{"entity": "journal", "iuid": "b299940c06b04f2ea2a81846770fc2e5", "timestamp": "2026-07-18T03:11:07.071Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Commun%20Med%20%28Lond%29.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Commun%20Med%20%28Lond%29"}}, "title": "Commun Med (Lond)", "issn": "2730-664X", "issn-l": null, "publications_count": 9, "publications": [{"entity": "publication", "iuid": "11b37392972444f5998ff8f14ca156cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11b37392972444f5998ff8f14ca156cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11b37392972444f5998ff8f14ca156cd"}}, "title": "An integrative molecular map of pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Enblad", "given": "Anna Pia", "initials": "AP"}, {"family": "Sulyaeva", "given": "Julia", "initials": "J"}, {"family": "Gogishvili", "given": "Dea", "initials": "D"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2026-04-11", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "6", "issue": "1", "issn-l": null}, "abstract": "The molecular landscape of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) has been extensively characterized through single-modality studies. However, the interplay between molecular modalities and their collective influence on treatment response and outcomes remains poorly understood.\n\nWe integrated genomic, epigenomic, transcriptomic, and ex vivo drug response data from 1231 patients diagnosed with BCP-ALL. Using Multi-Omics Factor Analysis, we identified signatures explaining key aspects of the integrative molecular landscape, referred to as cross-modal elements (CMEs). The CME-derived signatures were introduced into pathway and intermodal network analyses, while their impact on patient outcomes was assessed through survival modeling.\n\nPathway and network analyses annotate the resulting integrative CMEs, linking them to key biological processes, including disease development, cellular regulatory processes, metabolic pathways, and drug response. By leveraging correlations between DNA methylation and ex vivo response to doxorubicin, we stratify patients with hyperdiploidy into subgroups that differ in relapse-free survival. These signatures are independent of clinical variables. Survival models incorporating CME-selected ex-vivo drug responses combined with clinical data improve risk prediction compared to clinical models alone (FDR < 0.05), demonstrating the potential of integrative multiomics in refining risk stratification.\n\nOur study highlights the importance of multimodal data integration in BCP-ALL to provide biological insights with potential relevance for precision medicine.", "doi": "10.1038/s43856-026-01568-9", "pmid": "41965886", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13079846"}, {"db": "pii", "key": "10.1038/s43856-026-01568-9"}], "notes": [], "created": "2026-06-01T11:13:50.747Z", "modified": "2026-06-01T11:13:50.765Z"}, {"entity": "publication", "iuid": "b7284178e7704139b443a0f9e1f75614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7284178e7704139b443a0f9e1f75614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7284178e7704139b443a0f9e1f75614"}}, "title": "Homologous recombination deficiency in primary ER-positive and HER2-negative breast cancer.", "authors": [{"family": "Davies", "given": "Helen R", "initials": "HR", "orcid": "0000-0001-6381-3664", "researcher": {"href": "https://publications.scilifelab.se/researcher/e02b6738c9e140858456e24cef5d6b42.json"}}, {"family": "Black", "given": "Daniella", "initials": "D"}, {"family": "Kvist", "given": "Anders", "initials": "A", "orcid": "0000-0002-1358-0695", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e6b39bdc00c442f94caed782772a278.json"}}, {"family": "Sigurj\u00f3nsd\u00f3ttir", "given": "Krist\u00edn", "initials": "K"}, {"family": "Bosch", "given": "Ana", "initials": "A"}, {"family": "Bowden", "given": "Ramsay", "initials": "R", "orcid": "0000-0003-1138-4452", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b6effa9663145dabd83b3ced199385c.json"}}, {"family": "Memari", "given": "Yasin", "initials": "Y"}, {"family": "Chen", "given": "Ziqian", "initials": "Z"}, {"family": "Rinaldi", "given": "Giuseppe", "initials": "G", "orcid": "0000-0002-5650-6049", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7f30b3dfa5489ba61afa7840bc34c7.json"}}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"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": "Hohmann", "given": "Lennart", "initials": "L", "orcid": "0000-0002-0281-7140", "researcher": {"href": "https://publications.scilifelab.se/researcher/b605a3b893a24a238b5bb6eddd27b672.json"}}, {"family": "Nordborg", "given": "Nicklas", "initials": "N"}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J", "orcid": "0000-0002-8466-9179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b8605b9a7c74b20986146f020cf4b8f.json"}}, {"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": "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": "2026-02-16", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "6", "issue": "1", "pages": "118", "issn-l": null}, "abstract": "Homologous