", "given": "Noa", "initials": "N"}, {"family": "Vromen", "given": "Aviv", "initials": "A"}, {"family": "Friedler", "given": "Assaf", "initials": "A"}, {"family": "Str\u00f6mqvist", "given": "Johan", "initials": "J"}, {"family": "Wennmalm", "given": "Stefan", "initials": "S"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Schulte", "given": "Gunnar", "initials": "G"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-00253-9", "pmid": "28790300", "labels": {"Fluorescence Correlation Spectroscopy": "Collaborative", "Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-26T08:07:07.658Z", "modified": "2021-05-24T15:33:38.128Z"}, {"entity": "publication", "iuid": "42ab95d6b8f44dc38532ed2b323cc72e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42ab95d6b8f44dc38532ed2b323cc72e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42ab95d6b8f44dc38532ed2b323cc72e"}}, "title": "Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature", "authors": [{"family": "Martins", "given": "Sara", "initials": "S"}, {"family": "Montiel-Jorda", "given": "Alvaro", "initials": "A"}, {"family": "Cayrel", "given": "Anne", "initials": "A"}, {"family": "Huguet", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Roux", "given": "Christine Paysant Le", "initials": "CPL"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Vert", "given": "Gr\u00e9gory", "initials": "G"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-00355-4", "pmid": "28827608", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:33:46.381Z", "modified": "2025-10-17T13:03:18.458Z"}, {"entity": "publication", "iuid": "4b838933f7564dbcbb8d65bfc4f78b19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b838933f7564dbcbb8d65bfc4f78b19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b838933f7564dbcbb8d65bfc4f78b19"}}, "title": "Structural basis for dolichylphosphate mannose biosynthesis", "authors": [{"family": "Gandini", "given": "Rosaria", "initials": "R"}, {"family": "Reichenbach", "given": "Tom", "initials": "T"}, {"family": "Tan", "given": "Tien Chye", "initials": "TC"}, {"family": "Divne", "given": "Christina", "initials": "C"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-00187-2", "pmid": "28743912", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:44:20.090Z", "modified": "2017-11-09T13:21:29.760Z"}, {"entity": "publication", "iuid": "80c5501a15564f2eb10243009cd39671", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80c5501a15564f2eb10243009cd39671.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80c5501a15564f2eb10243009cd39671"}}, "title": "A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family", "authors": [{"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Zitnik", "given": "Marinka", "initials": "M"}, {"family": "Jemth", "given": "Ann Sofie", "initials": "AS"}, {"family": "Carter", "given": "Megan", "initials": "M"}, {"family": "Unterlass", "given": "Judith E", "initials": "JE"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Karem", "given": "Zhir", "initials": "Z"}, {"family": "Calder\u00f3n-Monta\u00f1o", "given": "Jos\u00e9 Manuel", "initials": "JM"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Edqvist", "given": "Per Henrik", "initials": "PH"}, {"family": "Matuszewski", "given": "Damian J", "initials": "DJ"}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Berntsson", "given": "Ronnie P A", "initials": "RPA"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "Studham", "given": "Matthew", "initials": "M"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P"}, {"family": "Zupan", "given": "Blaz", "initials": "B"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-01642-w", "pmid": "29142246", "labels": {"Protein Science Facility (PSF)": "Service", "BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Drug Discovery and Development": "Collaborative"}, "xrefs": [], "notes": "Biochemical and Cellular Screening", "created": "2017-11-16T10:37:23.396Z", "modified": "2025-10-17T13:05:08.653Z"}, {"entity": "publication", "iuid": "95ae32ed5cf940989a08d370d766bac4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95ae32ed5cf940989a08d370d766bac4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95ae32ed5cf940989a08d370d766bac4"}}, "title": "Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma", "authors": [{"family": "Sun", "given": "Yu", "initials": "Y"}, {"family": "Svedberg", "given": "Jesper", "initials": "J"}, {"family": "Hiltunen", "given": "Markus", "initials": "M"}, {"family": "Corcoran", "given": "P\u00e1draic", "initials": "P"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-01317-6", "pmid": "29074958", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2018-02-09T10:38:01.098Z", "modified": "2020-01-21T13:56:14.867Z"}, {"entity": "publication", "iuid": "f6edb416401d4e0c8654c1e81fba413e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6edb416401d4e0c8654c1e81fba413e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6edb416401d4e0c8654c1e81fba413e"}}, "title": "Microbial mineralization of cellulose in frozen soils.", "authors": [{"family": "Segura", "given": "Javier H", "initials": "JH"}, {"family": "Nilsson", "given": "Mats B", "initials": "MB"}, {"family": "Haei", "given": "Mahsa", "initials": "M"}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Mikkola", "given": "Jyri-Pekka", "initials": "JP"}, {"family": "Gr\u00e4svik", "given": "John", "initials": "J"}, {"family": "Schleucher", "given": "J\u00fcrgen", "initials": "J"}, {"family": "\u00d6quist", "given": "Mats G", "initials": "MG"}], "type": "journal article", "published": "2017-10-27", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "1154", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "High-latitude soils store ~40% of the global soil carbon and experience winters of up to 6 months or more. The winter soil CO2 efflux importantly contributes to the annual CO2 budget. Microorganisms can metabolize short chain carbon compounds in frozen soils. However, soil organic matter (SOM) is dominated by biopolymers, requiring exoenzymatic hydrolysis prior to mineralization. For winter SOM decomposition to have a substantial influence on soil carbon balances it is crucial whether or not biopolymers can be metabolized in frozen soils. We added 13C-labeled cellulose to frozen (-4 \u00b0C) mesocosms of boreal forest soil and followed its decomposition. Here we show that cellulose biopolymers are hydrolyzed under frozen conditions sustaining both CO2 production and microbial growth contributing to slow, but persistent, SOM mineralization. Given the long periods with frozen soils at high latitudes these findings are essential for understanding the contribution from winter to the global carbon balance.", "doi": "10.1038/s41467-017-01230-y", "pmid": "29074961", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-01230-y"}, {"db": "pmc", "key": "PMC5658388"}, {"db": "figshare", "key": "10.6084/m9.figshare.5318932"}], "notes": [], "created": "2017-10-31T12:11:16.407Z", "modified": "2025-10-17T13:03:59.540Z"}, {"entity": "publication", "iuid": "37e3547dbecb415db8dc52713feb0b69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37e3547dbecb415db8dc52713feb0b69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37e3547dbecb415db8dc52713feb0b69"}}, "title": "Efficient protein production by yeast requires global tuning of metabolism.", "authors": [{"family": "Huang", "given": "Mingtao", "initials": "M"}, {"family": "Bao", "given": "Jichen", "initials": "J"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Petranovic", "given": "Dina", "initials": "D"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-10-25", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "1131", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The biotech industry relies on cell factories for production of pharmaceutical proteins, of which several are among the top-selling medicines. There is, therefore, considerable interest in improving the efficiency of protein production by cell factories. Protein secretion involves numerous intracellular processes with many underlying mechanisms still remaining unclear. Here, we use RNA-seq to study the genome-wide transcriptional response to protein secretion in mutant yeast strains. We find that many cellular processes have to be attuned to support efficient protein secretion. In particular, altered energy metabolism resulting in reduced respiration and increased fermentation, as well as balancing of amino-acid biosynthesis and reduced thiamine biosynthesis seem to be particularly important. We confirm our findings by inverse engineering and physiological characterization and show that by tuning metabolism cells are able to efficiently secrete recombinant proteins. Our findings provide increased understanding of which cellular regulations and pathways are associated with efficient protein secretion.", "doi": "10.1038/s41467-017-00999-2", "pmid": "29070809", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-00999-2"}, {"db": "pmc", "key": "PMC5656615"}, {"db": "ENA", "description": "raw RNA-seq", "key": "ERP019558"}], "notes": [], "created": "2017-11-03T16:22:28.292Z", "modified": "2024-01-16T13:48:47.390Z"}, {"entity": "publication", "iuid": "badabce6ebc648ef88ba8754e445e30f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/badabce6ebc648ef88ba8754e445e30f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/badabce6ebc648ef88ba8754e445e30f"}}, "title": "The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus", "authors": [{"family": "Matzov", "given": "Donna", "initials": "D"}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Basu", "given": "Arnab", "initials": "A"}, {"family": "Zimmerman", "given": "Ella", "initials": "E"}, {"family": "Bashan", "given": "Anat", "initials": "A"}, {"family": "Yap", "given": "Mee Ngan F", "initials": "MNF", "orcid": "0000-0003-4213-4050", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2d55604c3f742569d9bf7cb2ad50cdf.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Yonath", "given": "Ada E", "initials": "AE"}], "type": "journal-article", "published": "2017-09-28", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "723", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.", "doi": "10.1038/s41467-017-00753-8", "pmid": "28959035", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5620080"}, {"db": "pii", "key": "10.1038/s41467-017-00753-8"}], "notes": [], "created": "2017-10-16T16:17:43.190Z", "modified": "2023-06-19T08:55:09.375Z"}, {"entity": "publication", "iuid": "8fbff4cafbc24d9294ca916bcd0620e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fbff4cafbc24d9294ca916bcd0620e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fbff4cafbc24d9294ca916bcd0620e2"}}, "title": "Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer.", "authors": [{"family": "Asim", "given": "Mohammad", "initials": "M", "orcid": "0000-0002-2074-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/493226a4e3fd47a88deb79a1a0e82674.json"}}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Zecchini", "given": "Heather I", "initials": "HI"}, {"family": "Sanjiv", "given": "Kumar", "initials": "K"}, {"family": "Gelali", "given": "Eleni", "initials": "E"}, {"family": "Massie", "given": "Charles E", "initials": "CE", "orcid": "0000-0003-2314-4843", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5d5818846044987b78e434586c54357.json"}}, {"family": "Baridi", "given": "Ajoeb", "initials": "A"}, {"family": "Warren", "given": "Anne Y", "initials": "AY"}, {"family": "Zhao", "given": "Wanfeng", "initials": "W"}, {"family": "Ogris", "given": "Christoph", "initials": "C"}, {"family": "McDuffus", "given": "Leigh-Anne", "initials": "LA"}, {"family": "Mascalchi", "given": "Patrice", "initials": "P"}, {"family": "Shaw", "given": "Greg", "initials": "G"}, {"family": "Dev", "given": "Harveer", "initials": "H"}, {"family": "Wadhwa", "given": "Karan", "initials": "K"}, {"family": "Wijnhoven", "given": "Paul", "initials": "P"}, {"family": "Forment", "given": "Josep V", "initials": "JV"}, {"family": "Lyons", "given": "Scott R", "initials": "SR"}, {"family": "Lynch", "given": "Andy G", "initials": "AG"}, {"family": "O'Neill", "given": "Cormac", "initials": "C"}, {"family": "Zecchini", "given": "Vincent R", "initials": "VR"}, {"family": "Rennie", "given": "Paul S", "initials": "PS"}, {"family": "Baniahmad", "given": "Aria", "initials": "A"}, {"family": "Tavar\u00e9", "given": "Simon", "initials": "S"}, {"family": "Mills", "given": "Ian G", "initials": "IG"}, {"family": "Galanty", "given": "Yaron", "initials": "Y"}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Neal", "given": "David", "initials": "D", "orcid": "0000-0002-6033-5086", "researcher": {"href": "https://publications.scilifelab.se/researcher/a32f7c812c7e40a78ee61a43bfa6c9fc.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2017-08-29", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "374", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Emerging data demonstrate homologous recombination (HR) defects in castration-resistant prostate cancers, rendering these tumours sensitive to PARP inhibition. Here we demonstrate a direct requirement for the androgen receptor (AR) to maintain HR gene expression and HR activity in prostate cancer. We show that PARP-mediated repair pathways are upregulated in prostate cancer following androgen-deprivation therapy (ADT). Furthermore, upregulation of PARP activity is essential for the survival of prostate cancer cells and we demonstrate a synthetic lethality between ADT and PARP inhibition in vivo. Our data suggest that ADT can functionally impair HR prior to the development of castration resistance and that, this potentially could be exploited therapeutically using PARP inhibitors in combination with androgen-deprivation therapy upfront in advanced or high-risk prostate cancer.Tumours with homologous recombination (HR) defects become sensitive to PARPi. Here, the authors show that androgen receptor (AR) regulates HR and AR inhibition activates the PARP pathway in vivo, thus inhibition of both AR and PARP is required for effective treatment of high risk prostate cancer.", "doi": "10.1038/s41467-017-00393-y", "pmid": "28851861", "labels": {"Advanced FISH Technologies": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-00393-y"}, {"db": "pmc", "key": "PMC5575038"}], "notes": [], "created": "2020-01-21T12:35:14.244Z", "modified": "2021-07-08T13:01:30.859Z"}, {"entity": "publication", "iuid": "2fc4e31b250e495ca1b009d046c37ce5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fc4e31b250e495ca1b009d046c37ce5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fc4e31b250e495ca1b009d046c37ce5"}}, "title": "Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.", "authors": [{"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Demissie", "given": "Serkalem", "initials": "S"}, {"family": "Hsu", "given": "Yi-Hsiang", "initials": "YH"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Chou", "given": "Wen-Chi", "initials": "WC"}, {"family": "Stolk", "given": "Lisette", "initials": "L"}, {"family": "Livshits", "given": "Gregory", "initials": "G"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Koller", "given": "Daniel L", "initials": "DL"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Malkin", "given": "Ida", "initials": "I"}, {"family": "Ried", "given": "Janina S", "initials": "JS"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Hua Zhao", "given": "Jing", "initials": "J"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Aghdassi", "given": "Ali", "initials": "A"}, {"family": "\u00c5kesson", "given": "Kristina", "initials": "K"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Baier", "given": "Leslie J", "initials": "LJ"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Bennett", "given": "David A", "initials": "DA"}, {"family": "Bertram", "given": "Lars", "initials": "L"}, {"family": "Biffar", "given": "Rainer", "initials": "R"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Buchman", "given": "Aron S", "initials": "AS"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Campos Obanda", "given": "Natalia", "initials": "N"}, {"family": "Cauley", "given": "Jane A", "initials": "JA"}, {"family": "Cawthon", "given": "Peggy M", "initials": "PM"}, {"family": "Cederberg", "given": "Henna", "initials": "H"}, {"family": "Chen", "given": "Zhao", "initials": "Z"}, {"family": "Cho", "given": "Nam H", "initials": "NH"}, {"family": "Jin Choi", "given": "Hyung", "initials": "H"}, {"family": "Claussnitzer", "given": "Melina", "initials": "M"}, {"family": "Collins", "given": "Francis", "initials": "F"}, {"family": "Cummings", "given": "Steven R", "initials": "SR"}, {"family": "De Jager", "given": "Philip L", "initials": "PL"}, {"family": "Demuth", "given": "Ilja", "initials": "I"}, {"family": "Dhonukshe-Rutten", "given": "Rosalie A M", "initials": "RAM"}, {"family": "Diatchenko", "given": "Luda", "initials": "L"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Enneman", "given": "Anke W", "initials": "AW"}, {"family": "Erdos", "given": "Mike", "initials": "M"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Eriksson", "given": "Joel", "initials": "J"}, {"family": "Estrada", "given": "Karol", "initials": "K"}, {"family": "Evans", "given": "Daniel S", "initials": "DS"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Fu", "given": "Mao", "initials": "M"}, {"family": "Garcia", "given": "Melissa", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Girke", "given": "Thomas", "initials": "T"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Grewal", "given": "Jagvir", "initials": "J"}, {"family": "Han", "given": "Bok-Ghee", "initials": "BG"}, {"family": "Hanson", "given": "Robert L", "initials": "RL"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Hoffman", "given": "Eric P", "initials": "EP"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Hsueh", "given": "Wen-Chi", "initials": "WC"}, {"family": "Hubal", "given": "Monica J", "initials": "MJ"}, {"family": "Hubbard", "given": "Alan", "initials": "A"}, {"family": "Huffman", "given": "Kim M", "initials": "KM"}, {"family": "Husted", "given": "Lise B", "initials": "LB"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Ittermann", "given": "Till", "initials": "T"}, {"family": "Jansson", "given": "John-Olov", "initials": "JO"}, {"family": "Jordan", "given": "Joanne M", "initials": "JM"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "Kloth", "given": "Jacqueline S L", "initials": "JSL"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA"}, {"family": "Kraus", "given": "William E", "initials": "WE"}, {"family": "Kritchevsky", "given": "Stephen", "initials": "S"}, {"family": "Kuulasmaa", "given": "Teemu", "initials": "T"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Lang", "given": "Thomas", "initials": "T"}, {"family": "Langdahl", "given": "Bente L", "initials": "BL"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Lee", "given": "Jong-Young", "initials": "JY"}, {"family": "Lerch", "given": "Markus M", "initials": "MM"}, {"family": "Lewis", "given": "Joshua R", "initials": "JR"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Liu", "given": "Tian", "initials": "T"}, {"family": "Liu", "given": "Youfang", "initials": "Y"}, {"family": "Ljunggren", "given": "\u00d6sten", "initials": "\u00d6"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Luben", "given": "Robert N", "initials": "RN"}, {"family": "Maixner", "given": "William", "initials": "W"}, {"family": "McGuigan", "given": "Fiona E", "initials": "FE"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Mellstr\u00f6m", "given": "Dan", "initials": "D"}, {"family": "Melov", "given": "Simon", "initials": "S"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Mosekilde", "given": "Leif", "initials": "L"}, {"family": "Newman", "given": "Anne", "initials": "A"}, {"family": "Nielson", "given": "Carrie M", "initials": "CM"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Orwoll", "given": "Eric S", "initials": "ES"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Parker", "given": "Stephen C J", "initials": "SCJ"}, {"family": "Peacock", "given": "Munro", "initials": "M"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Prince", "given": "Richard L", "initials": "RL"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Ralston", "given": "Stuart H", "initials": "SH"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Robbins", "given": "John A", "initials": "JA"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Satterfield", "given": "Suzanne", "initials": "S"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Schipf", "given": "Sabine", "initials": "S"}, {"family": "Scott", "given": "Laura", "initials": "L"}, {"family": "Sehmi", "given": "Joban", "initials": "J"}, {"family": "Shen", "given": "Jian", "initials": "J"}, {"family": "Soo Shin", "given": "Chan", "initials": "C"}, {"family": "Sigurdsson", "given": "Gunnar", "initials": "G"}, {"family": "Smith", "given": "Shad", "initials": "S"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Stan\u010d\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Steinhagen-Thiessen", "given": "Elisabeth", "initials": "E"}, {"family": "Streeten", "given": "Elizabeth A", "initials": "EA"}, {"family": "Styrkarsdottir", "given": "Unnur", "initials": "U"}, {"family": "Swart", "given": "Karin M A", "initials": "KMA"}, {"family": "Tan", "given": "Sian-Tsung", "initials": "ST"}, {"family": "Tarnopolsky", "given": "Mark A", "initials": "MA"}, {"family": "Thompson", "given": "Patricia", "initials": "P"}, {"family": "Thomson", "given": "Cynthia A", "initials": "CA"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Tranah", "given": "Gregory J", "initials": "GJ"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "van Schoor", "given": "Natasja M", "initials": "NM"}, {"family": "Verma", "given": "Arjun", "initials": "A"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wactawski-Wende", "given": "Jean", "initials": "J"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Weedon", "given": "Michael N", "initials": "MN"}, {"family": "Welch", "given": "Ryan", "initials": "R"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Williams", "given": "Frances M K", "initials": "FMK"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wright", "given": "Nicole C", "initials": "NC"}, {"family": "Xie", "given": "Weijia", "initials": "W"}, {"family": "Yu", "given": "Lei", "initials": "L"}, {"family": "Zhou", "given": "Yanhua", "initials": "Y"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Econs", "given": "Michael J", "initials": "MJ"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Ossowski", "given": "Vicky", "initials": "V"}, {"family": "Waterworth", "given": "Dawn", "initials": "D"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}], "type": "journal article", "published": "2017-07-19", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "80", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 \u00d7 10 -8) or suggestively genome wide (p < 2.3 \u00d7 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.Lean body mass is a highly heritable trait and is associated with various health conditions. Here, Kiel and colleagues perform a meta-analysis of genome-wide association studies for whole body lean body mass and find five novel genetic loci to be significantly associated.", "doi": "10.1038/s41467-017-00031-7", "pmid": "28724990", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-00031-7"}, {"db": "pmc", "key": "PMC5517526"}], "notes": [], "created": "2018-01-09T13:55:56.946Z", "modified": "2021-06-21T14:59:44.927Z"}, {"entity": "publication", "iuid": "c3577bba83a74b17857adfd5789c0771", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3577bba83a74b17857adfd5789c0771.