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"researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Gr\u00e4slund", "given": "Torbj\u00f6rn", "initials": "T", "orcid": "0000-0002-5391-600X", "researcher": {"href": "https://publications.scilifelab.se/researcher/52adbc739e274652bbf877facf4f0959.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Lund", "given": "Harald", "initials": "H", "orcid": "0000-0001-8046-0805", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fe4902c355449e4812008d4ad7a37e0.json"}}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P", "orcid": "0000-0003-1446-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/91c3e953634140b8974186ac0d7eac85.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Martin", "given": "Roland", "initials": "R"}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H", "orcid": "0000-0003-4882-7624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e701613f60249b793f2def737168a05.json"}}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b824181455243b19f4aa145a4545870.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2026-01-22", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "189", "issue": "2", "pages": "585-602.e38"}, "abstract": "Epstein-Barr virus (EBV) infection constitutes a prerequisite for multiple sclerosis (MS) development, and cross-reactivity between EBV nuclear antigen 1 (EBNA1) and anoctamin-2 (ANO2) antibodies was previously demonstrated in persons with MS (pwMS). Here, we show that ANO2-specific CD4+ T cells are more frequent in pwMS. Immunization of SJL/J mice with ANO2 or EBNA1 led to cross-reactive CD4+ T cell and antibody responses. ANO2 pre-immunization led to exacerbated experimental autoimmune encephalomyelitis (EAE), an effect mediated by CD4+ T cells, as confirmed by adoptive transfer experiments. T cell clones with cross-reactivity to EBNA1 and ANO2 could be isolated from natalizumab-treated pwMS, and sequencing of EBNA1- and ANO2-specific T cell receptors (TCRs) revealed a significant repertoire overlap. We thus report the first mechanistic evidence that EBNA1 CD4+ T cells can target the MS autoantigen ANO2, thereby establishing a link between EBV infection and neuroinflammation.", "doi": "10.1016/j.cell.2025.12.032", "pmid": "41534529", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)01481-3"}], "notes": [], "created": "2026-01-15T20:23:02.729Z", "modified": "2026-03-24T09:17:16.086Z"}, {"entity": "publication", "iuid": "20400326c0944ebda6e786a24f339e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26"}}, "title": "A human pan-disease blood atlas of the circulating proteome.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/648c9ed3483a4eb8a1d228cf7e59f6a7.json"}}, {"family": "Kenrick", "given": "Josefin", "initials": "J", "orcid": "0000-0002-0110-5192", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83beb37b7bc4e0aa84106bea7c6e0d0.json"}}, {"family": "Johansson", "given": "Emil", "initials": "E", "orcid": "0009-0003-1250-0678", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d953dd65ab24e8ab08aee7e7f101702.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": 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"given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Skoglund", "given": "Lovisa", "initials": "L", "orcid": "0009-0002-7863-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6bab6ea5e824b13ad5b77a6fa08523e.json"}}, {"family": "Smed-S\u00f6rensen", "given": "Anna", "initials": "A"}, {"family": "Sond\u00e9n", "given": "Klara", "initials": "K", "orcid": "0000-0003-1585-8475", "researcher": {"href": 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{"family": "Sutantiwanichkul", "given": "Thanadol", "initials": "T", "orcid": "0000-0002-1072-6863", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f33fff56f34d72bb1bbc88608ed914.json"}}, {"family": "Svedman", "given": "Fernanda Costa", "initials": "FC", "orcid": "0000-0001-8065-3375", "researcher": {"href": "https://publications.scilifelab.se/researcher/468b2e407aeb49a88b1ef0f7b1e02ce7.json"}}, {"family": "Svensson", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1695-7934", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3185cf86534a96983b39dd93df454a.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Tran-Minh", "given": "Khue Hua", "initials": "KH", "orcid": "0000-0002-8964-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/a94e99b0020f4ef28c00bb20e1a1c8ac.json"}}, {"family": "T\u00fcrkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbae52c6a22f4877b747a4de1ec1ca8a.json"}}, {"family": "Unge", "given": "Christian", "initials": "C"}, {"family": "Venge", "given": "Per", "initials": "P", "orcid": "0000-0001-5863-790X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1695020d4d724ba8b378c992e28e21b1.json"}}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Woessmann", "given": "Jakob", "initials": "J", "orcid": "0000-0002-2283-7237", "researcher": {"href": "https://publications.scilifelab.se/researcher/18460524ba914a91ad61dd2ec231c3a7.json"}}, {"family": "Yang", "given": "Hong", "initials": "H", "orcid": "0009-0002-0414-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52bdf7cbd1745e3a4578f17322c83f1.json"}}, {"family": "Ye\u015filkaya", "given": "Umit Haluk", "initials": "UH"}, {"family": "Yuan", "given": "Meng", "initials": "M", "orcid": "0000-0002-9248-3294", "researcher": {"href": "https://publications.scilifelab.se/researcher/befeb12cfba142eb9dadf81497d6c419.json"}}, {"family": "Zeybel", "given": "Mujdat", "initials": "M", "orcid": "0000-0001-5440-4623", "researcher": {"href": "https://publications.scilifelab.se/researcher/0559b83985134a0a9283ea39601a95a7.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2025-10-09", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": null, "issue": null, "pages": "eadx2678"}, "abstract": "The human blood proteome provides a holistic readout of health states through the assessment of thousands of circulating proteins. Here, we present a pan-disease resource to enable the study of diverse disease phenotypes within a harmonized proteomics dataset. By profiling protein concentrations across 59 diseases and healthy cohorts, we identified proteins associated with age, sex, and BMI, as well as disease-specific signatures. This study highlights shared and distinct protein patterns across conditions, demonstrating the power of a unified proteomics approach to uncover biological insights. The dataset, covering 8,262 individuals and up to 5,416 proteins, serves as an online resource for exploring disease-specific protein profiles and advancing precision medicine research.", "doi": "10.1126/science.adx2678", "pmid": "41066540", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-10T10:37:22.942Z", "modified": "2025-11-07T07:45:07.446Z"}, {"entity": "publication", "iuid": "c739e888429e49b782d4ec4455e72f97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c739e888429e49b782d4ec4455e72f97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c739e888429e49b782d4ec4455e72f97"}}, "title": "Correlation of autoantibody profiles with clinical parameters in exfoliative glaucoma patients.", "authors": [{"family": "Potter", "given": "Ryan", "initials": "R"}, {"family": "Ayala", "given": "Marcelo", "initials": "M"}, {"family": "Tilevik", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Int Ophthalmol", "issn": "1573-2630", "volume": "45", "issue": "1", "pages": "404", "issn-l": null}, "abstract": "Exfoliative glaucoma (XFG) is characterized by elevated intraocular pressure (IOP) caused by fibrous deposits obstructing aqueous humor drainage, traditionally emphasizing mechanical factors. In this study, we aim to investigate the relationships between clinical parameters and autoimmune activity in exfoliative glaucoma (XFG) patients, and identify patterns of autoantibody reactivity among patient subgroups with differing levels of overall autoimmune activity.\n\nWe analyzed serum autoantibody profiles against 92 antigens in 116 XFG patients using an xMAP suspension bead array. Spearman correlation analysis and PERMANOVA were applied to evaluate relationships between autoantibody reactivity and clinical parameters in glaucoma management. Hierarchical clustering was used to identify clusters of patients based on overall autoantibody reactivity levels, and network analysis using shortest path mapping was utilized to explore potential connections among the proteins associated with the antigens used in this study and other proteins not targeted in this study.\n\nSignificant positive correlations were found between the clinical parameter SE and autoantibodies targeting the proteins LOXL3, CYP39A1, and HYOU1. Clustering analysis revealed distinct subgroups of patients with differing overall autoantibody reactivity levels, notably showing significant negative correlations between broad autoantibody profiles and CCT exclusively within the subgroup characterized by higher autoimmune activity. Network analysis identified CTNNB1 as a prominent multi-path intermediary connecting disparate proteins, highlighting potential common regulatory pathways.\n\nThis study identifies novel correlations between clinical parameters and autoimmune activity in XFG, suggesting refractive changes and corneal structural characteristics may be influenced by specific immune mechanisms. These findings underscore the value of integrating immunological profiling with clinical glaucoma assessments, potentially enhancing patient stratification and identifying possible therapeutic targets.", "doi": "10.1007/s10792-025-03783-0", "pmid": "41042282", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12494623"}, {"db": "pii", "key": "10.1007/s10792-025-03783-0"}], "notes": [], "created": "2025-10-24T09:38:37.892Z", "modified": "2025-10-24T09:38:37.921Z"}, {"entity": "publication", "iuid": "d1f8810655e14e5896912d1b996ed6a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1f8810655e14e5896912d1b996ed6a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1f8810655e14e5896912d1b996ed6a7"}}, "title": "Immune-coagulation dynamics in severe COVID-19 revealed by autoantibody profiling and multi-omics integration.", "authors": [{"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Cederholm", "given": "Axel", "initials": "A", "orcid": "0009-0006-5973-9637", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2dffb2fd8e446d6a72c765602b97291.json"}}, {"family": "Rezene", "given": "Sefanit", "initials": "S"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M", "orcid": "0000-0003-0050-704X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65dc88b917274bc595daed855b63abab.json"}}, {"family": "Nordqvist", "given": "Hampus", "initials": "H"}, {"family": "Treutiger", "given": "Carl Johan", "initials": "CJ"}, {"family": "Lira-Junior", "given": "Ronaldo", "initials": "R"}, {"family": "Landegren", "given": "Nils", "initials": "N", "orcid": "0000-0002-6163-9540", "researcher": {"href": "https://publications.scilifelab.se/researcher/13ceacb17b7448709f9bfcd593bec1e2.json"}}, {"family": "Gupta", "given": "Soham", "initials": "S", "orcid": "0000-0003-1136-3010", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bbd430437164ba38676d7b94e2189ab.json"}}], "type": "journal article", "published": "2025-09-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "32149", "issn-l": "2045-2322"}, "abstract": "Severe COVID-19 is characterized by immune-coagulation dysregulation, yet the contribution of related autoantibodies remains poorly understood. We investigated relationships between plasma autoantibody reactivities, whole-blood transcriptomics, plasma proteomics, and clinical laboratory parameters in a cohort of hospitalized COVID-19 patients. Transcriptomic analysis revealed that 42 curated coagulation and complement cascade genes were upregulated in severe cases compared to healthy controls, with 15 genes, including CR1L, ELANE, ITGA2B, ITGB3, VWF, TFPI, PROS1, MMRN1, and SELP (> 1.2 log2 fold-change), also significantly different from mild cases. Autoantibody profiling against eight coagulation-related proteins (ADAMTS13, Factor V, Protein S, SERPINC1, Apo-H, PROC1, Prothrombin, and PF4) showed reactivities below positivity thresholds across all groups. Using an exploratory approach, in severe cases, subthreshold autoantibody candidates (FDR < 0.25) showed negative correlation trends with select gene expressions and inflammatory markers (Factor V with IL-6 and CXCL10), suggesting potential disease-specific immunomodulatory associations. In contrast, while mild cases exhibited stronger gene-protein correlations, they showed limited associations with antigen reactivities or clinical laboratory parameters. Additionally, no correlations were observed between autoantibodies and platelet-counts or Fibrin-D-dimer levels. Age-associated increases in antigen reactivities were noted in severe disease, implying a role for immunosenescence. These findings support further investigation into the role of subthreshold autoantibody candidates in thromboinflammatory COVID-19 pathogenesis.", "doi": "10.1038/s41598-025-17054-6", "pmid": "40890263", "labels": {"Autoimmunity and Serology Profiling": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12402181"}, {"db": "pii", "key": "10.1038/s41598-025-17054-6"}], "notes": [], "created": "2025-09-10T08:19:37.842Z", "modified": "2025-11-25T19:21:42.478Z"}, {"entity": "publication", "iuid": "a321ba70d5a8449193a0b042ea632cc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a321ba70d5a8449193a0b042ea632cc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a321ba70d5a8449193a0b042ea632cc6"}}, "title": "Sex Dependent and Sj\u00f6gren Disease Like Immune Responses Against Phosphoantigens in Balb/C Mice.", "authors": [{"family": "Czwakiel", "given": "Paulina", "initials": "P"}, {"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Eghbali", "given": "Atiyeh", "initials": "A"}, {"family": "Dircksen", "given": "Heinrich", "initials": "H"}, {"family": "Kamal", "given": "Kahkashan", "initials": "K", "orcid": "0000-0003-0968-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/56449fc911fd48b98b207c394d635507.json"}}, {"family": "Payandeh", "given": "Zahra", "initials": "Z"}, {"family": "Ozata", "given": "Deniz", "initials": "D", "orcid": "0000-0001-5215-8684", "researcher": {"href": "https://publications.scilifelab.se/researcher/933850bed34c4517b01e915cf8831686.json"}}, {"family": "Troye-Blomberg", "given": "Marita", "initials": "M"}, {"family": "Faye", "given": "Ingrid", "initials": "I", "orcid": "0000-0003-4382-7238", "researcher": {"href": "https://publications.scilifelab.se/researcher/28e762d6a5a845e79a7a107f700a82b5.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Scand. J. Immunol.", "issn": "1365-3083", "volume": "102", "issue": "3", "pages": "e70052", "issn-l": "0300-9475"}, "abstract": "The initial aim of this study on Balb/C mice was to investigate the putative effects on feeding and appetite of isopentenyl pyrophosphate (IPP) and E-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), also known as phosphoantigens (pAgs). HMBPP was recently shown to increase blood meal appetite in malaria mosquitoes. Both IPP and HMBPP are metabolites produced by the normal gut microbiota and apicomplexan parasites such as Plasmodium. To explore potential effects on appetite, male and female mice were treated by gavage with these metabolites, and body mass and gene expression were monitored in brain, stomach and small intestine at 3 h and 7 weeks. Body mass gain did not clearly differ between pAg-treated and water control mice. However, beginning between 4 and 7 weeks, the salivary glands of IPP-treated males began to swell. With the autoimmune Sj\u00f6gren disease (SjD) in mind, we subsequently investigated the salivary glands after 1, 4 and 7 weeks of IPP treatment. Fast gene set enrichment analysis (FGSEA) of marginal zone B-cell (MZB) transcripts from salivary glands, together with B-cell infiltration in both sexes at 4 weeks, suggested similarities to SjD pathology. Using ELISA, we measured serum autoantibodies against Ro52, Ro60 and La. Multivariate analysis at 7 weeks showed treatment-associated trends: levels of anti-Ro52 and anti-La tended to increase in IPP-treated males, but not in females. Notably, IL-6 serum levels displayed a sex-dependent pattern, and PCA analyses of transcriptomic data from brain, stomach and small intestine-though with some exceptions-also indicated differential responses to pAgs between males and females.", "doi": "10.1111/sji.70052", "pmid": "40898584", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12405675"}], "notes": [], "created": "2025-09-10T08:38:36.714Z", "modified": "2025-11-07T07:24:59.576Z"}, {"entity": "publication", "iuid": "85abd43001ea47faba9f42368da29448", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85abd43001ea47faba9f42368da29448.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85abd43001ea47faba9f42368da29448"}}, "title": "Idiopathic inflammatory myopathies lack neutralising autoantibodies to type- I, II and III interferons", "authors": [{"family": "Behere", "given": "Anish", "initials": "A", "orcid": "0000-0002-2424-3475", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c155029e86d458cad39ed4c2670c880.json"}}, {"family": "Mildner", "given": "Hedvig", "initials": "H"}, {"family": "Peralta Garcia", "given": "Irene", "initials": "I"}, {"family": "P\u00e9rez Bucio", "given": "C\u00e9sar", "initials": "C"}, {"family": "Lundberg", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}, {"family": "Horuluoglu", "given": "Begum", "initials": "B"}, {"family": "Landegren", "given": "Nils", "initials": "N"}], "type": "journal-article", "published": "2025-07-00", "journal": {"title": "RMD Open", "issn": "2056-5933", "volume": "11", "issue": "3", "pages": "e005836", "issn-l": "2056-5933"}, "abstract": null, "doi": "10.1136/rmdopen-2025-005836", "pmid": null, "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-03T09:44:26.353Z", "modified": "2025-12-03T09:44:26.437Z"}, {"entity": "publication", "iuid": "fcdd1bf8581f4524b781381b94a66ef9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcdd1bf8581f4524b781381b94a66ef9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcdd1bf8581f4524b781381b94a66ef9"}}, "title": "Evaluating IL1RA-Autoantibodies Across SARS-CoV-2-Related Diseases.", "authors": [{"family": "Behere", "given": "Anish", "initials": "A", "orcid": "0000-0002-2424-3475", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c155029e86d458cad39ed4c2670c880.json"}}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Cederholm", "given": "Axel", "initials": "A"}, {"family": "Cavalli", "given": "Marco", "initials": "M", "orcid": "0000-0003-1143-1431", "researcher": {"href": "https://publications.scilifelab.se/researcher/e35211c06385459baee12101121d2a15.json"}}, {"family": "Yalcinkaya", "given": "Ahmet", "initials": "A"}, {"family": "COVID\u2010HGE", "given": "", "initials": ""}, {"family": "Bastard", "given": "Paul", "initials": "P"}, {"family": "Puel", "given": "Anne", "initials": "A", "orcid": "0000-0003-2603-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bcef4c205904e5db9e36f3aadaa13bb.json"}}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Landegren", "given": "Nils", "initials": "N"}], "type": "letter", "published": "2025-07-00", "journal": {"title": "Scand. J. Immunol.", "issn": "1365-3083", "volume": "102", "issue": "1", "pages": "e70039", "issn-l": "0300-9475"}, "abstract": null, "doi": "10.1111/sji.70039", "pmid": "40556349", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12188108"}], "notes": [], "created": "2025-09-10T08:20:51.920Z", "modified": "2025-09-10T08:20:52.252Z"}, {"entity": "publication", "iuid": "d68819db6d2b4972833ed77bcff28ccc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d68819db6d2b4972833ed77bcff28ccc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d68819db6d2b4972833ed77bcff28ccc"}}, "title": "Human LY9 governs CD4+ T cell IFN-\u03b3 immunity to Mycobacterium tuberculosis.", "authors": [{"family": "Ogishi", "given": "Masato", "initials": "M", "orcid": "0000-0003-2421-7389", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9205246af72422f993f696135d03d00.json"}}, {"family": "Puchan", "given": "Julia", "initials": "J", "orcid": "0000-0003-0284-3629", "researcher": {"href": "https://publications.scilifelab.se/researcher/6067f38c03114b40981e92d0337479b0.json"}}, {"family": "Yang", "given": "Rui", "initials": "R", "orcid": "0000-0003-4427-2158", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e4faa40d4b94755a28e630d6e26c918.json"}}, {"family": "Arias", "given": "Andr\u00e9s Augusto", "initials": "AA"}, {"family": "Han", "given": "Ji Eun", "initials": "JE", "orcid": "0000-0003-1112-9320", "researcher": {"href": "https://publications.scilifelab.se/researcher/c81e24eb454147e1b68e642748424c0d.json"}}, {"family": "Nguyen", "given": "Tina", "initials": "T", "orcid": "0000-0003-0709-3636", "researcher": {"href": "https://publications.scilifelab.se/researcher/28a78707a08d4614bba6392434635526.json"}}, {"family": "Guti\u00e9rrez-C\u00f3zar", "given": "Rebeca", "initials": "R", "orcid": "0000-0003-0348-3223", "researcher": {"href": "https://publications.scilifelab.se/researcher/0042df6ba0b74d4aae8b17e7785b33ce.json"}}, {"family": "Conil", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Seeleuthner", "given": "Yoann", "initials": "Y"}, {"family": "Rinchai", "given": "Darawan", "initials": "D", "orcid": "0000-0001-8851-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/83435aa472e94885bf67a8cad09737fd.json"}}, {"family": "Zhang", "given": "Peng", "initials": "P", "orcid": "0000-0002-6129-567X", "researcher": {"href": "https://publications.scilifelab.se/researcher/20fcd31c47a940e8b72a8eb8d6e2a63b.json"}}, {"family": "Ponsin", "given": "Khoren", "initials": "K"}, {"family": "Chaldebas", "given": "Matthieu", "initials": "M", "orcid": "0000-0002-4920-3947", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ade171e91a94d3eac168e79443b954b.json"}}, {"family": "Feng", "given": "Yi", "initials": "Y", "orcid": "0000-0002-2393-1700", "researcher": {"href": "https://publications.scilifelab.se/researcher/779f0d6a0fda42e99f58a2f09f17b2d2.json"}}, {"family": "Neehus", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0002-8573-6820", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d78343f97c469cb88a2d38fd4945ec.json"}}, {"family": "Delmonte", "given": "Ottavia M", "initials": "OM", "orcid": "0000-0002-4772-0799", "researcher": {"href": "https://publications.scilifelab.se/researcher/8036b2ad257e4aa680127162020b0c28.json"}}, {"family": "Khan", "given": "Taushif", "initials": "T", "orcid": "0000-0002-7917-8965", "researcher": {"href": "https://publications.scilifelab.se/researcher/c19c3e42c4e9403eb5e37f3257ef1c04.json"}}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "Bohlen", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-0458-9484", "researcher": {"href": "https://publications.scilifelab.se/researcher/a740e67ef67a4958961dc5fbbf27c95f.json"}}, {"family": "Peel", "given": "Jessica N", "initials": "JN"}, {"family": "Fagniez", "given": "Iris", "initials": "I", "orcid": "0009-0009-9900-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea0a500efb1b48abac039da065cd95d8.json"}}, {"family": "Pelham", "given": "Simon J", "initials": "SJ", "orcid": "0000-0002-3119-662X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee668998ba674af5b89a2a8fb2d1e49d.json"}}, {"family": "Lei", "given": "Wei-Te", "initials": "WT", "orcid": "0000-0003-1677-8901", "researcher": {"href": "https://publications.scilifelab.se/researcher/84ba1115d51941bba83fdcab614d6005.json"}}, {"family": "Chrabieh", "given": "Maya", "initials": "M"}, {"family": "Laine", "given": "Candice", "initials": "C", "orcid": "0000-0003-3258-6969", "researcher": {"href": "https://publications.scilifelab.se/researcher/29a0e7587c494ae68155085ee0a1a1cd.json"}}, {"family": "Ouair", "given": "Hind", "initials": "H"}, {"family": "Benhsaien", "given": "Ibtihal", "initials": "I", "orcid": "0000-0001-5727-9629", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a7e07f8530c4d2482f60f8e60df5d46.json"}}, {"family": "Abid", "given": "Ahmed", "initials": "A", "orcid": "0000-0003-4885-6572", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b1708390385407cae181952bdcde860.json"}}, {"family": "Abderrhamani Ghorfi", "given": "Ismail", "initials": "I", "orcid": "0000-0001-6403-0098", "researcher": {"href": "https://publications.scilifelab.se/researcher/f040661497c2440da7a6f6687863df63.json"}}, {"family": "Souhi", "given": "Hicham", "initials": "H", "orcid": "0000-0003-3183-1627", "researcher": {"href": "https://publications.scilifelab.se/researcher/93ebbf18946842a3ada75998b5a95df9.json"}}, {"family": "Ouazzani", "given": "Hanane", "initials": "H"}, {"family": "Aniss", "given": "Rafik", "initials": "R"}, {"family": "Riminton", "given": "D Sean", "initials": "DS", "orcid": "0000-0002-9953-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f500629c8194268b99b12b9d6ce2970.json"}}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}, {"family": "Turvey", "given": "Stuart E", "initials": "SE", "orcid": "0000-0003-1599-1065", "researcher": {"href": "https://publications.scilifelab.se/researcher/55c5b74659bf4f9dac9e02826a9d6cec.json"}}, {"family": "Marr", "given": "Nico", "initials": "N", "orcid": "0000-0002-1927-7072", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cc63695a4ca4553ae5ed703ea6bdcf8.json"}}, {"family": "Notarangelo", "given": "Luigi D", "initials": "LD", "orcid": "0000-0002-8335-0262", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8d346e44c2d443ba3da3fcf2725b96c.json"}}, {"family": "Hatipoglu", "given": "Nevin", "initials": "N", "orcid": "0000-0003-2858-0150", "researcher": {"href": "https://publications.scilifelab.se/researcher/d396fdc46870452697c42b889866e40e.json"}}, {"family": "Bousfiha", "given": "Aziz", "initials": "A", "orcid": "0000-0002-5011-9873", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0206681da8543a39287d5b5d22f71fb.json"}}, {"family": "Ozcelik", "given": "Tayfun", "initials": "T", "orcid": "0000-0001-5937-1082", "researcher": {"href": "https://publications.scilifelab.se/researcher/251a5fd386594151b80b5a3a71f6ab58.json"}}, {"family": "El Baghdadi", "given": "Jamila", "initials": "J", "orcid": "0000-0002-1920-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9f21356552345c8a7f1085e5dc92d35.json"}}, {"family": "Cobat", "given": "Aurelie", "initials": "A", "orcid": "0000-0001-7209-6257", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaba2f9452294eec89161b589d96ff29.json"}}, {"family": "Ma", "given": "Cindy S", "initials": "CS", "orcid": "0000-0001-5387-8413", "researcher": {"href": "https://publications.scilifelab.se/researcher/398f17ef657242a1a091b04d05388cf9.json"}}, {"family": "Abel", "given": "Laurent", "initials": "L", "orcid": "0000-0001-7016-6493", "researcher": {"href": "https://publications.scilifelab.se/researcher/24ef4ca1eb3a4b1bbee73f07cd64fe92.json"}}, {"family": "Puel", "given": "Anne", "initials": "A", "orcid": "0000-0003-2603-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bcef4c205904e5db9e36f3aadaa13bb.json"}}, {"family": "Bustamante", "given": "Jacinta", "initials": "J", "orcid": "0000-0002-3439-2482", "researcher": {"href": "https://publications.scilifelab.se/researcher/152dc8084c1d4ba89ace373889bea81e.json"}}, {"family": "Engel", "given": "Pablo", "initials": "P", "orcid": "0000-0001-8410-252X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce0386cfa7d4851bfd8d16f2b0b8f71.json"}}, {"family": "Gros", "given": "Philippe", "initials": "P", "orcid": "0000-0002-0114-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0012dd9120a421ebdda3f5da528ec16.json"}}, {"family": "Tangye", "given": "Stuart G", "initials": "SG", "orcid": "0000-0002-5360-5180", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e3fa03cfc304a8aa0262e5f8c51665d.json"}}, {"family": "Sallusto", "given": "Federica", "initials": "F", "orcid": "0000-0003-3750-2752", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdca95394616420ba260e86d35809977.json"}}, {"family": "Boisson-Dupuis", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0002-7115-116X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5584eef132004c55a120c70d9a9f9eee.json"}}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL", "orcid": "0000-0002-7782-4169", "researcher": {"href": "https://publications.scilifelab.se/researcher/009e2306468648c08fb1eea319f0c488.json"}}], "type": "journal article", "published": "2025-05-30", "journal": {"title": "Sci Immunol", "issn": "2470-9468", "volume": "10", "issue": "107", "pages": "eads7377", "issn-l": null}, "abstract": "CD4+ T cells are indispensable for optimal immunity to Mycobacterium tuberculosis (M.tb), a pathogen that triggers tuberculosis (TB) in humans. M.tb-specific human CD4+ T cells are known to polarize toward an interferon-\u03b3 (IFN-\u03b3)-producing, CCR4-CCR6+CXCR3+T-bet+ROR\u03b3T+ T helper 1* cell (TH1*cell) memory phenotype. We report that autosomal recessive deficiency of the human lymphocytic surface receptor LY9 (SLAMF3 and CD229), which is found in less than 10-5 individuals in the general population, underlies TB in three unrelated patients due to selective impairment in IFN-\u03b3 production by TH1* cells. TH1* cells express higher levels of LY9 than other CD4+ T cells. Mechanistically, LY9 polarizes na\u00efve CD4+ T cells toward memory TH1* cells by inducing T-bet via signaling lymphocytic activation molecule (SLAM)-associated protein (SAP) and ROR\u03b3T (thymus-specific retinoid-related orphan receptor \u03b3) without SAP. LY9 costimulation enhances TCR-driven IFN-\u03b3 production of memory TH1*, but not TH1, cells in a T cell-intrinsic manner via NFAT1 (nuclear factor of activated T cells 1) and ROR\u03b3T. LY9 is likely to govern an optimal TH1* cell- and IFN-\u03b3-dependent protective immunity to M.tb in humans.", "doi": "10.1126/sciimmunol.ads7377", "pmid": "40446017", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2092213"}, {"db": "pmc", "key": "PMC12242830"}], "notes": [], "created": "2025-09-10T08:24:54.248Z", "modified": "2025-09-10T08:24:55.981Z"}, {"entity": "publication", "iuid": "1f4e4d96c44643488989943e6820d31a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f4e4d96c44643488989943e6820d31a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f4e4d96c44643488989943e6820d31a"}}, "title": "Antibody reactivity in cerebrospinal fluid and serum against the insulin-insulin-like growth factor 2 (INS-IGF2) protein is associated with psychotic symptomatology in patients with schizophrenia or related psychosis.", "authors": [{"family": "Melkersson", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2025-04-28", "journal": {"title": "Neuro Endocrinol. Lett.", "issn": "2354-4716", "volume": "46", "issue": "1", "pages": "1-14", "issn-l": "0172-780X"}, "abstract": "Evidence has accumulated that an autoimmune-mediated process may underlie development of schizophrenia, and in two recent studies, we found increased antibody reactivity against the insulin receptor-A (INSR-A) and insulin-like growth factor 1 receptor (IGF1R) and their ligands (insulin and insulin-like growth factor 1) in cerebrospinal fluid (CSF) and/ or serum from patients with schizophrenia or related psychosis. The aim of this study was to analyze antibody reactivity in schizophrenia against the insulin-insulin-like growth factor 2 (INS-IGF2) protein, which hypothetically also may be a ligand to INSR-A and IGF1R and involved in the pathogenesis of schizophrenia.\n\nPatients with schizophrenia or related psychosis and controls were analyzed regarding antibody reactivity against INS-IGF2 in CSF (n = 12/ n = 11) and serum (n = 17/ n = 11), using bead-based antigen arrays of one protein fragment and 24 peptides of this protein. Additionally, the patients were assessed for clinical symptoms with the Positive and Negative Syndrome Scale (PANSS) for schizophrenia.\n\nSignificantly higher antibody reactivity against the peptides 11 and 12 was found in patients in partial than full symptom remission. Patients' antibody reactivity against the peptides 5, 11 and 12 correlated positively to their PANSS scores of positive symptoms. Furthermore, significantly higher antibody reactivity against the peptides 2, 3, 10 and 22 was found in patients with, than without, heredity for diabetes mellitus type 1 or 2.\n\nThe findings in this study pointed that the INS-IGF2 protein may be present in the CNS and involved in the autoimmune-mediated process underlying the development of schizophrenia.", "doi": null, "pmid": "40319454", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "46012502"}], "notes": [], "created": "2025-09-10T08:13:51.362Z", "modified": "2025-09-10T08:13:51.369Z"}, {"entity": "publication", "iuid": "d7230d74309f4d7e9bc0c1654439db18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7230d74309f4d7e9bc0c1654439db18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7230d74309f4d7e9bc0c1654439db18"}}, "title": "Naturally acquired IgG responses to Plasmodium falciparum do not target the conserved termini of the malaria vaccine candidate Merozoite Surface Protein 2.", "authors": [{"family": "Zerebinski", "given": "Julia", "initials": "J"}, {"family": "Margerie", "given": "Lucille", "initials": "L"}, {"family": "Han", "given": "Nan Sophia", "initials": "NS"}, {"family": "Moll", "given": "Maximilian", "initials": "M"}, {"family": "Ritvos", "given": "Matias", "initials": "M"}, {"family": "Jahnmatz", "given": "Peter", "initials": "P"}, {"family": "Ahlborg", "given": "Niklas", "initials": "N"}, {"family": "Ngasala", "given": "Billy", "initials": "B"}, {"family": "Rooth", "given": "Ingegerd", "initials": "I"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Sundling", "given": "Christopher", "initials": "C", "orcid": "0000-0002-6138-690X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89c1e689a46b4b14adb0dc99e1c0a58c.json"}}, {"family": "Yman", "given": "Victor", "initials": "V", "orcid": "0000-0001-7267-0749", "researcher": {"href": "https://publications.scilifelab.se/researcher/c66cc2cb5f2c45cf903ca24d02ed3919.json"}}, {"family": "F\u00e4rnert", "given": "Anna", "initials": "A"}, {"family": "Plaza", "given": "David Fernando", "initials": "DF", "orcid": "0000-0003-0366-4112", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f09e7d9876344728f881fbb61c136f4.json"}}], "type": "journal article", "published": "2024-12-09", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "15", "pages": "1501700", "issn-l": "1664-3224"}, "abstract": "Malaria remains a significant burden, and a fully protective vaccine against Plasmodium falciparum is critical for reducing morbidity and mortality. Antibody responses against the blood-stage antigen Merozoite Surface Protein 2 (MSP2) are associated with protection from P. falciparum malaria, but its extensive polymorphism is a barrier to its development as a vaccine candidate. New tools, such as long-read sequencing and accurate protein structure modelling allow us to study the genetic diversity and immune responses towards antigens from clinical isolates with unprecedented detail. This study sought to better understand naturally acquired MSP2-specific antibody responses.