recombination deficiency (HRD) originating from inactivation of genes like BRCA1/BRCA2 is a targetable abnormality common in triple-negative breast cancer (TNBC). In estrogen-receptor (ER)-positive HER2-negative (ERpHER2n) breast cancer (BC), HRD prevalence and clinical impact are unclear.\n\nWe analyzed 502 ERpHER2n tumors from patients recruited via the population-representative Swedish SCAN-B study by whole genome sequencing (WGS), defining mutational signatures-based HRD, as well as matched transcriptional, DNA methylation, clinicopathological, adjuvant treatment, and outcome data.\n\nWe show that HRD is much less frequent in ERpHER2n BC (8.4%) compared to TNBC, though induced by similar genetic/epigenetic mechanisms acting on mainly BRCA1/BRCA2/RAD51C/PALB2 together, providing a plausible HR-inactivation mechanism for 71.4% of HRD tumors. Our modelled estimate of HRD in Western European/Nordic BC is ~10-13%. HRD tumors were observed across all PAM50 gene expression subtypes with the exception of Luminal A tumors ( < 1%) and did not exhibit a unique, defining transcriptional or DNA methylation profile. While HRD status was not statistically associated with differences in patient outcome for patients treated with combined chemotherapy and endocrine therapy, a nonsignificant trend of poorer outcome for patients with HRD tumors was observed for patients treated with adjuvant endocrine therapy only.\n\nERpHER2n HRD tumors show features of aggressive disease, but do not display a distinct transcriptional or DNA methylation profile that clearly differentiates them from HR-proficient tumors. Though numbers are limited, we present early evidence that HRD stratification by WGS could impact therapeutic strategies, as HRD BCs trended to poorer outcomes when not treated with chemotherapy.", "doi": "10.1038/s43856-026-01385-0", "pmid": "41699108", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12909304"}, {"db": "pii", "key": "10.1038/s43856-026-01385-0"}], "notes": [], "created": "2026-06-01T11:12:58.568Z", "modified": "2026-06-01T11:12:58.707Z"}, {"entity": "publication", "iuid": "aeb92fd9030f40e5b001042ea6594c76", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aeb92fd9030f40e5b001042ea6594c76.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aeb92fd9030f40e5b001042ea6594c76"}}, "title": "Developmental low-dose bisphenol A exposure leads to extensive transcriptome female masculinization and male feminization later in life.", "authors": [{"family": "Lind", "given": "Thomas", "initials": "T", "orcid": "0000-0003-2791-688X", "researcher": {"href": "https://publications.scilifelab.se/researcher/343532f8d9b44c848895493afbf32289.json"}}, {"family": "Dunder", "given": "Linda", "initials": "L"}, {"family": "Lejonklou", "given": "Margareta H", "initials": "MH"}, {"family": "Lind", "given": "P Monica", "initials": "PM"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Lind", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "410", "issn-l": null}, "abstract": "Bisphenol A (BPA) is an endocrine disruptor, and exposure to low doses in utero has been associated with the development of metabolic diseases. Previous studies have suggested that bone marrow (BM) may be particularly susceptible to BPA exposure.\n\nHere, we investigate how developmental exposure to low levels of BPA affects the BM transcriptome and the blood metabolic profile in Fischer 344 rats later in life. We compare these effects to those observed in human metabolic syndrome (MetS) using a population-based cohort.\n\nThe results show an unexpectedly extensive sex-biased effect on the BM transcriptome from a BPA dose approximately eight times lower than the recent temporary European Food Safety Authority (EFSA) human tolerable daily intake (TDI) and a higher dose considered safe in 2015. BPA exposure induces sex-specific changes in gene expression, progressing toward a hypometabolic cancer-like state in females and a hypermetabolic autoimmunity-like state in males, with a blood metabolic profile that significantly overlaps with human MetS in a cross-sectional study.