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3577bba83a74b17857adfd5789c0771"}}, "title": "Transancestral mapping and genetic load in systemic lupus erythematosus.", "authors": [{"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Ainsworth", "given": "Hannah C", "initials": "HC"}, {"family": "Cunninghame Graham", "given": "Deborah S", "initials": "DS"}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Comeau", "given": "Mary E", "initials": "ME"}, {"family": "Marion", "given": "Miranda C", "initials": "MC"}, {"family": "Howard", "given": "Timothy D", "initials": "TD"}, {"family": "Ramos", "given": "Paula S", "initials": "PS"}, {"family": "Croker", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0002-6292-4132", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdd33d806494a78901e9f697d49bfe1.json"}}, {"family": "Morris", "given": "David L", "initials": "DL"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Alml\u00f6f", "given": "Jonas Carlsson", "initials": "JC"}, {"family": "Acevedo-V\u00e1squez", "given": "Eduardo M", "initials": "EM"}, {"family": "Alarc\u00f3n", "given": "Graciela S", "initials": "GS"}, {"family": 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"Tushar", "initials": "T"}, {"family": "Oksenberg", "given": "Jorge R", "initials": "JR"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Gregersen", "given": "Peter K", "initials": "PK"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Jacob", "given": "Chaim O", "initials": "CO"}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}, {"family": "Tsao", "given": "Betty P", "initials": "BP"}, {"family": "Schanberg", "given": "Laura E", "initials": "LE"}, {"family": "Behrens", "given": "Timothy W", "initials": "TW"}, {"family": "Silverman", "given": "Earl D", "initials": "ED"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta E", "initials": "ME"}, {"family": "Kimberly", "given": "Robert P", "initials": "RP"}, {"family": "Harley", "given": "John B", "initials": "JB"}, {"family": "Wakeland", "given": "Edward K", "initials": "EK"}, {"family": "Graham", "given": "Robert R", "initials": "RR"}, {"family": "Gaffney", "given": "Patrick M", "initials": "PM"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "16021", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (\u223c50% of these regions have multiple independent associations); these include 24 novel SLE regions (P<5 \u00d7 10-8), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.", "doi": "10.1038/ncomms16021", "pmid": "28714469", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms16021"}, {"db": "pmc", "key": "PMC5520018"}], "notes": [], "created": "2017-10-25T15:18:21.921Z", "modified": "2024-01-16T13:48:47.734Z"}, {"entity": "publication", "iuid": "88adbd607a954e539fe5a35a01aba19a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88adbd607a954e539fe5a35a01aba19a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88adbd607a954e539fe5a35a01aba19a"}}, "title": "Genetic loci associated with heart rate variability and their effects on cardiac disease risk.", "authors": 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{"family": "Avery", "given": "Christy L", "initials": "CL"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Dierckx", "given": "Bram", "initials": "B"}, {"family": "van Dongen", "given": "Jenny", "initials": "J"}, {"family": "Gogarten", "given": "Stephanie M", "initials": "SM"}, {"family": "Goyette", "given": "Philippe", "initials": "P"}, {"family": "Hernesniemi", "given": "Jussi", "initials": "J"}, {"family": "Huikari", "given": "Ville", "initials": "V"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Jaju", "given": "Deepali", "initials": "D"}, {"family": "Kerr", "given": "Kathleen F", "initials": "KF"}, {"family": "Kluttig", "given": "Alexander", "initials": "A"}, {"family": "Krijthe", "given": "Bouwe P", "initials": "BP"}, {"family": "Kumar", "given": "Jitender", "initials": "J"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW", "orcid": "0000-0001-6888-1404", "researcher": {"href": 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"initials": "MF"}, {"family": "Siscovick", "given": "David", "initials": "D"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Soliman", "given": "Elsayed Z", "initials": "EZ", "orcid": "0000-0001-5632-8150", "researcher": {"href": "https://publications.scilifelab.se/researcher/96e79156ff664c509217e8834a728c79.json"}}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Staessen", "given": "Jan A", "initials": "JA"}, {"family": "Stein", "given": "Phyllis K", "initials": "PK"}, {"family": "Stilp", "given": "Adrienne M", "initials": "AM"}, {"family": "Stolarz-Skrzypek", "given": "Katarzyna", "initials": "K"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Swenne", "given": "Cees A", "initials": "CA"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": 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"initials": "BH"}, {"family": "Tiemeier", "given": "Henning", "initials": "H", "orcid": "0000-0002-4395-1397", "researcher": {"href": "https://publications.scilifelab.se/researcher/73e05bd74af344ba8d963463f49bb242.json"}}, {"family": "Vrijkotte", "given": "Tanja G M", "initials": "TGM"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW", "orcid": "0000-0002-1692-8669", "researcher": {"href": "https://publications.scilifelab.se/researcher/7037429ef1304bdaabd837d242b1e6f5.json"}}, {"family": "Brundel", "given": "Bianca J J M", "initials": "BJJM"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Whitsel", "given": "Eric A", "initials": "EA"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}], "type": "journal article", "published": "2017-06-14", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "15805", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Reduced cardiac vagal control reflected in low heart rate variability (HRV) is associated with greater risks for cardiac morbidity and mortality. In two-stage meta-analyses of genome-wide association studies for three HRV traits in up to 53,174 individuals of European ancestry, we detect 17 genome-wide significant SNPs in eight loci. HRV SNPs tag non-synonymous SNPs (in NDUFA11 and KIAA1755), expression quantitative trait loci (eQTLs) (influencing GNG11, RGS6 and NEO1), or are located in genes preferentially expressed in the sinoatrial node (GNG11, RGS6 and HCN4). Genetic risk scores account for 0.9 to 2.6% of the HRV variance. Significant genetic correlation is found for HRV with heart rate (-0.74<rg<-0.55) and blood pressure (-0.35<rg<-0.20). These findings provide clinically relevant biological insight into heritable variation in vagal heart rhythm regulation, with a key role for genetic variants (GNG11, RGS6) that influence G-protein heterotrimer action in GIRK-channel induced pacemaker membrane hyperpolarization.", "doi": "10.1038/ncomms15805", "pmid": "28613276", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms15805"}, {"db": "pmc", "key": "PMC5474732"}], "notes": [], "created": "2017-10-25T15:27:47.158Z", "modified": "2024-01-16T13:48:47.870Z"}, {"entity": "publication", "iuid": "dfc6452e87c54ae4a5a175da905f3a44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfc6452e87c54ae4a5a175da905f3a44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfc6452e87c54ae4a5a175da905f3a44"}}, "title": "Expression of CD226 is associated to but not required for NK cell education.", "authors": [{"family": "Wagner", "given": "Arnika K", "initials": "AK"}, {"family": "Kadri", "given": "Nadir", "initials": "N"}, {"family": "Sn\u00e4ll", "given": "Johanna", "initials": "J"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Gilfillan", "given": "Susan", "initials": "S"}, {"family": "Colonna", "given": "Marco", "initials": "M"}, {"family": "Bernhardt", "given": "G\u00fcnter", "initials": "G"}, {"family": "H\u00f6glund", "given": "Petter", "initials": "P"}, {"family": "K\u00e4rre", "given": "Klas", "initials": "K"}, {"family": "Chambers", "given": "Benedict J", "initials": "BJ"}], "type": "journal article", "published": "2017-05-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "8", "issue": null, "pages": "15627"}, "abstract": "DNAX accessory molecule-1 (DNAM-1, also known as CD226) is an activating receptor expressed on subsets of natural killer (NK) and T cells, interacts with its ligands CD155 or CD112, and has co-varied expression with inhibitory receptors. Since inhibitory receptors control NK-cell activation and are necessary for MHC-I-dependent education, we investigated whether DNAM-1 expression is also involved in NK-cell education. Here we show an MHC-I-dependent correlation between DNAM-1 expression and NK-cell education, and an association between DNAM-1 and NKG2A that occurs even in MHC class I deficient mice. DNAM-1 is expressed early during NK-cell development, precedes the expression of MHC-I-specific inhibitory receptors, and is modulated in an education-dependent fashion. Cd226-/- mice have missing self-responses and NK cells with a normal receptor repertoire. We propose a model in which NK-cell education prevents or delays downregulation of DNAM-1. This molecule endows educated NK cells with enhanced effector functions but is dispensable for education.", "doi": "10.1038/ncomms15627", "pmid": "28561023", "labels": {"Cellular Immunomonitoring": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms15627"}, {"db": "pmc", "key": "PMC5460037"}], "notes": [], "created": "2019-03-25T19:57:01.145Z", "modified": "2023-11-28T12:54:23.964Z"}, {"entity": "publication", "iuid": "307148582507404896332168f5379674", "links": {"self": {"href": "https://publications.scilifelab.se/publication/307148582507404896332168f5379674.json"}, "display": {"href": "https://publications.scilifelab.se/publication/307148582507404896332168f5379674"}}, "title": "Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits", "authors": [{"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Feitosa", "given": "Mary F", "initials": 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"initials": "A"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Wu", "given": "Joseph", "initials": "J"}, {"family": "Qi", "given": "Qibin", "initials": "Q"}, {"family": "Ahmad", "given": "Shafqat", "initials": "S"}, {"family": "Alfred", "given": "Tamuno", "initials": "T"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Bonnefond", "given": "Amelie", "initials": "A"}, {"family": "Bragg", "given": "Jennifer", "initials": "J"}, {"family": "Cadby", "given": "Gemma", "initials": "G"}, {"family": "Chittani", "given": "Martina", "initials": "M"}, {"family": "Coggeshall", "given": "Scott", "initials": "S"}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Direk", "given": "Nese", "initials": "N"}, {"family": "Eriksson", "given": "Joel", "initials": "J"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Neergaard Harder", "given": "Marie", "initials": "M"}, {"family": "Horikoshi", "given": "Momoko", "initials": "M"}, {"family": "Huang", "given": "Tao", "initials": "T"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Justesen", "given": "Johanne Marie", "initials": "JM"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Kinnunen", "given": "Leena", "initials": "L"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Komulainen", "given": "Pirjo", "initials": "P"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Lim", "given": "Unhee", "initials": "U"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Lyytik\u00e4inen", "given": "Leo Pekka", "initials": "LP"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Middelberg", "given": "Rita P S", "initials": "RPS"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "P\u00e9russe", "given": "Louis", "initials": "L"}, {"family": "Pervjakova", "given": "Natalia", "initials": "N"}, {"family": "Sarti", "given": "Cinzia", "initials": "C"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Stan\u010d\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Sung", "given": "Yun Ju", "initials": "YJ"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Vedantam", "given": "Sailaja L", "initials": "SL"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Vink", "given": "Jacqueline M", "initials": "JM"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Yengo", "given": "Loic", "initials": "L"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Hua Zhao", "given": "Jing", "initials": "J"}, {"family": "Zimmermann", "given": "Martina E", "initials": "ME"}, {"family": "Zubair", "given": "Niha", "initials": "N"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Adair", "given": "Linda S", "initials": "LS"}, {"family": "Afaq", "given": "Saima", "initials": "S"}, {"family": 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"FS"}, {"family": "Curran", "given": "Joanne E", "initials": "JE"}, {"family": "de Borst", "given": "Gert J", "initials": "GJ"}, {"family": "de Craen", "given": "Anton J M", "initials": "AJM"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "den Ruijter", "given": "Hester M", "initials": "HM"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Eriksson", "given": "Anna L", "initials": "AL"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Forrester", "given": "Terrence", "initials": "T"}, {"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Glorioso", "given": "Nicola", "initials": "N"}, {"family": "Gong", 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"M"}, {"family": "Holmen", "given": "Oddgeir L", "initials": "OL"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Jan Hottenga", "given": "Jouke", "initials": "J"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Hung", "given": "Joseph", "initials": "J"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "James", "given": "Alan L", "initials": "AL"}, {"family": "Jansson", "given": "John Olov", "initials": "JO"}, {"family": "Jarvelin", "given": "Marjo Riitta", "initials": "MR"}, {"family": "Jhun", "given": "Min A", "initials": "MA"}, {"family": "J\u00f8rgensen", "given": "Marit E", "initials": "ME"}, {"family": "Juonala", "given": "Markus", "initials": "M"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Kolovou", "given": "Genovefa", "initials": "G"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Kval\u00f8y", "given": "Kirsti", "initials": "K"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Lee", "given": "Nanette R", "initials": "NR"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Lobbens", "given": "Stephane", "initials": "S"}, {"family": "Loh", "given": "Marie", "initials": "M"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Luben", "given": "Robert", "initials": "R"}, {"family": "Lubke", "given": "Gitta", "initials": "G"}, {"family": "Ludolph-Donislawski", "given": "Anja", "initials": "A"}, {"family": "Lupoli", "given": "Sara", "initials": "S"}, {"family": "Madden", "given": "Pamela A F", "initials": "PAF"}, {"family": "M\u00e4nnikk\u00f6", "given": "Reija", "initials": "R"}, {"family": "Marques-Vidal", "given": "Pedro", "initials": "P"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "McKenzie", "given": "Colin A", "initials": "CA"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Mellstr\u00f6m", "given": "Dan", "initials": "D"}, {"family": "Menni", "given": "Cristina", "initials": "C"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Musk", "given": "AW (Bill)", "initials": "A("}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "Nauck", "given": "Matthias", 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{"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BHR"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Bouchard", "given": "Claude", "initials": "C"}, {"family": "Bruinenberg", "given": "Marcel", "initials": "M"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chen", "given": "Yii DerIda", "initials": "YD"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Cooper", "given": "Richard S", "initials": "RS"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Faire", "given": "Ulf de", "initials": "Ud"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Gordon-Larsen", "given": "Penny", "initials": "P"}, {"family": "Grabe", "given": "Hans J\u00f6rgen", "initials": "HJ"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Haiman", "given": "Christopher A", "initials": "CA"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Wouter Jukema", "given": "J", "initials": "J"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Marchand", "given": "Loic Le", "initials": "LL"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Pasterkamp", "given": "Gerard", "initials": "G"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Peters", "given": "Ulrike", "initials": "U"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Vestergaard", "given": "Henrik", "initials": "H"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Tyrrell", "given": "Jessica", "initials": "J"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Deloukas", "given": "Panagiotis", "initials": "P"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Hunter", "given": "David J", "initials": "DJ"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Marchini", "given": "Jonathan", "initials": "J"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Liu", "given": "Ching Ti", "initials": "CT"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}], "type": "journal-article", "published": "2017-04-26", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "14977", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/ncomms14977", "pmid": "28443625", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:33.062Z", "modified": "2020-01-21T13:56:11.704Z"}, {"entity": "publication", "iuid": "ce4c21c5846e448796cea17aa113b78f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce4c21c5846e448796cea17aa113b78f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce4c21c5846e448796cea17aa113b78f"}}, "title": "Light-sensing via hydrogen peroxide and a peroxiredoxin.", "authors": [{"family": "Bodvard", "given": "Kristofer", "initials": "K"}, {"family": "Peeters", "given": "Ken", "initials": "K"}, {"family": "Roger", "given": "Friederike", "initials": "F"}, {"family": "Romanov", "given": "Natalie", "initials": "N"}, {"family": "Igbaria", "given": "Aeid", "initials": "A"}, {"family": "Welkenhuysen", "given": "Niek", "initials": "N"}, {"family": "Palais", "given": "Ga\u00ebl", "initials": "G"}, {"family": "Reiter", "given": "Wolfgang", "initials": "W"}, {"family": "Toledano", "given": "Michel B", "initials": "MB"}, {"family": "K\u00e4ll", "given": "Mikael", "initials": "M"}, {"family": "Molin", "given": "Mikael", "initials": "M", "orcid": "0000-0002-3903-8503", "researcher": {"href": "https://publications.scilifelab.se/researcher/12e9dc11d1b047d88913ea3bcb2694be.json"}}], "type": "journal article", "published": "2017-03-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "8", "issue": "1", "pages": "14791", "issn-l": "2041-1723"}, "abstract": "Yeast lacks dedicated photoreceptors; however, blue light still causes pronounced oscillations of the transcription factor Msn2 into and out of the nucleus. Here we show that this poorly understood phenomenon is initiated by a peroxisomal oxidase, which converts light into a hydrogen peroxide (H 2O2) signal that is sensed by the peroxiredoxin Tsa1 and transduced to thioredoxin, to counteract PKA-dependent Msn2 phosphorylation. Upon H2O2, the nuclear retention of PKA catalytic subunits, which contributes to delayed Msn2 nuclear concentration, is antagonized in a Tsa1-dependent manner. Conversely, peroxiredoxin hyperoxidation interrupts the H2O2 signal and drives Msn2 oscillations by superimposing on PKA feedback regulation. Our data identify a mechanism by which light could be sensed in all cells lacking dedicated photoreceptors. In particular, the use of H2O2 as a second messenger in signalling is common to Msn2 oscillations and to light-induced entrainment of circadian rhythms and suggests conserved roles for peroxiredoxins in endogenous rhythms.", "doi": "10.1038/ncomms14791", "pmid": "28337980", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms14791"}, {"db": "pmc", "key": "PMC5376668"}], "notes": [], "created": "2020-01-23T16:34:25.369Z", "modified": "2021-06-21T15:40:28.799Z"}, {"entity": "publication", "iuid": "f5376f721608439b957f4647da281e62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5376f721608439b957f4647da281e62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5376f721608439b957f4647da281e62"}}, "title": "Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration", "authors": [{"family": "Sun", "given": "Xiaohuan", "initials": "X"}, {"family": "Cahill", "given": "James", "initials": "J"}, {"family": "Van Hautegem", "given": "Tom", "initials": "T"}, {"family": "Feys", "given": "Kim", "initials": "K"}, {"family": "Whipple", "given": "Clinton", "initials": "C"}, {"family": "Nov\u00e1k", "given": "Ondrej", "initials": "O"}, {"family": "Delbare", "given": "Sofie", "initials": "S"}, {"family": "Versteele", "given": "Charlot", "initials": "C"}, {"family": "Demuynck", "given": "Kirin", "initials": "K"}, {"family": "De Block", "given": "Jolien", "initials": "J"}, {"family": "Storme", "given": "Veronique", "initials": "V"}, {"family": "Claeys", "given": "Hannes", "initials": "H"}, {"family": "Van Lijsebettens", "given": "Mieke", "initials": "M"}, {"family": "Coussens", "given": "Griet", "initials": "G"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "De Vliegher", "given": "Alex", "initials": "A"}, {"family": "Muszynski", "given": "Michael", "initials": "M"}, {"family": "Inz\u00e9", "given": "Dirk", "initials": "D"}, {"family": "Nelissen", "given": "Hilde", "initials": "H"}], "type": "journal-article", "published": "2017-03-16", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "14752", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/ncomms14752", "pmid": "28300078", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:35:22.230Z", "modified": "2025-10-17T13:03:19.001Z"}, {"entity": "publication", "iuid": "29c7f4009ca84ed19064680dc486ca73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29c7f4009ca84ed19064680dc486ca73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29c7f4009ca84ed19064680dc486ca73"}}, "title": "Clonal reversal of ageing-associated stem cell lineage bias via a pluripotent intermediate.", "authors": [{"family": "Wahlestedt", "given": "Martin", "initials": "M"}, {"family": "Erlandsson", "given": "Eva", "initials": "E"}, {"family": "Kristiansen", "given": "Trine", "initials": "T"}, {"family": "Lu", "given": "Rong", "initials": "R"}, {"family": "Brakebusch", "given": "Cord", "initials": "C"}, {"family": "Weissman", "given": "Irving L", "initials": "IL"}, {"family": "Yuan", "given": "Joan", "initials": "J"}, {"family": "Martin-Gonzalez", "given": "Javier", "initials": "J"}, {"family": "Bryder", "given": "David", "initials": "D"}], "type": "journal article", "published": "2017-02-22", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "14533", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Ageing associates with significant alterations in somatic/adult stem cells and therapies to counteract these might have profound benefits for health. In the blood, haematopoietic stem cell (HSC) ageing is linked to several functional shortcomings. However, besides the recent realization that individual HSCs might be preset differentially already from young age, HSCs might also age asynchronously. Evaluating the prospects for HSC rejuvenation therefore ultimately requires approaching those HSCs that are functionally affected by age. Here we combine genetic barcoding of aged murine HSCs with the generation of induced pluripotent stem (iPS) cells. This allows us to specifically focus on aged HSCs presenting with a pronounced lineage skewing, a hallmark of HSC ageing. Functional and molecular evaluations reveal haematopoiesis from these iPS clones to be indistinguishable from that associating with young mice. Our data thereby provide direct support to the notion that several key functional attributes of HSC ageing can be reversed.", "doi": "10.1038/ncomms14533", "pmid": "28224997", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms14533"}, {"db": "pmc", "key": "PMC5322498"}], "notes": [], "created": "2017-10-17T09:41:51.769Z", "modified": "2024-01-16T13:48:48.396Z"}, {"entity": "publication", "iuid": "f38b315a15584e4396559e01b8376b10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f38b315a15584e4396559e01b8376b10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f38b315a15584e4396559e01b8376b10"}}, "title": "Novel genetic loci associated with hippocampal volume.", "authors": [{"family": "Hibar", "given": "Derrek P", "initials": "DP"}, {"family": "Adams", "given": "Hieab H H", "initials": "HH"}, {"family": "Jahanshad", "given": "Neda", "initials": "N"}, {"family": "Chauhan", "given": "Ganesh", "initials": "G"}, {"family": "Stein", "given": "Jason L", "initials": "JL"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Renteria", "given": "Miguel E", "initials": "ME"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Arias-Vasquez", "given": "Alejandro", "initials": "A"}, {"family": "Ikram", "given": "M Kamran", "initials": "MK"}, {"family": "Desrivi\u00e8res", "given": "Sylvane", "initials": "S"}, {"family": "Vernooij", "given": "Meike W", "initials": "MW"}, {"family": "Abramovic", "given": "Lucija", "initials": "L"}, {"family": "Alhusaini", "given": "Saud", "initials": "S"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Andersson", "given": "Micael", "initials": "M"}, {"family": "Arfanakis", "given": "Konstantinos", "initials": "K"}, {"family": "Aribisala", "given": "Benjamin