\n\nIgG responses against recombinantly expressed full-length, central polymorphic regions, and peptides derived from the conserved termini of MSP2 variants sequenced from patient isolates, were tested in plasma from travelers with recent, acute malaria and from individuals living in an endemic area of Tanzania.\n\nIgG responses towards full MSP2 and truncated MSP2 antigens were variant specific. IgG antibodies in the plasma of first-time infected or previously exposed travelers did not recognize the conserved termini of expressed MSP2 variants by ELISA, but they bound 13-amino acid long linear epitopes from the termini in a custom-made peptide array. Alphafold3 modelling suggests extensive structural heterogeneity in the conserved termini upon antigen oligomerization. IgG from individuals living in an endemic region, many who were asymptomatically infected, did not recognize the conserved termini by ELISA.\n\nOur results suggest that responses to the variable regions are critical for the development of naturally acquired immunity towards MSP2.", "doi": "10.3389/fimmu.2024.1501700", "pmid": "39717775", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11663719"}], "notes": [], "created": "2024-12-09T09:42:36.848Z", "modified": "2025-04-07T07:25:49.767Z"}, {"entity": "publication", "iuid": "bc60a0502a14498fbdae1579b2effdc2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc60a0502a14498fbdae1579b2effdc2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc60a0502a14498fbdae1579b2effdc2"}}, "title": "Autoantibodies against a subunit of mitochondrial respiratory chain complex I in inclusion body myositis.", "authors": [{"family": "Notarnicola", "given": "Antonella", "initials": "A", "orcid": "0000-0003-0272-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/42411ecc60cd4357930ff0e978b3fcd8.json"}}, {"family": "Hellstrom", "given": "Ceke", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Horuluoglu", "given": "Begum", "initials": "B"}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Preger", "given": "Charlotta", "initials": "C", "orcid": "0000-0002-1342-9135", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8519a1cc0e845c68b59d6ecdfea1a33.json"}}, {"family": "Bonomi", "given": "Francesco", "initials": "F"}, {"family": "De Paepe", "given": "Boel", "initials": "B"}, {"family": "De Bleecker", "given": "Jan L", "initials": "JL"}, {"family": "Van der Kooi", "given": "Anneke J", "initials": "AJ"}, {"family": "De Visser", "given": "Marianne", "initials": "M"}, {"family": "Sacconi", "given": "Sabrina", "initials": "S"}, {"family": "Machado", "given": "Pedro", "initials": "P"}, {"family": "Badrising", "given": "Umesh A", "initials": "UA"}, {"family": "Rietveld", "given": "Anke", "initials": "A"}, {"family": "Pruijn", "given": "Ger", "initials": "G"}, {"family": "Rothwell", "given": "Simon", "initials": "S", "orcid": "0000-0003-2123-9902", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39ce853a3d041b68e4d4e82e64e3703.json"}}, {"family": "Lilleker", "given": "James B", "initials": "JB"}, {"family": "Chinoy", "given": "Hector", "initials": "H", "orcid": "0000-0001-6492-1288", "researcher": {"href": "https://publications.scilifelab.se/researcher/03b0a1d459104296baba3dedebf10e08.json"}}, {"family": "Benveniste", "given": "Olivier", "initials": "O"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Idborg", "given": "Helena", "initials": "H", "orcid": "0000-0003-4041-4729", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb0d55d31d77413abaa72e76c0472dc1.json"}}, {"family": "Jakobsson", "given": "Per-Johan", "initials": "P", "orcid": "0000-0001-7665-9715", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb148e2233b4541bc7c8b340f0cf12c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}], "type": "journal article", "published": "2024-11-18", "journal": {"title": "J. Autoimmun.", "issn": "1095-9157", "issn-l": "0896-8411", "volume": "149", "issue": null, "pages": "103332"}, "abstract": "Autoantibodies are found in up to 80 % of patients with idiopathic inflammatory myopathies (IIM) and are associated with distinct clinical phenotypes. Autoantibodies targeting cytosolic 5'-nucleotidase 1A (anti-NT5C1A) are currently the only known serum biomarker for the subgroup inclusion body myositis (IBM), although detected even in other autoimmune diseases. The aim of the study was to identify new autoimmune targets in IIM.\r\n\r\nIn a first cross-sectional exploratory study, samples from 219 IIM (108 Polymyositis (PM), 80 Dermatomyositis (DM) and 31 IBM) patients, 349 Systemic Lupus Erythematosus (SLE) patients and 306 population controls were screened for IgG reactivity against a panel of 357 proteins using an antigen bead array. All samples were identified in the local biobank of the Rheumatology clinic, Karolinska University Hospital. Positive hits for the IBM subgroup were then validated in an independent larger cohort of 287 patients with IBM followed at nine European rheumatological or neurological centers. IBM serum samples were explored by antigen bead array and results validated by Western blot. As controls, sera from 29 patients with PM and 30 with DM, HLA-matched with the Swedish IBM cohort, were included. Demographics, laboratory, clinical, and muscle biopsy data of the IBM cohort was retrieved.\r\n\r\nIn the exploratory study, IgG reactivity towards NADH dehydrogenase 1 \u03b1 subcomplex 11 (NDUFA11), a subunit of the membrane-bound mitochondrial respiratory chain complex I, was discovered with higher frequency in the IBM (9.7 %) than PM (2.8 %) and DM samples (1.3 %), although the difference was not statistically significant. Anti-NDUFA11 IgG was also found in 1.4 % of SLE and 2.0 % of population control samples. In the validation study, anti-NDUFA11 autoantibodies were detected in 10/287 IBM patients (3.5 %), 0/29 p.m. and 0/30 DM patients. Reactivity against NDUFA11 could be confirmed by Western blot. No statistically significant differences were found between patients with and without anti-NDUFA11 antibodies when comparing clinical, laboratory and histological data. However, we observed a trend of higher frequency of distal lower extremity muscle weakness, ragged red fibers and higher CK levels at time of diagnosis in the anti-NDUFA11 positive group. Co-existence of anti-NDUFA11 and anti-NT5C1A antibodies was not observed in any IBM patient.\r\n\r\nOur results reveal a new autoimmune target in the mitochondrial respiratory chain complex I that might be specifically associated with IBM. This is of particular interest as mitochondrial abnormalities are known histological findings in muscle biopsies of IBM patients.", "doi": "10.1016/j.jaut.2024.103332", "pmid": "39561568", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0896-8411(24)00166-5"}], "notes": [], "created": "2024-11-25T12:19:45.739Z", "modified": "2025-04-07T09:26:23.573Z"}, {"entity": "publication", "iuid": "5a47b007d10f4537ab374a8782b3030c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a47b007d10f4537ab374a8782b3030c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a47b007d10f4537ab374a8782b3030c"}}, "title": "Incontinentia pigmenti underlies thymic dysplasia, autoantibodies to type I IFNs, and viral diseases.", "authors": [{"family": "Rosain", "given": "J\u00e9r\u00e9mie", "initials": "J", "orcid": "0000-0002-2822-161X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9648145c59af4d31b806ed93f5e2afd7.json"}}, {"family": "Le Voyer", "given": "Tom", "initials": "T", "orcid": "0000-0002-7253-3135", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ae9aa653f874c2cb1c68a2deb9357b8.json"}}, {"family": "Liu", "given": "Xian", "initials": "X", "orcid": "0000-0001-6546-3725", "researcher": {"href": "https://publications.scilifelab.se/researcher/67f9d4ef9f7149e1ae557cbc6375f935.json"}}, {"family": "Gervais", "given": "Adrian", "initials": "A", "orcid": "0000-0002-1083-5787", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4d47775a4da4ee6ac0ff7da16c0155c.json"}}, {"family": "Polivka", "given": "Laura", "initials": "L", "orcid": "0000-0002-5142-6234", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d02ad2da27342c9912f973a0b24edb1.json"}}, {"family": "Cederholm", "given": "Axel", "initials": "A", "orcid": "0009-0006-5973-9637", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2dffb2fd8e446d6a72c765602b97291.json"}}, {"family": "Berteloot", "given": "Laureline", "initials": "L", "orcid": "0000-0001-9681-3142", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0ce699420749dc97617accb080b2e8.json"}}, {"family": "Parent", "given": "Audrey V", "initials": "AV", "orcid": "0000-0003-4506-6268", "researcher": {"href": "https://publications.scilifelab.se/researcher/553847cbdc524ebf9d064078ce5ea089.json"}}, {"family": "Pescatore", "given": "Alessandra", "initials": "A", "orcid": "0000-0001-8453-8198", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bed07fa2f3b4bbd91f43b7ceab99180.json"}}, {"family": "Spinosa", "given": "Ezia", "initials": "E", "orcid": "0009-0000-4358-557X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f277842e8824bb99435d2fe0159404b.json"}}, {"family": "Minic", "given": "Snezana", "initials": "S", "orcid": "0000-0003-2185-9749", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd44dd110e0743cba754b54f396eb0f4.json"}}, {"family": "Kiszewski", "given": "Ana Elisa", "initials": "AE", "orcid": "0000-0002-6287-6302", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfab446653214f45b802e658ace9ddf1.json"}}, {"family": "Tsumura", "given": "Miyuki", "initials": "M", "orcid": "0000-0002-8272-9588", "researcher": {"href": "https://publications.scilifelab.se/researcher/0000b80ead774d0bae251fe78c315a7a.json"}}, {"family": "Thibault", "given": "Chlo\u00e9", "initials": "C", "orcid": "0000-0002-9420-4180", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4405cafc0ba4afab9732e6627be6fd3.json"}}, {"family": "Esnaola Azcoiti", "given": "Maria", "initials": "M", "orcid": "0000-0002-1499-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6b3a4104d464952a1f74486191d64d1.json"}}, {"family": "Martinovic", "given": "Jelena", "initials": "J", "orcid": "0000-0003-4595-7271", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7c283c428084ba185e28afccb22041e.json"}}, {"family": "Philippot", "given": "Quentin", "initials": "Q", "orcid": "0000-0003-3429-9605", "researcher": {"href": "https://publications.scilifelab.se/researcher/49fea9565657416ea5b12e31ff62177c.json"}}, {"family": "Khan", "given": "Taushif", "initials": "T", "orcid": "0000-0002-7917-8965", "researcher": {"href": "https://publications.scilifelab.se/researcher/c19c3e42c4e9403eb5e37f3257ef1c04.json"}}, {"family": "Marchal", "given": "Astrid", "initials": "A", "orcid": "0000-0003-0648-8126", "researcher": {"href": "https://publications.scilifelab.se/researcher/28c721f7c49542539df2986b4ff01c64.json"}}, {"family": "Charmeteau-De Muylder", "given": "B\u00e9n\u00e9dicte", "initials": "B", "orcid": "0009-0009-2692-781X", "researcher": {"href": "https://publications.scilifelab.se/researcher/083a77fab7094d4f9433fd498a5f1725.json"}}, {"family": "Bizien", "given": "Lucy", "initials": "L", "orcid": "0000-0001-9163-9122", "researcher": {"href": "https://publications.scilifelab.se/researcher/61953873d0704a21beb1769e160a8f9c.json"}}, {"family": "Deswarte", "given": "Caroline", "initials": "C", "orcid": "0000-0002-8775-3368", "researcher": {"href": "https://publications.scilifelab.se/researcher/cccc529fee1d460ca08d53b7299c0896.json"}}, {"family": "Hadjem", "given": "Lillia", "initials": "L", "orcid": "0009-0003-6990-5887", "researcher": {"href": "https://publications.scilifelab.se/researcher/b500ed1c08c14f1e94fc57d1cb3387fd.json"}}, {"family": "Fauvarque", "given": "Marie-Odile", "initials": "MO", "orcid": "0000-0001-5020-3701", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c4fdf162ffb430cabcb92b047662591.json"}}, {"family": "Dorgham", "given": "Karim", "initials": "K", "orcid": "0000-0001-9539-3203", "researcher": {"href": "https://publications.scilifelab.se/researcher/4468a96c2f1142bcb3828b9864bd6115.json"}}, {"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "Falcone", "given": "Emilia Liana", "initials": "EL", "orcid": "0000-0002-5486-1549", "researcher": {"href": "https://publications.scilifelab.se/researcher/37a07961f87c404596fd996f4bb3f820.json"}}, {"family": "Puel", "given": "Mathilde", "initials": "M", "orcid": "0009-0000-4972-6636", "researcher": {"href": "https://publications.scilifelab.se/researcher/617ce634a1614e19ba23f8e2d8ebfe3f.json"}}, {"family": "\u00dcnal", "given": "Sinem", "initials": "S", "orcid": "0009-0002-5460-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/38758f535ab9497e870a8cea680dcb2c.json"}}, {"family": "Geraldo", "given": "Amyrath", "initials": "A", "orcid": "0009-0005-9238-4447", "researcher": {"href": 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"Herv\u00e9", "initials": "H", "orcid": "0000-0003-4309-8338", "researcher": {"href": "https://publications.scilifelab.se/researcher/4045e579b374436294f5ef4811fe6fc3.json"}}, {"family": "Puel", "given": "Anne", "initials": "A", "orcid": "0000-0003-2603-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bcef4c205904e5db9e36f3aadaa13bb.json"}}, {"family": "Courtois", "given": "Gilles", "initials": "G", "orcid": "0000-0003-3117-9595", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f0a98c946c9408887e40f6e73f156c2.json"}}, {"family": "Bastard", "given": "Paul", "initials": "P", "orcid": "0000-0002-5926-8437", "researcher": {"href": "https://publications.scilifelab.se/researcher/3891533a59dc4185ba934b16e416e6ce.json"}}, {"family": "Landegren", "given": "Nils", "initials": "N", "orcid": "0000-0002-6163-9540", "researcher": {"href": "https://publications.scilifelab.se/researcher/13ceacb17b7448709f9bfcd593bec1e2.json"}}, {"family": "Anderson", "given": "Mark S", "initials": "MS", "orcid": "0000-0002-3093-4758", "researcher": {"href": "https://publications.scilifelab.se/researcher/4276efc31c1d4dbaaa242f11ef60c51e.json"}}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL", "orcid": "0000-0002-7782-4169", "researcher": {"href": "https://publications.scilifelab.se/researcher/009e2306468648c08fb1eea319f0c488.json"}}], "type": "journal article", "published": "2024-11-04", "journal": {"title": "J. Exp. Med.", "issn": "1540-9538", "volume": "221", "issue": "11", "issn-l": "0022-1007"}, "abstract": "Human inborn errors of thymic T cell tolerance underlie the production of autoantibodies (auto-Abs) neutralizing type I IFNs, which predispose to severe viral diseases. We analyze 131 female patients with X-linked dominant incontinentia pigmenti (IP), heterozygous for loss-of-function (LOF) NEMO variants, from 99 kindreds in 10 countries. Forty-seven of these patients (36%) have auto-Abs neutralizing IFN-\u03b1 and/or IFN-\u03c9, a proportion 23 times higher than that for age-matched female controls. This proportion remains stable from the age of 6 years onward. On imaging, female patients with IP have a small, abnormally structured thymus. Auto-Abs against type I IFNs confer a predisposition to life-threatening viral diseases. By contrast, patients with IP lacking auto-Abs against type I IFNs are at no particular risk of viral disease. These results suggest that IP accelerates thymic involution, thereby underlying the production of auto-Abs neutralizing type I IFNs in at least a third of female patients with IP, predisposing them to life-threatening viral diseases.", "doi": "10.1084/jem.20231152", "pmid": "39352576", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "277003"}], "notes": [], "created": "2024-10-03T15:01:34.155Z", "modified": "2024-10-03T15:01:41.828Z"}, {"entity": "publication", "iuid": "5a04bb7c654544609c10639696a8b1d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a04bb7c654544609c10639696a8b1d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a04bb7c654544609c10639696a8b1d8"}}, "title": "Autoantibodies to protein S may explain rare cases of coagulopathy following COVID-19 vaccination.", "authors": [{"family": "Yalcinkaya", "given": "Ahmet", "initials": "A"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M"}, {"family": "Cederholm", "given": "Axel", "initials": "A"}, {"family": "G\u00fcner", "given": "Almira", "initials": "A"}, {"family": "Rietrae", "given": "Isabel", "initials": "I"}, {"family": "Mildner", "given": "Hedvig", "initials": "H"}, {"family": "Behere", "given": "Anish", "initials": "A"}, {"family": "Eriksson", "given": "Oskar", "initials": "O"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Landegren", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2024-10-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "24512", "issn-l": "2045-2322"}, "abstract": "While Coronavirus disease 2019 (COVID-19) vaccines have proven to be both effective and generally safe, rare but severe adverse events following immunization (AEFIs) are described. Autoantibodies to platelet factor-4 are associated with catastrophic thrombotic AEFIs, but comprehensive investigations of other autoantibodies are lacking. We aimed to detect and describe autoantibodies targeting coagulation-related proteins in a population-wide cohort (SWEDEGENE) including AEFIs attributed to COVID-19 vaccines in Sweden. Subjects were recruited from December 2020 to October 2022 and were stratified based on diagnosis and COVID-19 exposure. Screening was carried out in two phases, with a multiplex bead-based assay in the first subset (until September 2021) and with targeted assays for the second (until October 2022). Positivity was defined based on absolute, relative, and biological/technical thresholds. Patients with coagulation-related AEFIs were older and the Vaxzevria vaccine was overrepresented in this group. Two cases had antiphospholipid antibodies but none had PF4 antibodies. We identified six positives for protein S autoantibodies. Protein S concentrations were negatively correlated with autoantibody response in patients with immunoreactivity and functional analysis revealed low protein S activity in three subjects. Our population-wide analysis reveals cases with autoantibodies against protein S which possibly underlie coagulopathic AEFIs.", "doi": "10.1038/s41598-024-75514-x", "pmid": "39424883", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11489816"}, {"db": "pii", "key": "10.1038/s41598-024-75514-x"}], "notes": [], "created": "2024-11-07T12:54:49.632Z", "modified": "2024-11-07T12:54:49.642Z"}, {"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": "184914c5984c485498ee2d2068a27342", "links": {"self": {"href": "https://publications.scilifelab.se/publication/184914c5984c485498ee2d2068a27342.json"}, "display": {"href": "https://publications.scilifelab.se/publication/184914c5984c485498ee2d2068a27342"}}, "title": "Autoantibodies towards HFE and SYT5 in anti-neutrophil cytoplasm antibody-associated vasculitis relapse.", "authors": [{"family": "Bayati", "given": "Shaghayegh", "initials": "S"}, {"family": "Nazeer", "given": "Jamsheela", "initials": "J"}, {"family": "Ng", "given": "James", "initials": "J"}, {"family": "George", "given": "Angel M", "initials": "AM"}, {"family": "Hayes", "given": "Michael", "initials": "M"}, {"family": "Little", "given": "Mark A", "initials": "MA"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}], "type": "journal article", "published": "2024-10-14", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "issn-l": "1462-0324", "volume": null, "issue": null, "pages": null}, "abstract": "Identification of those at high and low risk of disease relapse is a major unmet need in the management of patients with ANCA-associated vasculitis (AAV). Precise stratification would allow tailoring of immunosuppressive medication. We profiled the autoantibody repertoire of AAV patients in remission to identify novel autoantibodies associated with relapse risk.\r\n\r\nPlasma samples collected from 246 AAV patients in remission were screened for novel autoantibodies using in-house generated protein arrays including 42 000 protein fragments representing 18 000 unique human proteins. Patients were categorized based on the occurrence and frequency of relapses. We modelled the association between these antibodies and relapse occurrence using descriptive and high dimensional regression approaches.\r\n\r\nWe observed nine autoantibodies at higher frequency in samples from AAV patients experiencing multiple relapses compared with patients in long-term remission off therapy (LTROT). LASSO analysis identified six autoantibodies that exhibited an association with relapse occurrence after sample collection. Antibodies targeting HFE and SYT5 were identified as associated with relapse in both analyses.\r\n\r\nThrough a broad protein array-based autoantibody screening, we identified two novel autoantibodies directed against HFE and SYT5 as candidate biomarkers of relapse in AAV.", "doi": "10.1093/rheumatology/keae540", "pmid": "39400561", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7821207"}], "notes": [], "created": "2024-11-25T12:18:00.839Z", "modified": "2024-11-25T12:19:11.720Z"}, {"entity": "publication", "iuid": "03643ef7d9694de6b937dfdb8567206a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03643ef7d9694de6b937dfdb8567206a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03643ef7d9694de6b937dfdb8567206a"}}, "title": "IL-7-dependent and -independent lineages of IL-7R-dependent human T cells.", "authors": [{"family": "Arango-Franco", "given": "Carlos A", "initials": "CA"}, {"family": "Ogishi", "given": "Masato", "initials": "M"}, {"family": "Unger", "given": "Susanne", "initials": "S"}, {"family": "Delmonte", "given": "Ottavia M", "initials": "OM"}, {"family": "Orrego", "given": "Julio C\u00e9sar", "initials": "JC"}, {"family": "Yatim", "given": "Ahmad", "initials": "A"}, {"family": "Velasquez-Lopera", "given": "Margarita M", "initials": "MM"}, {"family": "Zea-Vera", "given": "Andr\u00e9s F", "initials": "AF"}, {"family": "Bohlen", "given": "Jonathan", "initials": "J"}, {"family": "Chbihi", "given": "Marwa", "initials": "M"}, {"family": "Fayand", "given": "Antoine", "initials": "A"}, {"family": "S\u00e1nchez", "given": "Juan Pablo", "initials": "JP"}, {"family": "Rojas", "given": "Julian", "initials": "J"}, {"family": "Seeleuthner", "given": "Yoann", "initials": "Y"}, {"family": "Le Voyer", "given": "Tom", "initials": "T"}, {"family": "Philippot", "given": "Quentin", "initials": "Q"}, {"family": "Payne", "given": "Kathryn J", "initials": "KJ"}, {"family": "Gervais", "given": "Adrian", "initials": "A"}, {"family": "Erazo-Borr\u00e1s", "given": "Lucia V", "initials": "LV"}, {"family": "Correa-Londo\u00f1o", "given": "Luis A", "initials": "LA"}, {"family": "Cederholm", "given": "Axel", "initials": "A"}, {"family": "Gall\u00f3n-Duque", "given": "Alejandro", "initials": "A"}, {"family": "Goncalves", "given": "Pedro", "initials": "P"}, {"family": "Doisne", "given": "Jean-Marc", "initials": "JM"}, {"family": "Horev", "given": "Liran", "initials": "L"}, {"family": "Charmeteau-de Muylder", "given": "B\u00e9n\u00e9dicte", "initials": "B"}, {"family": "\u00c1lvarez", "given": "Jes\u00fas \u00c1", "initials": "J\u00c1"}, {"family": "Arboleda", "given": "Diana M", "initials": "DM"}, {"family": "P\u00e9rez-Zapata", "given": "Lizet", "initials": "L"}, {"family": "V\u00e1squez-Echeverri", "given": "Estefan\u00eda", "initials": "E"}, {"family": "Moncada-V\u00e9lez", "given": "Marcela", "initials": "M"}, {"family": "L\u00f3pez", "given": "Juan A", "initials": "JA"}, {"family": "Caicedo", "given": "Yolanda", "initials": "Y"}, {"family": "Palterer", "given": "Boaz", "initials": "B"}, {"family": "Pati\u00f1o", "given": "Pablo J", "initials": "PJ"}, {"family": "Montoya", "given": "Carlos J", "initials": "CJ"}, {"family": "Chaldebas", "given": "Matthieu", "initials": "M"}, {"family": "Zhang", "given": "Peng", "initials": "P"}, {"family": "Nguyen", "given": "Tina", "initials": "T"}, {"family": "Ma", "given": "Cindy S", "initials": "CS"}, {"family": "Jeljeli", "given": "Mohamed", "initials": "M"}, {"family": "Alzate", "given": "Juan F", "initials": "JF"}, {"family": "Cabarcas", "given": "Felipe", "initials": "F"}, {"family": "Khan", "given": "Taushif", "initials": "T"}, {"family": "Rinchai", "given": "Darawan", "initials": "D"}, {"family": "Pr\u00e9tet", "given": "Jean-Luc", "initials": "JL"}, {"family": "Boisson", "given": "Bertrand", "initials": "B"}, {"family": "Generalized Verrucosis Japanese Consortium", "given": "", "initials": ""}, {"family": "Marr", "given": "Nico", "initials": "N"}, {"family": "Ibrahim", "given": "Ruba", "initials": "R"}, {"family": "Molho-Pessach", "given": "Vered", "initials": "V"}, {"family": "Boisson-Dupuis", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Kiritsi", "given": "Dimitra", "initials": "D"}, {"family": "Barata", "given": "Jo\u00e3o T", "initials": "JT"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Neven", "given": "B\u00e9n\u00e9dicte", "initials": "B"}, {"family": "Abel", "given": "Laurent", "initials": "L"}, {"family": "Lisco", "given": "Andrea", "initials": "A"}, {"family": "B\u00e9ziat", "given": "Vivien", "initials": "V"}, {"family": "Jouanguy", "given": "Emmanuelle", "initials": "E"}, {"family": "Bustamante", "given": "Jacinta", "initials": "J"}, {"family": "Di Santo", "given": "James P", "initials": "JP"}, {"family": "Tangye", "given": "Stuart G", "initials": "SG"}, {"family": "Notarangelo", "given": "Luigi D", "initials": "LD"}, {"family": "Cheynier", "given": "R\u00e9mi", "initials": "R"}, {"family": "Natsuga", "given": "Ken", "initials": "K"}, {"family": "Arias", "given": "Andr\u00e9s A", "initials": "AA"}, {"family": "Franco", "given": "Jos\u00e9 Luis", "initials": "JL"}, {"family": "Warnatz", "given": "Klaus", "initials": "K"}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL"}, {"family": "Puel", "given": "Anne", "initials": "A"}], "type": "journal article", "published": "2024-10-01", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "134", "issue": "19", "issn-l": "0021-9738"}, "abstract": "Infants with biallelic IL7R loss-of-function variants have severe combined immune deficiency (SCID) characterized by the absence of autologous T lymphocytes, but normal counts of circulating B and NK cells (T-B+NK+ SCID). We report 6 adults (aged 22 to 59 years) from 4 kindreds and 3 ancestries (Colombian, Israeli Arab, Japanese) carrying homozygous IL7 loss-of-function variants resulting in combined immunodeficiency (CID). Deep immunophenotyping revealed relatively normal counts and/or proportions of myeloid, B, NK, and innate lymphoid cells. By contrast, the patients had profound T cell lymphopenia, with low proportions of innate-like adaptive mucosal-associated invariant T and invariant NK T cells. They also had low blood counts of T cell receptor (TCR) excision circles, recent thymic emigrant T cells and naive CD4+ T cells, and low overall TCR repertoire diversity, collectively indicating impaired thymic output. The proportions of effector memory CD4+ and CD8+ T cells were high, indicating IL-7-independent homeostatic T cell proliferation in the periphery. Intriguingly, the proportions of other T cell subsets, including TCR\u03b3\u03b4+ T cells and some TCR\u03b1\u03b2+ T cell subsets (including Th1, Tfh, and Treg) were little affected. Peripheral CD4+ T cells displayed poor proliferation, but normal cytokine production upon stimulation with mitogens in vitro. Thus, inherited IL-7 deficiency impairs T cell development less severely and in a more subset-specific manner than IL-7R deficiency. These findings suggest that another IL-7R-binding cytokine, possibly thymic stromal lymphopoietin, governs an IL-7-independent pathway of human T cell development.", "doi": "10.1172/JCI180251", "pmid": "39352394", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "180251"}, {"db": "pmc", "key": "PMC11444196"}], "notes": [], "created": "2024-10-02T12:33:35.656Z", "modified": "2024-10-02T12:33:35.661Z"}, {"entity": "publication", "iuid": "85421d5b9d04415ba19ebdb36eeaee27", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85421d5b9d04415ba19ebdb36eeaee27.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85421d5b9d04415ba19ebdb36eeaee27"}}, "title": "Inherited human RelB deficiency impairs innate and adaptive immunity to infection.", "authors": [{"family": "Le Voyer", "given": "Tom", "initials": "T"}, {"family": "Maglorius Renkilaraj", "given": "Majistor Raj Luxman", "initials": "MRL"}, {"family": "Moriya", "given": "Kunihiko", "initials": "K"}, {"family": "P\u00e9rez Lorenzo", "given": "Malena", "initials": "M"}, {"family": "Nguyen", "given": "Tina", "initials": "T"}, {"family": "Gao", "given": "Liwei", "initials": "L"}, {"family": "Rubin", "given": "Tamar", "initials": "T"}, {"family": "Cederholm", "given": "Axel", "initials": "A"}, {"family": "Ogishi", "given": "Masato", "initials": "M", "orcid": "0000-0003-2421-7389", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9205246af72422f993f696135d03d00.json"}}, {"family": "Arango-Franco", "given": "Carlos A", "initials": "CA"}, {"family": "B\u00e9ziat", "given": "Vivien", "initials": "V", "orcid": "0000-0002-4020-824X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb59e3ecbbba41c98215a9424f82d70f.json"}}, {"family": "L\u00e9vy", "given": "Romain", "initials": "R"}, {"family": "Migaud", "given": "M\u00e9lanie", "initials": "M"}, {"family": "Rapaport", "given": "Franck", "initials": "F"}, {"family": "Itan", "given": "Yuval", "initials": "Y"}, {"family": "Deenick", "given": "Elissa K", "initials": "EK"}, {"family": "Cortese", "given": "Irene", "initials": "I"}, {"family": "Lisco", "given": "Andrea", "initials": "A"}, {"family": "Boztug", "given": "Kaan", "initials": "K"}, {"family": "Abel", "given": "Laurent", "initials": "L"}, {"family": "Boisson-Dupuis", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Boisson", "given": "Bertrand", "initials": "B", "orcid": "0000-0001-5240-3555", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7c47acbcc3346bcb65102b534b25cc8.json"}}, {"family": "Frosk", "given": "Patrick", "initials": "P"}, {"family": "Ma", "given": "Cindy S", "initials": "CS", "orcid": "0000-0001-5387-8413", "researcher": {"href": "https://publications.scilifelab.se/researcher/398f17ef657242a1a091b04d05388cf9.json"}}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Celmeli", "given": "Fatih", "initials": "F", "orcid": "0000-0002-2983-5058", "researcher": {"href": "https://publications.scilifelab.se/researcher/d10a5e911d694b9690bab499e0bbef99.json"}}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL", "orcid": "0000-0002-7782-4169", "researcher": {"href": "https://publications.scilifelab.se/researcher/009e2306468648c08fb1eea319f0c488.json"}}, {"family": "Tangye", "given": "Stuart G", "initials": "SG"}, {"family": "Puel", "given": "Anne", "initials": "A", "orcid": "0000-0003-2603-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bcef4c205904e5db9e36f3aadaa13bb.json"}}], "type": "journal article", "published": "2024-09-10", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "121", "issue": "37", "pages": "e2321794121", "issn-l": "0027-8424"}, "abstract": "We report two unrelated adults with homozygous (P1) or compound heterozygous (P2) private loss-of-function variants of V-Rel Reticuloendotheliosis Viral Oncogene Homolog B (RELB). The resulting deficiency of functional RelB impairs the induction of NFKB2 mRNA and NF-\u03baB2 (p100/p52) protein by lymphotoxin in the fibroblasts of the patients. These defects are rescued by transduction with wild-type RELB complementary DNA (cDNA). By contrast, the response of RelB-deficient fibroblasts to Tumor Necrosis Factor (TNF) or IL-1\u03b2 via the canonical NF-\u03baB pathway remains intact. P1 and P2 have low proportions of na\u00efve CD4+ and CD8+ T cells and of memory B cells. Moreover, their na\u00efve B cells cannot differentiate into immunoglobulin G (IgG)- or immunoglobulin A (IgA)-secreting cells in response to CD40L/IL-21, and the development of IL-17A/F-producing T cells is strongly impaired in vitro. Finally, the patients produce neutralizing autoantibodies against type I interferons (IFNs), even after hematopoietic stem cell transplantation, attesting to a persistent dysfunction of thymic epithelial cells in T cell selection and central tolerance to some autoantigens. Thus, inherited human RelB deficiency disrupts the alternative NF-\u03baB pathway, underlying a T- and B cell immunodeficiency, which, together with neutralizing autoantibodies against type I IFNs, confers a predisposition to viral, bacterial, and fungal infections.", "doi": "10.1073/pnas.2321794121", "pmid": "39231201", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11406260"}], "notes": [], "created": "2024-09-23T11:59:51.904Z", "modified": "2024-09-23T11:59:52.726Z"}, {"entity": "publication", "iuid": "ad8544dcfbdf4b14a12286065b365a09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad8544dcfbdf4b14a12286065b365a09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad8544dcfbdf4b14a12286065b365a09"}}, "title": "Type I Interferon Autoantibodies Correlate With Cellular Immune Alterations in Severe COVID-19.", "authors": [{"family": "Strunz", "given": "Benedikt", "initials": "B", "orcid": "0000-0001-9974-6133", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad80512007054aa9a3632660c0657c50.json"}}, {"family": "Maucourant", "given": "Christopher", "initials": "C"}, {"family": "Mehta", "given": "Adi", "initials": "A"}, {"family": "Wan", "given": "Hui", "initials": "H"}, {"family": "Du", "given": "Likun", "initials": "L"}, {"family": "Sun", "given": "Dan", "initials": "D"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Nordlander", "given": "Anna", "initials": "A"}, {"family": "Gao", "given": "Yu", "initials": "Y"}, {"family": "Cornillet", "given": "Martin", "initials": "M"}, {"family": "Bister", "given": "Jonna", "initials": "J"}, {"family": "Kvedaraite", "given": "Egle", "initials": "E"}, {"family": "Christ", "given": "Wanda", "initials": "W"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Geanon", "given": "Daniel", "initials": "D"}, {"family": "Parke", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Ekwall-Larson", "given": "Anna", "initials": "A"}, {"family": "Rivino", "given": "Laura", "initials": "L"}, {"family": "MacAry", "given": "Paul A", "initials": "PA"}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG"}, {"family": "Pan-Hammarstr\u00f6m", "given": "Qiang", "initials": "Q"}, {"family": "Lund-Johansen", "given": "Fridtjof", "initials": "F"}, {"family": "Str\u00e5lin", "given": "Kristoffer", "initials": "K"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK", "orcid": "0000-0002-0967-076X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf38521350ae490099f01bda1d10be4c.json"}}, {"family": "Karolinska KI/K COVID-19 Study Group\n", "given": "", "initials": ""}], "type": "journal article", "published": "2024-08-16", "journal": {"title": "J. Infect. Dis.", "issn": "1537-6613", "volume": "230", "issue": "2", "pages": "e318-e326", "issn-l": "0022-1899"}, "abstract": "Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to severe disease with increased morbidity and mortality among certain risk groups. The presence of autoantibodies against type I interferons (aIFN-Abs) is one mechanism that contributes to severe coronavirus disease 2019 (COVID-19).