\n\nWe conclude that developmental low-dose BPA exposure might induce metabolic syndrome specifically in males, possibly by affecting T cell activity in a sex-specific manner. Our study provides biologically plausible and convincing evidence for significant effects from low-dose BPA exposure, supporting the substantial lowering of the human BPA TDI by EFSA based on its critical effects on T cells.", "doi": "10.1038/s43856-025-01119-8", "pmid": "41034487", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Swedish Metabolomics Centre": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12488919"}, {"db": "pii", "key": "10.1038/s43856-025-01119-8"}], "notes": [], "created": "2025-11-17T15:52:20.678Z", "modified": "2025-11-27T08:05:30.935Z"}, {"entity": "publication", "iuid": "c86bd10726ee4bf092f5650e7a9e86a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c86bd10726ee4bf092f5650e7a9e86a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c86bd10726ee4bf092f5650e7a9e86a7"}}, "title": "The association between the gut microbiome and 24-h blood pressure measurements in the SCAPIS study.", "authors": [{"family": "Lin", "given": "Yi-Ting", "initials": "YT", "orcid": "0000-0002-5833-0040", "researcher": {"href": "https://publications.scilifelab.se/researcher/899debb5e314439c8f35f255445b3674.json"}}, {"family": "Sayols-Baixeras", "given": "Sergi", "initials": "S", "orcid": "0000-0002-1181-6262", "researcher": {"href": "https://publications.scilifelab.se/researcher/cde59259b02342deb13d78874ce93124.json"}}, {"family": "Baldanzi", "given": "Gabriel", "initials": "G", "orcid": "0000-0003-3962-3953", "researcher": {"href": "https://publications.scilifelab.se/researcher/577652ffb15442e1a47a9aaffc3b52e7.json"}}, {"family": "Dekkers", "given": "Koen F", "initials": "KF", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Nguyen", "given": "Diem", "initials": "D", "orcid": "0000-0002-9680-5772", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78958133e474831ac76dacc36f68cbb.json"}}, {"family": "Nielsen", "given": "Nynne", "initials": "N", "orcid": "0009-0003-5603-3514", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae270d751a64bef8e6ecf9b3a9b423b.json"}}, {"family": "Eklund", "given": "Aron C", "initials": "AC", "orcid": "0000-0003-0861-1001", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1b0f6b48de45f7916e14d6a4defb09.json"}}, {"family": "Varotsis", "given": "Georgios", "initials": "G", "orcid": "0000-0002-3320-2448", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3db146258e467ab67f8848a048baa3.json"}}, {"family": "Holm", "given": "Jacob B", "initials": "JB", "orcid": "0000-0003-1756-0875", "researcher": {"href": "https://publications.scilifelab.se/researcher/359fa6a18dc549a8852dd3990ccde1f1.json"}}, {"family": "Nielsen", "given": "H Bj\u00f8rn", "initials": "HB", "orcid": "0000-0003-2281-5713", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1d5f2e0565a46bcbccfc973eec9e838.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}], "type": "journal article", "published": "2025-07-07", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "276", "issn-l": null}, "abstract": "There is mounting evidence supporting the role of the microbiota in hypertension from experimental studies and population-based studies. We aimed to investigate the relationship between specific characteristics of the gut microbiome and 24-h ambulatory blood pressure measurements.\n\nThe association of gut microbial species and microbial functions, determined by shotgun metagenomic sequencing of fecal samples, with 24-h ambulatory blood pressure measurements in 3695 participants and office blood pressure was assessed in multivariable-adjusted models in 2770 participants without antihypertensive medication from the Swedish CArdioPulmonary bioImage Study.\n\nGut microbiome alpha diversity was negatively associated with diastolic blood pressure variability. Additionally, four microbial species were associated with at least one of the 24-h blood pressure traits. Streptococcus sp001556435 was associated with higher systolic blood pressure, Intestinimonas massiliensis and Dysosmobacter sp001916835 with lower systolic blood pressure, Dysosmobacter sp001916835 with lower diastolic blood pressure, and ER4 sp900317525 with lower systolic blood pressure variability. Moreover, office blood pressure data from a subsample without ambulatory blood pressure measurements replicated the association of Intestinimonas massiliensis with systolic blood pressure and Dysosmobacter sp001916835 with diastolic blood pressure. Species associated with 24-h blood pressure were linked to a similar pattern of metabolites.