S", "initials": "BS"}, {"family": "Armstrong", "given": "Nicola J", "initials": "NJ"}, {"family": "Athanasiu", "given": "Lavinia", "initials": "L"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Beecham", "given": "Ashley H", "initials": "AH"}, {"family": "Beiser", "given": "Alexa", "initials": "A"}, {"family": "Bernard", "given": "Manon", "initials": "M"}, {"family": "Blanton", "given": "Susan H", "initials": "SH"}, {"family": "Bohlken", "given": "Marc M", "initials": "MM"}, {"family": "Boks", "given": "Marco P", "initials": "MP"}, {"family": "Bralten", "given": "Janita", "initials": "J"}, {"family": "Brickman", "given": "Adam M", "initials": "AM"}, {"family": "Carmichael", "given": "Owen", "initials": "O"}, {"family": "Chakravarty", "given": "M Mallar", "initials": "MM"}, {"family": "Chen", "given": "Qiang", "initials": "Q"}, {"family": "Ching", "given": "Christopher R K", "initials": "CR"}, {"family": "Chouraki", "given": "Vincent", "initials": "V"}, {"family": "Cuellar-Partida", "given": "Gabriel", "initials": "G"}, {"family": "Crivello", "given": "Fabrice", "initials": "F"}, {"family": "Den Braber", "given": "Anouk", "initials": "A"}, {"family": "Doan", "given": "Nhat Trung", "initials": "NT"}, {"family": "Ehrlich", "given": "Stefan", "initials": "S"}, {"family": "Giddaluru", "given": "Sudheer", "initials": "S"}, {"family": "Goldman", "given": "Aaron L", "initials": "AL"}, {"family": "Gottesman", "given": "Rebecca F", "initials": "RF"}, {"family": "Grimm", "given": "Oliver", "initials": "O"}, {"family": "Griswold", "given": "Michael E", "initials": "ME"}, {"family": "Guadalupe", "given": "Tulio", "initials": "T"}, {"family": "Gutman", "given": "Boris A", "initials": "BA"}, {"family": "Hass", "given": "Johanna", "initials": "J"}, {"family": "Haukvik", "given": "Unn K", "initials": "UK"}, {"family": "Hoehn", "given": "David", "initials": "D"}, {"family": "Holmes", "given": "Avram J", "initials": "AJ"}, {"family": "Hoogman", "given": "Martine", "initials": "M"}, {"family": "Janowitz", "given": "Deborah", "initials": "D"}, {"family": "Jia", "given": "Tianye", "initials": "T"}, {"family": "J\u00f8rgensen", "given": "Kjetil N", "initials": "KN"}, {"family": "Karbalai", "given": "Nazanin", "initials": "N"}, {"family": "Kasperaviciute", "given": "Dalia", "initials": "D"}, {"family": "Kim", "given": "Sungeun", "initials": "S"}, {"family": "Klein", "given": "Marieke", "initials": "M"}, {"family": "Kraemer", "given": "Bernd", "initials": "B"}, {"family": "Lee", "given": "Phil H", "initials": "PH"}, {"family": "Liewald", "given": "David C M", "initials": "DC"}, {"family": "Lopez", "given": "Lorna M", "initials": "LM"}, {"family": "Luciano", "given": "Michelle", "initials": "M"}, {"family": "Macare", "given": "Christine", "initials": "C"}, {"family": "Marquand", "given": "Andre F", "initials": "AF"}, {"family": "Matarin", "given": "Mar", "initials": "M"}, {"family": "Mather", "given": "Karen A", "initials": "KA"}, {"family": "Mattheisen", "given": "Manuel", "initials": "M"}, {"family": "McKay", "given": "David R", "initials": "DR"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Mu\u00f1oz Maniega", "given": "Susana", "initials": "S"}, {"family": "Nho", "given": "Kwangsik", "initials": "K"}, {"family": "Nugent", "given": "Allison C", "initials": "AC"}, {"family": "Nyquist", "given": "Paul", "initials": "P"}, {"family": "Loohuis", "given": "Loes M Olde", "initials": "LM"}, {"family": "Oosterlaan", "given": "Jaap", "initials": "J"}, {"family": "Papmeyer", "given": "Martina", "initials": "M"}, {"family": "Pirpamer", "given": "Lukas", "initials": "L"}, {"family": "P\u00fctz", "given": "Benno", "initials": "B"}, {"family": "Ramasamy", "given": "Adaikalavan", "initials": "A"}, {"family": "Richards", "given": "Jennifer S", "initials": "JS"}, {"family": "Risacher", "given": "Shannon L", "initials": "SL"}, {"family": "Roiz-Santia\u00f1ez", "given": "Roberto", "initials": "R"}, {"family": "Rommelse", "given": "Nanda", "initials": "N"}, {"family": "Ropele", "given": "Stefan", "initials": "S"}, {"family": "Rose", "given": "Emma J", "initials": "EJ"}, {"family": "Royle", "given": "Natalie A", "initials": "NA"}, {"family": "Rundek", "given": "Tatjana", "initials": "T"}, {"family": "S\u00e4mann", "given": "Philipp G", "initials": "PG"}, {"family": "Saremi", "given": "Arvin", "initials": "A"}, {"family": "Satizabal", "given": "Claudia L", "initials": "CL"}, {"family": "Schmaal", "given": "Lianne", "initials": "L"}, {"family": "Schork", "given": "Andrew J", "initials": "AJ"}, {"family": "Shen", "given": "Li", "initials": "L"}, {"family": "Shin", "given": "Jean", "initials": "J"}, {"family": "Shumskaya", "given": "Elena", "initials": "E"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Sprooten", "given": "Emma", "initials": "E"}, {"family": "Strike", "given": "Lachlan T", "initials": "LT"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Tordesillas-Gutierrez", "given": "Diana", "initials": "D"}, {"family": "Toro", "given": "Roberto", "initials": "R"}, {"family": "Trabzuni", "given": "Daniah", "initials": "D"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Vaidya", "given": "Dhananjay", "initials": "D"}, {"family": "Van der Grond", "given": "Jeroen", "initials": "J"}, {"family": "Van der Lee", "given": "Sven J", "initials": "SJ"}, {"family": "Van der Meer", "given": "Dennis", "initials": "D"}, {"family": "Van Donkelaar", "given": "Marjolein M J", "initials": "MM"}, {"family": "Van Eijk", "given": "Kristel R", "initials": "KR"}, {"family": "Van Erp", "given": "Theo G M", "initials": "TG"}, {"family": "Van Rooij", "given": "Daan", "initials": "D"}, {"family": "Walton", "given": "Esther", "initials": "E"}, {"family": "Westlye", "given": "Lars T", "initials": "LT"}, {"family": "Whelan", "given": "Christopher D", "initials": "CD"}, {"family": "Windham", "given": "Beverly G", "initials": "BG"}, {"family": "Winkler", "given": "Anderson M", "initials": "AM"}, {"family": "Wittfeld", "given": "Katharina", "initials": "K"}, {"family": "Woldehawariat", "given": "Girma", "initials": "G"}, {"family": "Wolf", "given": "Christiane", "initials": "C"}, {"family": "Wolfers", "given": "Thomas", "initials": "T"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR"}, {"family": "Yang", "given": "Jingyun", "initials": "J"}, {"family": "Zijdenbos", "given": "Alex", "initials": "A"}, {"family": "Zwiers", "given": "Marcel P", "initials": "MP"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Almasy", "given": "Laura", "initials": "L"}, {"family": "Ames", "given": "David", "initials": "D"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Arepalli", "given": "Sampath", "initials": "S"}, {"family": "Assareh", "given": "Amelia A", "initials": "AA"}, {"family": "Barral", "given": "Sandra", "initials": "S"}, {"family": "Bastin", "given": "Mark E", "initials": "ME"}, {"family": "Becker", "given": "Diane M", "initials": "DM"}, {"family": "Becker", "given": "James T", "initials": "JT"}, {"family": "Bennett", "given": "David A", "initials": "DA"}, {"family": "Blangero", "given": "John", "initials": "J"}, {"family": "van Bokhoven", "given": "Hans", "initials": "H"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Brodaty", "given": "Henry", "initials": "H"}, {"family": "Brouwer", "given": "Rachel M", "initials": "RM"}, {"family": "Brunner", "given": "Han G", "initials": "HG"}, {"family": "Buckner", "given": "Randy L", "initials": "RL"}, {"family": "Buitelaar", "given": "Jan K", "initials": "JK"}, {"family": "Bulayeva", "given": "Kazima B", "initials": "KB"}, {"family": "Cahn", "given": "Wiepke", "initials": "W"}, {"family": "Calhoun", "given": "Vince D", "initials": "VD"}, {"family": "Cannon", "given": "Dara M", "initials": "DM"}, {"family": "Cavalleri", "given": "Gianpiero L", "initials": "GL"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Cichon", "given": "Sven", "initials": "S"}, {"family": "Cookson", "given": "Mark R", "initials": "MR"}, {"family": "Corvin", "given": "Aiden", "initials": "A"}, {"family": "Crespo-Facorro", "given": "Benedicto", "initials": "B"}, {"family": "Curran", "given": "Joanne E", "initials": "JE"}, {"family": "Czisch", "given": "Michael", "initials": "M"}, {"family": "Dale", "given": "Anders M", "initials": "AM"}, {"family": "Davies", "given": "Gareth E", "initials": "GE"}, {"family": "De Craen", "given": "Anton J M", "initials": "AJ"}, {"family": "De Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "De Jager", "given": "Philip L", "initials": "PL"}, {"family": "De Zubicaray", "given": "Greig I", "initials": "GI"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Debette", "given": "St\u00e9phanie", "initials": "S"}, {"family": "DeCarli", "given": "Charles", "initials": "C"}, {"family": "Delanty", "given": "Norman", "initials": "N"}, {"family": "Depondt", "given": "Chantal", "initials": "C"}, {"family": "DeStefano", "given": "Anita", "initials": "A"}, {"family": "Dillman", "given": "Allissa", "initials": "A"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Donohoe", "given": "Gary", "initials": "G"}, {"family": "Drevets", "given": "Wayne C", "initials": "WC"}, {"family": "Duggirala", "given": "Ravi", "initials": "R"}, {"family": "Dyer", "given": "Thomas D", "initials": "TD"}, {"family": "Enzinger", "given": "Christian", "initials": "C"}, {"family": "Erk", "given": "Susanne", "initials": "S"}, {"family": "Espeseth", "given": "Thomas", "initials": "T"}, {"family": "Fedko", "given": "Iryna O", "initials": "IO"}, {"family": "Fern\u00e1ndez", "given": "Guill\u00e9n", "initials": "G"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Fisher", "given": "Simon E", "initials": "SE"}, {"family": "Fleischman", "given": "Debra A", "initials": "DA"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Foroud", "given": "Tatiana M", "initials": "TM"}, {"family": "Fox", "given": "Peter T", "initials": "PT"}, {"family": "Francks", "given": "Clyde", "initials": "C"}, {"family": "Fukunaga", "given": "Masaki", "initials": "M"}, {"family": "Gibbs", "given": "J Raphael", "initials": "JR"}, {"family": "Glahn", "given": "David C", "initials": "DC"}, {"family": "Gollub", "given": "Randy L", "initials": "RL"}, {"family": "G\u00f6ring", "given": "Harald H H", "initials": "HH"}, {"family": "Green", "given": "Robert C", "initials": "RC"}, {"family": "Gruber", "given": "Oliver", "initials": "O"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Guelfi", "given": "Sebastian", "initials": "S"}, {"family": "H\u00e5berg", "given": "Asta K", "initials": "AK"}, {"family": "Hansell", "given": "Narelle K", "initials": "NK"}, {"family": "Hardy", "given": "John", "initials": "J"}, {"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Hashimoto", "given": "Ryota", "initials": "R"}, {"family": "Hegenscheid", "given": "Katrin", "initials": "K"}, {"family": "Heinz", "given": "Andreas", "initials": "A"}, {"family": "Le Hellard", "given": "Stephanie", "initials": "S"}, {"family": "Hernandez", "given": "Dena G", "initials": "DG"}, {"family": "Heslenfeld", "given": "Dirk J", "initials": "DJ"}, {"family": "Ho", "given": "Beng-Choon", "initials": "BC"}, {"family": "Hoekstra", "given": "Pieter J", "initials": "PJ"}, {"family": "Hoffmann", "given": "Wolfgang", "initials": "W"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Holsboer", "given": "Florian", "initials": "F"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Hosten", "given": "Norbert", "initials": "N"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Huentelman", "given": "Matthew", "initials": "M"}, {"family": "Pol", "given": "Hilleke E Hulshoff", "initials": "HE"}, {"family": "Ikeda", "given": "Masashi", "initials": "M"}, {"family": "Jack", "given": "Clifford R", "initials": "CR"}, {"family": "Jenkinson", "given": "Mark", "initials": "M"}, {"family": "Johnson", "given": "Robert", "initials": "R"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Kahn", "given": "Ren\u00e9 S", "initials": "RS"}, {"family": "Kanai", "given": "Ryota", "initials": "R"}, {"family": "Kloszewska", "given": "Iwona", "initials": "I"}, {"family": "Knopman", "given": "David S", "initials": "DS"}, {"family": "Kochunov", "given": "Peter", "initials": "P"}, {"family": "Kwok", "given": "John B", "initials": "JB"}, {"family": "Lawrie", "given": "Stephen M", "initials": "SM"}, {"family": "Lema\u00eetre", "given": "Herv\u00e9", "initials": "H"}, {"family": "Liu", "given": "Xinmin", "initials": "X"}, {"family": "Longo", "given": "Dan L", "initials": "DL"}, {"family": "Lopez", "given": "Oscar L", "initials": "OL"}, {"family": "Lovestone", "given": "Simon", "initials": "S"}, {"family": "Martinez", "given": "Oliver", "initials": "O"}, {"family": "Martinot", "given": "Jean-Luc", "initials": "JL"}, {"family": "Mattay", "given": "Venkata S", "initials": "VS"}, {"family": "McDonald", "given": "Colm", "initials": "C"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "McMahon", "given": "Francis J", "initials": "FJ"}, {"family": "McMahon", "given": "Katie L", "initials": "KL"}, {"family": "Mecocci", "given": "Patrizia", "initials": "P"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Meyer-Lindenberg", "given": "Andreas", "initials": "A"}, {"family": "Mohnke", "given": "Sebastian", "initials": "S"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Morris", "given": "Derek W", "initials": "DW"}, {"family": "Mosley", "given": "Thomas H", "initials": "TH"}, {"family": "M\u00fchleisen", "given": "Thomas W", "initials": "TW"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Nalls", "given": "Michael A", "initials": "MA"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Nichols", "given": "Thomas E", "initials": "TE"}, {"family": "Niessen", "given": "Wiro J", "initials": "WJ"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Nyberg", "given": "Lars", "initials": "L"}, {"family": "Ohi", "given": "Kazutaka", "initials": "K"}, {"family": "Olvera", "given": "Rene L", "initials": "RL"}, {"family": "Ophoff", "given": "Roel A", "initials": "RA"}, {"family": "Pandolfo", "given": "Massimo", "initials": "M"}, {"family": "Paus", "given": "Tomas", "initials": "T"}, {"family": "Pausova", "given": "Zdenka", "initials": "Z"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BW"}, {"family": "Pike", "given": "G Bruce", "initials": "GB"}, {"family": "Potkin", "given": "Steven G", "initials": "SG"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Reppermund", "given": "Simone", "initials": "S"}, {"family": "Rietschel", "given": "Marcella", "initials": "M"}, {"family": "Roffman", "given": "Joshua L", "initials": "JL"}, {"family": "Romanczuk-Seiferth", "given": "Nina", "initials": "N"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Ryten", "given": "Mina", "initials": "M"}, {"family": "Sacco", "given": "Ralph L", "initials": "RL"}, {"family": "Sachdev", "given": "Perminder S", "initials": "PS"}, {"family": "Saykin", "given": "Andrew J", "initials": "AJ"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schofield", "given": "Peter R", "initials": "PR"}, {"family": "Sigursson", "given": "Sigurdur", "initials": "S"}, {"family": "Simmons", "given": "Andrew", "initials": "A"}, {"family": "Singleton", "given": "Andrew", "initials": "A"}, {"family": "Sisodiya", "given": "Sanjay M", "initials": "SM"}, {"family": "Smith", "given": "Colin", "initials": "C"}, {"family": "Smoller", "given": "Jordan W", "initials": "JW"}, {"family": "Soininen", "given": "Hilkka", "initials": "H"}, {"family": "Steen", "given": "Vidar M", "initials": "VM"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Sussmann", "given": "Jessika E", "initials": "JE"}, {"family": "Thalamuthu", "given": "Anbupalam", "initials": "A"}, {"family": "Toga", "given": "Arthur W", "initials": "AW"}, {"family": "Traynor", "given": "Bryan J", "initials": "BJ"}, {"family": "Troncoso", "given": "Juan", "initials": "J"}, {"family": "Tsolaki", "given": "Magda", "initials": "M"}, {"family": "Tzourio", "given": "Christophe", "initials": "C"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Hern\u00e1ndez", "given": "Maria C Vald\u00e9s", "initials": "MC"}, {"family": "Van der Brug", "given": "Marcel", "initials": "M"}, {"family": "van der Lugt", "given": "Aad", "initials": "A"}, {"family": "van der Wee", "given": "Nic J A", "initials": "NJ"}, {"family": "Van Haren", "given": "Neeltje E M", "initials": "NE"}, {"family": "van 't Ent", "given": "Dennis", "initials": "D"}, {"family": "Van Tol", "given": "Marie-Jose", "initials": "MJ"}, {"family": "Vardarajan", "given": "Badri N", "initials": "BN"}, {"family": "Vellas", "given": "Bruno", "initials": "B"}, {"family": "Veltman", "given": "Dick J", "initials": "DJ"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Walter", "given": "Henrik", "initials": "H"}, {"family": "Wardlaw", "given": "Joanna M", "initials": "JM"}, {"family": "Wassink", "given": "Thomas H", "initials": "TH"}, {"family": "Weale", "given": "Michael E", "initials": "ME"}, {"family": "Weinberger", "given": "Daniel R", "initials": "DR"}, {"family": "Weiner", "given": "Michael W", "initials": "MW"}, {"family": "Wen", "given": "Wei", "initials": "W"}, {"family": "Westman", "given": "Eric", "initials": "E"}, {"family": "White", "given": "Tonya", "initials": "T"}, {"family": "Wong", "given": "Tien Y", "initials": "TY"}, {"family": "Wright", "given": "Clinton B", "initials": "CB"}, {"family": "Zielke", "given": "Ronald H", "initials": "RH"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Wright", "given": "Margaret J", "initials": "MJ"}, {"family": "Longstreth", "given": "W T", "initials": "WT"}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "Grabe", "given": "Hans J", "initials": "HJ"}, {"family": "Franke", "given": "Barbara", "initials": "B"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Thompson", "given": "Paul M", "initials": "PM"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}], "type": "journal article", "published": "2017-01-18", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "13624", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200\u2009kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg=-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness.", "doi": "10.1038/ncomms13624", "pmid": "28098162", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms13624"}, {"db": "pmc", "key": "PMC5253632"}], "notes": [], "created": "2017-10-25T15:54:13.732Z", "modified": "2024-01-16T13:48:48.676Z"}, {"entity": "publication", "iuid": "3581eb151b9748d899ada9189de921c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3581eb151b9748d899ada9189de921c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3581eb151b9748d899ada9189de921c6"}}, "title": "Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.", "authors": [{"family": "Corcoran", "given": "Martin M", "initials": "MM"}, {"family": "Phad", "given": "Ganesh E", "initials": "GE"}, {"family": "N\u00e9stor", "given": "V\u00e1zquez Bernat", "initials": "VB"}, {"family": "Stahl-Hennig", "given": "Christiane", "initials": "C"}, {"family": "Sumida", "given": "Noriyuki", "initials": "N"}, {"family": "Persson", "given": "Mats A A", "initials": "MA"}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB"}], "type": "journal article", "published": "2016-12-20", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "13642", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Comprehensive knowledge of immunoglobulin genetics is required to advance our understanding of B cell biology. Validated immunoglobulin variable (V) gene databases are close to completion only for human and mouse. We present a novel computational approach, IgDiscover, that identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species. Further, we describe a novel human IGHV3-21 allele and confirm significant gene differences between Balb/c and C57BL6 mouse strains, demonstrating the power of IgDiscover as a germline V gene discovery tool.", "doi": "10.1038/ncomms13642", "pmid": "27995928", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms13642"}, {"db": "pmc", "key": "PMC5187446"}], "notes": [], "created": "2017-05-08T07:55:57.438Z", "modified": "2020-01-21T13:53:21.083Z"}, {"entity": "publication", "iuid": "e019679b363f4778998bc039ebd9783c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e019679b363f4778998bc039ebd9783c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e019679b363f4778998bc039ebd9783c"}}, "title": "An oxygen-sensitive toxin-antitoxin system.", "authors": [{"family": "Marimon", "given": "Oriol", "initials": "O"}, {"family": "Teixeira", "given": "Jo\u00e3o M C", "initials": "JM"}, {"family": "Cordeiro", "given": "Tiago N", "initials": "TN"}, {"family": "Soo", "given": "Valerie W C", "initials": "VW"}, {"family": "Wood", "given": "Thammajun L", "initials": "TL"}, {"family": "Mayzel", "given": "Maxim", "initials": "M"}, {"family": "Amata", "given": "Irene", "initials": "I"}, {"family": "Garc\u00eda", "given": "Jes\u00fas", "initials": "J"}, {"family": "Morera", "given": "Ainara", "initials": "A"}, {"family": "Gay", "given": "Marina", "initials": "M"}, {"family": "Vilaseca", "given": "Marta", "initials": "M"}, {"family": "Orekhov", "given": "Vladislav Yu", "initials": "VY"}, {"family": "Wood", "given": "Thomas K", "initials": "TK"}, {"family": "Pons", "given": "Miquel", "initials": "M"}], "type": "journal article", "published": "2016-12-08", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "13634", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The Hha and TomB proteins from Escherichia coli form an oxygen-dependent toxin-antitoxin (TA) system. Here we show that YmoB, the Yersinia orthologue of TomB, and its single cysteine variant [C117S]YmoB can replace TomB as antitoxins in E. coli. In contrast to other TA systems, [C117S]YmoB transiently interacts with Hha (rather than forming a stable complex) and enhances the spontaneous oxidation of the Hha conserved cysteine residue to a -SOxH-containing species (sulfenic, sulfinic or sulfonic acid), which destabilizes the toxin. The nuclear magnetic resonance structure of [C117S]YmoB and the homology model of TomB show that the two proteins form a four-helix bundle with a conserved buried cysteine connected to the exterior by a channel with a diameter comparable to that of an oxygen molecule. The Hha interaction site is located on the opposite side of the helix bundle.", "doi": "10.1038/ncomms13634", "pmid": "27929062", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms13634"}, {"db": "pmc", "key": "PMC5155140"}], "notes": [], "created": "2017-05-08T08:00:12.767Z", "modified": "2025-10-17T13:04:00.267Z"}, {"entity": "publication", "iuid": "c280ce53dc7a48118050a900e613cf5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c280ce53dc7a48118050a900e613cf5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c280ce53dc7a48118050a900e613cf5b"}}, "title": "Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex.", "authors": [{"family": "Vijay", "given": "Nagarjun", "initials": "N"}, {"family": "Bossu", "given": "Christen M", "initials": "CM"}, {"family": "Poelstra", "given": "Jelmer W", "initials": "JW"}, {"family": "Weissensteiner", "given": "Matthias H", "initials": "MH", "orcid": "0000-0001-9302-798X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5550a93e906d4e25985cd7641f8be554.