\n\nThis study aimed to investigate the presence of aIFN-Abs in relation to the soluble proteome, circulating immune cell numbers, and cellular phenotypes, as well as development of adaptive immunity.\n\naIFN-Abs were more prevalent in critical compared to severe COVID-19 but largely absent in the other viral and bacterial infections studied here. The antibody and T-cell response to SARS-CoV-2 remained largely unaffected by the presence aIFN-Abs. Similarly, the inflammatory response in COVID-19 was comparable in individuals with and without aIFN-Abs. Instead, presence of aIFN-Abs had an impact on cellular immune system composition and skewing of cellular immune pathways.\n\nOur data suggest that aIFN-Abs do not significantly influence development of adaptive immunity but covary with alterations in immune cell numbers.", "doi": "10.1093/infdis/jiae036", "pmid": "38421006", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11326830"}, {"db": "pii", "key": "7616238"}], "notes": [], "created": "2024-10-22T09:29:19.468Z", "modified": "2024-10-22T09:29:19.486Z"}, {"entity": "publication", "iuid": "f15bd4cc0af84934af75b8818d57c833", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f15bd4cc0af84934af75b8818d57c833.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f15bd4cc0af84934af75b8818d57c833"}}, "title": "JAK inhibition decreases the autoimmune burden in Down syndrome", "authors": [{"family": "Rachubinski", "given": "Angela L", "initials": "AL"}, {"family": "Wallace", "given": "Elizabeth", "initials": "E"}, {"family": "Gurnee", "given": "Emily", "initials": "E"}, {"family": "Enriquez Estrada", "given": "Belinda A", "initials": "BA"}, {"family": "Worek", "given": "Kayleigh R", "initials": "KR"}, {"family": "Smith", "given": "Keith P", "initials": "KP"}, {"family": "Araya", "given": "Paula", "initials": "P"}, {"family": "Waugh", "given": "Katherine A", "initials": "KA"}, {"family": "Granrath", "given": "Ross E", "initials": "RE"}, {"family": "Britton", "given": "Eleanor", "initials": "E"}, {"family": "Lyford", "given": "Hannah R", "initials": "HR"}, {"family": "Donovan", "given": "Micah G", "initials": "MG"}, {"family": "Eduthan", "given": "Neetha Paul", "initials": "NP"}, {"family": "Hill", "given": "Amanda A", "initials": "AA"}, {"family": "Martin", "given": "Barry", "initials": "B"}, {"family": "Sullivan", "given": "Kelly D", "initials": "KD", "orcid": "0000-0003-2725-0205", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcb847c0e4a645879fef9ebd9cc78c8f.json"}}, {"family": "Patel", "given": "Lina", "initials": "L"}, {"family": "Fidler", "given": "Deborah J", "initials": "DJ"}, {"family": "Galbraith", "given": "Matthew D", "initials": "MD", "orcid": "0000-0003-0485-3927", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fee4421a3374b6cb0bc970f4a25a2a0.json"}}, {"family": "Dunnick", "given": "Cory A", "initials": "CA"}, {"family": "Norris", "given": "David A", "initials": "DA"}, {"family": "Espinosa", "given": "Joaquin M", "initials": "JM", "orcid": "0000-0001-9048-1941", "researcher": {"href": "https://publications.scilifelab.se/researcher/140e2a0067274d70943aa4ac0984f4d7.json"}}], "type": "posted-content", "published": "2024-08-08", "journal": {"title": "eLife", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.7554/elife.99323.1", "pmid": null, "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-01T12:10:58.656Z", "modified": "2025-12-18T19:26:30.694Z"}, {"entity": "publication", "iuid": "b256fd79deef4afa9342a5889196bf56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b256fd79deef4afa9342a5889196bf56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b256fd79deef4afa9342a5889196bf56"}}, "title": "Seroepidemiological assessment of the spread of SARS-CoV-2 among 25 and 28 year-old adult women in Finland between March 2020-June 2022.", "authors": [{"family": "Gray", "given": "Penelope", "initials": "P", "orcid": "0000-0001-9065-4734", "researcher": {"href": "https://publications.scilifelab.se/researcher/26b7c7b28e3a492f8a336203eef01ed9.json"}}, {"family": "Eriksson", "given": "Tiina", "initials": "T"}, {"family": "Skoglund", "given": "Lovisa", "initials": "L"}, {"family": "Lagheden", "given": "Camilla", "initials": "C"}, {"family": "Hellstr\u00f6m", "given": "Ceke", "initials": "C"}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Suomenrinne-Nordvik", "given": "Anna", "initials": "A", "orcid": "0000-0001-7678-6554", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8c2b8add04644429a01296f81e26d74.json"}}, {"family": "Pimenoff", "given": "Ville N", "initials": "VN", "orcid": "0000-0002-0813-7031", "researcher": {"href": "https://publications.scilifelab.se/researcher/96cbbc36d7214b94a798b4c63eeb6a3a.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Dillner", "given": "Joakim", "initials": "J"}, {"family": "Lehtinen", "given": "Matti", "initials": "M"}], "type": "journal article", "published": "2024-07-11", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "7", "pages": "e0305285", "issn-l": "1932-6203"}, "abstract": "Serological surveys of the prevalence of SARS-CoV-2 are instrumental to understanding the course of the COVID-19 epidemic. We evaluate the seroprevalence of SARS-CoV-2 among young adult Finnish females residing in 25 communities all over Finland from 2020 until 2022.\n\nBetween 1st March 2020 and 30th June 2022, 3589 blood samples were collected from 3583 women born in 1992-95 when aged 25 or 28 years old attending the follow-up of an ongoing population-based trial of cervical screening strategies. The crude and population standardized SARS-CoV-2 seroprevalence was measured using nucleocapsid (induced by infection) and spike wild-type (WT) protein (induced both by infection and by vaccination) antigens over time and stratified by place of residence (inside or outside the Helsinki metropolitan region).\n\nDuring 2020 (before vaccinations), spike-WT and nucleocapsid IgG antibodies followed each other closely, at very low levels (<5%). Spike-WT seropositivity increased rapidly concomitant with mass vaccinations in 2021 and reached 96.3% in the 2nd quartile of 2022. Antibodies to nucleocapsid IgG remained relatively infrequent throughput 2020-2021, increasing rapidly in the 1st and 2nd quartiles of 2022 (to 19.7% and 56.6% respectively). The nucleocapsid IgG seropositivity increased more profoundly in participants residing in the Helsinki metropolitan region (4.5%, 8.4% and 43.9% in 2020, 2021 and 2022 respectively) compared to those residing in communities outside the capital region (4.5%, 4.3% and 34.7%).\n\nLow SARS-CoV-2 infection-related seroprevalence during 2020-2021 suggest a comparatively successful infection control. Antibodies to the SARS-CoV-2 WT spike protein became extremely common among young women by the end of 2021, in line with the high uptake of SARS-CoV-2 vaccination. Finally, the rapid increase of seroprevalences to the SARS-CoV-2 nucleocapsid protein during the first and second quartile of 2022, imply a high incidence of infections with SARS-CoV-2 variants able to escape vaccine-induced protection.", "doi": "10.1371/journal.pone.0305285", "pmid": "38990856", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11238966"}, {"db": "pii", "key": "PONE-D-23-42685"}], "notes": [], "created": "2024-09-04T07:31:43.842Z", "modified": "2024-09-04T07:31:43.965Z"}, {"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": "d091485229d644619b14f8adc7d48630", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d091485229d644619b14f8adc7d48630.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d091485229d644619b14f8adc7d48630"}}, "title": "Neutralizing IFN-\u03b3 autoantibodies are rare and pathogenic in HLA-DRB1*15:02 or 16:02 individuals.", "authors": [{"family": "Peel", "given": "Jessica N", "initials": "JN"}, {"family": "Yang", "given": "Rui", "initials": "R"}, {"family": "Le Voyer", "given": "Tom", "initials": "T"}, {"family": "Gervais", "given": "Adrian", "initials": "A"}, {"family": "Rosain", "given": "J\u00e9r\u00e9mie", "initials": "J"}, {"family": "Bastard", "given": "Paul", "initials": "P"}, {"family": "Behere", "given": "Anish", "initials": "A"}, {"family": "Cederholm", "given": "Axel", "initials": "A"}, {"family": "Bodansky", "given": "Aaron", "initials": "A"}, {"family": "Seeleuthner", "given": "Yoann", "initials": "Y"}, {"family": "Conil", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Ding", "given": "Jing-Ya", "initials": "JY"}, {"family": "Lei", "given": "Wei-Te", "initials": "WT"}, {"family": "Bizien", "given": "Lucy", "initials": "L"}, {"family": "Soudee", "given": "Camille", "initials": "C"}, {"family": "Migaud", "given": "M\u00e9lanie", "initials": "M"}, {"family": "Ogishi", "given": "Masato", "initials": "M"}, {"family": "Yatim", "given": "Ahmad", "initials": "A"}, {"family": "Lee", "given": "Danyel", "initials": "D"}, {"family": "Bohlen", "given": "Jonathan", "initials": "J"}, {"family": "Perpoint", "given": "Thomas", "initials": "T"}, {"family": "Perez", "given": "Laura", "initials": "L"}, {"family": "Messina", "given": "Fernando", "initials": "F"}, {"family": "Genet", "given": "Roxana", "initials": "R"}, {"family": "Karkowski", "given": "Ludovic", "initials": "L"}, {"family": "Blot", "given": "Mathieu", "initials": "M"}, {"family": "Lafont", "given": "Emmanuel", "initials": "E"}, {"family": "Toullec", "given": "Laurie", "initials": "L"}, {"family": "Goulvestre", "given": "Claire", "initials": "C"}, {"family": "Mehlal-Sedkaoui", "given": "Souad", "initials": "S"}, {"family": "Sallette", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Martin", "given": "Fernando", "initials": "F"}, {"family": "Puel", "given": "Anne", "initials": "A"}, {"family": "Jouanguy", "given": "Emmanuelle", "initials": "E"}, {"family": "CONSTANCES cohort", "given": "", "initials": ""}, {"family": "3C-Dijon Study", "given": "", "initials": ""}, {"family": "Etablissement du Sang study group", "given": "", "initials": ""}, {"family": "Anderson", "given": "Mark S", "initials": "MS"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Tiberghien", "given": "Pierre", "initials": "P"}, {"family": "Abel", "given": "Laurent", "initials": "L"}, {"family": "Boisson-Dupuis", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Bustamante", "given": "Jacinta", "initials": "J"}, {"family": "Ku", "given": "Cheng-Lung", "initials": "CL"}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL"}], "type": "journal article", "published": "2024-03-12", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "134", "issue": "8", "issn-l": "0021-9738"}, "abstract": "BACKGROUNDWeakly virulent environmental mycobacteria (EM) can cause severe disease in HLA-DRB1*15:02 or 16:02 adults harboring neutralizing anti-IFN-\u03b3 autoantibodies (nAIGAs). The overall prevalence of nAIGAs in the general population is unknown, as are the penetrance of nAIGAs in HLA-DRB1*15:02 or 16:02 individuals and the proportion of patients with unexplained, adult-onset EM infections carrying nAIGAs.METHODSThis study analyzed the detection and neutralization of anti-IFN-\u03b3 autoantibodies (auto-Abs) from 8,430 healthy individuals of the general population, 257 HLA-DRB1*15:02 or 16:02 carriers, 1,063 patients with autoimmune disease, and 497 patients with unexplained severe disease due to EM.RESULTSWe found that anti-IFN-\u03b3 auto-Abs detected in 4,148 of 8,430 healthy individuals (49.2%) from the general population of an unknown HLA-DRB1 genotype were not neutralizing. Moreover, we did not find nAIGAs in 257 individuals carrying HLA-DRB1* 15:02 or 16:02. Additionally, nAIGAs were absent in 1,063 patients with an autoimmune disease. Finally, 7 of 497 patients (1.4%) with unexplained severe disease due to EM harbored nAIGAs.CONCLUSIONThese findings suggest that nAIGAs are isolated and that their penetrance in HLA-DRB1*15:02 or 16:02 individuals is low, implying that they may be triggered by rare germline or somatic variants. In contrast, the risk of mycobacterial disease in patients with nAIGAs is high, confirming that these nAIGAs are the cause of EM disease.FUNDINGThe Laboratory of Human Genetics of Infectious Diseases is supported by the Howard Hughes Medical Institute, the Rockefeller University, the St. Giles Foundation, the National Institutes of Health (NIH) (R01AI095983 and U19AIN1625568), the National Center for Advancing Translational Sciences (NCATS), the NIH Clinical and Translational Science Award (CTSA) program (UL1 TR001866), the French National Research Agency (ANR) under the \"Investments for the Future\" program (ANR-10-IAHU-01), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), ANR-GENMSMD (ANR-16-CE17-0005-01), ANR-MAFMACRO (ANR-22-CE92-0008), ANRSECTZ170784, the French Foundation for Medical Research (FRM) (EQU201903007798), the ANRS-COV05, ANR GENVIR (ANR-20-CE93-003), and ANR AI2D (ANR-22-CE15-0046) projects, the ANR-RHU program (ANR-21-RHUS-08-COVIFERON), the European Union's Horizon 2020 research and innovation program under grant agreement no. 824110 (EASI-genomics), the Square Foundation, Grandir - Fonds de solidarit\u00e9 pour l'enfance, the Fondation du Souffle, the SCOR Corporate Foundation for Science, the Battersea & Bowery Advisory Group, William E. Ford, General Atlantic's Chairman and Chief Executive Officer, Gabriel Caillaux, General Atlantic's Co-President, Managing Director, and Head of business in EMEA, and the General Atlantic Foundation, Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale (INSERM) and of Paris Cit\u00e9 University. JR was supported by the INSERM PhD program for doctors of pharmacy (poste d'accueil INSERM). JR and TLV were supported by the Bettencourt-Schueller Foundation and the MD-PhD program of the Imagine Institute. MO was supported by the David Rockefeller Graduate Program, the Funai Foundation for Information Technology (FFIT), the Honjo International Scholarship Foundation (HISF), and the New York Hideyo Noguchi Memorial Society (HNMS).", "doi": "10.1172/JCI178263", "pmid": "38470480", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11014650"}, {"db": "pii", "key": "178263"}], "notes": [], "created": "2024-09-23T11:54:48.929Z", "modified": "2024-09-23T11:54:48.935Z"}, {"entity": "publication", "iuid": "dfd2d4fbf6e741bda925e5f5b80c2649", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfd2d4fbf6e741bda925e5f5b80c2649.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfd2d4fbf6e741bda925e5f5b80c2649"}}, "title": "The serological immunogenicity of the third and fourth doses of COVID-19 vaccine in patients with inflammatory rheumatic diseases on different biologic or targeted DMARDs: a Swedish nationwide study (COVID-19-REUMA).", "authors": [{"family": "Frodlund", "given": "Martina", "initials": "M", "orcid": "0000-0001-7522-5069", "researcher": {"href": "https://publications.scilifelab.se/researcher/534858ebf9e943ec8085c7a24addba53.json"}}, {"family": "Nived", "given": "Per", "initials": "P"}, {"family": "Chatzidionysiou", "given": "Katerina", "initials": "K"}, {"family": "S\u00f6dergren", "given": "Anna", "initials": "A"}, {"family": "Klingberg", "given": "Eva", "initials": "E"}, {"family": "Hansson", "given": "Monica", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Bengtsson", "given": "Anders", "initials": "A"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Kapetanovic", "given": "Meliha", "initials": "M", "orcid": "0000-0002-7853-514X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb145f4fa71747749a8609a84fad5987.json"}}], "type": "journal article", "published": "2024-03-05", "journal": {"title": "Microbiol Spectr", "issn": "2165-0497", "pages": "e0298123", "issn-l": null}, "abstract": "Studies investigating the immunogenicity of additional COVID-19 vaccine doses in immunosuppressed patients with inflammatory rheumatic diseases (IRD) are still limited. The objective was to explore the antibody response including response to omicron virus subvariants (sBA.1 and sBS.2) after third and fourth COVID-19 vaccine doses in Swedish IRD patients treated with immunomodulating drugs compared to controls. Antibody levels to spike wild-type antigens (full-length protein and S1) and the omicron variants sBA.1 and sBA.2 (full-length proteins) were measured. A positive response was defined as having antibody levels over cut-off or \u2265fourfold increase in post-vaccination levels for both antigens. Patients with arthritis, vasculitis, and other autoimmune diseases (n = 414), and controls (n = 61) receiving biologic/targeted synthetic disease-modifying anti-rheumatic drugs (DMARDs) with or without conventional synthetic DMARDs participated. Of these, blood samples were available for 370 patients and 52 controls after three doses, and 65 patients and 15 controls after four doses. Treatment groups after three vaccine doses were rituximab (n = 133), abatacept (n = 22), IL6r inhibitors (n = 71), JAnus Kinase inhibitors (JAK-inhibitors) (n = 56), tumor necrosis factor inhibitor (TNF-inhibitors) (n = 61), IL12/23/17 inhibitors (n = 27), and controls (n = 52). The percentage of responders after three and four vaccine doses was lower in rituximab-treated patients (59% and 57%) compared to controls (100%) (P < 0.001). After three doses, the percentage of responders in all other groups was 100%, including response to omicron sBA.1 and sBA.2. In rituximab-treated patients, higher baseline immunoglobulin G (IgG) and longer time-period between rituximab and vaccination predicted better response. In this Swedish nationwide study including IRD patients three and four COVID-19 vaccine doses were immunogenic in patients treated with IL6r inhibitors, TNF-inhibitors, JAK-inhibitors, and IL12/23/17-inhibitors but not in rituximab. As >50% of rituximab patients responded to vaccines including omicron subvariants, these patients should be prioritized for additional vaccine doses.\n\nResults from this study provide further evidence that additional doses of COVID-19 vaccines are immunogenic and result in satisfactory antibody response in a majority of patients with inflammatory rheumatic diseases (IRD) receiving potent immunomodulating treatments such as biological or targeted disease-modifying anti-rheumatic drugs (DMARDs) given as monotherapy or combined with traditional DMARDs. We observed that rituximab treatment, both as monotherapy and combined with csDMARDs, impaired antibody response, and only roughly 50% of patients developed a satisfactory antibody response including response to omicron subvariants after the third vaccine. In addition, higher IgG levels at the last rituximab course before the third vaccine dose and a longer time after the last rituximab treatment increased the chance of a satisfactory antibody response. These results indicate that rituximab-treated patients should be prioritized for additional vaccine doses.\n\nEudraCT (European Union Drug Regulating Authorities Clinical Trials Database) with number 2021-000880-63.", "doi": "10.1128/spectrum.02981-23", "pmid": "38441463", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-10T06:07:47.558Z", "modified": "2024-03-10T06:07:47.994Z"}, {"entity": "publication", "iuid": "2c7e8f4c3e31469680b6105822961662", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c7e8f4c3e31469680b6105822961662.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c7e8f4c3e31469680b6105822961662"}}, "title": "No link between type I interferon autoantibody positivity and adverse reactions to COVID-19 vaccines.", "authors": [{"family": "Yalcinkaya", "given": "Ahmet", "initials": "A", "orcid": "0000-0002-1172-3330", "researcher": {"href": "https://publications.scilifelab.se/researcher/512b8aff987b407b81bb88460790769d.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Cederholm", "given": "Axel", "initials": "A", "orcid": "0009-0006-5973-9637", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2dffb2fd8e446d6a72c765602b97291.json"}}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M", "orcid": "0000-0003-0050-704X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65dc88b917274bc595daed855b63abab.json"}}, {"family": "Behere", "given": "Anish", "initials": "A", "orcid": "0000-0002-2424-3475", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c155029e86d458cad39ed4c2670c880.json"}}, {"family": "Mildner", "given": "Hedvig", "initials": "H", "orcid": "0009-0009-6636-2008", "researcher": {"href": "https://publications.scilifelab.se/researcher/a467c3b4499349daa62148a97e8f0e14.json"}}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Ekwall", "given": "Olov", "initials": "O"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}, {"family": "Bensing", "given": "Sophie", "initials": "S"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}, {"family": "Landegren", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2024-02-22", "journal": {"title": "NPJ Vaccines", "issn": "2059-0105", "volume": "9", "issue": "1", "pages": "42", "issn-l": null}, "abstract": "Type I interferons act as gatekeepers against viral infection, and autoantibodies that neutralize these signaling molecules have been associated with COVID-19 severity and adverse reactions to the live-attenuated yellow fever vaccine. On this background, we sought to examine whether autoantibodies against type I interferons were associated with adverse events following COVID-19 vaccination. Our nationwide analysis suggests that type I interferon autoantibodies were not associated with adverse events after mRNA or viral-vector COVID-19 vaccines.", "doi": "10.1038/s41541-024-00829-9", "pmid": "38388530", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10883980"}, {"db": "pii", "key": "10.1038/s41541-024-00829-9"}], "notes": [], "created": "2024-02-26T09:44:09.668Z", "modified": "2024-09-23T11:56:03.318Z"}, {"entity": "publication", "iuid": "5470201254594c14a5247faac7e19e36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5470201254594c14a5247faac7e19e36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5470201254594c14a5247faac7e19e36"}}, "title": "Xist ribonucleoproteins promote female sex-biased autoimmunity.", "authors": [{"family": "Dou", "given": "Diana R", "initials": "DR"}, {"family": "Zhao", "given": "Yanding", "initials": "Y"}, {"family": "Belk", "given": "Julia A", "initials": "JA"}, {"family": "Zhao", "given": "Yang", "initials": "Y"}, {"family": "Casey", "given": "Kerriann M", "initials": "KM"}, {"family": "Chen", "given": "Derek C", "initials": "DC"}, {"family": "Li", "given": "Rui", "initials": "R"}, {"family": "Yu", "given": "Bingfei", "initials": "B"}, {"family": "Srinivasan", "given": "Suhas", "initials": "S"}, {"family": "Abe", "given": "Brian T", "initials": "BT"}, {"family": "Kraft", "given": "Katerina", "initials": "K"}, {"family": "Hellstr\u00f6m", "given": "Ceke", "initials": "C"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R"}, {"family": "Chang", "given": "Sarah", "initials": "S"}, {"family": "Feng", "given": "Allan", "initials": "A"}, {"family": "Goldman", "given": "Daniel W", "initials": "DW"}, {"family": "Shah", "given": "Ami A", "initials": "AA"}, {"family": "Petri", "given": "Michelle", "initials": "M"}, {"family": "Chung", "given": "Lorinda S", "initials": "LS"}, {"family": "Fiorentino", "given": "David F", "initials": "DF"}, {"family": "Lundberg", "given": "Emma K", "initials": "EK"}, {"family": "Wutz", "given": "Anton", "initials": "A"}, {"family": "Utz", "given": "Paul J", "initials": "PJ"}, {"family": "Chang", "given": "Howard Y", "initials": "HY"}], "type": "journal article", "published": "2024-02-01", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "187", "issue": "3", "pages": "733-749.e16", "issn-l": "0092-8674"}, "abstract": "Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long non-coding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex comprising numerous autoantigenic components is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multi-organ pathology in a pristane-induced lupus model than wild-type males. Xist expression in males reprogrammed T and B cell populations and chromatin states to more resemble wild-type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.", "doi": "10.1016/j.cell.2023.12.037", "pmid": "38306984", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(24)00002-3"}], "notes": [], "created": "2024-02-05T10:51:52.183Z", "modified": "2024-02-05T10:51:52.189Z"}, {"entity": "publication", "iuid": "3a099c40d63f44ae80b30392bf18352f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a099c40d63f44ae80b30392bf18352f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a099c40d63f44ae80b30392bf18352f"}}, "title": "Identification of biomarker candidates for exfoliative glaucoma from autoimmunity profiling.", "authors": [{"family": "Potter", "given": "Ryan", "initials": "R"}, {"family": "Ayala", "given": "Marcelo", "initials": "M"}, {"family": "Tilevik", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2024-01-29", "journal": {"title": "BMC Ophthalmol", "issn": "1471-2415", "volume": "24", "issue": "1", "pages": "44", "issn-l": null}, "abstract": "Exfoliative glaucoma (XFG) is a subtype of open-angle glaucoma characterized by distinctive extracellular fibrils and a yet unknown pathogenesis potentially involving immune-related factors. The aim of this exploratory study was to identify biomarkers for XFG using data from autoimmunity profiling performed on blood samples from a Scandinavian cohort of patients.\n\nAutoantibody screening was analyzed against 258 different protein fragments in blood samples taken from 30 patients diagnosed with XFG and 30 healthy donors. The 258 protein fragments were selected based on a preliminary study performed on 3072 randomly selected antigens and antigens associated with the eye. The \"limma\" package was used to perform moderated t-tests on the proteomic data to identify differentially expressed reactivity between the groups.\n\nMultiple associated genes were highlighted as possible biomarker candidates including FUT2, CDH5, and the LOX family genes. Using seven variables, our binary logistic regression model was able to classify the cases from the controls with an AUC of 0.85, and our reduced model using only one variable corresponding to the FUT2 gene provided an AUC of 0.75, based on LOOCV. Furthermore, over-representation gene analysis was performed to identify pathways that were associated with antigens differentially bound to self-antibodies. This highlighted the enrichment of pathways related to collagen fibril formation and the regulatory molecules mir-3176 and mir-876-5p.\n\nThis study suggests several potential biomarkers that may be useful in developing further models of the pathology of XFG. In particular, CDH5, FUT2, and the LOX family seem to have a relationship which merits additional exploration.", "doi": "10.1186/s12886-024-03314-y", "pmid": "38287276", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10826272"}, {"db": "pii", "key": "10.1186/s12886-024-03314-y"}], "notes": [], "created": "2025-09-10T08:53:30.087Z", "modified": "2025-10-24T09:44:12.982Z"}, {"entity": "publication", "iuid": "936f5cb423c14280a19d6cd9d5cc66cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/936f5cb423c14280a19d6cd9d5cc66cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/936f5cb423c14280a19d6cd9d5cc66cc"}}, "title": "Identification of circulating autoantibodies to non-modified proteins associated with ACPA status in early rheumatoid arthritis.", "authors": [{"family": "Lourido", "given": "Luc\u00eda", "initials": "L"}, {"family": "Joshua", "given": "Vijay", "initials": "V"}, {"family": "Hansson", "given": "Monika", "initials": "M"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Ruiz-Romero", "given": "Cristina", "initials": "C"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Blanco", "given": "Francisco J", "initials": "FJ"}], "type": "journal article", "published": "2024-01-09", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "issn-l": "1462-0324"}, "abstract": "To discover autoantibodies to non-modified proteins associated with the presence/absence of anticitrullinated protein antibodies (ACPA) in rheumatoid arthritis (RA).\n\nThe autoantibody repertoire of 80 ACPA negative and 80 ACPA positive RA subjects from the Swedish population-based Epidemiological Investigation of RA (EIRA) cohort was screened using a suspension bead array built on protein fragments earlier described as autoimmunity targets. Four autoantibodies positive in the initial screening were validated in another set of EIRA samples containing 317 ACPA-positive, 302 ACPA-negative and 372 age- and sex-matched controls. The relationship between the four autoantibodies and lung abnormalities on high-resolution computed tomography (HRTC) was examined in 93 early RA patients from LURA cohort. Association between the autoantibodies, smoking and MHC class II alleles was assessed by logistic regression analysis.\n\n: Anti-ANOS1 and anti-MURC IgG levels were associated with ACPA-positive status (OR = 3.02; 95% CI 1.87-4.89; and OR = 1.86; 95% CI 1.16-2.97, respectively) and increased in ACPA-positive patients compared with controls. Anti-ANOS1 IgG was associated with smoking habit (OR = 2.11; 95% CI 1.22-3.69) and anti-MURC IgG with the presence of the MHC class II \"shared-epitope\" genes (OR = 1.95; 95% CI 1.11-3.46). Anti-TSPYL4 IgG was associated with ACPA-negative (OR = 0.41; 95% CI 0.19-0.89). Anti-TSPYL4 IgG and anti-MAP2K6 IgG levels were increased in the ACPA-negative patients compared with controls. Presence of anti-MAP2K6 IgG and anti-TSPYL4 IgG correlated negatively with HRCT-defined lung abnormalities.\n\nThese four autoantibodies may be useful in diagnostics and in predicting clinical phenotypes of RA.", "doi": "10.1093/rheumatology/keae007", "pmid": "38195995", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7513696"}], "notes": [], "created": "2024-09-04T07:30:38.578Z", "modified": "2024-09-04T07:30:38.582Z"}, {"entity": "publication", "iuid": "70a2b6c3bcec472da67434e6080095d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/70a2b6c3bcec472da67434e6080095d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/70a2b6c3bcec472da67434e6080095d4"}}, "title": "Influenza-A mediated pre-existing immunity levels to SARS-CoV-2 could predict early COVID-19 outbreak dynamics.", "authors": [{"family": "Almaz\u00e1n", "given": "Nerea Mart\u00edn", "initials": "NM"}, {"family": "Rahbar", "given": "Afsar", "initials": "A", "orcid": "0000-0003-1158-2512", "researcher": {"href": "https://publications.scilifelab.se/researcher/a65023dc25594ea3801d743aedeafe75.json"}}, {"family": "Carlsson", "given": "Marcus", "initials": "M"}, {"family": "Hoffman", "given": "Tove", "initials": "T"}, {"family": "Kolstad", "given": "Linda", "initials": "L"}, {"family": "R\u00f6nnberg", "given": "Bengt", "initials": "B"}, {"family": "Pantalone", "given": "Mattia Russel", "initials": "MR"}, {"family": "Fuchs", "given": "Ilona Lewensohn", "initials": "IL"}, {"family": "Naucl\u00e9r", "given": "Anna", "initials": "A"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}, {"family": "Sacharczuk", "given": "Mariusz", "initials": "M"}, {"family": "Religa", "given": "Piotr", "initials": "P"}, {"family": "Am\u00e9r", "given": "Stefan", "initials": "S"}, {"family": "Moln\u00e1r", "given": "Christian", "initials": "C"}, {"family": "Lundkvist", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Susrud", "given": "Andres", "initials": "A"}, {"family": "S\u00f6rensen", "given": "Birger", "initials": "B"}, {"family": "S\u00f6derberg-Naucl\u00e9r", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2023-12-15", "journal": {"title": "iScience", "issn": "2589-0042", "pages": "108441", "volume": "26", "issue": "12", "issn-l": "2589-0042"}, "abstract": "Susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is highly variable and could be mediated by a cross-protective pre-immunity. We identified 14 cross-reactive peptides between SARS-CoV-2 and influenza A H1N1, H3N2, and human herpesvirus (HHV)-6A/B with potential relevance. The H1N1 peptide NGVEGF was identical to a peptide in the most critical receptor binding motif in SARS-CoV-2 spike protein that interacts with the angiotensin converting enzyme 2 receptor. About 62%-73% of COVID-19-negative blood donors in Stockholm had antibodies to this peptide in the early pre-vaccination phase of the pandemic. Seasonal flu vaccination enhanced neutralizing capacity to SARS-CoV-2 and T cell immunity to this peptide. Mathematical modeling taking the estimated pre-immunity levels to flu into account could fully predict pre-Omicron SARS-CoV-2 outbreaks in Stockholm and India. This cross-immunity provides mechanistic explanations to the epidemiological observation that influenza vaccination protected people against early SARS-CoV-2 infections and implies that flu-mediated cross-protective immunity significantly dampened the first SARS-CoV-2 outbreaks.", "doi": "10.1016/j.isci.2023.108441", "pmid": "38144451", "labels": {"Autoimmunity and Serology Profiling": "Service", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10746369"}, {"db": "pii", "key": "S2589-0042(23)02518-X"}], "notes": [], "created": "2023-12-01T13:53:35.380Z", "modified": "2025-10-17T13:05:07.444Z"}, {"entity": "publication", "iuid": "80543734f42047bd8b359d3a2c96c420", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80543734f42047bd8b359d3a2c96c420.