\n\nIn this large cross-sectional analysis, gut microbiome alpha diversity negatively associates with diastolic blood pressure variability, and four gut microbial species associate with 24-h blood pressure traits.", "doi": "10.1038/s43856-025-00980-x", "pmid": "40624247", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12234806"}, {"db": "pii", "key": "10.1038/s43856-025-00980-x"}], "notes": [], "created": "2025-11-28T10:47:57.315Z", "modified": "2025-11-28T10:47:57.726Z"}, {"entity": "publication", "iuid": "5c24b2e6125b42d29feff583fc4f1da4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c24b2e6125b42d29feff583fc4f1da4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c24b2e6125b42d29feff583fc4f1da4"}}, "title": "Mosaic loss of chromosome Y in blood is associated with male susceptibility for idiopathic pulmonary fibrosis.", "authors": [{"family": "Bjurling", "given": "Josefin", "initials": "J", "orcid": "0009-0006-7675-429X", "researcher": {"href": "https://publications.scilifelab.se/researcher/442f42e953684bab8d50784c29c6e151.json"}}, {"family": "Chavkin", "given": "Nicholas W", "initials": "NW"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Thel", "given": "Mark C", "initials": "MC"}, {"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Kim", "given": "John S", "initials": "JS"}, {"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Ma", "given": "Shwu-Fan", "initials": "SF", "orcid": "0000-0002-3058-9480", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2346407b4814a0abe0415d60ec2b9fe.json"}}, {"family": "Martinez", "given": "Fernando J", "initials": "FJ", "orcid": "0000-0002-2412-3182", "researcher": {"href": "https://publications.scilifelab.se/researcher/81b4019b58504b3e84a228b7419d90a4.json"}}, {"family": "Anstrom", "given": "Kevin", "initials": "K"}, {"family": "Noth", "given": "Imre", "initials": "I"}, {"family": "Walsh", "given": "Kenneth", "initials": "K", "orcid": "0000-0001-7580-2276", "researcher": {"href": "https://publications.scilifelab.se/researcher/f06edcdf9ef24a1d9cadcb8ea3a30fff.json"}}, {"family": "Forsberg", "given": "Lars A", "initials": "LA", "orcid": "0000-0002-1701-755X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac2d8e983764a82982118b6db84029e.json"}}], "type": "journal article", "published": "2025-06-28", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "246", "issn-l": null}, "abstract": "The prevalence of idiopathic pulmonary fibrosis (IPF) is higher in men, a previously not well-understood sex bias that extends across severity and mortality. Mosaic loss of chromosome Y (mLOY) in blood is male-specific and associated with adverse outcomes, including IPF. In mLOY-mice, enhanced TGF-\u03b2 signaling has been reported to contribute to fibrosis of internal organs, but it is not known if such mLOY-driven disease mechanism exists in humans.\n\nWe focused here on IPF in men to investigate if mLOY contributes to fibrotic disease processes in humans, as demonstrated in mouse models. To this end, we investigated mLOY as a risk factor for male IPF in epidemiological and clinical datasets, as well as by re-analyses of published single-cell RNA sequencing (scRNAseq) datasets.\n\nWe find that men with mLOY in blood display an increased risk for IPF diagnosis and death caused by IPF in UK Biobank, and that mLOY is associated with reduced lung functions in two cohorts. Approximately 80% of the male excess in IPF prevalence occurs in the group of men with mLOY in blood leukocytes. Notably, scRNAseq analyses support that pulmonary leukocytes with Y loss exacerbate IPF by upregulating profibrotic genes and enhancing TGF-\u03b2 signaling.\n\nOur results contribute to explaining the profound sex bias in IPF and replicate a mLOY-driven profibrotic disease mechanism first identified in mice. Male IPF patients with mLOY represent a subgroup that may benefit from treatment with TGF-\u03b2 inhibitors.", "doi": "10.1038/s43856-025-00966-9", "pmid": "40581694", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12206232"}, {"db": "pii", "key": "10.1038/s43856-025-00966-9"}], "notes": [], "created": "2025-11-28T10:47:51.945Z", "modified": "2025-11-28T10:47:52.216Z"}, {"entity": "publication", "iuid": "5993e1e4e51044008a8a228e19ce6f0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5993e1e4e51044008a8a228e19ce6f0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5993e1e4e51044008a8a228e19ce6f0b"}}, "title": "Deep plasma proteomics identifies and validates an eight-protein biomarker panel that separate benign from malignant tumors in ovarian cancer.", "authors": [{"family": "Moskov", "given": "Mikaela", "initials": "M"}, {"family": "Hedlund Lindberg", "given": "Julia", "initials": "J"}, {"family": "Lycke", "given": "Maria", "initials": "M"}, {"family": "Ivansson", "given": "Emma", "initials": "E", "orcid": "0000-0002-4630-1576", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d2acd6a50fe49178f424c55df0a6b51.