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Kryukov", "given": "Alexey P", "initials": "AP"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JB"}], "type": "journal article", "published": "2016-10-31", "journal": {"volume": "7", "issn": "2041-1723", "issue": "1", "pages": "13195", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.", "doi": "10.1038/ncomms13195", "pmid": "27796282", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms13195"}, {"db": "pmc", "key": "PMC5095515"}], "notes": [], "created": "2017-10-30T09:31:42.595Z", "modified": "2021-06-21T15:54:31.307Z"}, {"entity": "publication", "iuid": "2e8f1d544b044178a9a6ac0e5f49534c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e8f1d544b044178a9a6ac0e5f49534c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e8f1d544b044178a9a6ac0e5f49534c"}}, "title": "Massive and parallel expression profiling using microarrayed single-cell sequencing.", "authors": [{"family": "Vickovic", "given": "Sanja", "initials": "S"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Giatrellis", "given": "Sarantis", "initials": "S"}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Navarro", "given": "Jos\u00e9 Fern\u00e1ndez", "initials": "JF"}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Sutton", "given": "Lesley-Ann", "initials": "L"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2016-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "7", "issue": null, "pages": "13182"}, "abstract": "Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. Here, we present a method enabling massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enables both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost (0.13 USD/cell), which is two orders of magnitude less than commercially available systems. Our novel approach provides data in a rapid and simple way. Therefore, MASC-seq has the potential to accelerate the study of subtle clonal dynamics and help provide critical insights into disease development and other biological processes.", "doi": "10.1038/ncomms13182", "pmid": "27739429", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Advanced FISH Technologies": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms13182"}, {"db": "pmc", "key": "PMC5067491"}], "notes": [], "created": "2017-05-03T12:59:57.922Z", "modified": "2024-01-16T13:48:49.157Z"}, {"entity": "publication", "iuid": "ef35bfff77544139a459abea6201ff56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef35bfff77544139a459abea6201ff56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef35bfff77544139a459abea6201ff56"}}, "title": "Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.", "authors": [{"family": "Bagnoud", "given": "Alexandre", "initials": "A"}, {"family": "Chourey", "given": "Karuna", "initials": "K"}, {"family": "Hettich", "given": "Robert L", "initials": "RL"}, {"family": "de Bruijn", "given": "Ino", "initials": "I"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Leupin", "given": "Olivier X", "initials": "OX"}, {"family": "Schwyn", "given": "Bernhard", "initials": "B"}, {"family": "Bernier-Latmani", "given": "Rizlan", "initials": "R"}], "type": "journal article", "published": "2016-10-14", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "12770", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.", "doi": "10.1038/ncomms12770", "pmid": "27739431", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms12770"}, {"db": "pmc", "key": "PMC5067608"}], "notes": [], "created": "2017-05-03T13:00:40.242Z", "modified": "2020-01-21T13:53:21.447Z"}, {"entity": "publication", "iuid": "318afc63a86d4e81b7be5c2ca07a9394", "links": {"self": {"href": "https://publications.scilifelab.se/publication/318afc63a86d4e81b7be5c2ca07a9394.json"}, "display": {"href": "https://publications.scilifelab.se/publication/318afc63a86d4e81b7be5c2ca07a9394"}}, "title": "Feralisation targets different genomic loci to domestication in the chicken.", "authors": [{"family": "Johnsson", "given": "M", "initials": "M"}, {"family": "Gering", "given": "E", "initials": "E"}, {"family": "Willis", "given": "P", "initials": "P"}, {"family": "Lopez", "given": "S", "initials": "S"}, {"family": "Van Dorp", "given": "L", "initials": "L"}, {"family": "Hellenthal", "given": "G", "initials": "G"}, {"family": "Henriksen", "given": "R", "initials": "R"}, {"family": "Friberg", "given": "U", "initials": "U"}, {"family": "Wright", "given": "D", "initials": "D"}], "type": "journal article", "published": "2016-09-30", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "12950", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Feralisation occurs when a domestic population recolonizes the wild, escaping its previous restricted environment, and has been considered as the reverse of domestication. We have previously shown that Kauai Island's feral chickens are a highly variable and admixed population. Here we map selective sweeps in feral Kauai chickens using whole-genome sequencing. The detected sweeps were mostly unique to feralisation and distinct to those selected for during domestication. To ascribe potential phenotypic functions to these genes we utilize a laboratory-controlled equivalent to the Kauai population-an advanced intercross between Red Junglefowl and domestic layer birds that has been used previously for both QTL and expression QTL studies. Certain sweep genes exhibit significant correlations with comb mass, maternal brooding behaviour and fecundity. Our analyses indicate that adaptations to feral and domestic environments involve different genomic regions and feral chickens show some evidence of adaptation at genes associated with sexual selection and reproduction.", "doi": "10.1038/ncomms12950", "pmid": "27686863", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms12950"}, {"db": "pmc", "key": "PMC5056458"}], "notes": [], "created": "2017-05-03T12:59:57.629Z", "modified": "2024-01-16T13:48:49.464Z"}, {"entity": "publication", "iuid": "e543ef21a04641fa8ec6cc59fb56125d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e543ef21a04641fa8ec6cc59fb56125d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e543ef21a04641fa8ec6cc59fb56125d"}}, "title": "Limited clonal relatedness between gut IgA plasma cells and memory B cells after oral immunization.", "authors": [{"family": "Bemark", "given": "Mats", "initials": "M", "orcid": "0000-0001-7416-9819", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a7ee472e2e0453b98ee9fdfc02de2b3.json"}}, {"family": "Hazanov", "given": "Helena", "initials": "H"}, {"family": "Str\u00f6mberg", "given": "Anneli", "initials": "A"}, {"family": "Komban", "given": "Rathan", "initials": "R"}, {"family": "Holmqvist", "given": "Joel", "initials": "J"}, {"family": "K\u00f6ster", "given": "Sofia", "initials": "S"}, {"family": "Mattsson", "given": "Johan", "initials": "J"}, {"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "Mehr", "given": "Ramit", "initials": "R"}, {"family": "Lycke", "given": "Nils Y", "initials": "NY"}], "type": "journal article", "published": "2016-09-06", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "12698", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Understanding how memory B cells are induced and relate to long-lived plasma cells is important for vaccine development. Immunity to oral vaccines has been considered short-lived because of a poor ability to develop IgA B-cell memory. Here we demonstrate that long-lived mucosal IgA memory is readily achieved by oral but not systemic immunization in mouse models with NP hapten conjugated with cholera toxin and transfer of B1-8(high)/GFP(+) NP-specific B cells. Unexpectedly, memory B cells are poorly related to long-lived plasma cells and less affinity-matured. They are \u03b14\u03b27-integrin(+)CD73(+)PD-L2(+)CD80(+) and at systemic sites mostly IgM(+), while 80% are IgA(+) in Peyer's patches. On reactivation, most memory B cells in Peyer's patches are GL7(-), but expand in germinal centres and acquire higher affinity and more mutations, demonstrating strong clonal selection. CCR9 expression is found only in Peyer's patches and appears critical for gut homing. Thus, gut mucosal memory possesses unique features not seen after systemic immunization.", "doi": "10.1038/ncomms12698", "pmid": "27596266", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms12698"}, {"db": "pmc", "key": "PMC5025876"}], "notes": [], "created": "2018-01-19T17:09:56.961Z", "modified": "2021-07-06T14:53:44.806Z"}, {"entity": "publication", "iuid": "8876c5f453b24b0f9219968d47dde812", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8876c5f453b24b0f9219968d47dde812.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8876c5f453b24b0f9219968d47dde812"}}, "title": "Stromal Hedgehog signalling is downregulated in colon cancer and its restoration restrains tumour growth.", "authors": [{"family": "Gerling", "given": "Marco", "initials": "M"}, {"family": "B\u00fcller", "given": "Nik\u00e8 V J A", "initials": "NV"}, {"family": "Kirn", "given": "Leonard M", "initials": "LM"}, {"family": "Joost", "given": "Simon", "initials": "S"}, {"family": "Frings", "given": "Oliver", "initials": "O"}, {"family": "Englert", "given": "Benjamin", "initials": "B"}, {"family": "Bergstr\u00f6m", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kuiper", "given": "Raoul V", "initials": "RV"}, {"family": "Blaas", "given": "Leander", "initials": "L"}, {"family": "Wielenga", "given": "Mattheus C B", "initials": "MC"}, {"family": "Almer", "given": "Sven", "initials": "S"}, {"family": "K\u00fchl", "given": "Anja A", "initials": "AA"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "van den Brink", "given": "Gijs R", "initials": "GR"}, {"family": "Toftg\u00e5rd", "given": "Rune", "initials": "R"}], "type": "journal article", "published": "2016-08-05", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "12321", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "A role for Hedgehog (Hh) signalling in the development of colorectal cancer (CRC) has been proposed. In CRC and other solid tumours, Hh ligands are upregulated; however, a specific Hh antagonist provided no benefit in a clinical trial. Here we use Hh reporter mice to show that downstream Hh activity is unexpectedly diminished in a mouse model of colitis-associated colon cancer, and that downstream Hh signalling is restricted to the stroma. Functionally, stroma-specific Hh activation in mice markedly reduces the tumour load and blocks progression of advanced neoplasms, partly via the modulation of BMP signalling and restriction of the colonic stem cell signature. By contrast, attenuated Hh signalling accelerates colonic tumourigenesis. In human CRC, downstream Hh activity is similarly reduced and canonical Hh signalling remains predominantly paracrine. Our results suggest that diminished downstream Hh signalling enhances CRC development, and that stromal Hh activation can act as a colonic tumour suppressor.", "doi": "10.1038/ncomms12321", "pmid": "27492255", "labels": {"Bioinformatics and Expression Analysis (BEA)": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms12321"}, {"db": "pmc", "key": "PMC4980446"}], "notes": [], "created": "2017-05-08T07:59:46.803Z", "modified": "2017-06-12T11:40:01.212Z"}, {"entity": "publication", "iuid": "969f9d959b2f42fb8c82e1acd010f3f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/969f9d959b2f42fb8c82e1acd010f3f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/969f9d959b2f42fb8c82e1acd010f3f3"}}, "title": "Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci.", "authors": [{"family": "Miller", "given": "Clint L", "initials": "CL"}, {"family": "Pjanic", "given": "Milos", "initials": "M"}, {"family": "Wang", "given": "Ting", "initials": "T"}, {"family": "Nguyen", "given": "Trieu", "initials": "T"}, {"family": "Cohain", "given": "Ariella", "initials": "A"}, {"family": "Lee", "given": "Jonathan D", "initials": "JD"}, {"family": "Perisic", "given": "Ljubica", "initials": "L"}, {"family": "Hedin", "given": "Ulf", "initials": "U"}, {"family": "Kundu", "given": "Ramendra K", "initials": "RK"}, {"family": "Majmudar", "given": "Deshna", "initials": "D"}, {"family": "Kim", "given": "Juyong B", "initials": "JB"}, {"family": "Wang", "given": "Oliver", "initials": "O"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Montgomery", "given": "Stephen B", "initials": "SB"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JL"}, {"family": "Quertermous", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2016-07-08", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "12092", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Coronary artery disease (CAD) is the leading cause of mortality and morbidity, driven by both genetic and environmental risk factors. Meta-analyses of genome-wide association studies have identified >150 loci associated with CAD and myocardial infarction susceptibility in humans. A majority of these variants reside in non-coding regions and are co-inherited with hundreds of candidate regulatory variants, presenting a challenge to elucidate their functions. Herein, we use integrative genomic, epigenomic and transcriptomic profiling of perturbed human coronary artery smooth muscle cells and tissues to begin to identify causal regulatory variation and mechanisms responsible for CAD associations. Using these genome-wide maps, we prioritize 64 candidate variants and perform allele-specific binding and expression analyses at seven top candidate loci: 9p21.3, SMAD3, PDGFD, IL6R, BMP1, CCDC97/TGFB1 and LMOD1. We validate our findings in expression quantitative trait loci cohorts, which together reveal new links between CAD associations and regulatory function in the appropriate disease context.", "doi": "10.1038/ncomms12092", "pmid": "27386823", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms12092"}, {"db": "pmc", "key": "PMC4941121"}], "notes": [], "created": "2017-05-03T13:01:36.255Z", "modified": "2020-01-21T13:56:03.870Z"}, {"entity": "publication", "iuid": "709d1e820d654284bdd12f0a6a293beb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/709d1e820d654284bdd12f0a6a293beb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/709d1e820d654284bdd12f0a6a293beb"}}, "title": "Genome-wide association study identifies multiple susceptibility loci for multiple myeloma.", "authors": [{"family": "Mitchell", "given": "Jonathan S", "initials": "JS"}, {"family": "Li", "given": "Ni", "initials": "N"}, {"family": "Weinhold", "given": "Niels", "initials": "N"}, {"family": "F\u00f6rsti", "given": "Asta", "initials": "A"}, {"family": "Ali", "given": "Mina", "initials": "M"}, {"family": "van Duin", "given": "Mark", "initials": "M"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Johnson", "given": "David C", "initials": "DC"}, {"family": "Chen", "given": "Bowang", "initials": "B"}, {"family": "Halvarsson", "given": "Britt-Marie", "initials": "BM"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Kuiper", "given": "Rowan", "initials": "R"}, {"family": "Stephens", "given": "Owen W", "initials": "OW"}, {"family": "Bertsch", "given": "Uta", "initials": "U"}, {"family": "Broderick", "given": "Peter", "initials": "P"}, {"family": "Campo", "given": "Chiara", "initials": "C"}, {"family": "Einsele", "given": "Hermann", "initials": "H"}, {"family": "Gregory", "given": "Walter A", "initials": "WA"}, {"family": "Gullberg", "given": "Urban", "initials": "U"}, {"family": "Henrion", "given": "Marc", "initials": "M"}, {"family": "Hillengass", "given": "Jens", "initials": "J"}, {"family": "Hoffmann", "given": "Per", "initials": "P"}, {"family": "Jackson", "given": "Graham H", "initials": "GH"}, {"family": "Johnsson", "given": "Ellinor", "initials": "E"}, {"family": "J\u00f6ud", "given": "Magnus", "initials": "M"}, {"family": "Kristinsson", "given": "Sigur\u00f0ur Y", "initials": "SY"}, {"family": "Lenhoff", "given": "Stig", "initials": "S"}, {"family": "Lenive", "given": "Oleg", "initials": "O"}, {"family": "Mellqvist", "given": "Ulf-Henrik", "initials": "UH"}, {"family": "Migliorini", "given": "Gabriele", "initials": "G"}, {"family": "Nahi", "given": "Hareth", "initials": "H"}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Nickel", "given": "Jolanta", "initials": "J"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Rafnar", "given": "Thorunn", "initials": "T"}, {"family": "Ross", "given": "Fiona M", "initials": "FM"}, {"family": "da Silva Filho", "given": "Miguel Inacio", "initials": "MI"}, {"family": "Swaminathan", "given": "Bhairavi", "initials": "B"}, {"family": "Thomsen", "given": "Hauke", "initials": "H"}, {"family": "Turesson", "given": "Ingemar", "initials": "I"}, {"family": "Vangsted", "given": "Annette", "initials": "A"}, {"family": "Vogel", "given": "Ulla", "initials": "U"}, {"family": "Waage", "given": "Anders", "initials": "A"}, {"family": "Walker", "given": "Brian A", "initials": "BA"}, {"family": "Wihlborg", "given": "Anna-Karin", "initials": "AK"}, {"family": "Broyl", "given": "Annemiek", "initials": "A"}, {"family": "Davies", "given": "Faith E", "initials": "FE"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Langer", "given": "Christian", "initials": "C"}, {"family": "Hansson", "given": "Markus", "initials": "M"}, {"family": "Kaiser", "given": "Martin", "initials": "M"}, {"family": "Sonneveld", "given": "Pieter", "initials": "P"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Morgan", "given": "Gareth J", "initials": "GJ"}, {"family": "Goldschmidt", "given": "Hartmut", "initials": "H"}, {"family": "Hemminki", "given": "Kari", "initials": "K"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Houlston", "given": "Richard S", "initials": "RS"}], "type": "journal article", "published": "2016-07-01", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "12050", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Multiple myeloma (MM) is a plasma cell malignancy with a significant heritable basis. Genome-wide association studies have transformed our understanding of MM predisposition, but individual studies have had limited power to discover risk loci. Here we perform a meta-analysis of these GWAS, add a new GWAS and perform replication analyses resulting in 9,866 cases and 239,188 controls. We confirm all nine known risk loci and discover eight new loci at 6p22.3 (rs34229995, P=1.31 \u00d7 10(-8)), 6q21 (rs9372120, P=9.09 \u00d7 10(-15)), 7q36.1 (rs7781265, P=9.71 \u00d7 10(-9)), 8q24.21 (rs1948915, P=4.20 \u00d7 10(-11)), 9p21.3 (rs2811710, P=1.72 \u00d7 10(-13)), 10p12.1 (rs2790457, P=1.77 \u00d7 10(-8)), 16q23.1 (rs7193541, P=5.00 \u00d7 10(-12)) and 20q13.13 (rs6066835, P=1.36 \u00d7 10(-13)), which localize in or near to JARID2, ATG5, SMARCD3, CCAT1, CDKN2A, WAC, RFWD3 and PREX1. These findings provide additional support for a polygenic model of MM and insight into the biological basis of tumour development.", "doi": "10.1038/ncomms12050", "pmid": "27363682", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms12050"}, {"db": "pmc", "key": "PMC4932178"}], "notes": [], "created": "2017-05-03T13:01:35.951Z", "modified": "2020-01-21T13:56:02.950Z"}, {"entity": "publication", "iuid": "53ddf8a681fc48a3b781d8d9364bfb2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53ddf8a681fc48a3b781d8d9364bfb2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53ddf8a681fc48a3b781d8d9364bfb2d"}}, "title": "Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia.", "authors": [{"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Henningsson", "given": "Rasmus", "initials": "R"}, {"family": "Hyrenius-Wittsten", "given": "Axel", "initials": "A"}, {"family": "Olsson", "given": "Linda", "initials": "L"}, {"family": "Orsmark-Pietras", "given": "Christina", "initials": "C"}, {"family": "von Palffy", "given": "Sofia", "initials": "S"}, {"family": "Askmyr", "given": "Maria", "initials": "M"}, {"family": "Rissler", "given": "Marianne", "initials": "M"}, {"family": "Schrappe", "given": "Martin", "initials": "M"}, {"family": "Cario", "given": "Gunnar", "initials": "G"}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Pronk", "given": "Cornelis J H", "initials": "CJ"}, {"family": "Behrendtz", "given": "Mikael", "initials": "M"}, {"family": "Mitelman", "given": "Felix", "initials": "F"}, {"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": "Andersson", "given": "Anna K", "initials": "AK"}, {"family": "Fontes", "given": "Magnus", "initials": "M"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}], "type": "journal article", "published": "2016-06-06", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "11790", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Fusion genes are potent driver mutations in cancer. In this study, we delineate the fusion gene landscape in a consecutive series of 195 paediatric B-cell precursor acute lymphoblastic leukaemia (BCP ALL). Using RNA sequencing, we find in-frame fusion genes in 127 (65%) cases, including 27 novel fusions. We describe a subtype characterized by recurrent IGH-DUX4 or ERG-DUX4 fusions, representing 4% of cases, leading to overexpression of DUX4 and frequently co-occurring with intragenic ERG deletions. Furthermore, we identify a subtype characterized by an ETV6-RUNX1-like gene-expression profile and coexisting ETV6 and IKZF1 alterations. Thus, this study provides a detailed overview of fusion genes in paediatric BCP ALL and adds new pathogenetic insights, which may improve risk stratification and provide therapeutic options for this disease.", "doi": "10.1038/ncomms11790", "pmid": "27265895", "labels": {"Clinical Genomics Lund": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms11790"}, {"db": "pmc", "key": "PMC4897744"}], "notes": [], "created": "2017-05-03T12:59:05.040Z", "modified": "2021-07-06T15:41:35.307Z"}, {"entity": "publication", "iuid": "aba97e54ec8741158ea6993bc199e7f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aba97e54ec8741158ea6993bc199e7f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aba97e54ec8741158ea6993bc199e7f1"}}, "title": "Pseudomonas aeruginosa elastase cleaves a C-terminal peptide from human thrombin that inhibits host inflammatory responses.", "authors": [{"family": "van der Plas", "given": "Mariena J A", "initials": "MJ"}, {"family": "Bhongir", "given": "Ravi K V", "initials": "RK"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Siller", "given": "Helena", "initials": "H"}, {"family": "Kasetty", "given": "Gopinath", "initials": "G"}, {"family": "M\u00f6rgelin", "given": "Matthias", "initials": "M"}, {"family": "Schmidtchen", "given": "Artur", "initials": "A"}], "type": "journal article", "published": "2016-05-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "7", "issue": null, "pages": "11567", "issn-l": "2041-1723"}, "abstract": "Pseudomonas aeruginosa is an opportunistic pathogen known for its immune evasive abilities amongst others by degradation of a large variety of host proteins. Here we show that digestion of thrombin by P. aeruginosa elastase leads to the release of the C-terminal thrombin-derived peptide FYT21, which inhibits pro-inflammatory responses to several pathogen-associated molecular patterns in vitro and in vivo by preventing toll-like receptor dimerization and subsequent activation of down-stream signalling pathways. Thus, P. aeruginosa 'hijacks' an endogenous anti-inflammatory peptide-based mechanism, thereby enabling modulation and circumvention of host responses.", "doi": "10.1038/ncomms11567", "pmid": "27181065", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms11567"}, {"db": "pmc", "key": "PMC4873665"}], "notes": [], "created": "2020-01-27T10:04:54.193Z", "modified": "2021-05-24T15:39:50.356Z"}, {"entity": "publication", "iuid": "9eadf5ffd77c4f54aef1ccdecf49859b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9eadf5ffd77c4f54aef1ccdecf49859b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9eadf5ffd77c4f54aef1ccdecf49859b"}}, "title": "A combined computational and structural model of the full-length human prolactin receptor.", "authors": [{"family": "Bugge", "given": "Katrine", "initials": "K"}, {"family": "Papaleo", "given": "Elena", "initials": "E"}, {"family": "Haxholm", "given": "Gitte W", "initials": "GW"}, {"family": "Hopper", "given": "Jonathan T S", "initials": "JT"}, {"family": "Robinson", "given": "Carol V", "initials": "CV"}, {"family": "Olsen", "given": "Johan G", "initials": "JG"}, {"family": "Lindorff-Larsen", "given": "Kresten", "initials": "K"}, {"family": "Kragelund", "given": "Birthe B", "initials": "BB"}], "type": "journal article", "published": "2016-05-13", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "11578", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg.", "doi": "10.1038/ncomms11578", "pmid": "27174498", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms11578"}, {"db": "pmc", "key": "PMC4869255"}], "notes": [], "created": "2017-05-03T13:02:53.074Z", "modified": "2025-10-17T13:04:00.524Z"}, {"entity": "publication", "iuid": "dfd19c39e64d4ddbab29c606e7641bb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfd19c39e64d4ddbab29c606e7641bb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfd19c39e64d4ddbab29c606e7641bb5"}}, "title": "Hypoxia regulates global membrane protein endocytosis through caveolin-1 in cancer cells.", "authors": [{"family": "Bourseau-Guilmain", "given": "E", "initials": "E"}, {"family": "Menard", "given": "J A", "initials": "JA"}, {"family": "Lindqvist", "given": "E", "initials": "E"}, {"family": "Indira Chandran", "given": "V", "initials": "V"}, {"family": "Christianson", "given": "H C", "initials": "HC"}, {"family": "Cerezo Maga\u00f1a", "given": "M", "initials": "M"}, {"family": "Lidfeldt", "given": "J", "initials": "J"}, {"family": "Marko-Varga", "given": "G", "initials": "G"}, {"family": "Welinder", "given": "C", "initials": "C"}, {"family": "Belting", "given": "M", "initials": "M"}], "type": "journal article", "published": "2016-04-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "7", "issue": null, "pages": "11371", "issn-l": "2041-1723"}, "abstract": "Hypoxia