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80543734f42047bd8b359d3a2c96c420"}}, "title": "Autoantibodies against type I IFNs in humans with alternative NF-\u03baB pathway deficiency.", "authors": [{"family": "Le Voyer", "given": "Tom", "initials": "T", "orcid": "0000-0002-7253-3135", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ae9aa653f874c2cb1c68a2deb9357b8.json"}}, {"family": "Parent", "given": "Audrey V", "initials": "AV", "orcid": "0000-0003-4506-6268", "researcher": {"href": "https://publications.scilifelab.se/researcher/553847cbdc524ebf9d064078ce5ea089.json"}}, {"family": "Liu", "given": "Xian", "initials": "X"}, {"family": "Cederholm", "given": "Axel", "initials": "A", "orcid": "0009-0006-5973-9637", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2dffb2fd8e446d6a72c765602b97291.json"}}, {"family": "Gervais", "given": "Adrian", "initials": "A"}, {"family": "Rosain", "given": "J\u00e9r\u00e9mie", "initials": "J"}, {"family": "Nguyen", "given": "Tina", "initials": "T"}, {"family": "Perez Lorenzo", "given": "Malena", "initials": "M", "orcid": "0000-0002-7933-5211", "researcher": {"href": "https://publications.scilifelab.se/researcher/62baf0182c984c9081911a2c6b3b18c1.json"}}, {"family": "Rackaityte", "given": "Elze", "initials": "E", "orcid": "0000-0003-3889-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ceee85bd2034a1892d6cbf35b7003b1.json"}}, {"family": "Rinchai", "given": "Darawan", "initials": "D"}, {"family": "Zhang", "given": "Peng", "initials": "P", "orcid": "0000-0002-6129-567X", "researcher": {"href": "https://publications.scilifelab.se/researcher/20fcd31c47a940e8b72a8eb8d6e2a63b.json"}}, {"family": "Bizien", "given": "Lucy", "initials": "L"}, {"family": "Hancioglu", "given": "Gonca", "initials": "G", "orcid": "0000-0003-4221-6232", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a9b9948d4114c17b7a86079fff8feb0.json"}}, {"family": "Ghillani-Dalbin", "given": "Pascale", "initials": "P"}, {"family": "Charuel", "given": "Jean-Luc", "initials": "JL"}, {"family": "Philippot", "given": "Quentin", 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"researcher": {"href": "https://publications.scilifelab.se/researcher/a4783c37a1ac4d528841846dbdbcc05c.json"}}, {"family": "Gray", "given": "Paul E", "initials": "PE", "orcid": "0000-0003-2057-3968", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5eca9282b664b5bbcc3510efc31c578.json"}}, {"family": "Belot", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-4902-5332", "researcher": {"href": "https://publications.scilifelab.se/researcher/155056471c474a8ca255b7cefd8c5cad.json"}}, {"family": "Kuehn", "given": "Hye Sun", "initials": "HS"}, {"family": "Rosenzweig", "given": "Sergio D", "initials": "SD"}, {"family": "Miyara", "given": "Makoto", "initials": "M"}, {"family": "Licciardi", "given": "Francesco", "initials": "F"}, {"family": "Servettaz", "given": "Am\u00e9lie", "initials": "A"}, {"family": "Barlogis", "given": "Vincent", "initials": "V"}, {"family": "Le Guenno", "given": "Guillaume", "initials": "G"}, {"family": "Herrmann", "given": "Vera-Maria", "initials": "VM"}, {"family": "Kuijpers", "given": "Taco", "initials": "T"}, {"family": "Ducoux", "given": "Gr\u00e9goire", "initials": "G"}, {"family": "Sarrot-Reynauld", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Schuetz", "given": "Catharina", "initials": "C"}, {"family": "Cunningham-Rundles", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-0725-0320", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f191aed462e40dba62ed32a771bbb0f.json"}}, {"family": "Rieux-Laucat", "given": "Fr\u00e9d\u00e9ric", "initials": "F", "orcid": "0000-0001-7858-7866", "researcher": {"href": "https://publications.scilifelab.se/researcher/abbce991c33c4908a575c148214fcc67.json"}}, {"family": "Tangye", "given": "Stuart G", "initials": "SG", "orcid": "0000-0002-5360-5180", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e3fa03cfc304a8aa0262e5f8c51665d.json"}}, {"family": "Sobacchi", "given": "Cristina", "initials": "C"}, {"family": "Doffinger", "given": "Rainer", "initials": "R"}, {"family": "Warnatz", "given": "Klaus", "initials": "K"}, {"family": "Grimbacher", "given": "Bodo", "initials": "B"}, {"family": "Fieschi", "given": "Claire", "initials": "C"}, {"family": "Berteloot", "given": "Laureline", "initials": "L", "orcid": "0000-0001-9681-3142", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0ce699420749dc97617accb080b2e8.json"}}, {"family": "Bryant", "given": "Vanessa L", "initials": "VL"}, {"family": "Trouillet Assant", "given": "Sophie", "initials": "S"}, {"family": "Su", "given": "Helen", "initials": "H", "orcid": "0000-0002-5582-9110", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f3b00f2707541b39b2205d70fd2d6f7.json"}}, {"family": "Neven", "given": "Benedicte", "initials": "B"}, {"family": "Abel", "given": "Laurent", "initials": "L"}, {"family": "Zhang", "given": "Qian", "initials": "Q"}, {"family": "Boisson", "given": "Bertrand", "initials": "B", "orcid": "0000-0001-5240-3555", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7c47acbcc3346bcb65102b534b25cc8.json"}}, {"family": "Cobat", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0001-7209-6257", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaba2f9452294eec89161b589d96ff29.json"}}, {"family": "Jouanguy", "given": "Emmanuelle", "initials": "E"}, {"family": "Kampe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}, {"family": "Bastard", "given": "Paul", "initials": "P"}, {"family": "Roifman", "given": "Chaim M", "initials": "CM"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Notarangelo", "given": "Luigi D", "initials": "LD", "orcid": "0000-0002-8335-0262", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8d346e44c2d443ba3da3fcf2725b96c.json"}}, {"family": "Anderson", "given": "Mark S", "initials": "MS", "orcid": "0000-0002-3093-4758", "researcher": {"href": "https://publications.scilifelab.se/researcher/4276efc31c1d4dbaaa242f11ef60c51e.json"}}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL", "orcid": "0000-0002-7782-4169", "researcher": {"href": "https://publications.scilifelab.se/researcher/009e2306468648c08fb1eea319f0c488.json"}}, {"family": "Puel", "given": "Anne", "initials": "A", "orcid": "0000-0003-2603-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bcef4c205904e5db9e36f3aadaa13bb.json"}}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "623", "issue": "7988", "pages": "803-813", "issn-l": "0028-0836"}, "abstract": "Patients with autoimmune polyendocrinopathy syndrome type 1 (APS-1) caused by autosomal recessive AIRE deficiency produce autoantibodies that neutralize type I interferons (IFNs)1,2, conferring a predisposition to life-threatening COVID-19 pneumonia3. Here we report that patients with autosomal recessive NIK or RELB deficiency, or a specific type of autosomal-dominant NF-\u03baB2 deficiency, also have neutralizing autoantibodies against type I IFNs and are at higher risk of getting life-threatening COVID-19 pneumonia. In patients with autosomal-dominant NF-\u03baB2 deficiency, these autoantibodies are found only in individuals who are heterozygous for variants associated with both transcription (p52 activity) loss of function (LOF) due to impaired p100 processing to generate p52, and regulatory (I\u03baB\u03b4 activity) gain of function (GOF) due to the accumulation of unprocessed p100, therefore increasing the inhibitory activity of I\u03baB\u03b4 (hereafter, p52LOF/I\u03baB\u03b4GOF). By contrast, neutralizing autoantibodies against type I IFNs are not found in individuals who are heterozygous for NFKB2 variants causing haploinsufficiency of p100 and p52 (hereafter, p52LOF/I\u03baB\u03b4LOF) or gain-of-function of p52 (hereafter, p52GOF/I\u03baB\u03b4LOF). In contrast to patients with APS-1, patients with disorders of NIK, RELB or NF-\u03baB2 have very few tissue-specific autoantibodies. However, their thymuses have an abnormal structure, with few AIRE-expressing medullary thymic epithelial cells. Human inborn errors of the alternative NF-\u03baB pathway impair the development of AIRE-expressing medullary thymic epithelial cells, thereby underlying the production of autoantibodies against type I IFNs and predisposition to viral diseases.", "doi": "10.1038/s41586-023-06717-x", "pmid": "37938781", "labels": {"Autoimmunity and Serology Profiling": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10665196"}, {"db": "pii", "key": "10.1038/s41586-023-06717-x"}], "notes": [], "created": "2023-11-16T13:27:25.515Z", "modified": "2024-11-28T18:23:58.185Z"}, {"entity": "publication", "iuid": "cbfa77436f394919be69926d5f93ccec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbfa77436f394919be69926d5f93ccec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbfa77436f394919be69926d5f93ccec"}}, "title": "Autoantibody Profiling and Anti-Kinesin Reactivity in ANCA-Associated Vasculitis.", "authors": [{"family": "Mescia", "given": "Federica", "initials": "F", "orcid": "0000-0002-2759-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c89c9c9abb44c59be30e792aa4a11ac.json"}}, {"family": "Bayati", "given": "Shaghayegh", "initials": "S"}, {"family": "Brouwer", "given": "Elisabeth", "initials": "E"}, {"family": "Heeringa", "given": "Peter", "initials": "P", "orcid": "0000-0001-8684-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/121f655c044d4b3894c195e3ffc2092a.json"}}, {"family": "Toonen", "given": "Erik J M", "initials": "EJM", "orcid": "0000-0001-9039-635X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d6d9551815f451b90c317b53766414e.json"}}, {"family": "Beenes", "given": "Marijke", "initials": "M"}, {"family": "Ball", "given": "Miriam J", "initials": "MJ"}, {"family": "Rees", "given": "Andrew J", "initials": "AJ"}, {"family": "Kain", "given": "Renate", "initials": "R", "orcid": "0000-0002-2428-543X", "researcher": {"href": "https://publications.scilifelab.se/researcher/87df5c95b8df4918ac438036cd7f2c58.json"}}, {"family": "Lyons", "given": "Paul A", "initials": "PA", "orcid": "0000-0001-7035-8997", "researcher": {"href": "https://publications.scilifelab.se/researcher/d405b26b9a714585b9db292bafd4892f.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}], "type": "journal article", "published": "2023-10-19", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "24", "issue": "20", "issn-l": null}, "abstract": "ANCA-associated vasculitides (AAV) are rare autoimmune diseases causing inflammation and damage to small blood vessels. New autoantibody biomarkers are needed to improve the diagnosis and treatment of AAV patients. In this study, we aimed to profile the autoantibody repertoire of AAV patients using in-house developed antigen arrays to identify previously unreported antibodies linked to the disease per se, clinical subgroups, or clinical activity. A total of 1743 protein fragments representing 1561 unique proteins were screened in 229 serum samples collected from 137 AAV patients at presentation, remission, and relapse. Additionally, serum samples from healthy individuals and patients with other type of vasculitis and autoimmune-inflammatory conditions were included to evaluate the specificity of the autoantibodies identified in AAV. Autoreactivity against members of the kinesin protein family were identified in AAV patients, healthy volunteers, and disease controls. Anti-KIF4A antibodies were significantly more prevalent in AAV. We also observed possible associations between anti-kinesin antibodies and clinically relevant features within AAV patients. Further verification studies will be needed to confirm these findings.", "doi": "10.3390/ijms242015341", "pmid": "37895021", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10607136"}, {"db": "pii", "key": "ijms242015341"}], "notes": [], "created": "2024-09-04T07:29:39.837Z", "modified": "2024-09-04T07:29:40.418Z"}, {"entity": "publication", "iuid": "c47a067012124fd3b1e0a4b3a87b6c30", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c47a067012124fd3b1e0a4b3a87b6c30.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c47a067012124fd3b1e0a4b3a87b6c30"}}, "title": "Cross-reactive EBNA1 immunity targets alpha-crystallin B and is associated with multiple sclerosis.", "authors": [{"family": "Thomas", "given": "Olivia G", "initials": "OG", "orcid": "0000-0002-2011-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea07f812ffee4db893c6f98548563525.json"}}, {"family": "Bronge", "given": "Mattias", "initials": "M", "orcid": "0000-0002-1258-3982", "researcher": {"href": "https://publications.scilifelab.se/researcher/691b77352a57408896ef1fb486980ccd.json"}}, {"family": "Tengvall", "given": "Katarina", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Akpinar", "given": "Birce", "initials": "B"}, {"family": "Nilsson", "given": "Ola B", "initials": "OB"}, {"family": "Holmgren", "given": "Erik", "initials": "E", "orcid": "0000-0002-2656-1864", "researcher": {"href": "https://publications.scilifelab.se/researcher/6160949c45cf4daaab3991d051db5a16.json"}}, {"family": "Hessa", "given": "Tara", "initials": "T"}, {"family": "Gafvelin", "given": "Guro", "initials": "G", "orcid": "0000-0003-1618-4011", "researcher": {"href": "https://publications.scilifelab.se/researcher/870294f4604744ccb212a3c299887ecc.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Martin", "given": "Roland", "initials": "R", "orcid": "0000-0002-0982-1329", "researcher": {"href": "https://publications.scilifelab.se/researcher/64b3f80280694b0399130e6eb26caf72.json"}}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b824181455243b19f4aa145a4545870.json"}}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H", "orcid": "0000-0003-4882-7624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e701613f60249b793f2def737168a05.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2938-1877", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9a20a941214f97a22f010df37cd8e1.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}], "type": "journal article", "published": "2023-05-19", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "20", "pages": "eadg3032", "issn-l": "2375-2548"}, "abstract": "Multiple sclerosis (MS) is an inflammatory disease of the central nervous system, for which and Epstein-Barr virus (EBV) infection is a likely prerequisite. Due to the homology between Epstein-Barr nuclear antigen 1 (EBNA1) and alpha-crystallin B (CRYAB), we examined antibody reactivity to EBNA1 and CRYAB peptide libraries in 713 persons with MS (pwMS) and 722 matched controls (Con). Antibody response to CRYAB amino acids 7 to 16 was associated with MS (OR = 2.0), and combination of high EBNA1 responses with CRYAB positivity markedly increased disease risk (OR = 9.0). Blocking experiments revealed antibody cross-reactivity between the homologous EBNA1 and CRYAB epitopes. Evidence for T cell cross-reactivity was obtained in mice between EBNA1 and CRYAB, and increased CRYAB and EBNA1 CD4+ T cell responses were detected in natalizumab-treated pwMS. This study provides evidence for antibody cross-reactivity between EBNA1 and CRYAB and points to a similar cross-reactivity in T cells, further demonstrating the role of EBV adaptive immune responses in MS development.", "doi": "10.1126/sciadv.adg3032", "pmid": "37196088", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10191428"}], "notes": [], "created": "2023-06-25T20:13:34.600Z", "modified": "2023-06-25T20:13:34.874Z"}, {"entity": "publication", "iuid": "1292ce8474234989b763b9a52fa7186c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1292ce8474234989b763b9a52fa7186c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1292ce8474234989b763b9a52fa7186c"}}, "title": "The impact of immunomodulating treatment on the immunogenicity of COVID-19 vaccines in patients with immune-mediated inflammatory rheumatic diseases compared to healthy controls. A Swedish nationwide study (COVID19-REUMA).", "authors": [{"family": "Frodlund", "given": "Martina", "initials": "M"}, {"family": "Nived", "given": "Per", "initials": "P", "orcid": "0000-0003-0879-8195", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6fb7542dac447caa7cce3ae562d60ec.json"}}, {"family": "Chatzidionysiou", "given": "Aikaterini", "initials": "A", "orcid": "0000-0002-2669-1247", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b9a88c2fbe94c3698e9681dff80fed5.json"}}, {"family": "S\u00f6dergren", "given": "Anna", "initials": "A", "orcid": "0000-0002-7436-7900", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d220b832fb45889249c243b179540f.json"}}, {"family": "Klingberg", "given": "Eva", "initials": "E", "orcid": "0000-0001-6858-6413", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0dbd5b2aa28413b97026db7b84ea412.json"}}, {"family": "Bengtsson", "given": "Anders", "initials": "A"}, {"family": "Hansson", "given": "Monika", "initials": "M"}, {"family": "Olsson", "given": "Sophie", "initials": "S"}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Kapetanovic", "given": "Meliha C", "initials": "MC", "orcid": "0000-0002-7853-514X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb145f4fa71747749a8609a84fad5987.json"}}], "type": "journal article", "published": "2023-05-11", "journal": {"title": "Vaccine", "issn": "1873-2518", "issn-l": null, "volume": "41", "issue": "20", "pages": "3247-3257"}, "abstract": "To elucidate antibody responses after the second and third dose of COVID-19 vaccine in patients with inflammatory rheumatic diseases (IRD) treated with biologic/targeted disease modifying anti-rheumatic drugs (b/ts DMARDs).\n\nAntibody levels to antigens representing spike full length protein and spike S1 were measured before vaccination, 2-12 weeks after the second dose, before and after the third dose using multiplex bead-based serology assay. Positive antibody response was defined as antibody levels over cut off (seropositivity) in seronegative individuals or \u2265 4-fold increase in antibodies in individuals seropositive for both spike proteins.\n\nPatients (n = 414) receiving b/ts DMARDs (283 had arthritis, 75 systemic vasculitis and 56 other autoimmune diseases) and controls (n = 61) from five Swedish regions participated. Treatments groups were: rituximab (n = 145); abatacept (n = 22); Interleukin 6 receptor inhibitors [IL6i (n = 79)]; JAnus Kinase Inhibitors [JAKi (n = 58)], Tumour Necrosis Factor inhibitor [TNFi (n = 68)] and Interleukin12/23/17 inhibitors [IL12/23/17i (n = 42)]. Percentage of patients with positive antibody response after two doses was significantly lower in rituximab (33,8%) and abatacept (40,9%) (p < 0,001) but not in IL12/23/17i, TNFi or JAKi groups compared to controls (80,3%). Higher age, rituximab treatment and shorter time between last rituximab course and vaccination predicted impaired antibody response. Antibody levels collected 21-40 weeks after second dose decreased significantly (IL6i: p = 0,02; other groups: p < 0,001) compared to levels at 2-12 week but most participants remained seropositive. Proportion of patients with positive antibody response increased after third dose but was still significantly lower in rituximab (p < 0,001).\n\nOlder individuals and patients on maintenance rituximab have an impaired response after two doses of COVID-19 vaccine which improves if the time between last rituximab course and vaccination extends and also after an additional vaccine dose. Rituximab patients should be prioritized for booster vaccine doses. TNFi, JAKi and IL12/23/17i does not diminished humoral response to primary and an additional vaccination.", "doi": "10.1016/j.vaccine.2023.03.065", "pmid": "37076360", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10070777"}, {"db": "pii", "key": "S0264-410X(23)00372-9"}], "notes": [], "created": "2023-04-08T19:24:09.107Z", "modified": "2023-06-19T13:39:51.077Z"}, {"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": "71a0bf37a08a4b598531df666d3e7a56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71a0bf37a08a4b598531df666d3e7a56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71a0bf37a08a4b598531df666d3e7a56"}}, "title": "Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis.", "authors": [{"family": "Geroldinger-Simi\u0107", "given": "Marija", "initials": "M", "orcid": "0000-0003-2789-1862", "researcher": {"href": "https://publications.scilifelab.se/researcher/e87141eb33c34783a5c051e604a087af.json"}}, {"family": "Bayati", "given": "Shaghayegh", "initials": "S", "orcid": "0000-0002-3745-4570", "researcher": {"href": "https://publications.scilifelab.se/researcher/219f304209674c4f9ed726cccb170998.json"}}, {"family": "Pohjanen", "given": "Emmie", "initials": "E"}, {"family": "Sepp", "given": "Norbert", "initials": "N"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}], "type": "journal article", "published": "2023-03-15", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "24", "issue": "6", "issn-l": null}, "abstract": "Systemic sclerosis (SSc) is a rare autoimmune systemic disease that leads to decreased survival and quality of life due to fibrosis, inflammation, and vascular damage in the skin and/or vital organs. Early diagnosis is crucial for clinical benefit in SSc patients. Our study aimed to identify autoantibodies in the plasma of SSc patients that are associated with fibrosis in SSc. Initially, we performed a proteome-wide screening on sample pools from SSc patients by untargeted autoantibody screening on a planar antigen array (including 42,000 antigens representing 18,000 unique proteins). The selection was complemented with proteins reported in the literature in the context of SSc. A targeted antigen bead array was then generated with protein fragments representing the selected proteins and used to screen 55 SSc plasma samples and 52 matched controls. We found eleven autoantibodies with a higher prevalence in SSc patients than in controls, eight of which bound to proteins associated with fibrosis. Combining these autoantibodies in a panel could lead to the subgrouping of SSc patients with fibrosis. Anti-Phosphatidylinositol-5-phosphate 4-kinase type 2 beta (PIP4K2B)- and anti-AKT Serine/Threonine Kinase 3 (AKT3)-antibodies should be further explored to confirm their association with skin and lung fibrosis in SSc patients.", "doi": "10.3390/ijms24065629", "pmid": "36982700", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10051301"}, {"db": "pii", "key": "ijms24065629"}], "notes": [], "created": "2023-04-08T19:25:04.020Z", "modified": "2023-04-08T19:25:04.134Z"}, {"entity": "publication", "iuid": "2b0f8e93d15043c893f2cf9373b87ac3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b0f8e93d15043c893f2cf9373b87ac3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b0f8e93d15043c893f2cf9373b87ac3"}}, "title": "Array-Based Multiplex and High-Throughput Serology Assays.", "authors": [{"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Hellstr\u00f6m", "given": "Ceke", "initials": "C"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Yousef", "given": "Jamil", "initials": "J"}, {"family": "Skoglund", "given": "Lovisa", "initials": "L"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Pin", "given": "Elisa", "initials": "E"}], "type": "journal article", "published": "2023-02-14", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2628", "pages": "535-553", "issn-l": "1064-3745"}, "abstract": "The detection of antibody responses using serological tests provides means to diagnose infections, follow disease transmission, and monitor vaccination responses. The coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 virus, highlighted the need for rapid development of robust and reliable serological tests to follow disease spreading. Moreover, the rise of SARS-CoV-2 variants emphasized the need to monitor their transmission and prevalence in the population. For this reason, multiplex and flexible serological assays are needed to allow for rapid inclusion of antigens representing new variants as soon as they appear. In this chapter, we describe the generation and application of a multiplex serological test, based on bead array technology, to detect anti-SARS-CoV-2 antibodies in a high-throughput manner, using only a few microliters of sample. This method is currently expanding to include a multi-disease antigen panel that will allow parallel detection of antibodies towards several infectious agents.", "doi": "10.1007/978-1-0716-2978-9_31", "pmid": "36781805", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2023-02-14T20:37:35.973Z", "modified": "2023-02-14T20:37:35.977Z"}, {"entity": "publication", "iuid": "3e2686f2fef94be1aa54fa18d30f71af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e2686f2fef94be1aa54fa18d30f71af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e2686f2fef94be1aa54fa18d30f71af"}}, "title": "Persistence of salivary antibody responses after COVID-19 vaccination is associated with oral microbiome variation in both healthy and people living with HIV.", "authors": [{"family": "Ghorbani", "given": "Mahin", "initials": "M"}, {"family": "Al-Manei", "given": "Khaled", "initials": "K"}, {"family": "Naud", "given": "Sabrina", "initials": "S"}, {"family": "Healy", "given": "Katie", "initials": "K"}, {"family": "Gabarrini", "given": "Giorgio", "initials": "G"}, {"family": "Sobkowiak", "given": "Michal Jacek", "initials": "MJ"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Ray", "given": "Shilpa", "initials": "S"}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Muschiol", "given": "Sandra", "initials": "S"}, {"family": "Bogdanovic", "given": "Gordana", "initials": "G"}, {"family": "Bergman", "given": "Peter", "initials": "P"}, {"family": "Ljungman", "given": "Per", "initials": "P"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M"}], "type": "clinical trial", "published": "2023-01-10", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "13", "pages": "1079995", "issn-l": "1664-3224"}, "abstract": "Coevolution of microbiome and immunity at mucosal sites is essential for our health. Whether the oral microbiome, the second largest community after the gut, contributes to the immunogenicity of COVID-19 vaccines is not known. We investigated the baseline oral microbiome in individuals in the COVAXID clinical trial receiving the BNT162b2 mRNA vaccine. Participants (n=115) included healthy controls (HC; n=57) and people living with HIV (PLHIV; n=58) who met the study selection criteria. Vaccine-induced Spike antibodies in saliva and serum from 0 to 6 months were assessed and comparative analyses were performed against the individual salivary 16S ASV microbiome diversity. High- versus low vaccine responders were assessed on general, immunological, and oral microbiome features. Our analyses identified oral microbiome features enriched in high- vs. low-responders among healthy and PLHIV participants. In low-responders, an enrichment of Gram-negative, anaerobic species with proteolytic activity were found including Campylobacter, Butyrivibrio, Selenomonas, Lachnoanaerobaculum, Leptotrichia, Megasphaera, Prevotella and Stomatobaculum. In high-responders, enriched species were mainly Gram-positive and saccharolytic facultative anaerobes: Abiotrophia, Corynebacterium, Gemella, Granulicatella, Rothia, and Haemophilus. Combining identified microbial features in a classifier using the area under the receiver operating characteristic curve (ROC AUC) yielded scores of 0.879 (healthy controls) to 0.82 (PLHIV), supporting the oral microbiome contribution in the long-term vaccination outcome. The present study is the first to suggest that the oral microbiome has an impact on the durability of mucosal immunity after Covid-19 vaccination. Microbiome-targeted interventions to enhance long-term duration of mucosal vaccine immunity may be exploited.", "doi": "10.3389/fimmu.2022.1079995", "pmid": "36703980", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9871925"}], "notes": [], "created": "2023-01-11T08:53:51.435Z", "modified": "2023-06-19T13:33:10.052Z"}, {"entity": "publication", "iuid": "a837cbec9e51416181d565a6ada77f43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a837cbec9e51416181d565a6ada77f43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a837cbec9e51416181d565a6ada77f43"}}, "title": "Identification of novel autoantigens as potential biomarkers in juvenile idiopathic arthritis associated uveitis.", "authors": [{"family": "Arve-Butler", "given": "Sabine", "initials": "S"}, {"family": "Mossberg", "given": "Anki", "initials": "A"}, {"family": "Kahn", "given": "Fredrik", "initials": "F"}, {"family": "Najibi", "given": "Seyed Morteza", "initials": "SM"}, {"family": "Berthold", "given": "Elisabet", "initials": "E"}, {"family": "Kr\u00f3l", "given": "Petra", "initials": "P"}, {"family": "M\u00e5nsson", "given": "Bengt", "initials": "B"}, {"family": "Kahn", "given": "Robin", "initials": "R"}], "type": "journal article", "published": "2023-01-09", "journal": {"title": "Front Pediatr", "issn": "2296-2360", "volume": "10", "pages": "1091308", "issn-l": null}, "abstract": "Many children with juvenile idiopathic arthritis (JIA) have autoantibodies, targeting nuclear components (anti-nuclear antibodies, ANA). ANA in JIA is associated with uveitis, an eye inflammation which may cause permanent vision impairment if not detected and treated. However, ANA-testing is neither specific nor sensitive enough to be a clinically reliable predictor of uveitis risk, and the precise autoantigens targeted by ANA in JIA are largely unknown. If identified, specific autoantibodies highly associated with uveitis could be used as biomarkers to facilitate identification of JIA patients at risk.\n\nAntibodies from six ANA-positive, oligoarticular JIA patients, with and without uveitis, were explored by two large-scale methods: (1) screening against 42,100 peptides on an autoimmunity profiling planar array, and (2) immunoprecipitations from cell lysates with antigen identification by mass spectrometry. Three hundred thirty-five peptide antigens, selected from proteins identified in the large-scale methods and the scientific literature were investigated using a bead-based array in a cohort of 56 patients with oligoarticular- or RF-negative polyarticular JIA, eight of which were having current or previous uveitis.\n\nIn the planar array, reactivity was detected against 332 peptide antigens. The immunoprecipitations identified reactivity towards 131 proteins. Only two proteins were identified by both methods. In the bead-based array of selected peptide antigens, patients with uveitis had a generally higher autoreactivity, seen as higher median fluorescence intensity (MFI) across all antigens, compared to patients without uveitis. Reactivity towards 17 specific antigens was significantly higher in patients with uveitis compared to patients without uveitis. Hierarchical clustering revealed that patients with uveitis clustered together.