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Sundfeldt", "given": "Karin", "initials": "K"}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}], "type": "journal article", "published": "2025-06-12", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "230", "issn-l": null}, "abstract": "Ovarian cancer has the highest mortality of all gynecological cancers and surgery is commonly used as final diagnostic. Available literature indicates that women with benign tumors could often be conservatively managed, but accurate molecular tests are needed for triaging when gold-standard imaging techniques are inconclusive or lacking.\n\nHere, we analyzed 5416 plasma proteins in two independent cohorts (N1 = 171, N2 = 233) with women surgically diagnosed with benign or malignant tumors. Using one cohort as discovery, we compared protein levels of benign tumors with early stage (I-II), late stage (III-IV) or any stage (I-IV) ovarian cancer and trained risk-score reporting multivariate models including a fixed cut-off for malignancy. Associations and model performance was then evaluated in the replication cohort.\n\nWe identify 327 biomarker associations, corresponding to 191 unique proteins, and replicate 326 (99.7%). By comparing the 191 proteins with their corresponding tumor gene expression we find that only 11% (21/191) have significant correlation. Through analyzes of protein-protein correlation networks, we find that 62 of the 191 proteins have high correlation with at least one other protein, suggesting that many of the associations are secondary effects. In the replication cohort, our model has areas under the curve (AUC = 0.96) corresponding to 97% sensitivity at 68% specificity. For early-stage tumors, we estimate the sensitivity to 91% at a specificity of 68% as compared to 85% and 54% for CA-125 alone.\n\nOur results indicates that up to one third of benign cases can be identified by molecular measures thereby reducing the need for diagnostic surgery.", "doi": "10.1038/s43856-025-00945-0", "pmid": "40506476", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12162877"}, {"db": "pii", "key": "10.1038/s43856-025-00945-0"}], "notes": [], "created": "2025-09-08T07:17:14.990Z", "modified": "2025-11-14T11:07:27.366Z"}, {"entity": "publication", "iuid": "eed9d79d809f4d5d864e6170b1dcfc20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eed9d79d809f4d5d864e6170b1dcfc20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eed9d79d809f4d5d864e6170b1dcfc20"}}, "title": "Titanium micro-particles are commonly found in soft tissues surrounding dental implants.", "authors": [{"family": "Dionigi", "given": "Carlotta", "initials": "C", "orcid": "0000-0002-4195-0729", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ee57750bddd48a3a323e397c64ba435.json"}}, {"family": "Nagy", "given": "Gyula", "initials": "G", "orcid": "0000-0003-3172-5736", "researcher": {"href": "https://publications.scilifelab.se/researcher/07c27d64291549dca9eda3709cbab30d.json"}}, {"family": "Derks", "given": "Jan", "initials": "J"}, {"family": "Ichioka", "given": "Yuki", "initials": "Y"}, {"family": "Tomasi", "given": "Cristiano", "initials": "C", "orcid": "0000-0002-3610-6574", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3067facfa6743db83d011e510fcddcf.json"}}, {"family": "Larsson", "given": "Lena", "initials": "L"}, {"family": "Primetzhofer", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5815-3742", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeed8e1ab76842eab7f052f57abcd960.json"}}, {"family": "Berglundh", "given": "Tord", "initials": "T", "orcid": "0000-0001-5864-6398", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d29bd79b2914b47b00a0c1005b30b43.json"}}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "78", "issn-l": null}, "abstract": "Dental implants are one of the most frequently used medical devices for therapeutic purposes in dentistry. Peri-implantitis is a severe, microbial biofilm-associated condition, characterized by inflammation in peri-implant soft tissues and destruction of supporting bone. It has been suggested that metal particles originating from the implant may influence the local host response to microbial biofilms.