promotes tumour aggressiveness and resistance of cancers to oncological treatment. The identification of cancer cell internalizing antigens for drug targeting to the hypoxic tumour niche remains a challenge of high clinical relevance. Here we show that hypoxia down-regulates the surface proteome at the global level and, more specifically, membrane proteome internalization. We find that hypoxic down-regulation of constitutive endocytosis is HIF-independent, and involves caveolin-1-mediated inhibition of dynamin-dependent, membrane raft endocytosis. Caveolin-1 overexpression inhibits protein internalization, suggesting a general negative regulatory role of caveolin-1 in endocytosis. In contrast to this global inhibitory effect, we identify several proteins that can override caveolin-1 negative regulation, exhibiting increased internalization at hypoxia. We demonstrate antibody-mediated cytotoxin delivery and killing specifically of hypoxic cells through one of these proteins, carbonic anhydrase IX. Our data reveal that caveolin-1 modulates cell-surface proteome turnover at hypoxia with potential implications for specific targeting of the hypoxic tumour microenvironment.", "doi": "10.1038/ncomms11371", "pmid": "27094744", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms11371"}, {"db": "pmc", "key": "PMC4842985"}], "notes": [], "created": "2020-01-27T10:11:19.802Z", "modified": "2021-05-24T15:39:50.407Z"}, {"entity": "publication", "iuid": "c368706e4e63422da6d309f637163d4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c368706e4e63422da6d309f637163d4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c368706e4e63422da6d309f637163d4e"}}, "title": "CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil.", "authors": [{"family": "Almqvist", "given": "Helena", "initials": "H"}, {"family": "Axelsson", "given": "Hanna", "initials": "H"}, {"family": "Jafari", "given": "Rozbeh", "initials": "R"}, {"family": "Dan", "given": "Chen", "initials": "C"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "Larsson", "given": "Andreas", "initials": "A"}, {"family": "Martinez Molina", "given": "Daniel", "initials": "D"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2016-03-24", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "11040", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Target engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen based on biophysical measurements of intracellular target binding, exemplified by human thymidylate synthase (TS). The screen selected accurately for all the tested known drugs acting on TS. We also identified TS inhibitors with novel chemistry and marketed drugs that were not previously known to target TS, including the DNA methyltransferase inhibitor decitabine. By following the cellular uptake and enzymatic conversion of known drugs we correlated the appearance of active metabolites over time with intracellular target engagement. These data distinguished a much slower activation of 5-fluorouracil when compared with nucleoside-based drugs. The approach establishes efficient means to associate drug uptake and activation with target binding during drug discovery.", "doi": "10.1038/ncomms11040", "pmid": "27010513", "labels": {"Protein Science Facility (PSF)": "Service", "Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms11040"}, {"db": "pmc", "key": "PMC4820820"}], "notes": "Laboratories for Chemical Biology at Karolinska Institutet (LCBKI)", "created": "2017-05-03T12:59:30.016Z", "modified": "2025-10-17T13:04:29.584Z"}, {"entity": "publication", "iuid": "81a49441bd744cc2a2236bfae261bc67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81a49441bd744cc2a2236bfae261bc67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81a49441bd744cc2a2236bfae261bc67"}}, "title": "VEGFR2 pY949 signalling regulates adherens junction integrity and metastatic spread.", "authors": [{"family": "Li", "given": "Xiujuan", "initials": "X"}, {"family": "Padhan", "given": "Narendra", "initials": "N"}, {"family": "Sj\u00f6str\u00f6m", "given": "Elisabet O", "initials": "EO"}, {"family": "Roche", "given": "Francis P", "initials": "FP"}, {"family": "Testini", "given": "Chiara", "initials": "C"}, {"family": "Honkura", "given": "Naoki", "initials": "N"}, {"family": "S\u00e1inz-Jaspeado", "given": "Miguel", "initials": "M"}, {"family": "Gordon", "given": "Emma", "initials": "E"}, {"family": "Bentley", "given": "Katie", "initials": "K"}, {"family": "Philippides", "given": "Andrew", "initials": "A"}, {"family": "Tolmachev", "given": "Vladimir", "initials": "V"}, {"family": "Dejana", "given": "Elisabetta", "initials": "E"}, {"family": "Stan", "given": "Radu V", "initials": "RV"}, {"family": "Vestweber", "given": "Dietmar", "initials": "D"}, {"family": "Ballmer-Hofer", "given": "Kurt", "initials": "K"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Pietras", "given": "Kristian", "initials": "K"}, {"family": "Jansson", "given": "Leif", "initials": "L"}, {"family": "Claesson-Welsh", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2016-03-23", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "11017", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The specific role of VEGFA-induced permeability and vascular leakage in physiology and pathology has remained unclear. Here we show that VEGFA-induced vascular leakage depends on signalling initiated via the VEGFR2 phosphosite Y949, regulating dynamic c-Src and VE-cadherin phosphorylation. Abolished Y949 signalling in the mouse mutant Vegfr2(Y949F/Y949F) leads to VEGFA-resistant endothelial adherens junctions and a block in molecular extravasation. Vessels in Vegfr2(Y949F/Y949F) mice remain sensitive to inflammatory cytokines, and vascular morphology, blood pressure and flow parameters are normal. Tumour-bearing Vegfr2(Y949F/Y949F) mice display reduced vascular leakage and oedema, improved response to chemotherapy and, importantly, reduced metastatic spread. The inflammatory infiltration in the tumour micro-environment is unaffected. Blocking VEGFA-induced disassembly of endothelial junctions, thereby suppressing tumour oedema and metastatic spread, may be preferable to full vascular suppression in the treatment of certain cancer forms.", "doi": "10.1038/ncomms11017", "pmid": "27005951", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms11017"}, {"db": "pmc", "key": "PMC4814575"}], "notes": [], "created": "2017-05-03T12:59:57.333Z", "modified": "2024-01-16T13:48:50.333Z"}, {"entity": "publication", "iuid": "8354dd110e2543798223953b699a47c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8354dd110e2543798223953b699a47c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8354dd110e2543798223953b699a47c3"}}, "title": "New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk", "authors": [{"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Day", "given": "Felix R", "initials": "FR", "orcid": "0000-0003-3789-7651", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d9ffc4d251a4469bcb97dd24dcc4218.json"}}, {"family": "Gustafsson", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5894-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a0552f8a6514baa9bdb6809148aaddc.json"}}, {"family": "Buchkovich", "given": "Martin L", "initials": "ML"}, {"family": "Na", "given": "Jianbo", "initials": "J"}, {"family": "Bataille", "given": "Veronique", "initials": "V"}, {"family": "Cousminer", "given": "Diana L", "initials": "DL"}, {"family": "Dastani", "given": "Zari", "initials": "Z"}, {"family": "Drong", "given": 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"given": "Andrew P", "initials": "AP"}, {"family": "Bishop", "given": "Julia A N", "initials": "JAN"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Prokopenko", "given": "Inga", "initials": "I", "orcid": "0000-0003-1624-7457", "researcher": {"href": "https://publications.scilifelab.se/researcher/d27906bec5a34e26a3a7a840002ecd08.json"}}, {"family": "Richards", "given": "J Brent", "initials": "JB"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Wid\u00e9n", "given": "Elisabeth", "initials": "E"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ", "orcid": "0000-0001-5645-4966", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a8e1d33146452b87e7e21eb5339f80.json"}}, {"family": "Yang", "given": "Jian", "initials": "J", "orcid": "0000-0003-2001-2474", "researcher": {"href": "https://publications.scilifelab.se/researcher/99b6239b59ad42248e8f18583b40777a.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Pospisilik", "given": "John Andrew", "initials": "JA", "orcid": "0000-0002-9745-0977", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e7b352d87ed446e8b3899f6281fa954.json"}}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas Oskari", "initials": "TO"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}], "type": "journal-article", "published": "2016-02-01", "journal": {"volume": "7", "issn": "2041-1723", "issue": "1", "pages": "10495", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 \u00d7 10(-8)), of which eight were previously associated with increased overall adiposity (BMI, BF%) and four (in or near COBLL1/GRB14, IGF2BP1, PLA2G6, CRTC1) were novel associations with BF%. Seven loci showed a larger effect on BF% than on BMI, suggestive of a primary association with adiposity, while five loci showed larger effects on BMI than on BF%, suggesting association with both fat and lean mass. In particular, the loci more strongly associated with BF% showed distinct cross-phenotype association signatures with a range of cardiometabolic traits revealing new insights in the link between adiposity and disease risk.", "doi": "10.1038/ncomms10495", "pmid": "26833246", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4740398"}, {"db": "pii", "key": "ncomms10495"}], "notes": [], "created": "2017-05-03T12:59:57.066Z", "modified": "2024-01-16T13:48:50.482Z"}, {"entity": "publication", "iuid": "db859ad32acb4306a79f04d94b558f17", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db859ad32acb4306a79f04d94b558f17.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db859ad32acb4306a79f04d94b558f17"}}, "title": "Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels.", "authors": [{"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Carli", "given": "Jayne F Martin", "initials": "JF"}, {"family": "Skowronski", "given": "Alicja A", "initials": "AA"}, {"family": "Sun", "given": "Qi", "initials": "Q"}, {"family": "Kriebel", "given": "Jennifer", "initials": "J"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Drong", "given": "Alexander W", "initials": "AW"}, {"family": "Hayes", "given": "James E", "initials": "JE"}, {"family": "Zhao", "given": "Jinghua", "initials": "J"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Schick", "given": "Ursula", "initials": "U"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Mangino", "given": "Massimo", 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{"family": "Vestergaard", "given": "Henrik", "initials": "H"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Eline Slagboom", "given": "P", "initials": "P"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Jukema", "given": "J W", "initials": "JW"}, {"family": "Klein", "given": "Robert J", "initials": "RJ"}, {"family": "Schadt", "given": "Erik E", "initials": "EE"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Leibel", "given": "Rudolph L", "initials": "RL"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}], "type": "journal article", "published": "2016-02-01", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "10494", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered. Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching P<10(-6) in 19,979 additional individuals. We identify five loci robustly associated (P<5 \u00d7 10(-8)) with leptin levels in/near LEP, SLC32A1, GCKR, CCNL1 and FTO. Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown experiments in mouse adipose tissue explants show convincing evidence for adipogenin, a regulator of adipocyte differentiation, as the novel causal gene in the SLC32A1 locus influencing leptin levels. Our findings provide novel insights into the regulation of leptin production by adipose tissue and open new avenues for examining the influence of variation in leptin levels on adiposity and metabolic health.", "doi": "10.1038/ncomms10494", "pmid": "26833098", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms10494"}, {"db": "pmc", "key": "PMC4740377"}], "notes": [], "created": "2017-05-03T12:59:56.718Z", "modified": "2024-01-16T13:48:50.493Z"}, {"entity": "publication", "iuid": "dfe06efb3c6746b1ba351aec04047a2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfe06efb3c6746b1ba351aec04047a2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfe06efb3c6746b1ba351aec04047a2f"}}, "title": "Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.", "authors": [{"family": "Pattaro", "given": "Cristian", "initials": "C", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Mijatovic", "given": "Vladan", "initials": "V"}, {"family": "Garnaas", "given": "Maija", "initials": "M"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "Sorice", "given": "Rossella", "initials": "R"}, {"family": "Li", "given": "Yong", "initials": "Y"}, {"family": "Taliun", "given": "Daniel", "initials": "D"}, {"family": "Olden", "given": 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{"family": "Adam", "given": "Martin", "initials": "M"}, {"family": "Cocca", "given": "Massimiliano", "initials": "M"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Imboden", "given": "Medea", "initials": "M"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Pruijm", "given": "Menno", "initials": "M"}, {"family": "Metzger", "given": "Marie", "initials": "M"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Sale", "given": "Michele M", "initials": "MM"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Boban", "given": "Mladen", "initials": "M"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Rheinberger", "given": "Myriam", "initials": "M"}, {"family": "Verweij", "given": "Niek", "initials": "N", "orcid": "0000-0002-4303-7685", "researcher": {"href": 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"initials": "PM"}, {"family": "Mitchell", "given": "Paul", "initials": "P"}, {"family": "Muntner", "given": "Paul", "initials": "P"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "ICBP Consortium", "given": "", "initials": ""}, {"family": "AGEN Consortium", "given": "", "initials": ""}, {"family": "CARDIOGRAM", "given": "", "initials": ""}, {"family": "CHARGe-Heart Failure Group", "given": "", "initials": ""}, {"family": "ECHOGen Consortium", "given": "", "initials": ""}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Biffar", "given": "Reiner", "initials": "R"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Middelberg", "given": "Rita P S", "initials": "RP"}, {"family": "Carroll", "given": "Robert J", "initials": "RJ"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Scott", "given": "Rodney J", "initials": "RJ"}, {"family": "Katz", "given": "Ronit", "initials": "R"}, {"family": "Sedaghat", "given": "Sanaz", "initials": "S"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SL"}, {"family": "Ulivi", "given": "Sheila", "initials": "S"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Kloiber", "given": "Stefan", "initials": "S"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Stengel", "given": "Benedicte", "initials": "B"}, {"family": "Hancock", "given": "Stephen J", "initials": "SJ"}, {"family": "Turner", "given": "Stephen T", "initials": "ST"}, {"family": "Rosas", "given": "Sylvia E", "initials": "SE"}, {"family": "Stracke", "given": "Sylvia", "initials": "S"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Aspelund", "given": "Thor", "initials": "T"}, {"family": "Nikopensius", "given": "Tiit", "initials": "T"}, {"family": "Esko", "given": "Tonu", "initials": "T"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Emilsson", "given": "Valur", "initials": "V"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Aalto", "given": "Ville", "initials": "V"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Chouraki", "given": "Vincent", "initials": "V"}, {"family": "Chen", "given": "Wei-Min", "initials": "WM"}, {"family": "Igl", "given": "Wilmar", "initials": "W"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Lieb", "given": "Wolfgang", "initials": "W"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Susztak", "given": "Katalin", "initials": "K"}, {"family": "Hamet", "given": "Pavel", "initials": "P"}, {"family": "Tremblay", "given": "Johanne", "initials": "J"}, {"family": "de Boer", "given": "Ian H", "initials": "IH"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Goessling", "given": "Wolfram", "initials": "W", "orcid": "0000-0001-9972-1569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5b458ffb873412681705bace6261451.json"}}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}], "type": "journal article", "published": "2016-01-21", "journal": {"volume": "7", "issn": "2041-1723", "issue": "1", "pages": "10023", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.", "doi": "10.1038/ncomms10023", "pmid": "26831199", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS733914"}, {"db": "pmc", "key": "PMC4735748"}, {"db": "pii", "key": "ncomms10023"}], "notes": [], "created": "2017-05-08T07:57:33.691Z", "modified": "2024-01-16T13:48:50.575Z"}, {"entity": "publication", "iuid": "84075ae7d7d1499899f56fdb73c9eaf4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84075ae7d7d1499899f56fdb73c9eaf4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84075ae7d7d1499899f56fdb73c9eaf4"}}, "title": "Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation.", "authors": [{"family": "Soler Artigas", "given": "Mar\u00eda", "initials": "M"}, {"family": "Wain", "given": "Louise V", "initials": "LV"}, {"family": "Miller", "given": "Suzanne", "initials": "S"}, {"family": "Kheirallah", "given": "Abdul Kader", "initials": "AK"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Shrine", "given": "Nick", "initials": "N"}, {"family": "Obeidat", "given": "Ma'en", "initials": "M"}, {"family": "Trochet", "given": "Holly", "initials": "H"}, {"family": "McArdle", "given": "Wendy L", "initials": "WL"}, {"family": "Alves", "given": "Alexessander Couto", "initials": "AC"}, {"family": "Hui", "given": "Jennie", "initials": "J"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Imboden", "given": "Medea", "initials": "M"}, {"family": "Rawal", "given": "Rajesh", "initials": "R"}, {"family": "Lopez", "given": "Lorna M", "initials": "LM"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Granell", "given": "Raquel", "initials": "R"}, {"family": "Hysi", "given": "Pirro G", "initials": "PG"}, {"family": "Flexeder", "given": "Claudia", "initials": "C"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Beilby", "given": "John", "initials": "J"}, {"family": "Boss\u00e9", "given": "Yohan", "initials": "Y"}, {"family": "Brandsma", "given": "Corry-Anke", "initials": "CA"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Gl\u00e4ser", "given": "Sven", "initials": "S"}, {"family": "Gonz\u00e1lez", "given": "Juan R", "initials": "JR"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Hammond", "given": "Chris J", "initials": "CJ"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Hartikainen", "given": "Anna-Liisa", "initials": "AL"}, {"family": "Heli\u00f6vaara", "given": "Markku", "initials": "M"}, {"family": "Henderson", "given": "John", "initials": "J"}, {"family": "Hocking", "given": "Lynne", "initials": "L"}, {"family": "Horikoshi", "given": "Momoko", "initials": "M"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kemp", "given": "John P", "initials": "JP"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Kumar", "given": "Ashish", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Musk", "given": "Arthur W", "initials": "AW"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Nickle", "given": "David C", "initials": "DC"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Ried", "given": "Janina S", "initials": "JS"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Schulz", "given": "Holger", "initials": "H"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Sin", "given": "Don D", "initials": "DD"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "UK BiLEVE", "given": null, "initials": null}, {"family": "Vi\u00f1uela", "given": "Ana", "initials": "A"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Jarvis", "given": "Deborah L", "initials": "DL"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Evans", "given": "David M", "initials": "DM"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Karrasch", "given": "Stefan", "initials": "S"}, {"family": "Probst-Hensch", "given": "Nicole M", "initials": "NM"}, {"family": "Heinrich", "given": "Joachim", "initials": "J"}, {"family": "Stubbe", "given": "Beate", "initials": "B"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "James", "given": "Alan L", "initials": "AL"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Sayers", "given": "Ian", "initials": "I"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Hall", "given": "Ian P", "initials": "IP"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}], "type": "journal article", "published": "2015-12-04", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "8658", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Lung function measures are used in the diagnosis of chronic obstructive pulmonary disease. In 38,199 European ancestry individuals, we studied genome-wide association of forced expiratory volume in 1\u2009s (FEV1), forced vital capacity (FVC) and FEV1/FVC with 1000 Genomes Project (phase 1)-imputed genotypes and followed up top associations in 54,550 Europeans. We identify 14 novel loci (P<5 \u00d7 10(-8)) in or near ENSA, RNU5F-1, KCNS3, AK097794, ASTN2, LHX3, CCDC91, TBX3, TRIP11, RIN3, TEKT5, LTBP4, MN1 and AP1S2, and two novel signals at known loci NPNT and GPR126, providing a basis for new understanding of the genetic determinants of these traits and pulmonary diseases in which they are altered.", "doi": "10.1038/ncomms9658", "pmid": "26635082", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ncomms9658"}, {"db": "pmc", "key": "PMC4686825"}], "notes": [], "created": "2017-05-02T12:56:31.958Z", "modified": "2020-01-21T13:56:03.408Z"}, {"entity": "publication", "iuid": "eddaaa22ebbe4684be096bfc736855bd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eddaaa22ebbe4684be096bfc736855bd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eddaaa22ebbe4684be096bfc736855bd"}}, "title": "Structural insights into the DNA-binding specificity of E2F family transcription factors.", "authors": [{"family": "Morgunova", "given": "Ekaterina", "initials": "E"}, {"family": "Yin", "given": "Yimeng", "initials": "Y"}, {"family": "Jolma", "given": "Arttu", "initials": "A"}, {"family": "Dave", "given": "Kashyap", "initials": "K"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Popov", "given": "Alexander", "initials": "A"}, {"family": "Eremina", "given": "Nadejda", "initials": "N"}, {"family": "Nilsson", "given": "Lennart", "initials": "L"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2015-12-03", "journal": {"volume": "6", "issn": "2041-1723", "issue": "1", "pages": "10050", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The mammalian cell cycle is controlled by the E2F family of transcription factors. Typical E2Fs bind to DNA as heterodimers with the related dimerization partner (DP) proteins, whereas the atypical E2Fs, E2F7 and E2F8 contain two DNA-binding domains (DBDs) and act as repressors. To understand the mechanism of repression, we have resolved the structure of E2F8 in complex with DNA at atomic resolution. We find that the first and second DBDs of E2F8 resemble the DBDs of typical E2F and DP proteins, respectively. Using molecular dynamics simulations, biochemical affinity measurements and chromatin immunoprecipitation, we further show that both atypical and typical E2Fs bind to similar DNA sequences in vitro and in vivo. Our results represent the first crystal structure of an E2F protein with two DBDs, and reveal the mechanism by which atypical E2Fs can repress canonical E2F target genes and exert their negative influence on cell cycle progression.", "doi": "10.1038/ncomms10050", "pmid": "26632596", "labels": {"Protein Science Facility (PSF)": null, "Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "ncomms10050"}, {"db": "pmc", "key": "PMC4686757"}, {"db": "BioProject", "key": "PRJEB8671"}, {"db": "PDB", "key": "4YO2"}], "notes": [], "created": "2017-05-02T12:56:56.387Z", "modified": "2021-07-06T14:42:14.622Z"}, {"entity": "publication", "iuid": "2f3d27778eb44d49b03e70d17cd679d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f3d27778eb44d49b03e70d17cd679d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f3d27778eb44d49b03e70d17cd679d7"}}, "title": "Meta-analysis identifies seven susceptibility loci involved in the atopic march.", "authors": [{"family": "Marenholz", "given": "Ingo", "initials": "I"}, {"family": "Esparza-Gordillo", "given": "Jorge", "initials": "J"}, {"family": "R\u00fcschendorf", "given": "Franz", "initials": "F"}, {"family": "Bauerfeind", "given": "Anja", "initials": "A"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Spycher", "given": "Ben D", "initials": "BD"}, {"family": "Baurecht", "given": "Hansj\u00f6rg", "initials": "H"}, {"family": "Margaritte-Jeannin", "given": "Patricia", "initials": "P"}, {"family": "S\u00e4\u00e4f", "given": "Annika", "initials": "A"}, {"family": "Kerkhof", "given": "Marjan", "initials": "M"}, {"family": "Ege", "given": "Markus", "initials": "M"}, {"family": "Baltic", "given": "Svetlana", "initials": "S"}, {"family": "Matheson", "given": "Melanie C", "initials": "MC"}, {"family": "Li", "given": "Jin", "initials": "J"}, {"family": "Michel", "given": "Sven", "initials": "S"}, {"family": "Ang", "given": "Wei Q", "initials": "WQ"}, {"family": "McArdle", "given": "Wendy", "initials": "W"}, {"family": "Arnold", "given": "Andreas", "initials": "A"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Demenais", "given": "Florence", "initials": "F"}, {"family": "Bouzigon", "given": "Emmanuelle", "initials": "E"}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "de Jongste", "given": "Johan C", "initials": "JC"}, {"family": "Postma", "given": "Dirkje S", "initials": "DS"}, {"family": "Braun-Fahrl\u00e4nder", "given": "Charlotte", "initials": "C"}, {"family": "Horak", "given": "Elisabeth", "initials": "E"}, {"family": "Ogorodova", "given": "Ludmila M", "initials": "LM"}, {"family": "Puzyrev", "given": "Valery P", "initials": "VP"}, {"family": "Bragina", "given": "Elena Yu", "initials": "EY"}, {"family": "Hudson", "given": "Thomas J", "initials": "TJ"}, {"family": "Morin", "given": "Charles", "initials": "C"}, {"family": "Duffy", "given": "David L", "initials": "DL", "orcid": "0000-0002-8875-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/dce1a0fd17154c73b30f23c2a58bd390.json"}}, {"family": "Marks", "given": "Guy B", "initials": "GB"}, {"family": "Robertson", "given": "Colin F", "initials": "CF"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Musk", "given": "Bill", "initials": "B"}, {"family": "Thompson", "given": "Philip J", "initials": "PJ"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "James", "given": "Alan", "initials": "A"}, {"family": "Sleiman", "given": "Patrick", "initials": "P"}, {"family": "Toskala", "given": "Elina", "initials": "E"}, {"family": "Rodriguez", "given": "Elke", "initials": "E"}, {"family": "F\u00f6lster-Holst", "given": "Regina", "initials": "R"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Lieb", "given": "Wolfgang", "initials": "W"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Heinzmann", "given": "Andrea", "initials": "A"}, {"family": "Rietschel", "given": "Ernst", "initials": "E"}, {"family": "Keil", "given": "Thomas", "initials": "T"}, {"family": "Cichon", "given": "Sven", "initials": "S"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Pennell", "given": "Craig E", "initials": "CE"}, {"family": "Sly", "given": "Peter D", "initials": "PD"}, {"family": "Schmidt", "given": "Carsten O", "initials": "CO"}, {"family": "Matanovic", "given": "Anja", "initials": "A"}, {"family": "Schneider", "given": "Valentin", "initials": "V"}, {"family": "Heinig", "given": "Matthias", "initials": "M"}, {"family": "H\u00fcbner", "given": "Norbert", "initials": "N"}, {"family": "Holt", "given": "Patrick G", "initials": "PG"}, {"family": "Lau", "given": "Susanne", "initials": "S"}, {"family": "Kabesch", "given": "Michael", "initials": "M"}, {"family": "Weidinger", "given": "Stefan", "initials": "S"}, {"family": "Hakonarson", "given": "Hakon", "initials": "H"}, {"family": "Ferreira", "given": "Manuel A R", "initials": "MA"}, {"family": "Laprise", "given": "Catherine", "initials": "C"}, {"family": "Freidin", "given": "Maxim B", "initials": "MB"}, {"family": "Genuneit", "given": "Jon", "initials": "J"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Dizier", "given": "Marie-H\u00e9l\u00e8ne", "initials": "MH"}, {"family": "Henderson", "given": "A John", "initials": "AJ"}, {"family": "Lee", "given": "Young Ae", "initials": "YA"}], "type": "journal article", "published": "2015-11-06", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "8804", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Eczema often precedes the development of asthma in a disease course called the 'atopic march'. To unravel the genes underlying this characteristic pattern of allergic disease, we conduct a multi-stage genome-wide association study on infantile eczema followed by childhood asthma in 12 populations including 2,428 cases and 17,034 controls. Here we report two novel loci specific for the combined eczema plus asthma phenotype, which are associated with allergic disease for the first time; rs9357733 located in EFHC1 on chromosome 6p12.3 (OR 1.27; P=2.1 \u00d7 10(-8)) and rs993226 between TMTC2 and SLC6A15 on chromosome 12q21.3 (OR 1.58; P=5.3 \u00d7 10(-9)). Additional susceptibility loci identified at genome-wide significance are FLG (1q21.3), IL4/KIF3A (5q31.1), AP5B1/OVOL1 (11q13.1), C11orf30/LRRC32 (11q13.5) and IKZF3 (17q21). We show that predominantly eczema loci increase the risk for the atopic march. Our findings suggest that eczema may play an important role in the development of asthma after eczema.", "doi": "10.1038/ncomms9804", "pmid": "26542096", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "ncomms9804"}, {"db": "pmc", "key": "PMC4667629"}], "notes": [], "created": "2017-05-02T12:57:59.687Z", "modified": "2023-06-19T10:55:16.441Z"}, {"entity": "publication", "iuid": "a037290156c84ac98879f71cfffcfeab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a037290156c84ac98879f71cfffcfeab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a037290156c84ac98879f71cfffcfeab"}}, "title": "Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.", "authors": [{"family": "St\u00f6dberg", "given": "Tommy", "initials": "T"}, {"family": "McTague", "given": "Amy", "initials": "A"}, {"family": "Ruiz", "given": "Arnaud J", "initials": "AJ"}, {"family": "Hirata", "given": "Hiromi", "initials": "H"}, {"family": "Zhen", "given": "Juan", "initials": "J"}, {"family": "Long", "given": "Philip", "initials": "P"}, {"family": "Farabella", "given": "Irene", "initials": "I"}, {"family": "Meyer", "given": "Esther", "initials": "E"}, {"family": "Kawahara", "given": "Atsuo", "initials": "A"}, {"family": "Vassallo", "given": "Grace", "initials": "G"}, {"family": "Stivaros", "given": "Stavros M", "initials": "SM"}, {"family": "Bjursell", "given": "Magnus K", "initials": "MK"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Tigerschi\u00f6ld", "given": "Stephanie", "initials": "S"}, {"family": "Persson", "given": "Bengt", "initials": "B"}, {"family": "Bangash", "given": "Iftikhar", "initials": "I"}, {"family": "Das", "given": "Krishna", "initials": "K"}, {"family": "Hughes", "given": "Deborah", "initials": "D"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Scott", "given": "Rod C", "initials": "RC"}, {"family": "Poduri", "given": "Annapurna", "initials": "A"}, {"family": "Scheffer", "given": "Ingrid E", "initials": "IE"}, {"family": "Smith", "given": "Holly", "initials": "H"}, {"family": "Gissen", "given": "Paul", "initials": "P", "orcid": "0000-0002-9712-6122", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca2717808896474eae93826d8b646e48.json"}}, {"family": "Schorge", "given": "Stephanie", "initials": "S"}, {"family": "Reith", "given": "Maarten E A", "initials": "ME"}, {"family": "Topf", "given": "Maya", "initials": "M"}, {"family": "Kullmann", "given": "Dimitri M", "initials": "DM"}, {"family": "Harvey", "given": "Robert J", "initials": "RJ"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Kurian", "given": "Manju A", "initials": "MA"}], "type": "journal article", "published": "2015-09-03", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "8038", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The potassium-chloride co-transporter KCC2, encoded by SLC12A5, plays a fundamental role in fast synaptic inhibition by maintaining a hyperpolarizing gradient for chloride ions. KCC2 dysfunction has been implicated in human epilepsy, but to date, no monogenic KCC2-related epilepsy disorders have been described. Here we show recessive loss-of-function SLC12A5 mutations in patients with a severe infantile-onset pharmacoresistant epilepsy syndrome, epilepsy of infancy with migrating focal seizures (EIMFS). Decreased KCC2 surface expression, reduced protein glycosylation and impaired chloride extrusion contribute to loss of KCC2 activity, thereby impairing normal synaptic inhibition and promoting neuronal excitability in this early-onset epileptic encephalopathy.", "doi": "10.1038/ncomms9038", "pmid": "26333769", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Clinical Genomics Stockholm": null, "Clinical Genomics": null}, "xrefs": [{"db": "pii", "key": "ncomms9038"}, {"db": "pmc", "key": "PMC4569694"}], "notes": [], "created": "2017-05-02T12:58:41.214Z", "modified": "2021-07-08T13:26:08.263Z"}, {"entity": "publication", "iuid": "4fdb10bc03be451bbcc19a17b12465ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4fdb10bc03be451bbcc19a17b12465ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4fdb10bc03be451bbcc19a17b12465ce"}}, "title": "Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2.", "authors": [{"family": "Carter", "given": "Megan", "initials": "M"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Hagenkort", "given": "Anna", "initials": "A"}, {"family": "Page", "given": "Brent D G", "initials": "BD"}, {"family": "Gustafsson", "given": "Robert", "initials": "R"}, {"family": "Griese", "given": "Julia J", "initials": "JJ"}, {"family": "Gad", "given": "Helge", "initials": "H"}, {"family": "Valerie", "given": "Nicholas C K", "initials": "NC"}, {"family": "Desroses", "given": "Matthieu", "initials": "M"}, {"family": "Bostr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Warpman Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P"}], "type": "journal article", "published": "2015-08-04", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "7871", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Deregulated redox metabolism in cancer leads to oxidative damage to cellular components including deoxyribonucleoside triphosphates (dNTPs). Targeting dNTP pool sanitizing enzymes, such as MTH1, is a highly promising anticancer strategy. The MTH2 protein, known as NUDT15, is described as the second human homologue of bacterial MutT with 8-oxo-dGTPase activity. We present the first NUDT15 crystal structure and demonstrate that NUDT15 prefers other nucleotide substrates over 8-oxo-dGTP. Key structural features are identified that explain different substrate preferences for NUDT15 and MTH1. We find that depletion of NUDT15 has no effect on incorporation of 8-oxo-dGTP into DNA and does not impact cancer cell survival in cell lines tested. NUDT17 and NUDT18 were also profiled and found to have far less activity than MTH1 against oxidized nucleotides. We show that NUDT15 is not a biologically relevant 8-oxo-dGTPase, and that MTH1 is the most prominent sanitizer of the cellular dNTP pool known to date.", "doi": "10.1038/ncomms8871", "pmid": "26238318", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "ncomms8871"}, {"db": "pmc", "key": "PMC4532830"}], "notes": [], "created": "2017-05-02T12:56:42.343Z", "modified": "2021-07-08T13:01:30.793Z"}, {"entity": "publication", "iuid": "7587d9b469b14d738cb51e3dfea1cfce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7587d9b469b14d738cb51e3dfea1cfce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7587d9b469b14d738cb51e3dfea1cfce"}}, "title": "Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.", "authors": [{"family": "Tan", "given": "Tien-Chye", "initials": "TC"}, {"family": "Kracher", "given": "Daniel", "initials": "D"}, {"family": "Gandini", "given": "Rosaria", "initials": "R"}, {"family": "Sygmund", "given": "Christoph", "initials": "C"}, {"family": "Kittl", "given": "Roman", "initials": "R"}, {"family": "Haltrich", "given": "Dietmar", "initials": "D"}, {"family": "H\u00e4llberg", "given": "B Martin", "initials": "BM"}, {"family": "Ludwig", "given": "Roland", "initials": "R"}, {"family": "Divne", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2015-07-07", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "7542", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH. CDH contains a haem-binding cytochrome (CYT) connected via a flexible linker to a flavin-dependent dehydrogenase (DH). Electrons are generated from cellobiose oxidation catalysed by DH and shuttled via CYT to LPMO. Here we present structural analyses that provide a comprehensive picture of CDH conformers, which govern the electron transfer between redox centres. Using structure-based site-directed mutagenesis, rapid kinetics analysis and molecular docking, we demonstrate that flavin-to-haem interdomain electron transfer (IET) is enabled by a haem propionate group and that rapid IET requires a closed CDH state in which the propionate is tightly enfolded by DH. Following haem reduction, CYT reduces LPMO to initiate oxygen activation at the copper centre and subsequent cellulose depolymerization.", "doi": "10.1038/ncomms8542", "pmid": "26151670", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "ncomms8542"}, {"db": "pmc", "key": "PMC4507011"}, {"db": "PDB", "key": "4QI3"}, {"db": "PDB", "key": "4QI4"}, {"db": "PDB", "key": "4QI5"}, {"db": "PDB", "key": "4QI6"}, {"db": "PDB", "key": "4QI7"}, {"db": "PDB", "key": "4QI8"}], "notes": [], "created": "2017-05-02T12:58:44.144Z", "modified": "2017-09-06T11:42:09.152Z"}, {"entity": "publication", "iuid": "d16c2a4a4c114d26aed8e150867bcbbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d16c2a4a4c114d26aed8e150867bcbbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d16c2a4a4c114d26aed8e150867bcbbb"}}, "title": "Proximity-dependent initiation of hybridization chain reaction.", "authors": [{"family": "Koos", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Cane", "given": "Ga\u00eblle", "initials": "G"}, {"family": "Grannas", "given": "Karin", "initials": "K"}, {"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Arng\u00e5rden", "given": "Linda", "initials": "L"}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Clausson", "given": "Carl-Magnus", "initials": "CM"}, {"family": "Klaesson", "given": "Axel", "initials": "A"}, {"family": "Hirvonen", "given": "M Karoliina", "initials": "MK"}, {"family": "de Oliveira", "given": "Felipe M S", "initials": "FM", "orcid": "0000-0001-6074-7462", "researcher": {"href": "https://publications.scilifelab.se/researcher/e21dfb5c78b94f9f8631d4bdba6cf9e6.json"}}, {"family": "Talibov", "given": "Vladimir O", "initials": "VO", "orcid": "0000-0002-1135-2744", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2cdaf464ed342d695baf33c19690518.json"}}, {"family": "Pham", "given": "Nhan T", "initials": "NT"}, {"family": "Auer", "given": "Manfred", "initials": "M"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}, {"family": "Haybaeck", "given": "Johannes", "initials": "J", "orcid": "0000-0001-5518-3359", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7ed164711b3491489b91d7ecc35f63b.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.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": "2015-06-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "6", "pages": "7294", "issn-l": "2041-1723"}, "abstract": "Sensitive detection of protein interactions and post-translational modifications of native proteins is a challenge for research and diagnostic purposes. A method for this, which could be used in point-of-care devices and high-throughput screening, should be reliable, cost effective and robust. To achieve this, here we design a method (proxHCR) that combines the need for proximal binding with hybridization chain reaction (HCR) for signal amplification. When two oligonucleotide hairpins conjugated to antibodies bind in close proximity, they can be activated to reveal an initiator sequence. This starts a chain reaction of hybridization events between a pair of fluorophore-labelled oligonucleotide hairpins, generating a fluorescent product. In conclusion, we show the applicability of the proxHCR method for the detection of protein interactions and posttranslational modifications in microscopy and flow cytometry. As no enzymes are needed, proxHCR may be an inexpensive and robust alternative to proximity ligation assays.", "doi": "10.1038/ncomms8294", "pmid": "26065580", "labels": {"PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4490387"}, {"db": "pii", "key": "ncomms8294"}], "notes": [], "created": "2023-06-16T12:43:37.596Z", "modified": "2023-06-16T12:44:14.437Z"}, {"entity": "publication", "iuid": "4fc3954e096f41c2822af003ff117b3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4fc3954e096f41c2822af003ff117b3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4fc3954e096f41c2822af003ff117b3d"}}, "title": "Phasing of single DNA molecules by massively parallel barcoding.", "authors": [{"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Redin", "given": "David", "initials": "D"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Berglund", "given": "Emelie", "initials": "E"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2015-06-09", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "7173", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.", "doi": "10.1038/ncomms8173", "pmid": "26055759", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ncomms8173"}, {"db": "pmc", "key": "PMC4468844"}, {"db": "SRA", "key": "SRA248941"}], "notes": [], "created": "2017-05-02T12:56:38.182Z", "modified": "2020-01-21T13:56:02.259Z"}, {"entity": "publication", "iuid": "7e5be0d2a9ae42819cedf06a84f51900", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e5be0d2a9ae42819cedf06a84f51900.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e5be0d2a9ae42819cedf06a84f51900"}}, "title": "Evolutionary analysis of the female-specific avian W chromosome.", "authors": [{"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Warmuth", "given": "Vera", "initials": "V"}, {"family": "Bolivar", "given": "Paulina", "initials": "P"}, {"family": "Uebbing", "given": "Severin", "initials": "S"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Nater", "given": "Alexander", "initials": "A"}, {"family": "Bure\u0161", "given": "Stanislav", "initials": "S"}, {"family": "Garamszegi", "given": "Laszlo Z", "initials": "LZ"}, {"family": "Hogner", "given": "Silje", "initials": "S"}, {"family": "Moreno", "given": "Juan", "initials": "J"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Ru\u017ei\u0107", "given": "Milan", "initials": "M"}, {"family": "S\u00e6ther", "given": "Stein-Are", "initials": "SA"}, {"family": "S\u00e6tre", "given": "Glenn-Peter", "initials": "GP"}, {"family": "T\u00f6r\u00f6k", "given": "Janos", "initials": "J"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2015-06-04", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "7330", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear-cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution.", "doi": "10.1038/ncomms8330", "pmid": "26040272", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ncomms8330"}, {"db": "pmc", "key": "PMC4468903"}, {"db": "mid", "key": "EMS63233"}, {"db": "BioProject", "key": "PRJEB7359"}], "notes": [], "created": "2017-05-02T12:58:36.293Z", "modified": "2020-01-21T13:56:03.269Z"}, {"entity": "publication", "iuid": "95d99038b0d24c8994108c7b2be420fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95d99038b0d24c8994108c7b2be420fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95d99038b0d24c8994108c7b2be420fa"}}, "title": "Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility.", "authors": [{"family": "Wessel", "given": "Jennifer", "initials": "J"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Wang", "given": "Shuai", "initials": "S"}, {"family": "Yaghootkar", "given": "Hanieh", "initials": "H"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Dauriz", "given": "Marco", "initials": "M"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Raghavan", "given": "Sridharan", "initials": "S"}, {"family": "Lipovich", "given": "Leonard", "initials": "L"}, {"family": "Hidalgo", "given": "Bertha", "initials": "B"}, {"family": "Fox", "given": "Keolu", "initials": "K"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "An", "given": "Ping", "initials": "P"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Rasmussen-Torvik", "given": "Laura J", "initials": "LJ"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Ehm", "given": "Margaret G", "initials": "MG"}, {"family": "Li", "given": "Li", "initials": "L"}, {"family": "Baldridge", "given": "Abigail S", "initials": "AS"}, {"family": "Stan\u010d\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Abrol", "given": "Ravinder", "initials": "R"}, {"family": "Besse", "given": "C\u00e9line", "initials": "C"}, {"family": "Boland", "given": "Anne", "initials": "A"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Freitag", "given": "Daniel F", "initials": "DF"}, {"family": "Garcia", "given": "Melissa E", "initials": "ME"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Hara", "given": "Kazuo", "initials": "K"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Jakobsdottir", "given": "Johanna", "initials": "J"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Layton", "given": "Jill C", "initials": "JC"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Hua Zhao", "given": "Jing", "initials": "J"}, {"family": "Meidtner", "given": "Karina", "initials": "K"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Peters", "given": "Marjolein J", "initials": "MJ"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Schurmann", "given": "Claudia", "initials": "C"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Southam", "given": "Lorraine", "initials": "L"}, {"family": "Stoiber", "given": "Marcus H", "initials": "MH"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Allin", "given": "Kristine H", "initials": "KH"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Aponte", "given": "Jennifer L", "initials": "JL"}, {"family": "Aung", "given": "Tin", "initials": "T"}, {"family": "Barbieri", "given": "Caterina", "initials": "C"}, {"family": "Bihlmeyer", "given": "Nathan A", "initials": "NA"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Bombieri", "given": "Cristina", "initials": "C"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "Burns", "given": "Sean M", "initials": "SM"}, {"family": "Chen", "given": "Yuning", "initials": "Y"}, {"family": "Chen", "given": "Yii-DerI", "initials": "YD"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Czajkowski", "given": "Jacek", "initials": "J"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Ehret", "given": "Georg B", "initials": "GB"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Escher", "given": "Stefan 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{"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "Karaleftheri", "given": "Maria", "initials": "M"}, {"family": "Khor", "given": "Chiea C", "initials": "CC"}, {"family": "Kirkpatrick", "given": "Andrea", "initials": "A"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Lange", "given": "Ethan M", "initials": "EM"}, {"family": "Lee", "given": "I T", "initials": "IT"}, {"family": "Lee", "given": "Wen-Jane", "initials": "WJ"}, {"family": "Leong", "given": "Aaron", "initials": "A"}, {"family": "Liao", "given": "Jiemin", "initials": "J"}, {"family": "Liu", "given": "Chunyu", "initials": "C"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Malerba", "given": "Giovanni", "initials": "G"}, {"family": "Mamakou", "given": "Vasiliki", "initials": "V"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Maruthur", "given": "Nisa