\n\nThis study investigated autoantigens in JIA and uveitis, by combining two exploratory methods and confirmation in a targeted array. JIA patients with current or a history of uveitis had significantly higher reactivity towards 17 autoantigens and a generally higher autoreactivity compared to JIA patients without uveitis. Hierarchical clustering suggests that a combination of certain autoantibodies, rather than reactivity towards one specific antigen, is associated with uveitis. Our analysis of autoantibodies associated with uveitis in JIA could be a starting point for identification of prognostic biomarkers useful in JIA clinical care.", "doi": "10.3389/fped.2022.1091308", "pmid": "36699287", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9869058"}], "notes": [], "created": "2023-09-20T09:05:35.928Z", "modified": "2023-09-20T09:05:35.958Z"}, {"entity": "publication", "iuid": "b180389c75874d4aa64b80bb8f0fcb9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b180389c75874d4aa64b80bb8f0fcb9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b180389c75874d4aa64b80bb8f0fcb9b"}}, "title": "Monitoring drug-target interactions through target engagement-mediated amplification on arrays and in situ.", "authors": [{"family": "Al-Amin", "given": "Rasel A", "initials": "RA", "orcid": "0000-0002-0762-9034", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c8aeb2e9852413c832cf1a05be12d2f.json"}}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Abdurakhmanov", "given": "Eldar", "initials": "E"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Arng\u00e5rden", "given": "Linda", "initials": "L"}, {"family": "Blokzijl", "given": "Andries", "initials": "A"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Hammond", "given": "Maria", "initials": "M"}, {"family": "L\u00f6nn", "given": "Peter", "initials": "P"}, {"family": "Haybaeck", "given": "Johannes", "initials": "J"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Jensen", "given": "Annika Jenmalm", "initials": "AJ"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2022-12-09", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "50", "issue": "22", "pages": "e129"}, "abstract": "Drugs are designed to bind their target proteins in physiologically relevant tissues and organs to modulate biological functions and elicit desirable clinical outcomes. Information about target engagement at cellular and subcellular resolution is therefore critical for guiding compound optimization in drug discovery, and for probing resistance mechanisms to targeted therapies in clinical samples. We describe a target engagement-mediated amplification (TEMA) technology, where oligonucleotide-conjugated drugs are used to visualize and measure target engagement in situ, amplified via rolling-circle replication of circularized oligonucleotide probes. We illustrate the TEMA technique using dasatinib and gefitinib, two kinase inhibitors with distinct selectivity profiles. In vitro binding by the dasatinib probe to arrays of displayed proteins accurately reproduced known selectivity profiles, while their differential binding to fixed adherent cells agreed with expectations from expression profiles of the cells. We also introduce a proximity ligation variant of TEMA to selectively investigate binding to specific target proteins of interest. This form of the assay serves to improve resolution of binding to on- and off-target proteins. In conclusion, TEMA has the potential to aid in drug development and clinical routine by conferring valuable insights in drug-target interactions at spatial resolution in protein arrays, cells and in tissues.", "doi": "10.1093/nar/gkac842", "pmid": "36189884", "labels": {"Autoimmunity and Serology Profiling": "Service", "Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9825164"}, {"db": "pii", "key": "6746875"}, {"db": "figshare", "key": "10.6084/m9.figshare.21107641.v1"}], "notes": [], "created": "2022-11-14T10:15:15.724Z", "modified": "2025-10-17T13:05:07.711Z"}, {"entity": "publication", "iuid": "1dd952ba69084ffca528e6af051188e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1dd952ba69084ffca528e6af051188e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1dd952ba69084ffca528e6af051188e0"}}, "title": "Autoantigenic properties of the aminoacyl tRNA synthetase family in idiopathic inflammatory myopathies.", "authors": [{"family": "Preger", "given": "Charlotta", "initials": "C", "orcid": "0000-0002-1342-9135", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8519a1cc0e845c68b59d6ecdfea1a33.json"}}, {"family": "Notarnicola", "given": "Antonella", "initials": "A"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Wigren", "given": "Edvard", "initials": "E"}, {"family": "Fernandes-Cerqueira", "given": "C\u00e1tia", "initials": "C"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Idborg", "given": "Helena", "initials": "H"}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Gr\u00e4slund", "given": "Susanne", "initials": "S"}, {"family": "Jakobsson", "given": "Per-Johan", "initials": "P"}], "type": "journal article", "published": "2022-12-02", "journal": {"title": "J. Autoimmun.", "issn": "1095-9157", "issn-l": "0896-8411", "volume": "134", "issue": null, "pages": "102951"}, "abstract": "Autoantibodies are thought to play a key role in the pathogenesis of idiopathic inflammatory myopathies (IIM). However, up to 40% of IIM patients, even those with clinical manifestations of anti-synthetase syndrome (ASSD), test seronegative to known myositis-specific autoantibodies. We hypothesized the existence of new potential autoantigens among human cytoplasmic aminoacyl tRNA synthetases (aaRS) in patients with IIM.\r\n\r\nPlasma samples from 217 patients with IIM according to 2017 EULAR/ACR criteria, including 50 patients with ASSD, 165 without, and two with unknown ASSD status were identified retrospectively, as well as age and gender-matched sera from 156 population controls, and 219 disease controls. Patients with previously documented ASSD had to test positive for at least one of the five most common anti-aaRS autoantibodies (anti-Jo1, -PL7, -PL12, -EJ, and -OJ) and present with one or more of the following clinical manifestations: interstitial lung disease, myositis, arthritis, Raynaud's phenomenon, fever, or mechanic's hands. Demographics, laboratory, and clinical data of the IIM cohort (ASSD and non-ASSD) were compared. Samples were screened using a multiplex bead array assay for presence of autoantibodies against a panel of 117 recombinant protein variants, representing 33 myositis-related proteins, including all nineteen cytoplasmic aaRS. Prospectively collected clinical data for the IIM cohort were retrieved and compared between groups within the IIM cohort and correlated with the results of the autoantibody screening. Principal component analysis was used to analyze clinical manifestations between ASSD, non-ASSD groups, and individuals with novel anti-aaRS autoantibodies.\r\n\r\nWe identified reactivity towards 16 aaRS in 72 of the 217 IIM patients. Twelve patients displayed reactivity against nine novel aaRS. The novel autoantibody specificities were detected in four previously seronegative patients for myositis-specific autoantibodies and eight with previously detected myositis-specific autoantibodies. IIM individuals with novel anti-aaRS autoantibodies (n = 12) all had signs of myositis, and they had either muscle weakness and/or muscle enzyme elevation, 2/12 had mechanic's hands, 3/12 had interstitial lung disease, and 2/12 had arthritis. The individuals with novel anti-aaRS and a pathological muscle biopsy all presented widespread up-regulation of major histocompatibility complex class I. The reactivities against novel aaRS could be confirmed in ELISA and western blot. Using the multiplex bead array assay, we could confirm previously known reactivities to four of the most common aaRS (Jo1, PL12, PL7, and EJ (n = 45)) and identified patients positive for anti-Zo, -KS, and -HA (n = 10) that were not previously tested. A low frequency of anti-aaRS autoantibodies was also detected in controls.\r\n\r\nOur results suggest that most, if not all, cytoplasmic aaRS may become autoantigenic. Autoantibodies against new aaRS may be found in plasma of patients previously classified as seronegative with potential high clinical relevance.", "doi": "10.1016/j.jaut.2022.102951", "pmid": "36470210", "labels": {"Autoimmunity and Serology Profiling": "Service", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0896-8411(22)00159-7"}], "notes": [], "created": "2022-12-05T11:42:17.752Z", "modified": "2025-10-17T13:05:07.724Z"}, {"entity": "publication", "iuid": "3f6dc136183e4058bd961f885dd3e501", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f6dc136183e4058bd961f885dd3e501.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f6dc136183e4058bd961f885dd3e501"}}, "title": "Seroprevalence of SARS-CoV-2 antibodies among public transport workers in Sweden.", "authors": [{"family": "Sj\u00f6rs Dahlman", "given": "Anna", "initials": "A", "orcid": "0000-0003-2530-4126", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9defcd11ae74aaf8ecf65e71b0ed094.json"}}, {"family": "Anund", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2022-12-00", "journal": {"title": "Journal of Transport &amp; Health", "issn": "2214-1405", "pages": "101508", "volume": "27", "issn-l": null}, "abstract": "Public transportation is an essential societal function in crisis situations like the coronavirus disease 2019 (COVID-19) pandemic. Bus drivers and other public transport workers are essential workers that need to keep working despite the risk of contagion. The SARS-CoV-2 virus may pose an occupational health risk to public transport workers and especially to bus drivers as they interact with passengers in a confined area. By analyzing antibodies towards SARS-CoV-2 proteins in blood samples it is possible to measure if an individual has been infected by COVID-19. Here, we report the prevalence of antibodies among bus drivers and other public transport employees in Stockholm, Sweden and relate it to socio-demographic factors.\n\nSeroprevalence of IgG antibodies towards SARS-CoV-2 proteins was investigated in a sample of 262 non-vaccinated public transport workers (182 men and 40 women) recruited between April 26 and May 7, 2021. Most of the participants were bus drivers (n = 222). The relationship between socio-demographic factors and seroprevalence was investigated with logistic regression.\n\nThe seroprevalence was 50% in the total sample of public transport workers. Among bus drivers, 51% were seropositive compared to 44% seropositive among the other public transport workers. The difference was not significant. The seroprevalence was higher than the national seroprevalence in Sweden during the same period (18.3% in non-vaccinated people aged 20-64 years). The logistic regression model using Wald forward selection showed that men had a higher risk of being seropositive (OR 2.7, 95% CI 1.3 - 5.8) and there was a higher risk with increasing number of people in the household (OR 1.3, 95% CI 1.1 - 1.6).\n\nThese findings could imply an occupational risk for COVID-19 infection among public transport workers. Infection control measures are warranted during virus epidemics to assure bus drives' safety and reduce transmission in public transport.", "doi": "10.1016/j.jth.2022.101508", "pmid": "36188635", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9515328"}, {"db": "pii", "key": "S2214-1405(22)00180-3"}], "notes": [], "created": "2022-10-02T20:49:40.446Z", "modified": "2023-06-02T10:29:40.260Z"}, {"entity": "publication", "iuid": "b887f906dec142239dbe61d55d203912", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b887f906dec142239dbe61d55d203912.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b887f906dec142239dbe61d55d203912"}}, "title": "Genetic and immunologic evaluation of children with inborn errors of immunity and severe or critical COVID-19.", "authors": [{"family": "Abolhassani", "given": "Hassan", "initials": "H"}, {"family": "Delavari", "given": "Samaneh", "initials": "S"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Shokri", "given": "Sima", "initials": "S"}, {"family": "Bastard", "given": "Paul", "initials": "P"}, {"family": "Du", "given": "Likun", "initials": "L"}, {"family": "Zuo", "given": "Fanglei", "initials": "F"}, {"family": "Hajebi", "given": "Reza", "initials": "R"}, {"family": "Abolnezhadian", "given": "Farhad", "initials": "F"}, {"family": "Iranparast", "given": "Sara", "initials": "S"}, {"family": "Modaresi", "given": "Mohammadreza", "initials": "M"}, {"family": "Vosughimotlagh", "given": "Ahmad", "initials": "A"}, {"family": "Salami", "given": "Fereshte", "initials": "F"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M"}, {"family": "Cobat", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Marcotte", "given": "Harold", "initials": "H"}, {"family": "Zhang", "given": "Shen-Ying", "initials": "SY"}, {"family": "Zhang", "given": "Qian", "initials": "Q"}, {"family": "Rezaei", "given": "Nima", "initials": "N"}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Pan-Hammarstr\u00f6m", "given": "Qiang", "initials": "Q"}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "J. Allergy Clin. Immunol.", "issn": "1097-6825", "volume": "150", "issue": "5", "pages": "1059-1073", "issn-l": "0091-6749"}, "abstract": "Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals are asymptomatic or only exhibit mild disease. In about 10% of cases, the infection leads to hypoxemic pneumonia, although it is much more rare in children.\n\nWe evaluated 31 young patients aged 0.5 to 19 years who had preexisting inborn errors of immunity (IEI) but lacked a molecular diagnosis and were later diagnosed with coronavirus disease 2019 (COVID-19) complications.\n\nGenetic evaluation by whole-exome sequencing was performed in all patients. SARS-CoV-2-specific antibodies, autoantibodies against type I IFN (IFN-I), and inflammatory factors in plasma were measured. We also reviewed COVID-19 disease severity/outcome in reported IEI patients.\n\nA potential genetic cause of the IEI was identified in 28 patients (90.3%), including mutations that may affect IFN signaling, T- and B-cell function, the inflammasome, and the complement system. From tested patients 65.5% had detectable virus-specific antibodies, and 6.8% had autoantibodies neutralizing IFN-I. Five patients (16.1%) fulfilled the diagnostic criteria of multisystem inflammatory syndrome in children. Eleven patients (35.4%) died of COVID-19 complications. All together, at least 381 IEI children with COVID-19 have been reported in the literature to date. Although many patients with asymptomatic or mild disease may not have been reported, severe presentation of COVID-19 was observed in 23.6% of the published cases, and the mortality rate was 8.7%.\n\nYoung patients with preexisting IEI may have higher mortality than children without IEI when infected with SARS-CoV-2. Elucidating the genetic basis of IEI patients with severe/critical COVID-19 may help to develop better strategies for prevention and treatment of severe COVID-19 disease and complications in pediatric patients.", "doi": "10.1016/j.jaci.2022.09.005", "pmid": "36113674", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "S0091-6749(22)01185-X"}, {"db": "pmc", "key": "PMC9472457"}], "notes": [], "created": "2022-11-10T22:45:49.416Z", "modified": "2022-11-10T22:45:49.419Z"}, {"entity": "publication", "iuid": "9daa6b181d8d4874a7834d3bce284468", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9daa6b181d8d4874a7834d3bce284468.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9daa6b181d8d4874a7834d3bce284468"}}, "title": "Anti-Spike Mucosal IgA Protection against SARS-CoV-2 Omicron Infection.", "authors": [{"family": "Havervall", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-1671-8183", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd194b3cef64f9f9341fd163a035235.json"}}, {"family": "Marking", "given": "Ulrika", "initials": "U"}, {"family": "Svensson", "given": "Julia", "initials": "J"}, {"family": "Greilert-Norin", "given": "Nina", "initials": "N"}, {"family": "Bacchus", "given": "Philip", "initials": "P", "orcid": "0000-0001-9800-1957", "researcher": {"href": "https://publications.scilifelab.se/researcher/287bafef8b584a5cbd7bee05dbe3b5d0.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Gordon", "given": "Max", "initials": "M"}, {"family": "Blom", "given": "Kim", "initials": "K"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Smed-S\u00f6rensen", "given": "Anna", "initials": "A"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "letter", "published": "2022-10-06", "journal": {"title": "N. Engl. J. Med.", "issn": "1533-4406", "volume": "387", "issue": "14", "pages": "1333-1336", "issn-l": "0028-4793"}, "abstract": null, "doi": "10.1056/NEJMc2209651", "pmid": "36103621", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9511632"}], "notes": [], "created": "2022-10-02T20:52:13.937Z", "modified": "2022-12-02T09:11:42.533Z"}, {"entity": "publication", "iuid": "6cc0ac07f09a4ceebc3c06cb9256e5cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cc0ac07f09a4ceebc3c06cb9256e5cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cc0ac07f09a4ceebc3c06cb9256e5cb"}}, "title": "Hybrid immunity in immunocompromised patients with CLL after SARS-CoV-2 infection followed by booster mRNA vaccination.", "authors": [{"family": "Lisa", "given": "Blixt", "initials": "B"}, {"family": "Gao", "given": "Yu", "initials": "Y", "orcid": "0000-0002-4615-3614", "researcher": {"href": "https://publications.scilifelab.se/researcher/3915993e75dc4151bfc8ccab93895a40.json"}}, {"family": "Wullimann", "given": "David", "initials": "D", "orcid": "0000-0003-1632-0394", "researcher": {"href": "https://publications.scilifelab.se/researcher/349d6f425343417a93a83093b8863391.json"}}, {"family": "Mur\u00e9n Ingelman-Sundberg", "given": "Hanna", "initials": "H"}, {"family": "Muschiol", "given": "Sandra", "initials": "S"}, {"family": "Healy", "given": "Katie", "initials": "K", "orcid": "0000-0002-7242-6604", "researcher": {"href": "https://publications.scilifelab.se/researcher/399f5a83e04a4929ae03f265d57da92a.json"}}, {"family": "Bogdanovic", "given": "Gordana", "initials": "G"}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Kjellander", "given": "Christian", "initials": "C"}, {"family": "Grifoni", "given": "Alba", "initials": "A"}, {"family": "Sette", "given": "Alessandro", "initials": "A"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M", "orcid": "0000-0002-3793-4064", "researcher": {"href": "https://publications.scilifelab.se/researcher/af31e38e29a24d208df80184c563357f.json"}}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "H"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Hansson", "given": "Lotta", "initials": "L", "orcid": "0000-0001-6614-5737", "researcher": {"href": "https://publications.scilifelab.se/researcher/754f78f2a56143b4a3fe80294227f7ae.json"}}, {"family": "Osterborg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2022-09-23", "journal": {"title": "Blood", "issn": "1528-0020", "issn-l": "0006-4971", "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1182/blood.2022016815", "pmid": "36150168", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "486704"}, {"db": "pmc", "key": "PMC9512527"}], "notes": [], "created": "2022-10-02T20:55:03.352Z", "modified": "2023-06-27T07:07:12.345Z"}, {"entity": "publication", "iuid": "9de5d70a240743dd9a671e5e9fe20877", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9de5d70a240743dd9a671e5e9fe20877.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9de5d70a240743dd9a671e5e9fe20877"}}, "title": "B-cell repopulation dynamics and drug pharmacokinetics impact SARS-CoV-2 vaccine efficacy in anti-CD20-treated multiple sclerosis patients.", "authors": [{"family": "Asplund H\u00f6gelin", "given": "Klara", "initials": "K", "orcid": "0000-0002-3696-355X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a0642ad3dcd48bcb32acac944de9c31.json"}}, {"family": "Ruffin", "given": "Nicolas", "initials": "N"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Starvaggi Cucuzza", "given": "Chiara", "initials": "C"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Piehl", "given": "Fredrik", "initials": "F"}, {"family": "Al Nimer", "given": "Faiez", "initials": "F"}], "type": "journal article", "published": "2022-07-08", "journal": {"title": "Eur. J. Neurol.", "issn": "1468-1331", "issn-l": "1351-5101"}, "abstract": "Recent findings document a blunted humoral response to SARS-CoV-2 vaccination in patients on anti-CD20 treatment. Although most patients develop a cellular response, it is still important to identify predictors of seroconversion to optimize vaccine responses.\n\nWe determined antibody responses after SARS-CoV-2 vaccination in a real-world cohort of multiple sclerosis patients (n = 94) treated with anti-CD20, mainly rituximab, with variable treatment duration (median = 2.9, range = 0.4-9.6 years) and time from last anti-CD20 infusion to vaccination (median = 190, range = 60-1032 days).\n\nWe find that presence of B cells and/or rituximab in blood predict seroconversion better than time since last infusion. Using multiple logistic regression, presence of >0.5% B cells increased probability of seroconversion with an odds ratio (OR) of 5.0 (95% confidence interval [CI] = 1.0-28.1, p = 0.055), whereas the corresponding OR for \u22656 months since last infusion was 1.45 (95% CI = 0.20-10.15, p = 0.705). In contrast, detectable rituximab levels were negatively associated with seroconversion (OR = 0.05, 95% CI = 0.002-0.392, p = 0.012). Furthermore, na\u00efve and memory IgG+ B cells correlated with antibody levels. Although retreatment with rituximab at 4 weeks or more after booster depleted spike-specific B cells, it did not noticeably affect the rate of decline in antibody titers. Interferon-\u03b3 and/or interleukin-13 T-cell responses to the spike S1 domain were observed in most patients, but with no correlation to spike antibody levels.\n\nThese findings are relevant for providing individualized guidance to patients and planning of vaccination schemes, in turn optimizing benefit-risk with anti-CD20.", "doi": "10.1111/ene.15492", "pmid": "35808856", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9349816"}], "notes": [], "created": "2022-08-08T12:57:24.608Z", "modified": "2022-08-08T12:57:24.673Z"}, {"entity": "publication", "iuid": "a0f9f52f37ba4168a47b6bbaa3ea93fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0f9f52f37ba4168a47b6bbaa3ea93fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0f9f52f37ba4168a47b6bbaa3ea93fb"}}, "title": "Immune responses after omicron infection in triple-vaccinated health-care workers with and without previous SARS-CoV-2 infection.", "authors": [{"family": "Blom", "given": "Kim", "initials": "K"}, {"family": "Marking", "given": "Ulrika", "initials": "U"}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Norin", "given": "Nina Greilert", "initials": "NG"}, {"family": "Gordon", "given": "Max", "initials": "M"}, {"family": "Garc\u00eda", "given": "Marina", "initials": "M"}, {"family": "Tecleab", "given": "Teghesti", "initials": "T"}, {"family": "Christ", "given": "Wanda", "initials": "W"}, {"family": "Forsell", "given": "Mattias", "initials": "M"}, {"family": "Phillipson", "given": "Mia", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Mangsbo", "given": "Sara", "initials": "S"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "letter", "published": "2022-07-00", "journal": {"title": "Lancet Infect Dis", "issn": "1474-4457", "issn-l": null, "volume": "22", "issue": "7", "pages": "943-945"}, "abstract": null, "doi": "10.1016/S1473-3099(22)00362-0", "pmid": "35691303", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9183210"}, {"db": "pii", "key": "S1473-3099(22)00362-0"}], "notes": [], "created": "2022-08-08T12:56:32.449Z", "modified": "2022-12-02T09:11:41.215Z"}, {"entity": "publication", "iuid": "387be3d37549490b96f97b6b0818f875", "links": {"self": {"href": "https://publications.scilifelab.se/publication/387be3d37549490b96f97b6b0818f875.json"}, "display": {"href": "https://publications.scilifelab.se/publication/387be3d37549490b96f97b6b0818f875"}}, "title": "Identification of four novel T cell autoantigens and personal autoreactive profiles in multiple sclerosis.", "authors": [{"family": "Bronge", "given": "Mattias", "initials": "M", "orcid": "0000-0002-1258-3982", "researcher": {"href": "https://publications.scilifelab.se/researcher/691b77352a57408896ef1fb486980ccd.json"}}, {"family": "H\u00f6gelin", "given": "Klara Asplund", "initials": "KA"}, {"family": "Thomas", "given": "Olivia G", "initials": "OG", "orcid": "0000-0002-2011-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea07f812ffee4db893c6f98548563525.json"}}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Carvalho-Queiroz", "given": "Claudia", "initials": "C"}, {"family": "Nilsson", "given": "Ola B", "initials": "OB"}, {"family": "Kaiser", "given": "Andreas", "initials": "A"}, {"family": "Zeitelhofer", "given": "Manuel", "initials": "M"}, {"family": "Holmgren", "given": "Erik", "initials": "E", "orcid": "0000-0002-2656-1864", "researcher": {"href": "https://publications.scilifelab.se/researcher/6160949c45cf4daaab3991d051db5a16.json"}}, {"family": "Linnerbauer", "given": "Mathias", "initials": "M", "orcid": "0000-0002-5528-5141", "researcher": {"href": "https://publications.scilifelab.se/researcher/27c1386bf72f4371acb131d333314da2.json"}}, {"family": "Adzemovic", "given": "Milena Z", "initials": "MZ"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Jelcic", "given": "Ivan", "initials": "I", "orcid": "0000-0002-6187-7098", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b5547919d474434bddd217865f1fb8e.json"}}, {"family": "Liu", "given": "Hao", "initials": "H", "orcid": "0000-0001-6572-2870", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3f8f259e77d4e208a4c838de8a7c7de.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Hillert", "given": "Jan", "initials": "J", "orcid": "0000-0002-7386-6732", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb4f3ad8831d430e8327dd457d43834b.json"}}, {"family": "Brundin", "given": "Lou", "initials": "L", "orcid": "0000-0003-4408-7817", "researcher": {"href": "https://publications.scilifelab.se/researcher/9181d700c722427099d882b3b40eb91e.json"}}, {"family": "Fink", "given": "Katharina", "initials": "K"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Tengvall", "given": "Katarina", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Martin", "given": "Roland", "initials": "R"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Gr\u00e4slund", "given": "Torbj\u00f6rn", "initials": "T", "orcid": "0000-0002-5391-600X", "researcher": {"href": "https://publications.scilifelab.se/researcher/52adbc739e274652bbf877facf4f0959.json"}}, {"family": "Al Nimer", "given": "Faiez", "initials": "F", "orcid": "0000-0003-0937-5995", "researcher": {"href": "https://publications.scilifelab.se/researcher/743a318b1c64432280e3999fb57c9a18.json"}}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b824181455243b19f4aa145a4545870.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Gafvelin", "given": "Guro", "initials": "G", "orcid": "0000-0003-1618-4011", "researcher": {"href": "https://publications.scilifelab.se/researcher/870294f4604744ccb212a3c299887ecc.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2938-1877", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9a20a941214f97a22f010df37cd8e1.json"}}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H", "orcid": "0000-0003-4882-7624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e701613f60249b793f2def737168a05.json"}}], "type": "journal article", "published": "2022-04-29", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "17", "pages": "eabn1823", "issn-l": "2375-2548"}, "abstract": "Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS), in which pathological T cells, likely autoimmune, play a key role. Despite its central importance, the autoantigen repertoire remains largely uncharacterized. Using a novel in vitro antigen delivery method combined with the Human Protein Atlas library, we screened for T cell autoreactivity against 63 CNS-expressed proteins. We identified four previously unreported autoantigens in MS: fatty acid-binding protein 7, prokineticin-2, reticulon-3, and synaptosomal-associated protein 91, which were verified to induce interferon-\u03b3 responses in MS in two cohorts. Autoreactive profiles were heterogeneous, and reactivity to several autoantigens was MS-selective. Autoreactive T cells were predominantly CD4+ and human leukocyte antigen-DR restricted. Mouse immunization induced antigen-specific responses and CNS leukocyte infiltration. This represents one of the largest systematic efforts to date in the search for MS autoantigens, demonstrates the heterogeneity of autoreactive profiles, and highlights promising targets for future diagnostic tools and immunomodulatory therapies in MS.", "doi": "10.1126/sciadv.abn1823", "pmid": "35476434", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-04-28T11:23:43.022Z", "modified": "2022-04-28T11:23:43.509Z"}, {"entity": "publication", "iuid": "515134db32a844d79ba99c6f199c37d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/515134db32a844d79ba99c6f199c37d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/515134db32a844d79ba99c6f199c37d6"}}, "title": "Impact of SARS-CoV-2 infection on vaccine-induced immune responses over time.", "authors": [{"family": "Havervall", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-1671-8183", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd194b3cef64f9f9341fd163a035235.json"}}, {"family": "Marking", "given": "Ulrika", "initials": "U"}, {"family": "Greilert-Norin", "given": "Nina", "initials": "N"}, {"family": "Gordon", "given": "Max", "initials": "M"}, {"family": "Ng", "given": "Henry", "initials": "H"}, {"family": "Christ", "given": "Wanda", "initials": "W"}, {"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": "Blom", "given": "Kim", "initials": "K"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Mangsbo", "given": "Sara", "initials": "S"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2022-04-18", "journal": {"title": "Clin Transl Immunology", "issn": "2050-0068", "volume": "11", "issue": "4", "pages": "e1388", "issn-l": null}, "abstract": "To determine the long-term impact of prior SARS-CoV-2 infection on immune responses after COVID-19 vaccination.\n\nUsing longitudinally collected blood samples from the COMMUNITY study, we determined binding (WHO BAU mL-1) and neutralising antibody titres against ten SARS-CoV-2 variants over 7 months following BNT162b2 in SARS-CoV-2-recovered (n = 118) and SARS-CoV-2-na\u00efve (n = 289) healthcare workers with confirmed prior SARS-CoV-2 infection. A smaller group with (n = 47) and without (n = 60) confirmed prior SARS-CoV-2 infection receiving ChAdOx1 nCoV-19 was followed for 3 months. SARS-CoV-2-specific memory T-cell responses were investigated in a subset of SARS-CoV-2-na\u00efve and SARS-CoV-2-recovered vaccinees.\n\nVaccination with both vaccine platforms resulted in substantially enhanced T-cell responses, anti-spike IgG responses and neutralising antibodies effective against ten SARS-CoV-2 variants in SARS-CoV-2-recovered participants as compared to SARS-CoV-2-na\u00efve participants. The enhanced immune responses sustained over 7 months following vaccination.\n\nThese findings imply that prior SARS-CoV-2 infection should be taken into consideration when planning booster doses and design of current and future COVID-19 vaccine programmes.", "doi": "10.1002/cti2.1388", "pmid": "35444806", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9015077"}, {"db": "pii", "key": "CTI21388"}], "notes": [], "created": "2022-04-22T10:27:53.070Z", "modified": "2022-12-02T09:11:39.950Z"}, {"entity": "publication", "iuid": "302e1f949c0e46a9b094509df48e8bc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/302e1f949c0e46a9b094509df48e8bc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/302e1f949c0e46a9b094509df48e8bc9"}}, "title": "SLC38A10 Regulate Glutamate Homeostasis and Modulate the AKT/TSC2/mTOR Pathway in Mouse Primary Cortex Cells.", "authors": [{"family": "Tripathi", "given": "Rekha", "initials": "R"}, {"family": "Aggarwal", "given": "Tanya", "initials": "T"}, {"family": "Lindberg", "given": "Frida A", "initials": "FA"}, {"family": "Klemm", "given": "Anna H", "initials": "AH"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2022-04-05", "journal": {"title": "Front Cell Dev Biol", "issn": "2296-634X", "volume": "10", "pages": "854397", "issn-l": null}, "abstract": "Glutamate acts as a critical regulator of neurotransmitter balance, recycling, synaptic function and homeostasis in the brain and glutamate transporters control glutamate levels in the brain. SLC38A10 is a member of the SLC38 family and regulates protein synthesis and cellular stress responses. Here, we uncover the role of SLC38A10 as a transceptor involved in glutamate-sensing signaling pathways that control both the glutamate homeostasis and mTOR-signaling. The culture of primary cortex cells from SLC38A10 knockout mice had increased intracellular glutamate. In addition, under nutrient starvation, KO cells had an impaired response in amino acid-dependent mTORC1 signaling. Combined studies from transcriptomics, protein arrays and metabolomics established that SLC38A10 is involved in mTOR signaling and that SLC38A10 deficient primary cortex cells have increased protein synthesis. Metabolomic data showed decreased cholesterol levels, changed fatty acid synthesis, and altered levels of fumaric acid, citrate, 2-oxoglutarate and succinate in the TCA cycle. These data suggests that SLC38A10 may act as a modulator of glutamate homeostasis, and mTOR-sensing and loss of this transceptor result in lower cholesterol, which could have implications in neurodegenerative diseases.", "doi": "10.3389/fcell.2022.854397", "pmid": "35450293", "labels": {"Autoimmunity and Serology Profiling": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9017388"}, {"db": "pii", "key": "854397"}], "notes": [], "created": "2022-11-24T10:51:46.853Z", "modified": "2025-10-17T13:03:15.188Z"}, {"entity": "publication", "iuid": "d8c307b538944e43b439658ee0a24270", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d8c307b538944e43b439658ee0a24270.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d8c307b538944e43b439658ee0a24270"}}, "title": "Long-term SARS-CoV-2-specific and cross-reactive cellular immune responses correlate with humoral responses, disease severity, and symptomatology.", "authors": [{"family": "Laur\u00e9n", "given": "Ida", "initials": "I", "orcid": "0000-0003-0041-6084", "researcher": {"href": "https://publications.scilifelab.se/researcher/37ecae2143cf4534935defaca37e85ca.json"}}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Ng", "given": "Henry", "initials": "H", "orcid": "0000-0003-2873-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcb12c664a64724b5cd42a1267a5bea.json"}}, {"family": "Lord", "given": "Martin", "initials": "M"}, {"family": "Pettke", "given": "Aleksandra", "initials": "A"}, {"family": "Greilert-Norin", "given": "Nina", "initials": "N"}, {"family": "Gabrielsson", "given": "Lena", "initials": "L"}, {"family": "Chourlia", "given": "Aikaterini", "initials": "A"}, {"family": "Amo\u00eado-Leite", "given": "Catarina", "initials": "C"}, {"family": "Josyula", "given": "Vijay S", "initials": "VS"}, {"family": "Eltahir", "given": "Mohamed", "initials": "M"}, {"family": "Kerzeli", "given": "Iliana", "initials": "I"}, {"family": "Falk", "given": "August J", "initials": "AJ", "orcid": "0000-0002-7773-1851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe6400bde68b46899515cef5bea05fca.json"}}, {"family": "Hober", "given": "Jonathan", "initials": "J"}, {"family": "Christ", "given": "Wanda", "initials": "W"}, {"family": "Wiberg", "given": "Anna", "initials": "A"}, {"family": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Burman", "given": "Joachim", "initials": "J"}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Christoffersson", "given": "Gustaf", "initials": "G"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Philipson", "given": "Mia", "initials": "M"}, {"family": "D\u00f6nnes", "given": "Pierre", "initials": "P"}, {"family": "Lindsay", "given": "Robin", "initials": "R"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}, {"family": "Mangsbo", "given": "Sara", "initials": "S", "orcid": "0000-0002-1355-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/c743bbcad6554f049c8fc5f64a6801bc.json"}}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Immun Inflamm Dis", "issn": "2050-4527", "volume": "10", "issue": "4", "pages": "e595", "issn-l": null}, "abstract": "Cellular immune memory responses post coronavirus disease 2019 (COVID-19) have been difficult to assess due to the risks of contaminating the immune response readout with memory responses stemming from previous exposure to endemic coronaviruses. The work herein presents a large-scale long-term follow-up study investigating the correlation between symptomology and cellular immune responses four to five months post seroconversion based on a unique severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific peptide pool that contains no overlapping peptides with endemic human coronaviruses.