\n\nSoft tissue biopsies were collected from implant sites with and without peri-implantitis in 21 patients. Micro Proton-induced X-ray Emission (\u00b5-PIXE) analysis was used to localize, quantify and characterize titanium micro-particles within tissues. RNA sequencing was performed to evaluate potential associations between titanium micro-particles and gene expression profiles in peri-implantitis lesions.\n\nTitanium micro-particles are consistent findings in soft tissues surrounding dental implants. Their occurrence varies across patients but not between sites with and without peri-implantitis within the same individual. Most particles reside in a 2-mm wide tissue portion close to the implant/tissue interface. The time in function of the implants does not influence the volumetric density of titanium micro-particles, while implant systems do. Fourteen differentially expressed genes are identified when comparing peri-implantitis samples with high and low densities of titanium micro-particles. The gene-set enrichment analysis reveals functions related to the regulation of the immune response and epithelial development.\n\nThe present results indicate that titanium micro-particles are commonly found in tissues surrounding dental implants and are not associated with the occurrence of peri-implantitis.", "doi": "10.1038/s43856-025-00756-3", "pmid": "40102654", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service", "Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11920262"}, {"db": "pii", "key": "10.1038/s43856-025-00756-3"}], "notes": [], "created": "2025-07-08T13:53:22.922Z", "modified": "2025-11-05T13:50:37.870Z"}, {"entity": "publication", "iuid": "111154cd228d47fabf63f871f677a0d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/111154cd228d47fabf63f871f677a0d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/111154cd228d47fabf63f871f677a0d7"}}, "title": "Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections.", "authors": [{"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "Dahl", "given": "Leo", "initials": "L", "orcid": "0000-0003-1492-3052", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4df506f315c4289935b935a503efd56.json"}}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Albrecht", "given": "Vincent", "initials": "V", "orcid": "0009-0003-1985-7733", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d422e623e9e449f98853e6830cdd401.json"}}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Thomas", "given": "Cecilia E", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1156f987764218af202efbd76c31fd.json"}}, {"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-0504-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcf3474dc7054c598cbe3a195deb8a1b.json"}}, {"family": "Gisslen", "given": "Magnus", "initials": "M"}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2024-04-02", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "issn-l": null, "volume": "4", "issue": "1", "pages": "55"}, "abstract": "Self-sampling of dried blood spots (DBS) offers new routes to gather valuable health-related information from the general population. Yet, the utility of using deep proteome profiling from home-sampled DBS to obtain clinically relevant insights about SARS-CoV-2 infections remains largely unexplored.\r\n\r\nOur study involved 228 individuals from the general Swedish population who used a volumetric DBS sampling device and completed questionnaires at home during spring 2020 and summer 2021. Using multi-analyte COVID-19 serology, we stratified the donors by their response phenotypes, divided them into three study sets, and analyzed 276 proteins by proximity extension assays (PEA). After normalizing the data to account for variances in layman-collected samples, we investigated the association of DBS proteomes with serology and self-reported information.\r\n\r\nOur three studies display highly consistent variance of protein levels and share associations of proteins with sex (e.g., MMP3) and age (e.g., GDF-15). Studying seropositive (IgG+) and seronegative (IgG-) donors from the first pandemic wave reveals a network of proteins reflecting immunity, inflammation, coagulation, and stress response. A comparison of the early-infection phase (IgM+IgG-) with the post-infection phase (IgM-IgG+) indicates several proteins from the respiratory system. In DBS from the later pandemic wave, we find that levels of a virus receptor on B-cells differ between seropositive (IgG+) and seronegative (IgG-) donors.