M", "initials": "NM"}, {"family": "Matchan", "given": "Angela", "initials": "A"}, {"family": "McKean-Cowdin", "given": "Roberta", "initials": "R"}, {"family": "McLeod", "given": "Olga", "initials": "O"}, {"family": "Metcalf", "given": "Ginger A", "initials": "GA"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Muzny", "given": "Donna M", "initials": "DM"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Palmer", "given": "Nicholette D", "initials": "ND"}, {"family": "Pasko", "given": "Dorota", "initials": "D"}, {"family": "Peter", "given": "Andreas", "initials": "A"}, {"family": "Rayner", "given": "Nigel W", "initials": "NW"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Rice", "given": "Ken", "initials": "K"}, {"family": "Sala", "given": "Cinzia F", "initials": "CF"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Serafetinidis", "given": "Ioannis", "initials": "I"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "Stahl", "given": "Eli A", "initials": "EA"}, {"family": "Stirrups", "given": "Kathleen", "initials": "K"}, {"family": "Tentolouris", "given": "Nikos", "initials": "N"}, {"family": "Thanopoulou", "given": "Anastasia", "initials": "A"}, {"family": "Torres", "given": "Mina", "initials": "M"}, {"family": "Traglia", "given": "Michela", "initials": "M"}, {"family": "Tsafantakis", "given": "Emmanouil", "initials": "E"}, {"family": "Javad", "given": "Sundas", "initials": "S"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR"}, {"family": "Zengini", "given": "Eleni", "initials": "E"}, {"family": "Becker", "given": "Diane M", "initials": "DM"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Brown", "given": "James B", "initials": "JB"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Karter", "given": "Andrew J", "initials": "AJ"}, {"family": "Lorenzo", "given": "Carlos", "initials": "C"}, {"family": "Mathias", "given": "Rasika A", "initials": "RA"}, {"family": "Norris", "given": "Jill M", "initials": "JM"}, {"family": "Peloso", "given": "Gina M", "initials": "GM"}, {"family": "Sheu", "given": "Wayne H-H", "initials": "WH"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Vaidya", "given": "Dhananjay", "initials": "D"}, {"family": "Varma", "given": "Rohit", "initials": "R"}, {"family": "Wagenknecht", "given": "Lynne E", "initials": "LE"}, {"family": "Boeing", "given": "Heiner", "initials": "H"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Ferrannini", "given": "Ele", "initials": "E"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Gibbs", "given": "Richard A", "initials": "RA"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hattersley", "given": "Andrew T", "initials": "AT"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Jansson", "given": "Jan-H\u00e5kan", "initials": "JH"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "O'Rahilly", "given": "Stephen", "initials": "S"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Wong", "given": "Tien Y", "initials": "TY"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "EPIC-InterAct Consortium", "given": "", "initials": ""}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}], "type": "journal article", "published": "2015-01-29", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "5897", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Fasting glucose and insulin are intermediate traits for type 2 diabetes. Here we explore the role of coding variation on these traits by analysis of variants on the HumanExome BeadChip in 60,564 non-diabetic individuals and in 16,491 T2D cases and 81,877 controls. We identify a novel association of a low-frequency nonsynonymous SNV in GLP1R (A316T; rs10305492; MAF=1.4%) with lower FG (\u03b2=-0.09\u00b10.01\u2009mmol\u2009l(-1), P=3.4 \u00d7 10(-12)), T2D risk (OR[95%CI]=0.86[0.76-0.96], P=0.010), early insulin secretion (\u03b2=-0.07\u00b10.035\u2009pmolinsulin mmolglucose(-1), P=0.048), but higher 2-h glucose (\u03b2=0.16\u00b10.05\u2009mmol\u2009l(-1), P=4.3 \u00d7 10(-4)). We identify a gene-based association with FG at G6PC2 (pSKAT=6.8 \u00d7 10(-6)) driven by four rare protein-coding SNVs (H177Y, Y207S, R283X and S324P). We identify rs651007 (MAF=20%) in the first intron of ABO at the putative promoter of an antisense lncRNA, associating with higher FG (\u03b2=0.02\u00b10.004\u2009mmol\u2009l(-1), P=1.3 \u00d7 10(-8)). Our approach identifies novel coding variant associations and extends the allelic spectrum of variation underlying diabetes-related quantitative traits and T2D susceptibility.", "doi": "10.1038/ncomms6897", "pmid": "25631608", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms6897"}, {"db": "pmc", "key": "PMC4311266"}, {"db": "mid", "key": "NIHMS642453"}], "notes": [], "created": "2017-10-30T13:12:56.257Z", "modified": "2020-01-21T13:56:08.162Z"}, {"entity": "publication", "iuid": "f0030f2c2a5446f0b28876e29f1b16f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0030f2c2a5446f0b28876e29f1b16f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0030f2c2a5446f0b28876e29f1b16f4"}}, "title": "Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer.", "authors": [{"family": "Mengelbier", "given": "Linda Holmquist", "initials": "LH"}, {"family": "Karlsson", "given": "Jenny", "initials": "J"}, {"family": "Lindgren", "given": "David", "initials": "D"}, {"family": "Valind", "given": "Anders", "initials": "A"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Jansson", "given": "Caroline", "initials": "C"}, {"family": "Bexell", "given": "Daniel", "initials": "D"}, {"family": "Braekeveldt", "given": "No\u00e9mie", "initials": "N"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Jonson", "given": "Tord", "initials": "T"}, {"family": "Kultima", "given": "Hanna G\u00f6ransson", "initials": "HG"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Asmundsson", "given": "Jurate", "initials": "J"}, {"family": "Versteeg", "given": "Rogier", "initials": "R"}, {"family": "Rissler", "given": "Marianne", "initials": "M"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Sandstedt", "given": "Bengt", "initials": "B"}, {"family": "B\u00f6rjesson", "given": "Anna", "initials": "A"}, {"family": "Backman", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Pal", "given": "Niklas", "initials": "N"}, {"family": "\u00d8ra", "given": "Ingrid", "initials": "I"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Gisselsson", "given": "David", "initials": "D"}], "type": "journal article", "published": "2015-01-27", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "6125", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Genetic differences among neoplastic cells within the same tumour have been proposed to drive cancer progression and treatment failure. Whether data on intratumoral diversity can be used to predict clinical outcome remains unclear. We here address this issue by quantifying genetic intratumoral diversity in a set of chemotherapy-treated childhood tumours. By analysis of multiple tumour samples from seven patients we demonstrate intratumoral diversity in all patients analysed after chemotherapy, typically presenting as multiple clones within a single millimetre-sized tumour sample (microdiversity). We show that microdiversity often acts as the foundation for further genome evolution in metastases. In addition, we find that microdiversity predicts poor cancer-specific survival (60%; P=0.009), independent of other risk factors, in a cohort of 44 patients with chemotherapy-treated childhood kidney cancer. Survival was 100% for patients lacking microdiversity. Thus, intratumoral genetic diversity is common in childhood cancers after chemotherapy and may be an important factor behind treatment failure.", "doi": "10.1038/ncomms7125", "pmid": "25625758", "labels": {"National Genomics Infrastructure": null, "Array and Analysis Facility": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ncomms7125"}], "notes": [], "created": "2017-05-02T12:57:43.059Z", "modified": "2021-07-07T14:37:06.646Z"}, {"entity": "publication", "iuid": "63b0dfa07cb74dd9bdd4c6ff30277415", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63b0dfa07cb74dd9bdd4c6ff30277415.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63b0dfa07cb74dd9bdd4c6ff30277415"}}, "title": "Biological interpretation of genome-wide association studies using predicted gene functions.", "authors": [{"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Karjalainen", "given": "Juha M", "initials": "JM"}, {"family": "Chan", "given": "Yingleong", "initials": "Y"}, {"family": "Westra", "given": "Harm-Jan", "initials": "HJ"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Lui", "given": "Julian C", "initials": "JC"}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Esko", "given": "Tonu", "initials": "T"}, {"family": "Frayling", "given": "Tim", "initials": "T"}, {"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "Genetic Investigation of ANthropometric Traits (GIANT) Consortium", "given": "", "initials": ""}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Raychaudhuri", "given": "Soumya", "initials": "S"}, {"family": "Fehrmann", "given": "Rudolf S N", "initials": "RS"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Franke", "given": "Lude", "initials": "L"}], "type": "journal article", "published": "2015-01-19", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "5890", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The main challenge for gaining biological insights from genetic associations is identifying which genes and pathways explain the associations. Here we present DEPICT, an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes.", "doi": "10.1038/ncomms6890", "pmid": "25597830", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms6890"}, {"db": "pmc", "key": "PMC4420238"}, {"db": "mid", "key": "NIHMS682773"}], "notes": [], "created": "2017-10-30T13:12:55.291Z", "modified": "2020-01-21T13:56:08.174Z"}, {"entity": "publication", "iuid": "422ac06b69a9438ab2116ba55bd587c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/422ac06b69a9438ab2116ba55bd587c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/422ac06b69a9438ab2116ba55bd587c7"}}, "title": "The statistical geometry of transcriptome divergence in cell-type evolution and cancer.", "authors": [{"family": "Liang", "given": "Cong", "initials": "C"}, {"family": "FANTOM Consortium", "given": null, "initials": null}, {"family": "Forrest", "given": "Alistair R R", "initials": "AR"}, {"family": "Wagner", "given": "G\u00fcnter P", "initials": "GP"}], "type": "journal article", "published": "2015-01-14", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "6066", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination.", "doi": "10.1038/ncomms7066", "pmid": "25585899", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "ncomms7066"}], "notes": [], "created": "2017-05-02T12:57:47.832Z", "modified": "2020-01-21T13:53:20.481Z"}, {"entity": "publication", "iuid": "7fc7fd871da94b569b401dea2017da23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fc7fd871da94b569b401dea2017da23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fc7fd871da94b569b401dea2017da23"}}, "title": "Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes", "authors": [{"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Bolivar", "given": "Paulina", "initials": "P"}, {"family": "Husby", "given": "Arild", "initials": "A"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Uebbing", "given": "Severin", "initials": "S"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2014-11-07", "journal": {"volume": "5", "issn": "2041-1723", "issue": null, "pages": "5448", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/ncomms6448", "pmid": "25378102", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:37:10.825Z", "modified": "2020-01-21T13:56:09.958Z"}, {"entity": "publication", "iuid": "ec9a4e98da2445e2b76c2a3e03754045", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec9a4e98da2445e2b76c2a3e03754045.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec9a4e98da2445e2b76c2a3e03754045"}}, "title": "Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.", "authors": [{"family": "Ghoussaini", "given": "Maya", "initials": "M"}, {"family": "Edwards", "given": "Stacey L", "initials": "SL"}, {"family": "Michailidou", "given": "Kyriaki", "initials": "K"}, {"family": "Nord", "given": "Silje", "initials": "S"}, {"family": "Cowper-Sal Lari", "given": "Richard", "initials": "R"}, {"family": "Desai", "given": "Kinjal", "initials": "K"}, {"family": "Kar", "given": "Siddhartha", "initials": "S"}, {"family": "Hillman", "given": "Kristine M", "initials": "KM"}, {"family": "Kaufmann", "given": "Susanne", "initials": "S"}, {"family": "Glubb", "given": "Dylan M", "initials": "DM"}, {"family": "Beesley", "given": "Jonathan", "initials": "J"}, {"family": "Dennis", "given": "Joe", "initials": "J"}, {"family": "Bolla", "given": "Manjeet K", "initials": "MK"}, {"family": "Wang", "given": "Qin", "initials": "Q"}, {"family": "Dicks", "given": "Ed", "initials": "E"}, {"family": "Guo", "given": "Qi", "initials": "Q"}, {"family": "Schmidt", "given": "Marjanka K", "initials": "MK"}, {"family": "Shah", "given": "Mitul", "initials": "M"}, {"family": "Luben", "given": "Robert", "initials": "R"}, {"family": "Brown", "given": "Judith", "initials": "J"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Darabi", "given": "Hatef", "initials": "H"}, {"family": "Eriksson", "given": "Mikael", "initials": "M"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Bojesen", "given": "Stig E", "initials": "SE"}, {"family": "Nordestgaard", "given": "B\u00f8rge G", "initials": "BG"}, {"family": "Nielsen", "given": "Sune F", "initials": "SF"}, {"family": "Flyger", "given": "Henrik", "initials": "H"}, {"family": "Lambrechts", "given": "Diether", "initials": "D"}, {"family": "Thienpont", "given": "Bernard", "initials": "B"}, {"family": "Neven", "given": "Patrick", "initials": "P"}, {"family": "Wildiers", "given": "Hans", "initials": "H"}, {"family": "Broeks", "given": "Annegien", "initials": "A"}, {"family": "Van't Veer", "given": "Laura J", "initials": "LJ"}, {"family": "Th Rutgers", "given": "Emiel J", "initials": "EJ"}, {"family": "Couch", "given": "Fergus J", "initials": "FJ"}, {"family": "Olson", "given": "Janet E", "initials": "JE"}, {"family": "Hallberg", "given": "Emily", "initials": "E"}, {"family": "Vachon", "given": "Celine", "initials": "C"}, {"family": "Chang-Claude", "given": "Jenny", "initials": "J"}, {"family": "Rudolph", "given": "Anja", "initials": "A"}, {"family": "Seibold", "given": "Petra", "initials": "P"}, {"family": "Flesch-Janys", "given": "Dieter", "initials": "D"}, {"family": "Peto", "given": "Julian", "initials": "J"}, {"family": "Dos-Santos-Silva", "given": "Isabel", "initials": "I"}, {"family": "Gibson", "given": "Lorna", "initials": "L"}, {"family": "Nevanlinna", "given": "Heli", "initials": "H"}, {"family": "Muranen", "given": "Taru A", "initials": "TA"}, {"family": "Aittom\u00e4ki", "given": "Kristiina", "initials": "K"}, {"family": "Blomqvist", "given": "Carl", "initials": "C"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Li", "given": "Jingmei", "initials": "J"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Humphreys", "given": "Keith", "initials": "K"}, {"family": "Kang", "given": "Daehee", "initials": "D"}, {"family": "Choi", "given": "Ji-Yeob", "initials": "JY"}, {"family": "Park", "given": "Sue K", "initials": "SK"}, {"family": "Noh", "given": "Dong-Young", "initials": "DY"}, {"family": "Matsuo", "given": "Keitaro", "initials": "K"}, {"family": "Ito", "given": "Hidemi", "initials": "H"}, {"family": "Iwata", "given": "Hiroji", "initials": "H"}, {"family": "Yatabe", "given": "Yasushi", "initials": "Y"}, {"family": "Gu\u00e9nel", "given": "Pascal", "initials": "P"}, {"family": "Truong", "given": "Th\u00e9r\u00e8se", "initials": "T"}, {"family": "Menegaux", "given": "Florence", "initials": "F"}, {"family": "Sanchez", "given": "Marie", "initials": "M"}, {"family": "Burwinkel", "given": "Barbara", "initials": "B"}, {"family": "Marme", "given": "Frederik", "initials": "F"}, {"family": "Schneeweiss", "given": "Andreas", "initials": "A"}, {"family": "Sohn", "given": "Christof", "initials": "C"}, {"family": "Wu", "given": "Anna H", "initials": "AH"}, {"family": "Tseng", "given": "Chiu-Chen", "initials": "CC"}, {"family": "Van Den Berg", "given": "David", "initials": "D"}, {"family": "Stram", "given": "Daniel O", "initials": "DO"}, {"family": "Benitez", "given": "Javier", "initials": "J"}, {"family": "Zamora", "given": "M Pilar", "initials": "MP"}, {"family": "Perez", "given": "Jose Ignacio Arias", "initials": "JI"}, {"family": "Men\u00e9ndez", "given": "Primitiva", "initials": "P"}, {"family": "Shu", "given": "Xiao-Ou", "initials": "XO"}, {"family": "Lu", "given": "Wei", "initials": "W"}, {"family": "Gao", "given": "Yu-Tang", "initials": "YT"}, {"family": "Cai", "given": "Qiuyin", "initials": "Q"}, {"family": "Cox", "given": "Angela", "initials": "A"}, {"family": "Cross", "given": "Simon S", "initials": "SS"}, {"family": "Reed", "given": "Malcolm W R", "initials": "MW"}, {"family": "Andrulis", "given": "Irene L", "initials": "IL"}, {"family": "Knight", "given": "Julia A", "initials": "JA"}, {"family": "Glendon", "given": "Gord", "initials": "G"}, {"family": "Tchatchou", "given": "Sandrine", "initials": "S"}, {"family": "Sawyer", "given": "Elinor J", "initials": "EJ"}, {"family": "Tomlinson", "given": "Ian", "initials": "I"}, {"family": "Kerin", "given": "Michael J", "initials": "MJ"}, {"family": "Miller", "given": "Nicola", "initials": "N"}, {"family": "Haiman", "given": "Christopher A", "initials": "CA"}, {"family": "Henderson", "given": "Brian E", "initials": "BE"}, {"family": "Schumacher", "given": "Fredrick", "initials": "F"}, {"family": "Le Marchand", "given": "Loic", "initials": "L"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}, {"family": "Margolin", "given": "Sara", "initials": "S"}, {"family": "Teo", "given": "Soo Hwang", "initials": "SH"}, {"family": "Yip", "given": "Cheng Har", "initials": "CH"}, {"family": "Lee", "given": "Daphne S C", "initials": "DS"}, {"family": "Wong", "given": "Tien Y", "initials": "TY"}, {"family": "Hooning", "given": "Maartje J", "initials": "MJ"}, {"family": "Martens", "given": "John W M", "initials": "JW"}, {"family": "Coll\u00e9e", "given": "J Margriet", "initials": "JM"}, {"family": "van Deurzen", "given": "Carolien H M", "initials": "CH"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Southey", "given": "Melissa C", "initials": "MC"}, {"family": "Tsimiklis", "given": "Helen", "initials": "H"}, {"family": "Kapuscinski", "given": "Miroslav K", "initials": "MK"}, {"family": "Shen", "given": "Chen-Yang", "initials": "CY"}, {"family": "Wu", "given": "Pei-Ei", "initials": "PE"}, {"family": "Yu", "given": "Jyh-Cherng", "initials": "JC"}, {"family": "Chen", "given": "Shou-Tung", "initials": "ST"}, {"family": "Aln\u00e6s", "given": "Grethe Grenaker", "initials": "GG"}, {"family": "Borresen-Dale", "given": "Anne-Lise", "initials": "AL"}, {"family": "Giles", "given": "Graham G", "initials": "GG"}, {"family": "Milne", "given": "Roger L", "initials": "RL"}, {"family": "McLean", "given": "Catriona", "initials": "C"}, {"family": "Muir", "given": "Kenneth", "initials": "K"}, {"family": "Lophatananon", "given": "Artitaya", "initials": "A"}, {"family": "Stewart-Brown", "given": "Sarah", "initials": "S"}, {"family": "Siriwanarangsan", "given": "Pornthep", "initials": "P"}, {"family": "Hartman", "given": "Mikael", "initials": "M"}, {"family": "Miao", "given": "Hui", "initials": "H"}, {"family": "Buhari", "given": "Shaik Ahmad Bin Syed", "initials": "SA"}, {"family": "Teo", "given": "Yik Ying", "initials": "YY"}, {"family": "Fasching", "given": "Peter A", "initials": "PA"}, {"family": "Haeberle", "given": "Lothar", "initials": "L"}, {"family": "Ekici", "given": "Arif B", "initials": "AB"}, {"family": "Beckmann", "given": "Matthias W", "initials": "MW"}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Dieffenbach", "given": "Aida Karina", "initials": "AK"}, {"family": "Arndt", "given": "Volker", "initials": "V"}, {"family": "Stegmaier", "given": "Christa", "initials": "C"}, {"family": "Swerdlow", "given": "Anthony", "initials": "A"}, {"family": "Ashworth", "given": "Alan", "initials": "A"}, {"family": "Orr", "given": "Nick", "initials": "N"}, {"family": "Schoemaker", "given": "Minouk J", "initials": "MJ"}, {"family": "Garc\u00eda-Closas", "given": "Montserrat", "initials": "M"}, {"family": "Figueroa", "given": "Jonine", "initials": "J"}, {"family": "Chanock", "given": "Stephen J", "initials": "SJ"}, {"family": "Lissowska", "given": "Jolanta", "initials": "J"}, {"family": "Simard", "given": "Jacques", "initials": "J"}, {"family": "Goldberg", "given": "Mark S", "initials": "MS"}, {"family": "Labr\u00e8che", "given": "France", "initials": "F"}, {"family": "Dumont", "given": "Martine", "initials": "M"}, {"family": "Winqvist", "given": "Robert", "initials": "R"}, {"family": "Pylk\u00e4s", "given": "Katri", "initials": "K"}, {"family": "Jukkola-Vuorinen", "given": "Arja", "initials": "A"}, {"family": "Brauch", "given": "Hiltrud", "initials": "H"}, {"family": "Br\u00fcning", "given": "Thomas", "initials": "T"}, {"family": "Koto", "given": "Yon-Dschun", "initials": "YD"}, {"family": "Radice", "given": "Paolo", "initials": "P"}, {"family": "Peterlongo", "given": "Paolo", "initials": "P"}, {"family": "Bonanni", "given": "Bernardo", "initials": "B"}, {"family": "Volorio", "given": "Sara", "initials": "S"}, {"family": "D\u00f6rk", "given": "Thilo", "initials": "T"}, {"family": "Bogdanova", "given": "Natalia V", "initials": "NV"}, {"family": "Helbig", "given": "Sonja", "initials": "S"}, {"family": "Mannermaa", "given": "Arto", "initials": "A"}, {"family": "Kataja", "given": "Vesa", "initials": "V"}, {"family": "Kosma", "given": "Veli-Matti", "initials": "VM"}, {"family": "Hartikainen", "given": "Jaana M", "initials": "JM"}, {"family": "Devilee", "given": "Peter", "initials": "P"}, {"family": "Tollenaar", "given": "Robert A E M", "initials": "RA"}, {"family": "Seynaeve", "given": "Caroline", "initials": "C"}, {"family": "Van Asperen", "given": "Christi J", "initials": "CJ"}, {"family": "Jakubowska", "given": "Anna", "initials": "A"}, {"family": "Lubinski", "given": "Jan", "initials": "J"}, {"family": "Jaworska-Bieniek", "given": "Katarzyna", "initials": "K"}, {"family": "Durda", "given": "Katarzyna", "initials": "K"}, {"family": "Slager", "given": "Susan", "initials": "S"}, {"family": "Toland", "given": "Amanda E", "initials": "AE"}, {"family": "Ambrosone", "given": "Christine B", "initials": "CB"}, {"family": "Yannoukakos", "given": "Drakoulis", "initials": "D"}, {"family": "Sangrajrang", "given": "Suleeporn", "initials": "S"}, {"family": "Gaborieau", "given": "Valerie", "initials": "V"}, {"family": "Brennan", "given": "Paul", "initials": "P"}, {"family": "McKay", "given": "James", "initials": "J"}, {"family": "Hamann", "given": "Ute", "initials": "U"}, {"family": "Torres", "given": "Diana", "initials": "D"}, {"family": "Zheng", "given": "Wei", "initials": "W"}, {"family": "Long", "given": "Jirong", "initials": "J"}, {"family": "Anton-Culver", "given": "Hoda", "initials": "H"}, {"family": "Neuhausen", "given": "Susan L", "initials": "SL"}, {"family": "Luccarini", "given": "Craig", "initials": "C"}, {"family": "Baynes", "given": "Caroline", "initials": "C"}, {"family": "Ahmed", "given": "Shahana", "initials": "S"}, {"family": "Maranian", "given": "Mel", "initials": "M"}, {"family": "Healey", "given": "Catherine S", "initials": "CS"}, {"family": "Gonz\u00e1lez-Neira", "given": "Anna", "initials": "A"}, {"family": "Pita", "given": "Guillermo", "initials": "G"}, {"family": "Alonso", "given": "M Rosario", "initials": "MR"}, {"family": "Alvarez", "given": "Nuria", "initials": "N"}, {"family": "Herrero", "given": "Daniel", "initials": "D"}, {"family": "Tessier", "given": "Daniel C", "initials": "DC"}, {"family": "Vincent", "given": "Daniel", "initials": "D"}, {"family": "Bacot", "given": "Francois", "initials": "F"}, {"family": "de Santiago", "given": "Ines", "initials": "I"}, {"family": "Carroll", "given": "Jason", "initials": "J"}, {"family": "Caldas", "given": "Carlos", "initials": "C"}, {"family": "Brown", "given": "Melissa A", "initials": "MA"}, {"family": "Lupien", "given": "Mathieu", "initials": "M"}, {"family": "Kristensen", "given": "Vessela N", "initials": "VN"}, {"family": "Pharoah", "given": "Paul D P", "initials": "PD"}, {"family": "Chenevix-Trench", "given": "Georgia", "initials": "G"}, {"family": "French", "given": "Juliet D", "initials": "JD"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Dunning", "given": "Alison M", "initials": "AM"}, {"family": "Australian Ovarian Cancer Management Group", "given": "", "initials": ""}], "type": "journal article", "published": "2014-09-23", "journal": {"volume": "4", "issn": "2041-1723", "issue": "1", "pages": "4999", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "GWAS have identified a breast cancer susceptibility locus on 2q35. Here we report the fine mapping of this locus using data from 101,943 subjects from 50 case-control studies. We genotype 276 SNPs using the 'iCOGS' genotyping array and impute genotypes for a further 1,284 using 1000 Genomes Project data. All but two, strongly correlated SNPs (rs4442975 G/T and rs6721996 G/A) are excluded as candidate causal variants at odds against >100:1. The best functional candidate, rs4442975, is associated with oestrogen receptor positive (ER+) disease with an odds ratio (OR) in Europeans of 0.85 (95% confidence interval=0.84-0.87; P=1.7 \u00d7 10(-43)) per t-allele. This SNP flanks a transcriptional enhancer that physically interacts with the promoter of IGFBP5 (encoding insulin-like growth factor-binding protein 5) and displays allele-specific gene expression, FOXA1 binding and chromatin looping. Evidence suggests that the g-allele confers increased breast cancer susceptibility through relative downregulation of IGFBP5, a gene with known roles in breast cell biology.", "doi": "10.1038/ncomms5999", "pmid": "25248036", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "mid", "key": "NIHMS654459"}, {"db": "pmc", "key": "PMC4321900"}, {"db": "pii", "key": "ncomms5999"}], "notes": [], "created": "2017-05-04T14:58:46.423Z", "modified": "2023-06-19T11:18:30.504Z"}, {"entity": "publication", "iuid": "04969cb9430a410798ba87f6a197d420", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04969cb9430a410798ba87f6a197d420.