\n\nPeptide stimulated memory T cell responses were assessed with dual interferon-gamma (IFN\u03b3) and interleukin (IL)-2 Fluorospot. Serological analyses were performed using a multiplex antigen bead array.\n\nOur work demonstrates that long-term SARS-CoV-2-specific memory T cell responses feature dual IFN\u03b3 and IL-2 responses, whereas cross-reactive memory T cell responses primarily generate IFN\u03b3 in response to SARS-CoV-2 peptide stimulation. T cell responses correlated to long-term humoral immune responses. Disease severity as well as specific COVID-19 symptoms correlated with the magnitude of the SARS-CoV-2-specific memory T cell response four to five months post seroconversion.\n\nUsing a large cohort and a SARS-CoV-2-specific peptide pool we were able to substantiate that initial disease severity and symptoms correlate with the magnitude of the SARS-CoV-2-specific memory T cell responses.", "doi": "10.1002/iid3.595", "pmid": "35349756", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-03-31T06:07:11.524Z", "modified": "2022-03-31T06:07:11.636Z"}, {"entity": "publication", "iuid": "f42de6731b7b459b96b1816ead8dbcac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f42de6731b7b459b96b1816ead8dbcac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f42de6731b7b459b96b1816ead8dbcac"}}, "title": "Inherited IFNAR1 Deficiency in a Child with Both Critical COVID-19 Pneumonia and Multisystem Inflammatory Syndrome", "authors": [{"family": "Abolhassani", "given": "Hassan", "initials": "H"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Bastard", "given": "Paul", "initials": "P"}, {"family": "Materna", "given": "Marie", "initials": "M"}, {"family": "Modaresi", "given": "Mohammadreza", "initials": "M"}, {"family": "Du", "given": "Likun", "initials": "L"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M"}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Zuo", "given": "Fanglei", "initials": "F"}, {"family": "Zhang", "given": "Peng", "initials": "P"}, {"family": "Marcotte", "given": "Harold", "initials": "H"}, {"family": "Marr", "given": "Nico", "initials": "N"}, {"family": "Khan", "given": "Taushif", "initials": "T"}, {"family": "Ata", "given": "Manar", "initials": "M"}, {"family": "Al-Ali", "given": "Fatima", "initials": "F"}, {"family": "Pescarmona", "given": "Remi", "initials": "R"}, {"family": "Belot", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-4902-5332", "researcher": {"href": "https://publications.scilifelab.se/researcher/155056471c474a8ca255b7cefd8c5cad.json"}}, {"family": "B\u00e9ziat", "given": "Vivien", "initials": "V"}, {"family": "Zhang", "given": "Qian", "initials": "Q"}, {"family": "Casanova", "given": "Jean Laurent", "initials": "JL"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Zhang", "given": "Shen Ying", "initials": "SY"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Pan-Hammarstr\u00f6m", "given": "Qiang", "initials": "Q", "orcid": "0000-0003-1990-8804", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9d3baa27411425a8b8f63f3c3230964.json"}}], "type": "journal-article", "published": "2022-04-00", "journal": {"title": "J Clin Immunol", "issn": "0271-9142", "issn-l": null, "volume": "42", "issue": "3", "pages": "471-483"}, "abstract": "Inborn errors of immunity (IEI) and autoantibodies to type I interferons (IFNs) underlie critical COVID-19 pneumonia in at least 15% of the patients, while the causes of multisystem inflammatory syndrome in children (MIS-C) remain elusive.\n\nTo detect causal genetic variants in very rare cases with concomitant critical COVID-19 pneumonia and MIS-C.\n\nWhole exome sequencing was performed, and the impact of candidate gene variants was investigated. Plasma levels of cytokines, specific antibodies against the virus, and autoantibodies against type I IFNs were also measured.\n\nWe report a 3-year-old child who died on day 56 of SARS-CoV-2 infection with an unusual clinical presentation, combining both critical COVID-19 pneumonia and MIS-C. We identified a large, homozygous loss-of-function deletion in IFNAR1, underlying autosomal recessive IFNAR1 deficiency.\n\nOur findings confirm that impaired type I IFN immunity can underlie critical COVID-19 pneumonia, while suggesting that it can also unexpectedly underlie concomitant MIS-C. Our report further raises the possibility that inherited or acquired dysregulation of type I IFN immunity might contribute to MIS-C in other patients.", "doi": "10.1007/s10875-022-01215-7", "pmid": "35091979", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8798309"}, {"db": "pii", "key": "10.1007/s10875-022-01215-7"}], "notes": [], "created": "2022-01-31T10:27:07.869Z", "modified": "2023-06-19T09:13:02.921Z"}, {"entity": "publication", "iuid": "b724ea57b7804942a3a4c7845bd72891", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b724ea57b7804942a3a4c7845bd72891.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b724ea57b7804942a3a4c7845bd72891"}}, "title": "Linear Epitope Binding Patterns of Grass Pollen-Specific Antibodies in Allergy and in Response to Allergen-Specific Immunotherapy.", "authors": [{"family": "Th\u00f6rnqvist", "given": "Linnea", "initials": "L"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "van Hage", "given": "Marianne", "initials": "M"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2022-03-31", "journal": {"title": "Front. Allergy", "issn": "2673-6101", "issn-l": null, "volume": "3", "issue": null, "pages": "859126"}, "abstract": "Allergic diseases affect many individuals world-wide and are dependent on the interaction between allergens and antibodies of the IgE isotype. Allergen-specific immunotherapy (AIT) can alter the development of the disease, e.g., through induction of allergen-specific IgG that block allergen-IgE interactions. The knowledge of epitopes recognized by allergy-causing and protective antibodies are limited. Therefore, we developed an allergome-wide peptide microarray, aiming to track linear epitope binding patterns in allergic diseases and during AIT. Here, we focused on immune responses to grass pollen allergens and found that such epitopes were commonly recognized before initiation of AIT and that AIT commonly resulted in increased antibody production against additional epitopes already after 1 year of treatment. The linear epitope binding patterns were highly individual, both for subjects subjected to and for individuals not subjected to AIT. Still, antibodies against some linear epitopes were commonly developed during AIT. For example, the two rigid domains found in grass pollen group 5 allergens have previously been associated to a diversity of discontinuous epitopes. Here, we present evidence that also the flexible linker, connecting these domains, contains regions of linear epitopes against which antibodies are developed during AIT. We also describe some commonly recognized linear epitopes on Phl p 2 and suggest how antibodies against these epitopes may contribute to or prevent allergy in relation to a well-defined stereotyped/public IgE response against the same allergen. Finally, we identify epitopes that induce cross-reactive antibodies, but also antibodies that exclusively bind one of two highly similar variants of a linear epitope. Our findings highlight the complexity of antibody recognition of linear epitopes, with respect to both the studied individuals and the examined allergens. We expect that many of the findings in this study can be generalized also to discontinuous epitopes and that allergen peptide microarrays provide an important tool for enhancing the understanding of allergen-specific antibodies in allergic disease and during AIT.", "doi": "10.3389/falgy.2022.859126", "pmid": "35769580", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9234942"}], "notes": [], "created": "2022-04-04T07:45:58.570Z", "modified": "2025-10-17T13:05:07.795Z"}, {"entity": "publication", "iuid": "e981886f12a74ccd99562804b814129a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e981886f12a74ccd99562804b814129a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e981886f12a74ccd99562804b814129a"}}, "title": "Broad anti-SARS-CoV-2 antibody immunity induced by heterologous ChAdOx1/mRNA-1273 vaccination.", "authors": [{"family": "Kaku", "given": "Chengzi I", "initials": "CI", "orcid": "0000-0002-9854-8351", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa373156aa094c7b91e621eaf7d7add9.json"}}, {"family": "Champney", "given": "Elizabeth R", "initials": "ER"}, {"family": "Normark", "given": "Johan", "initials": "J", "orcid": "0000-0001-5831-4369", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ff458cccc2a422ca28ba878e98afb9c.json"}}, {"family": "Garcia", "given": "Marina", "initials": "M", "orcid": "0000-0002-9130-3933", "researcher": {"href": "https://publications.scilifelab.se/researcher/20fa6d5f40764b32a70f792f29d97e60.json"}}, {"family": "Johnson", "given": "Carl E", "initials": "CE"}, {"family": "Ahlm", "given": "Clas", "initials": "C", "orcid": "0000-0003-2018-8592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0add593fb7a74193afa74ff553aaa322.json"}}, {"family": "Christ", "given": "Wanda", "initials": "W", "orcid": "0000-0003-3886-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe3a44fdb547b885cce5b6f490b2bc.json"}}, {"family": "Sakharkar", "given": "Mrunal", "initials": "M", "orcid": "0000-0002-2717-5201", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a93fe70686e477f9e6951a650818d08.json"}}, {"family": "Ackerman", "given": "Margaret E", "initials": "ME", "orcid": "0000-0002-4253-3476", "researcher": {"href": "https://publications.scilifelab.se/researcher/2457511cf8d249c5bc962d3991354175.json"}}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Forsell", "given": "Mattias N E", "initials": "MNE", "orcid": "0000-0001-6904-742X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5947732f625a43e8a08055fc214649b6.json"}}, {"family": "Walker", "given": "Laura M", "initials": "LM", "orcid": "0000-0001-7704-3197", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec65711d236a41c3b2b3098f6ae34b84.json"}}], "type": "journal article", "published": "2022-03-04", "journal": {"title": "Science", "issn": "1095-9203", "volume": "375", "issue": "6584", "pages": "1041-1047", "issn-l": "0036-8075"}, "abstract": "Heterologous prime-boost immunization strategies have the potential to augment COVID-19 vaccine efficacy. We longitudinally profiled severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S)-specific serological and memory B cell (MBC) responses in individuals who received either homologous (ChAdOx1:ChAdOx1) or heterologous (ChAdOx1:mRNA-1273) prime-boost vaccination. Heterologous messenger RNA (mRNA) booster immunization induced higher serum neutralizing antibody and MBC responses against SARS-CoV-2 variants of concern (VOCs) compared with that of homologous ChAdOx1 boosting. Specificity mapping of circulating B cells revealed that mRNA-1273 boost immunofocused ChAdOx1-primed responses onto epitopes expressed on prefusion-stabilized S. Monoclonal antibodies isolated from mRNA-1273-boosted participants displayed overall higher binding affinities and increased breadth of reactivity against VOCs relative to those isolated from ChAdOx1-boosted individuals. Overall, the results provide molecular insight into the enhanced quality of the B cell response induced after heterologous mRNA booster vaccination.", "doi": "10.1126/science.abn2688", "pmid": "35143256", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8939765"}], "notes": [], "created": "2023-04-08T19:26:07.659Z", "modified": "2023-04-08T19:26:07.828Z"}, {"entity": "publication", "iuid": "7fbc2682596149a09196893f53e4a15e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fbc2682596149a09196893f53e4a15e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fbc2682596149a09196893f53e4a15e"}}, "title": "Duration of SARS-CoV-2 Immune Responses Up to Six Months Following Homologous or Heterologous Primary Immunization with ChAdOx1 nCoV-19 and BNT162b2 mRNA Vaccines.", "authors": [{"family": "Marking", "given": "Ulrika", "initials": "U"}, {"family": "Havervall", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-1671-8183", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd194b3cef64f9f9341fd163a035235.json"}}, {"family": "Greilert-Norin", "given": "Nina", "initials": "N"}, {"family": "Ng", "given": "Henry", "initials": "H", "orcid": "0000-0003-2873-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcb12c664a64724b5cd42a1267a5bea.json"}}, {"family": "Blom", "given": "Kim", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Phillipson", "given": "Mia", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Nilsson", "given": "Charlotta", "initials": "C"}, {"family": "Mangsbo", "given": "Sara", "initials": "S"}, {"family": "Christ", "given": "Wanda", "initials": "W"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Gordon", "given": "Max", "initials": "M"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2022-02-24", "journal": {"title": "Vaccines (Basel)", "issn": "2076-393X", "volume": "10", "issue": "3", "issn-l": null}, "abstract": "Heterologous primary immunization against SARS-CoV-2 is part of applied recommendations. However, little is known about duration of immune responses after heterologous vaccine regimens. To evaluate duration of immune responses after primary vaccination with homologous adeno-vectored ChAdOx1 nCoV-19 vaccine (ChAd) or heterologous ChAd/BNT162b2 mRNA vaccine (BNT), anti-spike-IgG and SARS-CoV-2 VOC-neutralizing antibody responses were measured in 354 healthcare workers (HCW) at 2 weeks, 3 months, 5 months and 6 months after the second vaccine dose. T-cell responses were investigated using a whole blood interferon gamma (IFN-\u03b3) release assay 2 weeks and 3 months post second vaccine dose. Two hundred and ten HCW immunized with homologous BNT were enrolled for comparison of antibody responses. In study participants na\u00efve to SARS-CoV-2 prior to vaccination, heterologous ChAd/BNT resulted in 6-fold higher peak anti-spike IgG antibody titers compared to homologous ChAd vaccination. The half-life of antibody titers was 3.1 months (95% CI 2.8-3.6) following homologous ChAd vaccination and 1.9 months (95% CI 1.7-2.1) after heterologous vaccination, reducing the GMT difference between the groups to 3-fold 6 months post vaccination. Peak T-cell responses were stronger in ChAd/BNT vaccinees, but no significant difference was observed 3 months post vaccination. SARS-CoV-2 infection prior to vaccination resulted in substantially higher peak GMTs and IFN-\u03b3 levels and enhanced SARS-CoV-2 specific antibody and T cell responses over time. Heterologous primary SARS-CoV-2 immunization with ChAd and BNT elicits a stronger initial immune response compared to homologous vaccination with ChAd. However, although the differences in humoral responses remain over 6 months, the difference in SARS-CoV-2 specific T cell responses are no longer significant three months after vaccination.", "doi": "10.3390/vaccines10030359", "pmid": "35334989", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8953845"}, {"db": "pii", "key": "vaccines10030359"}], "notes": [], "created": "2022-03-31T06:08:32.766Z", "modified": "2022-12-02T09:11:38.547Z"}, {"entity": "publication", "iuid": "d05ad8156c2c4552aa167cc2f77c5f92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d05ad8156c2c4552aa167cc2f77c5f92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d05ad8156c2c4552aa167cc2f77c5f92"}}, "title": "Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort", "authors": [{"family": "Carapito", "given": "Raphael", "initials": "R", "orcid": "0000-0002-7036-442X", "researcher": {"href": "https://publications.scilifelab.se/researcher/76903b22cdeb455e836b9653637e5863.json"}}, {"family": "Li", "given": "Richard", "initials": "R", "orcid": "0000-0003-0741-337X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6beb7b6fa854ea1894e2f4d73f960e6.json"}}, {"family": "Helms", "given": "Julie", "initials": "J"}, {"family": "Carapito", "given": "Christine", "initials": "C", "orcid": "0000-0002-0079-319X", "researcher": {"href": "https://publications.scilifelab.se/researcher/40c906d688c94e41946b96261474db92.json"}}, {"family": "Gujja", "given": "Sharvari", "initials": "S"}, {"family": "Rolli", "given": "V\u00e9ronique", "initials": "V", "orcid": "0000-0002-1215-9436", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eaa0e60b3cb41a78f4d8dcb40e917cc.json"}}, {"family": "Guimaraes", "given": "Raony", "initials": "R"}, {"family": "Malagon-Lopez", "given": "Jose", "initials": "J"}, {"family": "Spinnhirny", "given": "Perrine", "initials": "P"}, {"family": "Lederle", "given": "Alexandre", "initials": "A"}, {"family": "Mohseninia", "given": "Razieh", "initials": "R"}, {"family": "Hirschler", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0001-5066-6263", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd804c98aada4e44976c12dd2912c38d.json"}}, {"family": "Muller", "given": "Leslie", "initials": "L"}, {"family": "Bastard", "given": "Paul", "initials": "P", "orcid": "0000-0002-5926-8437", "researcher": {"href": "https://publications.scilifelab.se/researcher/3891533a59dc4185ba934b16e416e6ce.json"}}, {"family": "Gervais", "given": "Adrian", "initials": "A", "orcid": "0000-0002-1083-5787", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4d47775a4da4ee6ac0ff7da16c0155c.json"}}, {"family": "Zhang", "given": "Qian", "initials": "Q", "orcid": "0000-0002-9040-3289", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bee352280384ad99b180f4f4bac42f5.json"}}, {"family": "Danion", "given": "Fran\u00e7ois", "initials": "F", "orcid": "0000-0003-3907-0658", "researcher": {"href": "https://publications.scilifelab.se/researcher/010a92d1146e4dd484553305bf3d5c74.json"}}, {"family": "Ruch", "given": "Yvon", "initials": "Y", "orcid": "0000-0002-4713-9478", "researcher": {"href": "https://publications.scilifelab.se/researcher/866834d1c2554ce2aa0d9e3823aa4c10.json"}}, {"family": "Schenck", "given": "Maleka", "initials": "M", "orcid": "0000-0002-1043-6452", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdf8cad93b2b492ab7c6a86f6fb8109d.json"}}, {"family": "Collange", "given": "Olivier", "initials": "O"}, {"family": "Chamaraux-Tran", "given": "Thi\u00ean Nga", "initials": "TN"}, {"family": "Molitor", "given": "Anne", "initials": "A", "orcid": "0000-0003-1646-2325", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1348a6ee6524f8886c48fd1c2b73b28.json"}}, {"family": "Pichot", "given": "Ang\u00e9lique", "initials": "A", "orcid": "0000-0003-2515-5538", "researcher": {"href": "https://publications.scilifelab.se/researcher/4aacb269ddaf4f5a8f2209b8f547a6a9.json"}}, {"family": "Bernard", "given": "Alice", "initials": "A"}, {"family": "Tahar", "given": "Ouria", "initials": "O", "orcid": "0000-0002-0075-2590", "researcher": {"href": "https://publications.scilifelab.se/researcher/a804ab13daff43f3b6888cd27b766b91.json"}}, {"family": "Bibi-Triki", "given": "Sabrina", "initials": "S"}, {"family": "Wu", "given": "Haiguo", "initials": "H"}, {"family": "Paul", "given": "Nicod\u00e8me", "initials": "N", "orcid": "0000-0003-4680-3012", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9d8924cb3264f119c43c97feb3257b3.json"}}, {"family": "Mayeur", "given": "Sylvain", "initials": "S"}, {"family": "Larnicol", "given": "Annabel", "initials": "A"}, {"family": "Laumond", "given": "G\u00e9raldine", "initials": "G"}, {"family": "Frappier", "given": "Julia", "initials": "J", "orcid": "0000-0003-2618-8817", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3ece157db0949298e13cc370703b60f.json"}}, {"family": "Schmidt", "given": "Sylvie", "initials": "S"}, {"family": "Hanauer", "given": "Antoine", "initials": "A"}, {"family": "Macquin", "given": "C\u00e9cile", "initials": "C", "orcid": "0000-0003-3194-7080", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbcf074bed9b46e0872d01c65a91cb76.json"}}, {"family": "Stemmelen", "given": "Tristan", "initials": "T", "orcid": "0000-0002-4382-1277", "researcher": {"href": "https://publications.scilifelab.se/researcher/a821c104c65e48dead6301338168a18b.json"}}, {"family": "Simons", "given": "Michael", "initials": "M", "orcid": "0000-0003-0348-7734", "researcher": {"href": "https://publications.scilifelab.se/researcher/19fa7012d92c41cda7c5757a2c50c5be.json"}}, {"family": "Mariette", "given": "Xavier", "initials": "X", "orcid": "0000-0002-4244-5417", "researcher": {"href": "https://publications.scilifelab.se/researcher/13855fe7b68b4235a48a8dda9a0d5fd6.json"}}, {"family": "Hermine", "given": "Olivier", "initials": "O", "orcid": "0000-0003-2574-3874", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1bbf2973ff4bababdb07cc23398dd9.json"}}, {"family": "Fafi-Kremer", "given": "Samira", "initials": "S", "orcid": "0000-0003-3886-7833", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb83f475c4ad4c3c80df18c9d3451652.json"}}, {"family": "Goichot", "given": "Bernard", "initials": "B", "orcid": "0000-0001-7794-1683", "researcher": {"href": "https://publications.scilifelab.se/researcher/29d2670d923f4bbd99a441bbf425584c.json"}}, {"family": "Drenou", "given": "Bernard", "initials": "B", "orcid": "0000-0002-2175-6785", "researcher": {"href": "https://publications.scilifelab.se/researcher/8250de3cdb9a4fc3be54b7e3e8fd1eef.json"}}, {"family": "Kuteifan", "given": "Khaldoun", "initials": "K", "orcid": "0000-0002-0428-7016", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8d76418273b4af1bf4e69d098f3007c.json"}}, {"family": "Pottecher", "given": "Julien", "initials": "J"}, {"family": "Mertes", "given": "Paul Michel", "initials": "PM", "orcid": "0000-0002-6060-9438", "researcher": {"href": "https://publications.scilifelab.se/researcher/f147972b91414f6b87477b0859897927.json"}}, {"family": "Kailasan", "given": "Shweta", "initials": "S"}, {"family": "Aman", "given": "M Javad", "initials": "MJ"}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Thomas", "given": "Anne", "initials": "A", "orcid": "0000-0001-6901-3844", "researcher": {"href": "https://publications.scilifelab.se/researcher/3242b86e2de84178a74c1c199f1910f6.json"}}, {"family": "Viari", "given": "Alain", "initials": "A", "orcid": "0000-0002-1329-7777", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b361fcd1ef94feaae3458693899a858.json"}}, {"family": "Sanlaville", "given": "Damien", "initials": "D"}, {"family": "Schneider", "given": "Francis", "initials": "F"}, {"family": "Sibilia", "given": "Jean", "initials": "J"}, {"family": "Tharaux", "given": "Pierre Louis", "initials": "PL", "orcid": "0000-0002-6062-5905", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d6e1c79e38f4a4d83c19dcd0def5f32.json"}}, {"family": "Casanova", "given": "Jean Laurent", "initials": "JL", "orcid": "0000-0002-7782-4169", "researcher": {"href": "https://publications.scilifelab.se/researcher/009e2306468648c08fb1eea319f0c488.json"}}, {"family": "Hansmann", "given": "Yves", "initials": "Y", "orcid": "0000-0001-8903-0027", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e05e2d28e154aa5a19eacd5690e109d.json"}}, {"family": "Lidar", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1671-1515", "researcher": {"href": "https://publications.scilifelab.se/researcher/d213f3e38f4d40b49056ff57ae662764.json"}}, {"family": "Radosavljevic", "given": "Mirjana", "initials": "M", "orcid": "0000-0003-3925-0640", "researcher": {"href": "https://publications.scilifelab.se/researcher/b455278e8bf7496f8beff983485dace4.json"}}, {"family": "Gulcher", "given": "Jeffrey R", "initials": "JR"}, {"family": "Meziani", "given": "Ferhat", "initials": "F"}, {"family": "Moog", "given": "Christiane", "initials": "C", "orcid": "0000-0002-0916-156X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe7d5553a9d24a0b83ad2f7ecc18a526.json"}}, {"family": "Chittenden", "given": "Thomas W", "initials": "TW"}, {"family": "Bahram", "given": "Seiamak", "initials": "S", "orcid": "0000-0002-6928-9952", "researcher": {"href": "https://publications.scilifelab.se/researcher/151805ef1f8142baab4c253b50680d18.json"}}], "type": "journal-article", "published": "2022-01-19", "journal": {"title": "Sci. Transl. Med.", "issn": "1946-6234", "pages": "eabj7521", "volume": "14", "issue": "628", "issn-l": "1946-6234"}, "abstract": "The drivers of critical coronavirus disease 2019 (COVID-19) remain unknown. Given major confounding factors such as age and comorbidities, true mediators of this condition have remained elusive. We used a multi-omics analysis combined with artificial intelligence in a young patient cohort where major comorbidities were excluded at the onset. The cohort included 47 \u201ccritical\u201d (in the intensive care unit under mechanical ventilation) and 25 \u201cnon-critical\u201d (in a non-critical care ward) patients with COVID-19 and 22 healthy individuals. The analyses included whole-genome sequencing, whole-blood RNA sequencing, plasma and blood mononuclear cell proteomics, cytokine profiling, and high-throughput immunophenotyping. An ensemble of machine learning, deep learning, quantum annealing, and structural causal modeling were used. Patients with critical COVID-19 were characterized by exacerbated inflammation, perturbed lymphoid and myeloid compartments, increased coagulation, and viral cell biology. Among differentially expressed genes, we observed up-regulation of the metalloprotease ADAM9. This gene signature was validated in a second independent cohort of 81 critical and 73 recovered patients with COVID-19 and was further confirmed at the transcriptional and protein level and by proteolytic activity. Ex vivo ADAM9 inhibition decreased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake and replication in human lung epithelial cells. In conclusion, within a young, otherwise healthy, cohort of individuals with COVID-19, we provide the landscape of biological perturbations in vivo where a unique gene signature differentiated critical from non-critical patients. We further identified ADAM9 as a driver of disease severity and a candidate therapeutic target.", "doi": "10.1126/scitranslmed.abj7521", "pmid": "34698500", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [], "notes": [], "created": "2021-11-09T06:20:06.651Z", "modified": "2023-06-19T11:35:21.919Z"}, {"entity": "publication", "iuid": "998ee78639d54b3a9729c42c99deb02c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/998ee78639d54b3a9729c42c99deb02c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/998ee78639d54b3a9729c42c99deb02c"}}, "title": "SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection.", "authors": [{"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Jernbom Falk", "given": "August", "initials": "A", "orcid": "0000-0002-7773-1851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe6400bde68b46899515cef5bea05fca.json"}}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Ng", "given": "Henry", "initials": "H", "orcid": "0000-0003-2873-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcb12c664a64724b5cd42a1267a5bea.json"}}, {"family": "Greilert-Norin", "given": "Nina", "initials": "N"}, {"family": "Gabrielsson", "given": "Lena", "initials": "L"}, {"family": "Salomonsson", "given": "Ann-Christin", "initials": "AC"}, {"family": "Isaksson", "given": "Eva", "initials": "E", "orcid": "0000-0003-0289-8750", "researcher": {"href": "https://publications.scilifelab.se/researcher/f82b765ab5e64c7589dfe9f14db8478a.json"}}, {"family": "Rudberg", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Andersson", "given": "Eni", "initials": "E", "orcid": "0000-0002-5115-0637", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef94cf857c3746088cd01cee49242f24.json"}}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Skoglund", "given": "Lovisa", "initials": "L"}, {"family": "Yousef", "given": "Jamil", "initials": "J", "orcid": "0000-0001-5915-1258", "researcher": {"href": "https://publications.scilifelab.se/researcher/86be17c932614797a876bb55c7ce566e.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Christ", "given": "Wanda", "initials": "W", "orcid": "0000-0003-3886-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe3a44fdb547b885cce5b6f490b2bc.json"}}, {"family": "Olausson", "given": "Mikaela", "initials": "M"}, {"family": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Mangsbo", "given": "Sara", "initials": "S"}, {"family": "Phillipson", "given": "Mia", "initials": "M"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2022-01-12", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "17", "issue": "1", "pages": "e0262169", "issn-l": "1932-6203"}, "abstract": "Current SARS-CoV-2 serological assays generate discrepant results, and the longitudinal characteristics of antibodies targeting various antigens after asymptomatic to mild COVID-19 are yet to be established. This longitudinal cohort study including 1965 healthcare workers, of which 381 participants exhibited antibodies against the SARS-CoV-2 spike antigen at study inclusion, reveal that these antibodies remain detectable in most participants, 96%, at least four months post infection, despite having had no or mild symptoms. Virus neutralization capacity was confirmed by microneutralization assay in 91% of study participants at least four months post infection. Contrary to antibodies targeting the spike protein, antibodies against the nucleocapsid protein were only detected in 80% of previously anti-nucleocapsid IgG positive healthcare workers. Both anti-spike and anti-nucleocapsid IgG levels were significantly higher in previously hospitalized COVID-19 patients four months post infection than in healthcare workers four months post infection (p = 2*10-23 and 2*10-13 respectively). Although the magnitude of humoral response was associated with disease severity, our findings support a durable and functional humoral response after SARS-CoV-2 infection even after no or mild symptoms. We further demonstrate differences in antibody kinetics depending on the antigen, arguing against the use of the nucleocapsid protein as target antigen in population-based SARS-CoV-2 serological surveys.", "doi": "10.1371/journal.pone.0262169", "pmid": "35020778", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-21-27419"}], "notes": [], "created": "2022-01-14T08:23:14.930Z", "modified": "2022-01-14T08:23:15.078Z"}, {"entity": "publication", "iuid": "40debb001133430dacf91ed1b897a801", "links": {"self": {"href": "https://publications.scilifelab.se/publication/40debb001133430dacf91ed1b897a801.json"}, "display": {"href": "https://publications.scilifelab.se/publication/40debb001133430dacf91ed1b897a801"}}, "title": "Salivary IgG to SARS-CoV-2 indicates seroconversion and correlates to serum neutralization in mRNA-vaccinated immunocompromised individuals", "authors": [{"family": "Healy", "given": "Katie", "initials": "K"}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "S\u00f6derdahl", "given": "Gunnar", "initials": "G"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}, {"family": "Mielke", "given": "Stephan", "initials": "S", "orcid": "0000-0002-8325-9215", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbb6778eb9964f9cbd9ffc260892d609.json"}}, {"family": "Hansson", "given": "Lotta", "initials": "L"}, {"family": "Bergman", "given": "Peter", "initials": "P", "orcid": "0000-0003-3306-3713", "researcher": {"href": "https://publications.scilifelab.se/researcher/397d11713c80456bb600b1e4c88ff843.json"}}, {"family": "Smith", "given": "C I Edvard", "initials": "CIE"}, {"family": "Ljungman", "given": "Per", "initials": "P"}, {"family": "Valentini", "given": "Davide", "initials": "D"}, {"family": "Blennow", "given": "Ola", "initials": "O", "orcid": "0000-0002-7167-7882", "researcher": {"href": "https://publications.scilifelab.se/researcher/08ed03f808e84f50a0b599ce28b29d7d.json"}}, {"family": "\u00d6sterborg", "given": "Anders", "initials": "A"}, {"family": "Gabarrini", "given": "Giorgio", "initials": "G", "orcid": "0000-0001-6936-4919", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbb92481579b4a23afefbbed5ad59a9a.json"}}, {"family": "Al-Manei", "given": "Khaled", "initials": "K", "orcid": "0000-0003-0787-5849", "researcher": {"href": "https://publications.scilifelab.se/researcher/289ad83f90da43adb6634178107db3de.json"}}, {"family": "Alkharaan", "given": "Hassan", "initials": "H"}, {"family": "Sobkowiak", "given": "Michal Jacek", "initials": "MJ", "orcid": "0000-0003-2932-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/14f1eb990edf472cac56f24d7cae330c.json"}}, {"family": "Yousef", "given": "Jamil", "initials": "J"}, {"family": "Mravinacova", "given": "Sara", "initials": "S"}, {"family": "Cuapio", "given": "Angelica", "initials": "A"}, {"family": "Xu", "given": "Xinling", "initials": "X"}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K", "orcid": "0000-0001-7679-9494", "researcher": {"href": "https://publications.scilifelab.se/researcher/737245a5bc2144bd90be71487cbb3192.json"}}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Muschiol", "given": "Sandra", "initials": "S"}, {"family": "Bogdanovic", "given": "Gordana", "initials": "G"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Ljunggren", "given": "Hans Gustaf", "initials": "HG"}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Aleman", "given": "Soo", "initials": "S", "orcid": "0000-0003-0461-4870", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a125a916b34de985de977dd8384650.json"}}, {"family": "Chen", "given": "Margaret S\u00e4llberg", "initials": "MS"}], "type": "journal-article", "published": "2022-01-00", "journal": {"title": "Med", "issn": "2666-6340", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1016/j.medj.2022.01.001", "pmid": "35075450", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-01-26T08:48:19.747Z", "modified": "2022-01-26T08:51:23.010Z"}, {"entity": "publication", "iuid": "662e6300d57a45818e6a52bf43aa890a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/662e6300d57a45818e6a52bf43aa890a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/662e6300d57a45818e6a52bf43aa890a"}}, "title": "Robust humoral and cellular immune responses and low risk for reinfection at least 8 months following asymptomatic to mild COVID-19.", "authors": [{"family": "Havervall", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-1671-8183", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd194b3cef64f9f9341fd163a035235.json"}}, {"family": "Ng", "given": "Henry", "initials": "H", "orcid": "0000-0003-2873-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcb12c664a64724b5cd42a1267a5bea.json"}}, {"family": "Jernbom Falk", "given": "August", "initials": "A", "orcid": "0000-0002-7773-1851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe6400bde68b46899515cef5bea05fca.json"}}, {"family": "Greilert-Norin", "given": "Nina", "initials": "N", "orcid": "0000-0003-1492-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0c03be884e4ae8840d0e0d04c411dd.