\r\n\r\nProteome analysis of volumetric self-sampled DBS facilitates precise analysis of clinically relevant proteins, including those secreted into the circulation or found on blood cells, augmenting previous COVID-19 reports with clinical blood collections. Our population surveys support the usefulness of DBS, underscoring the role of timing the sample collection to complement clinical and precision health monitoring initiatives.", "doi": "10.1038/s43856-024-00480-4", "pmid": "38565620", "labels": {"Affinity Proteomics Stockholm": "Technology development", "Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10987641"}, {"db": "pii", "key": "10.1038/s43856-024-00480-4"}], "notes": [], "created": "2024-04-18T09:27:59.211Z", "modified": "2024-08-28T11:04:43.993Z"}, {"entity": "publication", "iuid": "7344de1a6fea4d8e8b4e7972f2c93e6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7344de1a6fea4d8e8b4e7972f2c93e6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7344de1a6fea4d8e8b4e7972f2c93e6f"}}, "title": "The development of blood protein profiles in extremely preterm infants follows a stereotypic evolution pattern.", "authors": [{"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "Brusselaers", "given": "Nele", "initials": "N", "orcid": "0000-0003-0137-447X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cb44146e4e943a589f38cd31beae2a0.json"}}, {"family": "Wackernagel", "given": "Dirk", "initials": "D"}, {"family": "Sj\u00f6bom", "given": "Ulrika", "initials": "U"}, {"family": "S\u00e4vman", "given": "Karin", "initials": "K"}, {"family": "Hansen Pupp", "given": "Ingrid", "initials": "I"}, {"family": "Ley", "given": "David", "initials": "D"}, {"family": "Nilsson", "given": "Anders K", "initials": "AK", "orcid": "0000-0003-3631-0783", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7c743e9c8e4acc985b22d1a3b4827d.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"}}, {"family": "Hellstr\u00f6m", "given": "Ann", "initials": "A", "orcid": "0000-0002-9259-1244", "researcher": {"href": "https://publications.scilifelab.se/researcher/59eda2822ead4300a3ebfa8e80e4e191.json"}}], "type": "journal article", "published": "2023-08-02", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "3", "issue": "1", "pages": "107", "issn-l": null}, "abstract": "Preterm birth is the leading cause of neonatal mortality and morbidity. Early diagnosis and interventions are critical to improving the clinical outcomes of extremely premature infants. Blood protein profiling during the first months of life in preterm infants can shed light on the role of early extrauterine development and provide an increased understanding of maturation after extremely preterm birth and the underlying mechanisms of prematurity-related disorders.\n\nWe have investigated the blood protein profiles during the first months of life in preterm infants on the role of early extrauterine development. The blood protein levels were analyzed using next generation blood profiling on 1335 serum samples, collected longitudinally at nine time points from birth to full-term from 182 extremely preterm infants.\n\nThe protein analysis reveals evident predestined serum evolution patterns common for all included infants. The majority of the variations in blood protein expression are associated with the postnatal age of the preterm infants rather than any other factors. There is a uniform protein pattern on postnatal day 1 and after 30 weeks postmenstrual age (PMA), independent of gestational age (GA). However, during the first month of life, GA had a significant impact on protein variability.\n\nThe unified pattern of protein development for all included infants suggests an age-dependent stereotypic development of blood proteins after birth. This knowledge should be considered in neonatal settings and might alter the clinical approach within neonatology, where PMA is today the most dominant age variable.", "doi": "10.1038/s43856-023-00338-1", "pmid": "37532738", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10397184"}, {"db": "pii", "key": "10.1038/s43856-023-00338-1"}], "notes": [], "created": "2023-08-10T09:21:14.958Z", "modified": "2023-08-10T09:21:15.252Z"}], "created": "2023-08-10T09:21:15.241Z", "modified": "2023-08-10T09:21:15.241Z"}