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04969cb9430a410798ba87f6a197d420"}}, "title": "The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.", "authors": [{"family": "Ahola", "given": "Virpi", "initials": "V"}, {"family": "Lehtonen", "given": "Rainer", "initials": "R"}, {"family": "Somervuo", "given": "Panu", "initials": "P"}, {"family": "Salmela", "given": "Leena", "initials": "L"}, {"family": "Koskinen", "given": "Patrik", "initials": "P"}, {"family": "Rastas", "given": "Pasi", "initials": "P"}, {"family": "V\u00e4lim\u00e4ki", "given": "Niko", "initials": "N"}, {"family": "Paulin", "given": "Lars", "initials": "L"}, {"family": "Kvist", "given": "Jouni", "initials": "J"}, {"family": "Wahlberg", "given": "Niklas", "initials": "N"}, {"family": "Tanskanen", "given": "Jaakko", "initials": "J"}, {"family": "Hornett", "given": "Emily A", "initials": "EA"}, {"family": "Ferguson", "given": "Laura C", "initials": "LC"}, {"family": "Luo", "given": "Shiqi", "initials": "S"}, {"family": "Cao", "given": "Zijuan", "initials": "Z"}, {"family": "de Jong", "given": "Maaike A", "initials": "MA"}, {"family": "Duplouy", "given": "Anne", "initials": "A"}, {"family": "Smolander", "given": "Olli-Pekka", "initials": "OP"}, {"family": "Vogel", "given": "Heiko", "initials": "H"}, {"family": "McCoy", "given": "Rajiv C", "initials": "RC"}, {"family": "Qian", "given": "Kui", "initials": "K"}, {"family": "Chong", "given": "Wong Swee", "initials": "WS"}, {"family": "Zhang", "given": "Qin", "initials": "Q"}, {"family": "Ahmad", "given": "Freed", "initials": "F"}, {"family": "Haukka", "given": "Jani K", "initials": "JK"}, {"family": "Joshi", "given": "Aruj", "initials": "A"}, {"family": "Saloj\u00e4rvi", "given": "Jarkko", "initials": "J"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Grosse-Wilde", "given": "Ewald", "initials": "E"}, {"family": "Hughes", "given": "Daniel", "initials": "D"}, {"family": "Katainen", "given": "Riku", "initials": "R"}, {"family": "Pitk\u00e4nen", "given": "Esa", "initials": "E"}, {"family": "Ylinen", "given": "Johannes", "initials": "J"}, {"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "V\u00e4h\u00e4rautio", "given": "Anna", "initials": "A"}, {"family": "Ojanen", "given": "Sami P", "initials": "SP"}, {"family": "Schulman", "given": "Alan H", "initials": "AH"}, {"family": "Taipale", "given": "Minna", "initials": "M"}, {"family": "Lawson", "given": "Daniel", "initials": "D"}, {"family": "Ukkonen", "given": "Esko", "initials": "E"}, {"family": "M\u00e4kinen", "given": "Veli", "initials": "V"}, {"family": "Goldsmith", "given": "Marian R", "initials": "MR"}, {"family": "Holm", "given": "Liisa", "initials": "L"}, {"family": "Auvinen", "given": "Petri", "initials": "P"}, {"family": "Frilander", "given": "Mikko J", "initials": "MJ"}, {"family": "Hanski", "given": "Ilkka", "initials": "I"}], "type": "journal article", "published": "2014-09-05", "journal": {"volume": "5", "issn": "2041-1723", "issue": null, "pages": "4737", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393\u2009Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n=31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n=31 for at least 140\u2009My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.", "doi": "10.1038/ncomms5737", "pmid": "25189940", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "ncomms5737"}, {"db": "pmc", "key": "PMC4164777"}, {"db": "mid", "key": "EMS59677"}, {"db": "GENBANK", "key": "APLT00000000"}], "notes": [], "created": "2017-05-04T14:57:08.111Z", "modified": "2017-05-30T14:30:23.346Z"}, {"entity": "publication", "iuid": "14dd4b04dcad4612b4f6ca37502797fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14dd4b04dcad4612b4f6ca37502797fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14dd4b04dcad4612b4f6ca37502797fc"}}, "title": "Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs.", "authors": [{"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Enroth", "given": "Sofia Bosdotter", "initials": "SB"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2014-08-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "5", "issue": "1", "pages": "4684"}, "abstract": "Ideal biomarkers used for disease diagnosis should display deviating levels in affected individuals only and be robust to factors unrelated to the disease. Here we show the impact of genetic, clinical and lifestyle factors on circulating levels of 92 protein biomarkers for cancer and inflammation, using a population-based cohort of 1,005 individuals. For 75% of the biomarkers, the levels are significantly heritable and genome-wide association studies identifies 16 novel loci and replicate 2 previously known loci with strong effects on one or several of the biomarkers with P-values down to 4.4 \u00d7 10(-58). Integrative analysis attributes as much as 56.3% of the observed variance to non-disease factors. We propose that information on the biomarker-specific profile of major genetic, clinical and lifestyle factors should be used to establish personalized clinical cutoffs, and that this would increase the sensitivity of using biomarkers for prediction of clinical end points.", "doi": "10.1038/ncomms5684", "pmid": "25147954", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms5684"}, {"db": "pmc", "key": "PMC4143927"}], "notes": [], "created": "2020-01-23T15:05:43.720Z", "modified": "2023-04-14T13:56:27.513Z"}, {"entity": "publication", "iuid": "71be83e00a0e48cb9666dd6c698a7d62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71be83e00a0e48cb9666dd6c698a7d62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71be83e00a0e48cb9666dd6c698a7d62"}}, "title": "Sequential pH-driven dimerization and stabilization of the N-terminal domain enables rapid spider silk formation.", "authors": [{"family": "Kronqvist", "given": "Nina", "initials": "N"}, {"family": "Otikovs", "given": "Martins", "initials": "M"}, {"family": "Chmyrov", "given": "Volodymyr", "initials": "V"}, {"family": "Chen", "given": "Gefei", "initials": "G"}, {"family": "Andersson", "given": "Marlene", "initials": "M"}, {"family": "Nordling", "given": "Kerstin", "initials": "K"}, {"family": "Landreh", "given": "Michael", "initials": "M"}, {"family": "Sarr", "given": "M\u00e9doune", "initials": "M"}, {"family": "J\u00f6rnvall", "given": "Hans", "initials": "H"}, {"family": "Wennmalm", "given": "Stefan", "initials": "S"}, {"family": "Widengren", "given": "Jerker", "initials": "J"}, {"family": "Meng", "given": "Qing", "initials": "Q"}, {"family": "Rising", "given": "Anna", "initials": "A"}, {"family": "Otzen", "given": "Daniel", "initials": "D"}, {"family": "Knight", "given": "Stefan D", "initials": "SD"}, {"family": "Jaudzems", "given": "Kristaps", "initials": "K"}, {"family": "Johansson", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2014-02-11", "journal": {"volume": "5", "issn": "2041-1723", "issue": null, "pages": "3254", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The mechanisms controlling the conversion of spider silk proteins into insoluble fibres, which happens in a fraction of a second and in a defined region of the silk glands, are still unresolved. The N-terminal domain changes conformation and forms a homodimer when pH is lowered from 7 to 6; however, the molecular details still remain to be determined. Here we investigate site-directed mutants of the N-terminal domain from Euprosthenops australis major ampullate spidroin 1 and find that the charged residues D40, R60 and K65 mediate intersubunit electrostatic interactions. Protonation of E79 and E119 is required for structural conversions of the subunits into a dimer conformation, and subsequent protonation of E84 around pH 5.7 leads to the formation of a fully stable dimer. These residues are highly conserved, indicating that the now proposed three-step mechanism prevents premature aggregation of spidroins and enables fast formation of spider silk fibres in general.", "doi": "10.1038/ncomms4254", "pmid": "24510122", "labels": {"Fluorescence Correlation Spectroscopy": "Collaborative", "Integrated Microscopy Technologies Stockholm": null}, "xrefs": [{"db": "pii", "key": "ncomms4254"}], "notes": [], "created": "2017-05-04T14:56:13.026Z", "modified": "2021-05-24T15:33:38.192Z"}, {"entity": "publication", "iuid": "2a7f0a52b8574df7b032a4e7b53db095", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a7f0a52b8574df7b032a4e7b53db095.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a7f0a52b8574df7b032a4e7b53db095"}}, "title": "Metabolic enzyme expression highlights a key role for MTHFD2 and the mitochondrial folate pathway in cancer.", "authors": [{"family": "Nilsson", "given": "Roland", "initials": "R"}, {"family": "Jain", "given": "Mohit", "initials": "M"}, {"family": "Madhusudhan", "given": "Nikhil", "initials": "N"}, {"family": "Sheppard", "given": "Nina Gustafsson", "initials": "NG"}, {"family": "Strittmatter", "given": "Laura", "initials": "L"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Huang", "given": "Jenny", "initials": "J"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Mootha", "given": "Vamsi K", "initials": "VK"}], "type": "journal article", "published": "2014-01-24", "journal": {"volume": "5", "issn": "2041-1723", "issue": null, "pages": "3128", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Metabolic remodeling is now widely regarded as a hallmark of cancer, but it is not clear whether individual metabolic strategies are frequently exploited by many tumours. Here we compare messenger RNA profiles of 1,454 metabolic enzymes across 1,981 tumours spanning 19 cancer types to identify enzymes that are consistently differentially expressed. Our meta-analysis recovers established targets of some of the most widely used chemotherapeutics, including dihydrofolate reductase, thymidylate synthase and ribonucleotide reductase, while also spotlighting new enzymes, such as the mitochondrial proline biosynthetic enzyme PYCR1. The highest scoring pathway is mitochondrial one-carbon metabolism and is centred on MTHFD2. MTHFD2 RNA and protein are markedly elevated in many cancers and correlated with poor survival in breast cancer. MTHFD2 is expressed in the developing embryo, but is absent in most healthy adult tissues, even those that are proliferating. Our study highlights the importance of mitochondrial compartmentalization of one-carbon metabolism in cancer and raises important therapeutic hypotheses.", "doi": "10.1038/ncomms4128", "pmid": "24451681", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "ncomms4128"}, {"db": "pmc", "key": "PMC4106362"}, {"db": "mid", "key": "NIHMS550439"}], "notes": [], "created": "2017-05-04T14:56:09.415Z", "modified": "2017-05-30T12:52:35.256Z"}, {"entity": "publication", "iuid": "54e26e482cb24dc7af06502b2d69948a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54e26e482cb24dc7af06502b2d69948a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54e26e482cb24dc7af06502b2d69948a"}}, "title": "Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease.", "authors": [{"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Agren", "given": "Rasmus", "initials": "R"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "comparative study", "published": "2014-01-15", "journal": {"volume": "5", "issn": "2041-1723", "issue": null, "pages": "3083", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Several liver disorders result from perturbations in the metabolism of hepatocytes, and their underlying mechanisms can be outlined through the use of genome-scale metabolic models (GEMs). Here we reconstruct a consensus GEM for hepatocytes, which we call iHepatocytes2322, that extends previous models by including an extensive description of lipid metabolism. We build iHepatocytes2322 using Human Metabolic Reaction 2.0 database and proteomics data in Human Protein Atlas, which experimentally validates the incorporated reactions. The reconstruction process enables improved annotation of the proteomics data using the network centric view of iHepatocytes2322. We then use iHepatocytes2322 to analyse transcriptomics data obtained from patients with non-alcoholic fatty liver disease. We show that blood concentrations of chondroitin and heparan sulphates are suitable for diagnosing non-alcoholic steatohepatitis and for the staging of non-alcoholic fatty liver disease. Furthermore, we observe serine deficiency in patients with NASH and identify PSPH, SHMT1 and BCAT1 as potential therapeutic targets for the treatment of non-alcoholic steatohepatitis.", "doi": "10.1038/ncomms4083", "pmid": "24419221", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "ncomms4083"}], "notes": [], "created": "2017-05-04T14:56:09.113Z", "modified": "2021-07-08T13:44:33.268Z"}, {"entity": "publication", "iuid": "1a635d4304824c54b6edcca43eb98c0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a635d4304824c54b6edcca43eb98c0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a635d4304824c54b6edcca43eb98c0e"}}, "title": "Hydrogenosomes in the diplomonad Spironucleus salmonicida.", "authors": [{"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Einarsson", "given": "Elin", "initials": "E"}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Hjort", "given": "Karin", "initials": "K"}, {"family": "Ek", "given": "Bo", "initials": "B"}, {"family": "Steinhauf", "given": "Daniel", "initials": "D"}, {"family": "Hultenby", "given": "Kjell", "initials": "K"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Andersson", "given": "Jan O", "initials": "JO"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "journal article", "published": "2013-09-18", "journal": {"volume": "4", "issn": "2041-1723", "issue": null, "pages": "2493", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Acquisition of the mitochondrion is a key event in the evolution of the eukaryotic cell, but diversification of the organelle has occurred during eukaryotic evolution. One example of such mitochondria-related organelles (MROs) are hydrogenosomes, which produce ATP by substrate-level phosphorylation with hydrogen as a byproduct. The diplomonad parasite Giardia intestinalis harbours mitosomes, another type of MRO. Here we identify MROs in the salmon parasite Spironucleus salmonicida with similar protein import and Fe-S cluster assembly machineries as in Giardia mitosomes. We find that hydrogen production is prevalent in the diplomonad genus Spironucleus, and that S. salmonicida MROs contain enzymes characteristic of hydrogenosomes. Evolutionary analyses of known hydrogenosomal components indicate their presence in the diplomonad ancestor, and subsequent loss in Giardia. Our results suggest that hydrogenosomes are metabolic adaptations predating the split between parabasalids and diplomonads, which is deeper than the split between animals and fungi in the eukaryotic tree.", "doi": "10.1038/ncomms3493", "pmid": "24042146", "labels": {"Mass Spectrometry-based Proteomics, Uppsala": null}, "xrefs": [{"db": "pii", "key": "ncomms3493"}, {"db": "pmc", "key": "PMC3778541"}], "notes": [], "created": "2017-05-04T15:03:26.011Z", "modified": "2017-05-30T12:43:14.061Z"}, {"entity": "publication", "iuid": "64b1a650dbca4d7fae474646e27d6298", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64b1a650dbca4d7fae474646e27d6298.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64b1a650dbca4d7fae474646e27d6298"}}, "title": "Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.", "authors": [{"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "Sanchez", "given": "Betzabe C", "initials": "BC"}, {"family": "Mundt", "given": "Filip", "initials": "F"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "Kovacs", "given": "Aniko", "initials": "A"}, {"family": "Panizza", "given": "Elena", "initials": "E"}, {"family": "Hultin-Rosenberg", "given": "Lina", "initials": "L"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "M\u00e1th\u00e9", "given": "Gy\u00f6ngyv\u00e9r", "initials": "G"}, {"family": "Yakhini", "given": "Zohar", "initials": "Z"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Krawiec", "given": "Kamilla", "initials": "K"}, {"family": "Kanter", "given": "Lena", "initials": "L"}, {"family": "Hjerpe", "given": "Anders", "initials": "A"}, {"family": "St\u00e5l", "given": "Olle", "initials": "O"}, {"family": "Linderholm", "given": "Barbro K", "initials": "BK"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2013-07-23", "journal": {"volume": "4", "issn": "2041-1723", "issue": null, "pages": "2175", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "About one-third of oestrogen receptor alpha-positive breast cancer patients treated with tamoxifen relapse. Here we identify the nuclear receptor retinoic acid receptor alpha as a marker of tamoxifen resistance. Using quantitative mass spectrometry-based proteomics, we show that retinoic acid receptor alpha protein networks and levels differ in a tamoxifen-sensitive (MCF7) and a tamoxifen-resistant (LCC2) cell line. High intratumoural retinoic acid receptor alpha protein levels also correlate with reduced relapse-free survival in oestrogen receptor alpha-positive breast cancer patients treated with adjuvant tamoxifen solely. A similar retinoic acid receptor alpha expression pattern is seen in a comparable independent patient cohort. An oestrogen receptor alpha and retinoic acid receptor alpha ligand screening reveals that tamoxifen-resistant LCC2 cells have increased sensitivity to retinoic acid receptor alpha ligands and are less sensitive to oestrogen receptor alpha ligands compared with MCF7 cells. Our data indicate that retinoic acid receptor alpha may be a novel therapeutic target and a predictive factor for oestrogen receptor alpha-positive breast cancer patients treated with adjuvant tamoxifen.", "doi": "10.1038/ncomms3175", "pmid": "23868472", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms3175"}, {"db": "pmc", "key": "PMC3759040"}], "notes": "Biochemical and Cellular Screening", "created": "2017-05-04T14:57:01.894Z", "modified": "2025-10-17T13:05:09.700Z"}, {"entity": "publication", "iuid": "6cb6fb789ed643b2ab8c7387bb5a3546", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cb6fb789ed643b2ab8c7387bb5a3546.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cb6fb789ed643b2ab8c7387bb5a3546"}}, "title": "Symptomatic atherosclerosis is associated with an altered gut metagenome.", "authors": [{"family": "Karlsson", "given": "Fredrik H", "initials": "FH"}, {"family": "F\u00e5k", "given": "Frida", "initials": "F"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Fagerberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Petranovic", "given": "Dina", "initials": "D"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2012-12-06", "journal": {"volume": "3", "issn": "2041-1723", "issue": null, "pages": "1245", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Recent findings have implicated the gut microbiota as a contributor of metabolic diseases through the modulation of host metabolism and inflammation. Atherosclerosis is associated with lipid accumulation and inflammation in the arterial wall, and bacteria have been suggested as a causative agent of this disease. Here we use shotgun sequencing of the gut metagenome to demonstrate that the genus Collinsella was enriched in patients with symptomatic atherosclerosis, defined as stenotic atherosclerotic plaques in the carotid artery leading to cerebrovascular events, whereas Roseburia and Eubacterium were enriched in healthy controls. Further characterization of the functional capacity of the metagenomes revealed that patient gut metagenomes were enriched in genes encoding peptidoglycan synthesis and depleted in phytoene dehydrogenase; patients also had reduced serum levels of \u03b2-carotene. Our findings suggest that the gut metagenome is associated with the inflammatory status of the host and patients with symptomatic atherosclerosis harbor characteristic changes in the gut metagenome.", "doi": "10.1038/ncomms2266", "pmid": "23212374", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ncomms2266"}, {"db": "pmc", "key": "PMC3538954"}], "notes": [], "created": "2017-05-04T14:57:38.926Z", "modified": "2021-07-05T13:05:37.669Z"}, {"entity": "publication", "iuid": "2e8a48c6bcb0435e81f13645120db225", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e8a48c6bcb0435e81f13645120db225.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e8a48c6bcb0435e81f13645120db225"}}, "title": "Proteomic screen reveals Fbw7 as a modulator of the NF-\u03baB pathway.", "authors": [{"family": "Arabi", "given": "Azadeh", "initials": "A"}, {"family": "Ullah", "given": "Karim", "initials": "K"}, {"family": "Branca", "given": "Rui M M", "initials": "RM"}, {"family": "Johansson", "given": "Johan", "initials": "J"}, {"family": "Bandarra", "given": "Daniel", "initials": "D"}, {"family": "Haneklaus", "given": "Moritz", "initials": "M"}, {"family": "Fu", "given": "Jing", "initials": "J"}, {"family": "Ari\u00ebs", "given": "Ingrid", "initials": "I"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Den Boer", "given": "Monique L", "initials": "ML"}, {"family": "Pokrovskaja", "given": "Katja", "initials": "K"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "Xiao", "given": "Gutian", "initials": "G"}, {"family": "Rocha", "given": "Sonia", "initials": "S"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Sangfelt", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2012-08-07", "journal": {"volume": "3", "issn": "2041-1723", "issue": null, "pages": "976", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Fbw7 is a ubiquitin-ligase that targets several oncoproteins for proteolysis, but the full range of Fbw7 substrates is not known. Here we show that by performing quantitative proteomics combined with degron motif searches, we effectively screened for a more complete set of Fbw7 targets. We identify 89 putative Fbw7 substrates, including several disease-associated proteins. The transcription factor NF-\u03baB2 (p100/p52) is one of the candidate Fbw7 substrates. We show that Fbw7 interacts with p100 via a conserved degron and that it promotes degradation of p100 in a GSK3\u03b2 phosphorylation-dependent manner. Fbw7 inactivation increases p100 levels, which in the presence of NF-\u03baB pathway stimuli, leads to increased p52 levels and activity. Accordingly, the apoptotic threshold can be increased by loss of Fbw7 in a p100-dependent manner. In conclusion, Fbw7-mediated destruction of p100 is a regulatory component restricting the response to NF-\u03baB2 pathway stimulation.", "doi": "10.1038/ncomms1975", "pmid": "22864569", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "ncomms1975"}, {"db": "pmc", "key": "PMC4354031"}], "notes": [], "created": "2017-05-04T14:56:18.815Z", "modified": "2021-07-08T11:36:15.152Z"}], "created": "2017-05-09T09:12:08.433Z", "modified": "2020-11-27T13:14:08.691Z"}