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d155273b5b54e61b773f263e4f2ce9b.json"}}, {"family": "Marking", "given": "Ulrika", "initials": "U"}, {"family": "Laur\u00e9n", "given": "Ida", "initials": "I"}, {"family": "Gabrielsson", "given": "Lena", "initials": "L"}, {"family": "Salomonsson", "given": "Ann-Christin", "initials": "AC"}, {"family": "Aguilera", "given": "Katherina", "initials": "K"}, {"family": "Kihlgren", "given": "Martha", "initials": "M"}, {"family": "M\u00e5nsson", "given": "Maja", "initials": "M"}, {"family": "Rosell", "given": "Axel", "initials": "A", "orcid": "0000-0001-6280-0562", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcddaba7a96a406b994756ab71427baf.json"}}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Olofsson", "given": "Jennie", "initials": "J", "orcid": "0000-0002-8593-9089", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2b59febdeec4df99bf3a0d5480df305.json"}}, {"family": "Skoglund", "given": "Lovisa", "initials": "L"}, {"family": "Yousef", "given": "Jamil", "initials": "J", "orcid": "0000-0001-5915-1258", "researcher": {"href": "https://publications.scilifelab.se/researcher/86be17c932614797a876bb55c7ce566e.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Lord", "given": "Martin", "initials": "M", "orcid": "0000-0002-3238-3187", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e14847c142f4c359f2d531601436897.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "D\u00f6nnes", "given": "Pierre", "initials": "P", "orcid": "0000-0002-4613-2952", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d32d60f9b547be8096c448fc013246.json"}}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Mangsbo", "given": "Sara", "initials": "S", "orcid": "0000-0002-1355-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/c743bbcad6554f049c8fc5f64a6801bc.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": "2022-01-00", "journal": {"title": "J. Intern. Med.", "issn": "1365-2796", "issn-l": "0954-6820", "volume": "291", "issue": "1", "pages": "72-80"}, "abstract": "Emerging data support detectable immune responses for months after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination, but it is not yet established to what degree and for how long protection against reinfection lasts.\n\nWe investigated SARS-CoV-2-specific humoral and cellular immune responses more than 8 months post-asymptomatic, mild and severe infection in a cohort of 1884 healthcare workers (HCW) and 51 hospitalized COVID-19 patients. Possible protection against SARS-CoV-2 reinfection was analyzed by a weekly 3-month polymerase chain reaction (PCR) screening of 252 HCW that had seroconverted 7 months prior to start of screening and 48 HCW that had remained seronegative at multiple time points.\n\nAll COVID-19 patients and 96% (355/370) of HCW who were anti-spike IgG positive at inclusion remained anti-spike IgG positive at the 8-month follow-up. Circulating SARS-CoV-2-specific memory T cell responses were detected in 88% (45/51) of COVID-19 patients and in 63% (233/370) of seropositive HCW. The cumulative incidence of PCR-confirmed SARS-CoV-2 infection was 1% (3/252) among anti-spike IgG positive HCW (0.13 cases per 100 weeks at risk) compared to 23% (11/48) among anti-spike IgG negative HCW (2.78 cases per 100 weeks at risk), resulting in a protective effect of 95.2% (95% CI 81.9%-99.1%).\n\nThe vast majority of anti-spike IgG positive individuals remain anti-spike IgG positive for at least 8 months regardless of initial COVID-19 disease severity. The presence of anti-spike IgG antibodies is associated with a substantially reduced risk of reinfection up to 9 months following asymptomatic to mild COVID-19.", "doi": "10.1111/joim.13387", "pmid": "34459525", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8661920"}], "notes": [], "created": "2021-08-31T10:38:04.811Z", "modified": "2022-12-02T10:46:29.165Z"}, {"entity": "publication", "iuid": "f71763d565f84b18be09dab6512e64ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f71763d565f84b18be09dab6512e64ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f71763d565f84b18be09dab6512e64ea"}}, "title": "Differences in risk for SARS-CoV-2 infection among healthcare workers.", "authors": [{"family": "Elfstr\u00f6m", "given": "K Miriam", "initials": "KM"}, {"family": "Blomqvist", "given": "Jonas", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Pimenoff", "given": "Ville N", "initials": "VN", "orcid": "0000-0002-0813-7031", "researcher": {"href": "https://publications.scilifelab.se/researcher/96cbbc36d7214b94a798b4c63eeb6a3a.json"}}, {"family": "Arroyo M\u00fchr", "given": "Laila Sara", "initials": "LS"}, {"family": "Lundgren", "given": "Kalle Conneryd", "initials": "KC"}, {"family": "Dillner", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Prev Med Rep", "issn": "2211-3355", "issn-l": null, "volume": "24", "issue": null, "pages": "101518"}, "abstract": "Healthcare workers (HCWs) are a risk group for SARS-CoV-2 infection, but which healthcare work that conveys risk and to what extent such risk can be prevented is not clear. Starting on April 24th, 2020, all employees at work (n = 15,300) at the Karolinska University Hospital, Stockholm, Sweden were invited and 92% consented to participate in a SARS-CoV-2 cohort study. Complete SARS-CoV-2 serology was available for n = 12,928 employees and seroprevalences were analyzed by age, sex, profession, patient contact, and hospital department. Relative risks were estimated to examine the association between type of hospital department as a proxy for different working environment exposure and risk for seropositivity, adjusting for age, sex, sampling week, and profession. Wards that were primarily responsible for COVID-19 patients were at increased risk (adjusted OR 1.95 (95% CI 1.65-2.32) with the notable exception of the infectious diseases and intensive care units (adjusted OR 0.86 (95% CI 0.66-1.13)), that were not at increased risk despite being highly exposed. Several units with similar types of work varied greatly in seroprevalences. Among the professions examined, nurse assistants had the highest risk (adjusted OR 1.62 (95% CI 1.38-1.90)). Although healthcare workers, in particular nurse assistants, who attend to COVID-19 patients are a risk group for SARS-CoV-2 infection, several units caring for COVID-19 patients had no excess risk. Large variations in seroprevalences among similar units suggest that healthcare work-related risk of SARS-CoV-2 infection may be preventable.", "doi": "10.1016/j.pmedr.2021.101518", "pmid": "34458081", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-3355(21)00208-4"}, {"db": "pmc", "key": "PMC8379088"}], "notes": [], "created": "2021-08-31T10:37:30.851Z", "modified": "2021-12-03T14:26:19.323Z"}, {"entity": "publication", "iuid": "21e4f30aade1496eb1c236fc2c632024", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21e4f30aade1496eb1c236fc2c632024.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21e4f30aade1496eb1c236fc2c632024"}}, "title": "Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health.", "authors": [{"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "James", "given": "Tojo", "initials": "T"}, {"family": "Karhu", "given": "Anu", "initials": "A"}, {"family": "Virtanen", "given": "Heidi", "initials": "H"}, {"family": "Kettunen", "given": "Kaisa", "initials": "K"}, {"family": "Stenlund", "given": "Hans", "initials": "H"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Mills", "given": "Robert", "initials": "R"}, {"family": "Perheentupa", "given": "Teemu", "initials": "T"}, {"family": "Laivuori", "given": "Hannele", "initials": "H"}, {"family": "Helkkula", "given": "Pyry", "initials": "P"}, {"family": "Byrne", "given": "Myles", "initials": "M"}, {"family": "Jokinen", "given": "Ilkka", "initials": "I"}, {"family": "Honko", "given": "Harri", "initials": "H"}, {"family": "Kallonen", "given": "Antti", "initials": "A"}, {"family": "Ermes", "given": "Miikka", "initials": "M"}, {"family": "Simil\u00e4", "given": "Heidi", "initials": "H"}, {"family": "Lindholm", "given": "Mikko", "initials": "M"}, {"family": "Wid\u00e9n", "given": "Elisabeth", "initials": "E"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Per\u00e4l\u00e4-Heape", "given": "Maritta", "initials": "M"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Moritz", "given": "Thomas", "initials": "T"}, {"family": "Miettinen", "given": "Timo", "initials": "T"}, {"family": "Sallinen", "given": "Riitta", "initials": "R"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}], "type": "journal article", "published": "2021-11-30", "journal": {"title": "Cell Syst", "issn": "2639-5460", "issn-l": "2405-4712"}, "abstract": "We explored opportunities for personalized and predictive health care by collecting serial clinical measurements, health surveys, genomics, proteomics, autoantibodies, metabolomics, and gut microbiome data from 96 individuals who participated in a data-driven health coaching program over a 16-month period with continuous digital monitoring of activity and sleep. We generated a resource of >20,000 biological samples from this study and a compendium of >53 million primary data points for 558,032 distinct features. Multiomics factor analysis revealed distinct and independent molecular factors linked to obesity, diabetes, liver function, cardiovascular disease, inflammation, immunity, exercise, diet, and hormonal effects. For example, ethinyl estradiol, a common oral contraceptive, produced characteristic molecular and physiological effects, including increased levels of inflammation and impact on thyroid, cortisol levels, and pulse, that were distinct from other sources of variability observed in our study. In total, this work illustrates the value of combining deep molecular and digital monitoring of human health. A record of this paper's transparent peer review process is included in the supplemental information.", "doi": "10.1016/j.cels.2021.11.001", "pmid": "34856119", "labels": {"Autoimmunity and Serology Profiling": "Service", "Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2405-4712(21)00451-8"}], "notes": [], "created": "2021-12-07T12:27:49.709Z", "modified": "2025-10-17T13:03:15.531Z"}, {"entity": "publication", "iuid": "74942a3c449d4077b680af0a5d959dea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74942a3c449d4077b680af0a5d959dea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74942a3c449d4077b680af0a5d959dea"}}, "title": "Safety and efficacy of the mRNA BNT162b2 vaccine against SARS-CoV-2 in five groups of immunocompromised patients and healthy controls in a prospective open-label clinical trial.", "authors": [{"family": "Bergman", "given": "Peter", "initials": "P"}, {"family": "Blennow", "given": "Ola", "initials": "O"}, {"family": "Hansson", "given": "Lotta", "initials": "L"}, {"family": "Mielke", "given": "Stephan", "initials": "S"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "S\u00f6derdahl", "given": "Gunnar", "initials": "G"}, {"family": "\u00d6sterborg", "given": "Anders", "initials": "A"}, {"family": "Smith", "given": "C I Edvard", "initials": "CIE"}, {"family": "Wullimann", "given": "David", "initials": "D"}, {"family": "Vesterbacka", "given": "Jan", "initials": "J"}, {"family": "Lindgren", "given": "Gustaf", "initials": "G"}, {"family": "Blixt", "given": "Lisa", "initials": "L"}, {"family": "Friman", "given": "Gustav", "initials": "G"}, {"family": "Wahren-Borgstr\u00f6m", "given": "Emilie", "initials": "E"}, {"family": "Nordlander", "given": "Anna", "initials": "A"}, {"family": "Gomez", "given": "Angelica Cuapio", "initials": "AC"}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Valentini", "given": "Davide", "initials": "D"}, {"family": "Norlin", "given": "Anna-Carin", "initials": "AC"}, {"family": "Thalme", "given": "Anders", "initials": "A"}, {"family": "Bogdanovic", "given": "Gordana", "initials": "G"}, {"family": "Muschiol", "given": "Sandra", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K"}, {"family": "Chen", "given": "Margaret S\u00e4llberg", "initials": "MS"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG"}, {"family": "Ljungman", "given": "Per", "initials": "P"}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "COVAXID-collaborator group (shown separately)", "given": "", "initials": ""}], "type": "journal article", "published": "2021-11-29", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "74", "pages": "103705", "issn-l": "2352-3964"}, "abstract": "Patients with immunocompromised disorders have mainly been excluded from clinical trials of vaccination against COVID-19. Thus, the aim of this prospective clinical trial was to investigate safety and efficacy of BNT162b2 mRNA vaccination in five selected groups of immunocompromised patients and healthy controls.\n\n539 study subjects (449 patients and 90 controls) were included. The patients had either primary (n=90), or secondary immunodeficiency disorders due to human immunodeficiency virus infection (n=90), allogeneic hematopoietic stem cell transplantation/CAR T cell therapy (n=90), solid organ transplantation (SOT) (n=89), or chronic lymphocytic leukemia (CLL) (n=90). The primary endpoint was seroconversion rate two weeks after the second dose. The secondary endpoints were safety and documented SARS-CoV-2 infection.\n\nAdverse events were generally mild, but one case of fatal suspected unexpected serious adverse reaction occurred. 72.2% of the immunocompromised patients seroconverted compared to 100% of the controls (p=0.004). Lowest seroconversion rates were found in the SOT (43.4%) and CLL (63.3%) patient groups with observed negative impact of treatment with mycophenolate mofetil and ibrutinib, respectively.\n\nThe results showed that the mRNA BNT162b2 vaccine was safe in immunocompromised patients. Rate of seroconversion was substantially lower than in healthy controls, with a wide range of rates and antibody titres among predefined patient groups and subgroups. This clinical trial highlights the need for additional vaccine doses in certain immunocompromised patient groups to improve immunity.\n\nKnut and Alice Wallenberg Foundation, the Swedish Research Council, Nordstjernan AB, Region Stockholm, Karolinska Institutet, and organizations for PID/CLL-patients in Sweden.", "doi": "10.1016/j.ebiom.2021.103705", "pmid": "34861491", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2352-3964(21)00499-0"}], "notes": [], "created": "2021-12-07T12:29:21.945Z", "modified": "2021-12-07T12:29:21.950Z"}, {"entity": "publication", "iuid": "8c8a0954f8e7418499ebb5efc5d2460f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c8a0954f8e7418499ebb5efc5d2460f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c8a0954f8e7418499ebb5efc5d2460f"}}, "title": "Multiomics Profiling of Alzheimer's Disease Serum for the Identification of Autoantibody Biomarkers.", "authors": [{"family": "San Segundo-Acosta", "given": "Pablo", "initials": "P"}, {"family": "Montero-Calle", "given": "Ana", "initials": "A"}, {"family": "Jernbom-Falk", "given": "August", "initials": "A", "orcid": "0000-0002-7773-1851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe6400bde68b46899515cef5bea05fca.json"}}, {"family": "Alonso-Navarro", "given": "Miren", "initials": "M"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "S\u00e1nchez-Mart\u00ednez", "given": "MariCruz", "initials": "M"}, {"family": "R\u00e1bano", "given": "Alberto", "initials": "A"}, {"family": "Sol\u00eds-Fern\u00e1ndez", "given": "Guillermo", "initials": "G"}, {"family": "Pel\u00e1ez-Garc\u00eda", "given": "Alberto", "initials": "A"}, {"family": "Mart\u00ednez-Useros", "given": "Javier", "initials": "J"}, {"family": "Fern\u00e1ndez-Ace\u00f1ero", "given": "Mar\u00eda Jes\u00fas", "initials": "MJ"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Barderas", "given": "Rodrigo", "initials": "R", "orcid": "0000-0003-3539-7469", "researcher": {"href": "https://publications.scilifelab.se/researcher/99cd10d411ea49a5bbeee8367fcce1b8.json"}}], "type": "journal article", "published": "2021-11-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "20", "issue": "11", "pages": "5115-5130", "issn-l": "1535-3893"}, "abstract": "New biomarkers of Alzheimer's disease (AD) with a diagnostic value in preclinical and prodromal stages are urgently needed. AD-related serum autoantibodies are potential candidate biomarkers. Here, we aimed at identifying AD-related serum autoantibodies using protein microarrays and mass spectrometry-based methods. To this end, an untargeted complementary screening using high-density (42,100 antigens) and low-density (384 antigens) planar protein-epitope signature tag (PrEST) arrays and an immunoprecipitation protocol coupled to mass spectrometry analysis were used for serum autoantibody profiling. From the untargeted screening phase, 377 antigens corresponding to 338 proteins were selected for validation. Out of them, IVD, CYFIP1, and ADD2 seroreactivity was validated using 128 sera from AD patients and controls by PrEST-suspension bead arrays, and ELISA or luminescence Halotag-based bead immunoassay using full-length recombinant proteins. Importantly, IVD, CYFIP1, and ADD2 showed in combination a noticeable AD diagnostic ability. Moreover, IVD protein abundance in the prefrontal cortex was significantly two-fold higher in AD patients than in controls by western blot and immunohistochemistry, whereas CYFIP1 and ADD2 were significantly down-regulated in AD patients. The panel of AD-related autoantigens identified by a comprehensive multiomics approach may provide new insights of the disease and should help in the blood-based diagnosis of Alzheimer's disease. Mass spectrometry raw data are available in the ProteomeXchange database with the access number PXD028392.", "doi": "10.1021/acs.jproteome.1c00630", "pmid": "34628858", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-11-09T06:20:50.146Z", "modified": "2021-11-10T12:21:31.532Z"}, {"entity": "publication", "iuid": "026de8bcc2504d949e7041d1ba43ddb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/026de8bcc2504d949e7041d1ba43ddb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/026de8bcc2504d949e7041d1ba43ddb8"}}, "title": "Risk of SARS-CoV-2 exposure among hospital healthcare workers in relation to patient contact and type of care.", "authors": [{"family": "Klevebro", "given": "Susanna", "initials": "S", "orcid": "0000-0002-1261-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cace10c20c847f6a04259937e74891e.json"}}, {"family": "Bahram", "given": "Fuad", "initials": "F"}, {"family": "Elfstr\u00f6m", "given": "K Miriam", "initials": "KM"}, {"family": "Hellberg", "given": "Ulrika", "initials": "U"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK"}, {"family": "Kull", "given": "Inger", "initials": "I"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Tornvall", "given": "Per", "initials": "P"}, {"family": "Wang", "given": "Gang", "initials": "G"}, {"family": "Conneryd Lundgren", "given": "Kalle", "initials": "K"}, {"family": "Ponzer", "given": "Sari", "initials": "S"}, {"family": "Dillner", "given": "Joakim", "initials": "J"}, {"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": "2021-11-00", "journal": {"title": "Scand J Public Health", "issn": "1651-1905", "pages": "707-712", "volume": "49", "issue": "7", "issn-l": null}, "abstract": "We aimed to assess prevalence of IgG antibodies to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and factors associated with seropositivity in a large cohort of healthcare workers (HCWs).\r\n\r\nFrom 11 May until 11 June 2020, 3981 HCWs at a large Swedish emergency care hospital provided serum samples and questionnaire data. Presence of IgG antibodies to SARS-CoV-2 was measured as an indicator of SARS-CoV-2 exposure.\r\n\r\nThe total seroprevalence was 18% and increased during the study period. Among the seropositive HCWs, 11% had been entirely asymptomatic. Participants who worked with COVID-19 patients had higher odds for seropositivity: adjusted odds ratio 1.96 (95% confidence intervals 1.59-2.42). HCWs from three of the departments managing COVID-19 patients had significantly higher seroprevalences, whereas the prevalence among HCWs from the intensive care unit (also managing COVID-19 patients) was significantly lower.\r\n\r\nHCWs in contact with SARS-CoV-2 infected patients had a variable, but on average higher, likelihood for SARS-CoV-2 infections.", "doi": "10.1177/14034948211022434", "pmid": "34148454", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8521364"}], "notes": [], "created": "2021-06-22T11:52:27.525Z", "modified": "2021-12-09T08:53:11.156Z"}, {"entity": "publication", "iuid": "dd873fd96ae643718c643fc7b4e6d2e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd873fd96ae643718c643fc7b4e6d2e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd873fd96ae643718c643fc7b4e6d2e9"}}, "title": "X-Linked TLR7 Deficiency Underlies Critical COVID-19 Pneumonia in a Male Patient with Ataxia-Telangiectasia.", "authors": [{"family": "Abolhassani", "given": "Hassan", "initials": "H"}, {"family": "Vosughimotlagh", "given": "Ahmad", "initials": "A"}, {"family": "Asano", "given": "Takaki", "initials": "T"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Boisson", "given": "Bertrand", "initials": "B"}, {"family": "Delavari", "given": "Samaneh", "initials": "S"}, {"family": "Bastard", "given": "Paul", "initials": "P"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M"}, {"family": "Wang", "given": "Yating", "initials": "Y"}, {"family": "Zuo", "given": "Fanglei", "initials": "F"}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Marcotte", "given": "Harold", "initials": "H"}, {"family": "Du", "given": "Likun", "initials": "L"}, {"family": "Zhang", "given": "Shen-Ying", "initials": "SY"}, {"family": "Zhang", "given": "Qian", "initials": "Q"}, {"family": "Rezaei", "given": "Nima", "initials": "N"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Casanova", "given": "Jean-Laurent", "initials": "JL"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Pan-Hammarstr\u00f6m", "given": "Qiang", "initials": "Q", "orcid": "0000-0003-1990-8804", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9d3baa27411425a8b8f63f3c3230964.json"}}], "type": "journal article", "published": "2021-10-23", "journal": {"title": "J Clin Immunol", "issn": "1573-2592", "issn-l": "0271-9142"}, "abstract": "Coronavirus disease 2019 (COVID-19) exhibits a wide spectrum of clinical manifestations, ranging from asymptomatic to critical conditions. Understanding the mechanism underlying life-threatening COVID-19 is instrumental for disease prevention and treatment in individuals with a high risk.\n\nWe aimed to identify the genetic cause for critical COVID-19 pneumonia in a patient with a preexisting inborn error of immunity (IEI).\n\nSerum levels of specific antibodies against the virus and autoantibodies against type I interferons (IFNs) were measured. Whole exome sequencing was performed, and the impacts of candidate gene variants were investigated. We also evaluated 247 ataxia-telangiectasia (A-T) patients in the Iranian IEI registry.\n\nWe report a 7-year-old Iranian boy with a preexisting hyper IgM syndrome who developed critical COVID-19 pneumonia. IgM only specific COVID-19 immune response was detected but no autoantibodies against type I IFN were observed. A homozygous deleterious mutation in the ATM gene was identified, which together with his antibody deficiency, radiosensitivity, and neurological signs, established a diagnosis of A-T. Among the 247 A-T patients evaluated, 36 had SARS-CoV-2 infection, but all had mild symptoms or were asymptomatic except the index patient. A hemizygous deleterious mutation in the TLR7 gene was subsequently identified in the patient.\n\nWe report a unique IEI patient with combined ATM and TLR7 deficiencies. The two genetic defects underlie A-T and critical COVID-19 in this patient, respectively.", "doi": "10.1007/s10875-021-01151-y", "pmid": "34686943", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s10875-021-01151-y"}, {"db": "pmc", "key": "PMC8536475"}], "notes": [], "created": "2021-11-08T12:54:06.187Z", "modified": "2021-11-10T12:21:37.499Z"}, {"entity": "publication", "iuid": "7d99cf0771284a35b64a21dd96e44e8f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d99cf0771284a35b64a21dd96e44e8f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d99cf0771284a35b64a21dd96e44e8f"}}, "title": "A cell-free high throughput assay for assessment of SARS-CoV-2 neutralizing antibodies.", "authors": [{"family": "Mravinacova", "given": "Sara", "initials": "S"}, {"family": "J\u00f6nsson", "given": "Malin", "initials": "M"}, {"family": "Christ", "given": "Wanda", "initials": "W"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Yousef", "given": "Jamil", "initials": "J"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Hober", "given": "Sophia", "initials": "S"}], "type": "journal article", "published": "2021-10-07", "journal": {"title": "N Biotechnol", "issn": "1876-4347", "volume": "66", "pages": "46-52", "issn-l": "1871-6784"}, "abstract": "Highly accurate serological tests are key to assessing the prevalence of SARS-CoV-2 antibodies and the level of immunity in the population. This is important to predict the current and future status of the pandemic. With the recent emergence of new and more infectious SARS-CoV-2 variants, assays allowing for high throughput analysis of antibodies able to neutralize SARS-CoV-2 become even more important. Here, we report the development and validation of a robust, high throughput method, which enables the assessment of antibodies inhibiting the binding between the SARS-CoV-2 spike protein and angiotensin converting enzyme 2 (ACE2). The assay uses recombinantly produced spike-f and ACE2 and is performed in a bead array format, which allows analysis of up to 384 samples in parallel per instrument over seven hours, demanding only one hour of manual handling. The method is compared to a microneutralization assay utilising live SARS-CoV-2 and is shown to deliver highly correlating data. Further, a comparison with a serological method that measures all antibodies recognizing the spike protein shows that this type of assessment provides important insights into the neutralizing efficiency of the antibodies, especially for individuals with low antibody levels. This method can be an important and valuable tool for large-scale assessment of antibody-based neutralization, including neutralization of new spike variants that might emerge.", "doi": "10.1016/j.nbt.2021.10.002", "pmid": "34628049", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(21)00091-1"}, {"db": "pmc", "key": "PMC8495044"}], "notes": [], "created": "2021-11-09T06:21:16.024Z", "modified": "2021-11-10T12:21:43.185Z"}, {"entity": "publication", "iuid": "34832c01dbff4e7394549cc3c1f7bc36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34832c01dbff4e7394549cc3c1f7bc36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34832c01dbff4e7394549cc3c1f7bc36"}}, "title": "An evaluation of a FluoroSpot assay as a diagnostic tool to determine SARS-CoV-2 specific T cell responses.", "authors": [{"family": "Mangsbo", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-1355-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/c743bbcad6554f049c8fc5f64a6801bc.json"}}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Laur\u00e9n", "given": "Ida", "initials": "I"}, {"family": "Lindsay", "given": "Robin", "initials": "R", "orcid": "0000-0001-7867-8653", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0be8216b4c14ad4a02ef037a61a32b3.json"}}, {"family": "Jernbom Falk", "given": "August", "initials": "A", "orcid": "0000-0002-7773-1851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe6400bde68b46899515cef5bea05fca.json"}}, {"family": "Marking", "given": "Ulrika", "initials": "U"}, {"family": "Lord", "given": "Martin", "initials": "M", "orcid": "0000-0002-3238-3187", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e14847c142f4c359f2d531601436897.json"}}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "D\u00f6nnes", "given": "Pierre", "initials": "P"}, {"family": "Christoffersson", "given": "Gustaf", "initials": "G"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Phillipson", "given": "Mia", "initials": "M"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "evaluation study", "published": "2021-09-30", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "16", "issue": "9", "pages": "e0258041", "issn-l": "1932-6203"}, "abstract": "Numerous assays evaluating serological and cellular responses have been developed to characterize immune responses against SARS-CoV-2. Serological assays are both cost- and time-effective compared to cellular assays, but cellular immune responses may provide a diagnostic value to determine previous SARS-CoV-2 infection in seronegative individuals. However, potential cross-reactive T cell responses stemming from prior encounters with human coronaviruses (HCoVs) may affect assay specificity. In this study, we evaluated the specificity and sensitivity of a SARS-CoV-2 IFN-\u03b3 Release Assay (IGRA) based on the FluoroSpot method employing commercially available SARS-CoV-2-specific peptide pools, as well as an in-house designed SARS-CoV-2 peptide pool restricted to 5 amino acid stretches or less aligning with endemic HCoVs. Blood samples were obtained from healthcare workers (HCW) 5-6 months post SARS-CoV-2 spike (S) IgG and nucleocapsid (N) IgG dual seroconversion (n = 187) and HCW who had been S IgG and N IgG dual seronegative at repeated occasions, including the current sampling time point (n = 102). In addition, samples were obtained 4 to 5 months post infection from 55 polymerase chain reaction (PCR)-confirmed COVID-19 patients. Assay specificity and sensitivity were calculated with serology as a reference standard for HCW. The in-house generated peptide pool displayed a specificity of 96.1%, while the commercially available peptide pools displayed specificities of 80.4% and 85.3%, respectively. Sensitivity was higher in a cohort of previously hospitalized COVID-19 patients (96.4% and 84.0% for the commercially available peptide pools and 92.7% for the in-house generated peptide pool) compared to the HCW cohort (92.0% and 66.8% for the commercially available peptide pools and 76.0% for the in-house generated peptide pool). Based on these findings, the individual diagnostic value of T cell immune responses against SARS-CoV-2 currently appears to be limited but remain an important research tool ahead.", "doi": "10.1371/journal.pone.0258041", "pmid": "34591918", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "PONE-D-21-19070"}, {"db": "pmc", "key": "PMC8483319"}], "notes": [], "created": "2021-11-09T06:21:46.471Z", "modified": "2021-11-10T12:21:51.168Z"}, {"entity": "publication", "iuid": "ff6107395ef8440ebc36c976bc2ec0dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff6107395ef8440ebc36c976bc2ec0dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff6107395ef8440ebc36c976bc2ec0dd"}}, "title": "Covid-19 in patients with chronic lymphocytic leukemia: clinical outcome and B- and T-cell immunity during 13 months in consecutive patients.", "authors": [{"family": "Blixt", "given": "Lisa", "initials": "L"}, {"family": "Bogdanovic", "given": "Gordana", "initials": "G"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Gao", "given": "Yu", "initials": "Y"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Healy", "given": "Katie", "initials": "K"}, {"family": "Johansson", "given": "Hemming", "initials": "H"}, {"family": "Kjellander", "given": "Christian", "initials": "C"}, {"family": "Mravinacova", "given": "Sara", "initials": "S", "orcid": "0000-0003-1848-910X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fd872e0772d43e1b6ab4c2a87306755.json"}}, {"family": "Muschiol", "given": "Sandra", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Palma", "given": "Marzia", "initials": "M", "orcid": "0000-0003-4287-3179", "researcher": {"href": "https://publications.scilifelab.se/researcher/f376e77de1a54c748b710baaa570cc7f.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Smith", "given": "C I Edvard", "initials": "CIE", "orcid": "0000-0003-1907-3392", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3ea998a87b44c218f91701cf3019af1.json"}}, {"family": "Stromberg", "given": "Olga", "initials": "O"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M", "orcid": "0000-0002-3793-4064", "researcher": {"href": "https://publications.scilifelab.se/researcher/af31e38e29a24d208df80184c563357f.json"}}, {"family": "Zain", "given": "Rula", "initials": "R", "orcid": "0000-0001-8327-846X", "researcher": {"href": "https://publications.scilifelab.se/researcher/debf02201d0b46d7a9b65dab9a29d55f.json"}}, {"family": "Hansson", "given": "Lotta", "initials": "L", "orcid": "0000-0001-6614-5737", "researcher": {"href": "https://publications.scilifelab.se/researcher/754f78f2a56143b4a3fe80294227f7ae.json"}}, {"family": "\u00d6sterborg", "given": "Anders", "initials": "A", "orcid": "0000-0001-6489-4865", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a1df5f584834eec8d7f90ab421a31ec.json"}}], "type": "journal article", "published": "2021-09-25", "journal": {"title": "Leukemia", "issn": "1476-5551", "issn-l": "0887-6924", "volume": null, "issue": null, "pages": null}, "abstract": "We studied clinical and immunological outcome of Covid-19 in consecutive CLL patients from a well-defined area during month 1-13 of the pandemic. Sixty patients (median age 71 y, range 43-97) were identified. Median CIRS was eight (4-20). Patients had indolent CLL (n = 38), had completed (n = 12) or ongoing therapy (n = 10). Forty-six patients (77%) were hospitalized due to severe Covid-19 and 11 were admitted to ICU. Severe Covid-19 was equally distributed across subgroups irrespective of age, gender, BMI, CLL status except CIRS (p < 0.05). Fourteen patients (23%) died; age \u226575 y was the only significant risk factor (p < 0.05, multivariate analysis with limited power). Comparing month 1-6 vs 7-13 of the pandemic, deaths were numerically reduced from 32% to 18%, ICU admission from 37% to 15% whereas hospitalizations remained frequent (86% vs 71%). Seroconversion occurred in 33/40 patients (82%) and anti-SARS-CoV-2 antibodies were detectable at six and 12 months in 17/22 and 8/11 patients, respectively. Most (13/17) had neutralizing antibodies and 19/28 had antibodies in saliva. SARS-CoV-2-specific T-cells (ELISpot) were detected in 14/17 patients. Covid-19 continued to result in high admission even among consecutive and young early- stage CLL patients. A robust and durable B and/or T cell immunity was observed in most convalescents.", "doi": "10.1038/s41375-021-01424-w", "pmid": "34564699", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41375-021-01424-w"}, {"db": "pmc", "key": "PMC8475381"}], "notes": [], "created": "2021-09-27T10:49:23.183Z", "modified": "2021-12-09T13:48:57.010Z"}, {"entity": "publication", "iuid": "7fb644cfeba54e11b4880535c18e290d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fb644cfeba54e11b4880535c18e290d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fb644cfeba54e11b4880535c18e290d"}}, "title": "Development of humoral and cellular immunological memory against SARS-CoV-2 despite B cell depleting treatment in multiple sclerosis.", "authors": [{"family": "Asplund H\u00f6gelin", "given": "Klara", "initials": "K"}, {"family": "Ruffin", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3698-5505", "researcher": {"href": "https://publications.scilifelab.se/researcher/991af3c2719f4c0b9d4feeae24c5161a.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Gafvelin", "given": "Guro", "initials": "G"}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Piehl", "given": "Fredrik", "initials": "F"}, {"family": "Al Nimer", "given": "Faiez", "initials": "F"}], "type": "journal article", "published": "2021-09-24", "journal": {"title": "iScience", "issn": "2589-0042", "pages": "103078", "volume": "24", "issue": "9", "issn-l": "2589-0042"}, "abstract": "B cell depleting therapies (BCDTs) are widely used as immunomodulating agents for autoimmune diseases such as multiple sclerosis. Their possible impact on development of immunity to severe acute respiratory syndrome virus-2 (SARS-CoV-2) has raised concerns with the coronavirus disease 2019 (COVID-19) pandemic. We here evaluated the frequency of COVID-19-like symptoms and determined immunological responses in participants of an observational trial comprising several multiple sclerosis disease modulatory drugs (COMBAT-MS; NCT03193866) and in eleven patients after vaccination, with a focus on BCDT. Almost all seropositive and 17.9% of seronegative patients on BCDT, enriched for a history of COVID-19-like symptoms, developed anti-SARS-CoV-2 T cell memory, and T cells displayed functional similarity to controls producing IFN-\u03b3 and TNF. Following vaccination, vaccine-specific humoral memory was impaired, while all patients developed a specific T cell response. These results indicate that BCDTs do not abrogate SARS-CoV-2 cellular memory and provide a possible explanation as to why the majority of patients on BCDTs recover from COVID-19.", "doi": "10.1016/j.isci.2021.103078", "pmid": "34490414", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2589-0042(21)01046-4"}, {"db": "pmc", "key": "PMC8410640"}], "notes": [], "created": "2021-09-08T10:30:28.258Z", "modified": "2021-11-10T12:22:14.144Z"}, {"entity": "publication", "iuid": "1d1abfbe6bf14f89a16e62a59302a18f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d1abfbe6bf14f89a16e62a59302a18f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d1abfbe6bf14f89a16e62a59302a18f"}}, "title": "Autoantibody profiles associated with clinical features in psychotic disorders.", "authors": [{"family": "Jernbom Falk", "given": "August", "initials": "A", "orcid": "0000-0002-7773-1851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe6400bde68b46899515cef5bea05fca.json"}}, {"family": "Galletly", "given": "Cherrie", "initials": "C", "orcid": "0000-0001-6185-9677", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadd383f017b42378128e92766c3d451.json"}}, {"family": "Just", "given": "David", "initials": "D", "orcid": "0000-0001-6126-2256", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f687d3a9cf4400932c75510807c764.json"}}, {"family": "Toben", "given": "Catherine", "initials": "C"}, {"family": "Baune", "given": "Bernhard T", "initials": "BT"}, {"family": "Clark", "given": "Scott R", "initials": "SR", "orcid": "0000-0003-1640-5611", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d99798c02a2436ea76de86f381750b4.json"}}, {"family": "Liu", "given": "Dennis", "initials": "D"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d155273b5b54e61b773f263e4f2ce9b.json"}}, {"family": "Schubert", "given": "K Oliver", "initials": "KO", "orcid": "0000-0003-1690-0209", "researcher": {"href": "https://publications.scilifelab.se/researcher/740bdd06c28b47f9bfcc37a1e3e084bf.json"}}], "type": "journal article", "published": "2021-09-13", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "issn-l": "2158-3188", "volume": "11", "issue": "1", "pages": "474"}, "abstract": "Autoimmune processes are suspected to play a role in the pathophysiology of psychotic disorders. Better understanding of the associations between auto-immunoglobulin G (IgG) repertoires and clinical features of mental illness could yield novel models of the pathophysiology of psychosis, and markers for biological patient stratification. We undertook cross-sectional detection and quantification of auto-IgGs in peripheral blood plasma of 461 people (39% females) with established psychotic disorder diagnoses. Broad screening of 24 individuals was carried out on group level in eight clinically defined groups using planar protein microarrays containing 42,100 human antigens representing 18,914 proteins. Autoantibodies indicated by broad screening and in the previous literature were measured using a 380-plex bead-based array for autoantibody profiling of all 461 individuals. Associations between autoantibody profiles and dichotomized clinical characteristics were assessed using a stepwise selection procedure. Broad screening and follow-up targeted analyses revealed highly individual autoantibody profiles. Females, and people with family histories of obesity or of psychiatric disorders other than schizophrenia had the highest overall autoantibody counts. People who had experienced subjective thought disorder and/or were treated with clozapine (trend) had the lowest overall counts. Furthermore, six autoantibodies were associated with specific psychopathology symptoms: anti-AP3B2 (persecutory delusions), anti-TDO2 (hallucinations), anti-CRYGN (initial insomnia); anti-APMAP (poor appetite), anti-OLFM1 (above-median cognitive function), and anti-WHAMMP3 (anhedonia and dysphoria). Future studies should clarify whether there are causal biological relationships, and whether autoantibodies could be used as clinical markers to inform diagnostic patient stratification and choice of treatment.", "doi": "10.1038/s41398-021-01596-0", "pmid": "34518517", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-021-01596-0"}, {"db": "pmc", "key": "PMC8438048"}], "notes": [], "created": "2021-09-15T10:19:31.008Z", "modified": "2021-12-09T13:48:43.908Z"}, {"entity": "publication", "iuid": "b6d27f8c7d2c449ca75863e2f4bec72f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6d27f8c7d2c449ca75863e2f4bec72f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6d27f8c7d2c449ca75863e2f4bec72f"}}, "title": "Increased antibody reactivity against insulin receptor-A and insulin like growth factor 1 receptor and their ligands in cerebrospinal fluid and serum of patients with schizophrenia or related psychosis.", "authors": [{"family": "Melkersson", "given": "Kristina", "initials": "K"}, {"family": "Bensing", "given": "Sophie", "initials": "S", "orcid": "0000-0002-9193-2860", "researcher": {"href": "https://publications.scilifelab.se/researcher/acae2ad8ca844588b2b850c863034b7b.json"}}], "type": "journal article", "published": "2021-09-10", "journal": {"title": "Neuro Endocrinol. Lett.", "issn": "2354-4716", "issn-l": "0172-780X", "volume": "42", "issue": "5", "pages": "339-358"}, "abstract": "Evidence has accumulated that an autoimmune-mediated process in the central nervous system may underlie the development of schizophrenia. Various antibodies have also previously been detected in serum of patients with schizophrenia. Therefore, the aim of this study was to analyze antibody reactivity against proteins, selected based on potential schizophrenia disease relevance, in both cerebrospinal fluid and serum of patients with schizophrenia.\r\n\r\nCerebrospinal fluid and serum from 17 patients with schizophrenia or related psychosis and 12 controls were analyzed regarding antibody reactivity, using bead-based antigen arrays of protein fragments or peptides of 21 selected proteins. Additionally, the patients were accessed for clinical symptoms with the Positive and Negative Syndrome Scale (PANSS) for schizophrenia.\r\n\r\nIncreased antibody reactivity was found in patients compared to controls against the insulin receptor (INSR), PAGE2B;2;5 and heat shock proteins (HSPs) in both cerebrospinal fluid and serum, and against the insulin like growth factor 1 receptor (IGF1R), insulin (INS), insulin like growth factor 1 (IGF1), cadherin 5 (CDH5), nerve growth factor (NGF) and vascular endothelial growth factor A (VEGFA) in serum alone. Moreover, patients' antibody reactivity in serum against PAGE2B;2;5, IGF1R or NGF correlated positively to their PANSS scores.\r\n\r\nTaken together, these results point to that an autoimmune-mediated process underlies the development of a core group of schizophrenia cases and that the INSR and IGF1R, their ligands (INS and IGF1) and related inter- and intracellular proteins (CDH5, PAGE2B;2;5, HSPs, NGF and VEGFA) may constitute antigen targets.", "doi": null, "pmid": "34506098", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "NEL420521A09"}], "notes": [], "created": "2021-12-01T08:57:34.170Z", "modified": "2025-11-17T10:02:08.406Z"}, {"entity": "publication", "iuid": "49f178b8e80b4b5fa88aeada66e2e92e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49f178b8e80b4b5fa88aeada66e2e92e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49f178b8e80b4b5fa88aeada66e2e92e"}}, "title": "Immunoglobulin A Autoreactivity toward Brain Enriched and Apoptosis-Regulating Proteins in Saliva of Athletes after Acute Concussion and Subconcussive Impacts.", "authors": [{"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Petricoin", "given": "Emanuel F", "initials": "EF"}, {"family": "Cortes", "given": "Nelson", "initials": "N"}, {"family": "Bowman", "given": "Thomas G", "initials": "TG"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"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": "Caswell", "given": "Shane V", "initials": "SV"}], "type": "journal article", "published": "2021-09-01", "journal": {"title": "J. Neurotrauma", "issn": "1557-9042", "volume": "38", "issue": "17", "pages": "2373-2383", "issn-l": "0897-7151"}, "abstract": "The diagnosis and management of concussion is hindered by its diverse clinical presentation and assessment tools reliant on subjectively experienced symptoms. The biomechanical threshold of concussion is also not well understood, and asymptomatic concussion or \"subconcussive impacts\" of variable magnitudes are common in contact sports. Concerns have risen because athletes returning to activity too soon have an increased risk of prolonged recovery or long-term adverse health consequences. To date, little is understood on a molecular level regarding concussion and subconcussive impacts. Recent research suggests that neuroinflammatory mechanisms may serve an important role subsequent to concussion and possibly to subconcussive impacts. These studies suggest that autoantibodies may be a valuable tool for detection of acute concussion and monitoring for changes caused by cumulative exposure to subconcussive impacts. Hence, we aimed to profile the immunoglobulin (Ig)A autoantibody repertoire in saliva by screening a unique sport-related head trauma biobank. Saliva samples (n = 167) were donated by male and female participants enrolled in either the concussion (24-48 h post-injury) or subconcussion (non-concussed participants having moderate or high cumulative subconcussive impact exposure) cohorts. Study design included discovery and verification phases. Discovery aimed to identify new candidate autoimmune targets of IgA. Verification tested whether concussion and subconcussion cohorts increased IgA reactivity and whether cohorts showed similarities. The results show a significant increase in the prevalence of IgA toward protein fragments representing 5-hydroxytryptamine receptor 1A (HTR1A), serine/arginine repetitive matrix 4 (SRRM4) and FAS (tumor necrosis factor receptor superfamily member 6) after concussion and subconcussion. These results may suggest that concussion and subconcussion induce similar physiological effects, especially in terms of immune response. Our study demonstrates that saliva is a potential biofluid for autoantibody detection in concussion and subconcussion. After rigorous confirmation in much larger independent study sets, a validated salivary autoantibody assay could provide a non-subjective quantitative means of assessing concussive and subconcussive events.", "doi": "10.1089/neu.2020.7375", "pmid": "33858214", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-04-17T20:45:31.849Z", "modified": "2021-11-10T12:24:41.204Z"}, {"entity": "publication", "iuid": "b1bbc99bd90b49fba5442516412ee4c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1bbc99bd90b49fba5442516412ee4c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1bbc99bd90b49fba5442516412ee4c0"}}, "title": "Persisting Salivary IgG Against SARS-CoV-2 at 9 Months After Mild COVID-19: A Complementary Approach to Population Surveys.", "authors": [{"family": "Alkharaan", "given": "Hassan", "initials": "H"}, {"family": "Bayati", "given": "Shaghayegh", "initials": "S"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "Olsson", "given": "Annika", "initials": "A"}, {"family": "Lindahl", "given": "Karin", "initials": "K"}, {"family": "Bogdanovic", "given": "Gordana", "initials": "G"}, {"family": "Healy", "given": "Katie", "initials": "K"}, {"family": "Tsilingaridis", "given": "Georgios", "initials": "G"}, {"family": "De Palma", "given": "Patricia", "initials": "P"}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "M\u00e5nberg", "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": "Pin", "given": "Elisa", "initials": "E"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M", "orcid": "0000-0002-3793-4064", "researcher": {"href": "https://publications.scilifelab.se/researcher/af31e38e29a24d208df80184c563357f.json"}}], "type": "journal article", "published": "2021-08-02", "journal": {"title": "J. Infect. Dis.", "issn": "1537-6613", "issn-l": "0022-1899", "volume": "224", "issue": "3", "pages": "407-414"}, "abstract": "Declining humoral immunity in coronavirus disease 2019 (COVID-19) patients and possible reinfection have raised concern. Mucosal immunity, particularly salivary antibodies, may be short lived although long-term studies are lacking.\n\nUsing a multiplex bead-based array platform, we investigated antibodies specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins in 256 saliva samples from convalescent patients 1-9 months after symptomatic COVID-19 (n = 74, cohort 1), undiagnosed individuals with self-reported questionnaires (n = 147, cohort 2), and individuals sampled prepandemic (n = 35, cohort 3).\n\nSalivary IgG antibody responses in cohort 1 (mainly mild COVID-19) were detectable up to 9 months postrecovery, with high correlations between spike and nucleocapsid specificity. At 9 months, IgG remained in blood and saliva in most patients. Salivary IgA was rarely detected at this time point. In cohort 2, salivary IgG and IgA responses were significantly associated with recent history of COVID-19-like symptoms. Salivary IgG tolerated temperature and detergent pretreatments.\n\nUnlike SARS-CoV-2 salivary IgA that appeared short lived, specific saliva IgG appeared stable even after mild COVID-19, as for blood serology. This noninvasive saliva-based SARS-CoV-2 antibody test with home self-collection may be a complementary alternative to conventional blood serology.", "doi": "10.1093/infdis/jiab256", "pmid": "33978762", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6274637"}, {"db": "pmc", "key": "PMC8244549"}], "notes": [], "created": "2021-05-18T10:20:22.106Z", "modified": "2021-11-10T12:24:53.416Z"}, {"entity": "publication", "iuid": "d6aab70d22e14fdb8abd33c99edee34e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6aab70d22e14fdb8abd33c99edee34e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6aab70d22e14fdb8abd33c99edee34e"}}, "title": "SARS-CoV-2 infections amongst personnel providing home care services for older persons in Stockholm, Sweden.", "authors": [{"family": "Hassan", "given": "S S", "initials": "SS"}, {"family": "Seigerud", "given": "\u00c5", "initials": "\u00c5"}, {"family": "Abdirahman", "given": "R", "initials": "R"}, {"family": "Arroyo M\u00fchr", "given": "L S", "initials": "LS"}, {"family": "Nordqvist Kleppe", "given": "S", "initials": "S"}, {"family": "Pin", "given": "E", "initials": "E"}, {"family": "M\u00e5nberg", "given": "A", "initials": "A"}, {"family": "Hober", "given": "S", "initials": "S"}, {"family": "Nilsson", "given": "P", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Engstrand", "given": "L", "initials": "L"}, {"family": "Miriam Elfstr\u00f6m", "given": "K", "initials": "K"}, {"family": "Blomqvist", "given": "J", "initials": "J"}, {"family": "Conneryd Lundgren", "given": "K", "initials": "K"}, {"family": "Dillner", "given": "J", "initials": "J", "orcid": "0000-0001-8588-6506", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b5c258635ad412f9e79994dcee4e323.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "J. Intern. Med.", "issn": "1365-2796", "volume": "290", "issue": "2", "pages": "430-436", "issn-l": "0954-6820"}, "abstract": "In Sweden, home care services is a major external contact for older persons.\n\nFive home care service companies in Stockholm, Sweden, enrolled 405 employees to a study including serum IgG to SARS-CoV-2 and SARS-CoV-2 virus in throat swabs.\n\n20.1% (81/403) of employees were seropositive, about twice as many as in a simultaneously enrolled reference population (healthcare workers entirely without patient contact, n = 3671; 9.7% seropositivity). 13/379 employees (3.4%) had a current infection (PCR positivity). Amongst these, 5 were also seropositive and 3 were positive with low amounts of virus. High amounts of virus and no antibodies (a characteristic for presymptomatic COVID-19) were present in 5 employees (1.3%).\n\nPersonnel providing home services for older persons appear to be a risk group for SARS-CoV-2. Likely presymptomatic employees can be readily identified by screening. Increased protection of employees and of the older persons they serve is warranted.", "doi": "10.1111/joim.13274", "pmid": "33843090", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8250663"}], "notes": [], "created": "2021-04-13T10:22:39.926Z", "modified": "2021-11-10T12:25:49.835Z"}, {"entity": "publication", "iuid": "92a25ccfb56c4600b8ba78521ed05f2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92a25ccfb56c4600b8ba78521ed05f2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92a25ccfb56c4600b8ba78521ed05f2c"}}, "title": "Antibody responses after a single dose of ChAdOx1 nCoV-19 vaccine in healthcare workers previously infected with SARS-CoV-2.", "authors": [{"family": "Havervall", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-1671-8183", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd194b3cef64f9f9341fd163a035235.json"}}, {"family": "Marking", "given": "Ulrika", "initials": "U"}, {"family": "Greilert-Norin", "given": "Nina", "initials": "N"}, {"family": "Ng", "given": "Henry", "initials": "H", "orcid": "0000-0003-2873-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcb12c664a64724b5cd42a1267a5bea.json"}}, {"family": "Gordon", "given": "Max", "initials": "M"}, {"family": "Salomonsson", "given": "Ann-Christin", "initials": "AC"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Blom", "given": "Kim", "initials": "K"}, {"family": "Mangsbo", "given": "Sara", "initials": "S"}, {"family": "Phillipson", "given": "Mia", "initials": "M"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"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": "2021-08-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "70", "pages": "103523", "issn-l": "2352-3964"}, "abstract": "Recent reports demonstrate robust serological responses to a single dose of messenger RNA (mRNA) vaccines in individuals previously infected with SARS-CoV-2. Data on immune responses following a single-dose adenovirus-vectored vaccine expressing the SARS-CoV-2 spike protein (ChAdOx1 nCoV-19) in individuals with previous SARS-CoV-2 infection are however limited, and current guidelines recommend a two-dose regimen regardless of preexisting immunity.\n\nWe compared RBD-specific IgG and RBD-ACE2 blocking antibodies against SARS-CoV-2 wild type and variants of concern following two doses of the mRNA vaccine BNT162b2 in SARS-CoV-2 na\u00efve healthcare workers (n=65) and a single dose of the adenovector vaccine ChAdOx1 nCoV-19 in 82 healthcare workers more than (n=45) and less than (n=37) 11 months post mild SARS-CoV-2 infection at time of vaccination.\n\nThe post-vaccine levels of RBD-specific IgG and neutralizing antibodies against the SARS-CoV-2 wild type and variants of concern including Delta lineage 1.617.2 were similar or higher in participants receiving a single dose of ChAdOx1 nCoV-19 vaccine post SARS-CoV-2 infection (both more than and less than 11 months post infection) compared to SARS-CoV-2 na\u00efve participants who received two doses of BNT162b2 vaccine.\n\nOur data support that a single dose ChAdOx1 nCoV-19 vaccine that is administered up to at least 11 months post SARS-CoV-2 infection serves as an effective immune booster. This provides a possible rationale for a single-dose vaccine regimen.\n\nA full list of funding bodies that contributed to this study can be found in the Acknowledgements section.", "doi": "10.1016/j.ebiom.2021.103523", "pmid": "34391088", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2352-3964(21)00316-9"}, {"db": "pmc", "key": "PMC8357428"}], "notes": [], "created": "2021-08-15T21:19:37.358Z", "modified": "2021-12-10T10:31:23.212Z"}, {"entity": "publication", "iuid": "9d0f9b6ced5447dfab67df3380c65330", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d0f9b6ced5447dfab67df3380c65330.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d0f9b6ced5447dfab67df3380c65330"}}, "title": "Systematic evaluation of SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay.", "authors": [{"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Olofsson", "given": "Jennie", "initials": "J", "orcid": "0000-0002-8593-9089", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2b59febdeec4df99bf3a0d5480df305.json"}}, {"family": "Andersson", "given": "Eni", "initials": "E", "orcid": "0000-0002-5115-0637", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef94cf857c3746088cd01cee49242f24.json"}}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/648c9ed3483a4eb8a1d228cf7e59f6a7.json"}}, {"family": "Jernbom Falk", "given": "August", "initials": "A", "orcid": "0000-0002-7773-1851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe6400bde68b46899515cef5bea05fca.json"}}, {"family": "Bayati", "given": "Shaghayegh", "initials": "S"}, {"family": "Mravinacova", "given": "Sara", "initials": "S"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Yousef", "given": "Jamil", "initials": "J", "orcid": "0000-0001-5915-1258", "researcher": {"href": "https://publications.scilifelab.se/researcher/86be17c932614797a876bb55c7ce566e.json"}}, {"family": "Skoglund", "given": "Lovisa", "initials": "L"}, {"family": "Kanje", "given": "Sara", "initials": "S"}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Jensen", "given": "Gabriella", "initials": "G"}, {"family": "Enstedt", "given": "Henric", "initials": "H"}, {"family": "Afshari", "given": "Delaram", "initials": "D"}, {"family": "Xu", "given": "Lan Lan", "initials": "LL"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Hanke", "given": "Leo", "initials": "L"}, {"family": "Murrell", "given": "Ben", "initials": "B"}, {"family": "McInerney", "given": "Gerald", "initials": "G"}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB"}, {"family": "Lendel", "given": "Christofer", "initials": "C"}, {"family": "Roth", "given": "Robert G", "initials": "RG"}, {"family": "Skoog", "given": "Ingmar", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Fogdell-Hahn", "given": "Anna", "initials": "A"}, {"family": "Lindroth", "given": "Ylva", "initials": "Y"}, {"family": "Lundgren", "given": "Maria", "initials": "M"}, {"family": "Maleki", "given": "Kimia T", "initials": "KT"}, {"family": "Lagerqvist", "given": "Nina", "initials": "N"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Da Silva Rodrigues", "given": "Rui", "initials": "R"}, {"family": "Muschiol", "given": "Sandra", "initials": "S"}, {"family": "Bogdanovic", "given": "Gordana", "initials": "G"}, {"family": "Arroyo M\u00fchr", "given": "Laila Sara", "initials": "LS"}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Lagheden", "given": "Camilla", "initials": "C"}, {"family": "Dillner", "given": "Joakim", "initials": "J"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Havervall", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-1671-8183", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd194b3cef64f9f9341fd163a035235.json"}}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-1345-6491", "researcher": {"href": "https://publications.scilifelab.se/researcher/130fb6ef6b774613a767e98f9f9b2eb4.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d155273b5b54e61b773f263e4f2ce9b.json"}}, {"family": "Hedhammar", "given": "My", "initials": "M", "orcid": "0000-0003-0140-419X", "researcher": {"href": "https://publications.scilifelab.se/researcher/061cceecaf0e4bed8efabca146e5b235.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": "2021-07-19", "journal": {"title": "Clin Transl Immunology", "issn": "2050-0068", "volume": "10", "issue": "7", "pages": "e1312", "issn-l": null}, "abstract": "The COVID-19 pandemic poses an immense need for accurate, sensitive and high-throughput clinical tests, and serological assays are needed for both overarching epidemiological studies and evaluating vaccines. Here, we present the development and validation of a high-throughput multiplex bead-based serological assay.\n\nMore than 100 representations of SARS-CoV-2 proteins were included for initial evaluation, including antigens produced in bacterial and mammalian hosts as well as synthetic peptides. The five best-performing antigens, three representing the spike glycoprotein and two representing the nucleocapsid protein, were further evaluated for detection of IgG antibodies in samples from 331 COVID-19 patients and convalescents, and in 2090 negative controls sampled before 2020.\n\nThree antigens were finally selected, represented by a soluble trimeric form and the S1-domain of the spike glycoprotein as well as by the C-terminal domain of the nucleocapsid. The sensitivity for these three antigens individually was found to be 99.7%, 99.1% and 99.7%, and the specificity was found to be 98.1%, 98.7% and 95.7%. The best assay performance was although achieved when utilising two antigens in combination, enabling a sensitivity of up to 99.7% combined with a specificity of 100%. Requiring any two of the three antigens resulted in a sensitivity of 99.7% and a specificity of 99.4%.\n\nThese observations demonstrate that a serological test based on a combination of several SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay.", "doi": "10.1002/cti2.1312", "pmid": "34295471", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "CTI21312"}, {"db": "pmc", "key": "PMC8288725"}], "notes": [], "created": "2021-07-25T21:30:22.465Z", "modified": "2021-11-10T12:23:19.192Z"}, {"entity": "publication", "iuid": "9ece3f643ded46e68cafc8c075b59335", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ece3f643ded46e68cafc8c075b59335.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ece3f643ded46e68cafc8c075b59335"}}, "title": "High Amounts of SARS-CoV-2 Precede Sickness Among Asymptomatic Health Care Workers.", "authors": [{"family": "Dillner", "given": "Joakim", "initials": "J"}, {"family": "Elfstr\u00f6m", "given": "K Miriam", "initials": "KM"}, {"family": "Blomqvist", "given": "Jonas", "initials": "J"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Lagheden", "given": "Camilla", "initials": "C"}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "Nordqvist-Kleppe", "given": "Sara", "initials": "S"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Falk", "given": "August Jernbom", "initials": "AJ"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Hultin", "given": "Emilie", "initials": "E"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Pimenoff", "given": "Ville N", "initials": "VN"}, {"family": "Hassan", "given": "Sadaf", "initials": "S"}, {"family": "M\u00e5nberg", "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": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Mattsson", "given": "Johan", "initials": "J"}, {"family": "Arroyo M\u00fchr", "given": "Laila Sara", "initials": "LS"}, {"family": "Lundgren", "given": "Kalle Conneryd", "initials": "KC"}], "type": "journal article", "published": "2021-07-02", "journal": {"title": "J. Infect. Dis.", "issn": "1537-6613", "volume": "224", "issue": "1", "pages": "14-20", "issn-l": "0022-1899"}, "abstract": "Whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity among asymptomatic subjects reflects past or future disease may be difficult to ascertain.\n\nWe tested 9449 employees at Karolinska University Hospital, Stockholm, Sweden for SARS-CoV-2 RNA and antibodies, linked the results to sick leave records, and determined associations with past or future sick leave using multinomial logistic regression.\n\nSubjects with high amounts of SARS-CoV-2 virus, indicated by polymerase chain reaction (PCR) cycle threshold (Ct) value, had the highest risk for sick leave in the 2 weeks after testing (odds ratio [OR], 11.97; 95% confidence interval [CI], 6.29-22.80) whereas subjects with low amounts of virus had the highest risk for sick leave in the 3 weeks before testing (OR, 6.31; 95% CI, 4.38-9.08). Only 2.5% of employees were SARS-CoV-2 positive while 10.5% were positive by serology and 1.2% were positive in both tests. Serology-positive subjects were not at excess risk for future sick leave (OR, 1.06; 95% CI, .71-1.57).\n\nHigh amounts of SARS-CoV-2 virus, as determined using PCR Ct values, was associated with development of sickness in the next few weeks. Results support the concept that PCR Ct may be informative when testing for SARS-CoV-2. Clinical Trials Registration. NCT04411576.", "doi": "10.1093/infdis/jiab099", "pmid": "33580261", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "6134453"}, {"db": "pmc", "key": "PMC7928785"}, {"db": "ClinicalTrials.gov", "key": "NCT04411576"}], "notes": [], "created": "2021-02-14T17:57:35.852Z", "modified": "2021-11-10T12:26:59.324Z"}, {"entity": "publication", "iuid": "e430feac4bdd43b18fefd962d8122973", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e430feac4bdd43b18fefd962d8122973.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e430feac4bdd43b18fefd962d8122973"}}, "title": "Severe COVID-19 in an APS1 patient with interferon autoantibodies treated with plasmapheresis", "authors": [{"family": "Lemarquis", "given": "Andri", "initials": "A", "orcid": "0000-0001-5165-0247", "researcher": {"href": "https://publications.scilifelab.se/researcher/776e9a2ecebf446ba4d0e3d20c8d793c.json"}}, {"family": "Campbell", "given": "Tessa", "initials": "T", "orcid": "0000-0002-7737-2123", "researcher": {"href": "https://publications.scilifelab.se/researcher/649b3cbdbb894026ba87a79e6834e651.json"}}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M", "orcid": "0000-0003-0050-704X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65dc88b917274bc595daed855b63abab.json"}}, {"family": "Hennings", "given": "Viktoria", "initials": "V"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}, {"family": "Blennow", "given": "Kaj", "initials": "K", "orcid": "0000-0002-1890-4193", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e646be026ce42ecbfd4d62eca3f9bce.json"}}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}, {"family": "Wenner\u00e5s", "given": "Christine", "initials": "C"}, {"family": "Eriksson", "given": "Kristina", "initials": "K"}, {"family": "Landegren", "given": "Nils", "initials": "N", "orcid": "0000-0002-6163-9540", "researcher": {"href": "https://publications.scilifelab.se/researcher/13ceacb17b7448709f9bfcd593bec1e2.json"}}, {"family": "Bryceson", "given": "Yenan", "initials": "Y", "orcid": "0000-0002-7783-9934", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce63349a03924444836215ffd201d2e3.json"}}, {"family": "Berg", "given": "Stefan", "initials": "S"}, {"family": "Ekwall", "given": "Olov", "initials": "O", "orcid": "0000-0002-4506-9955", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d7af11d7d30410d8fe5f3b5fbd0ba1d.json"}}], "type": "journal-article", "published": "2021-07-00", "journal": {"title": "Journal of Allergy and Clinical Immunology", "issn": "1085-8725", "volume": "148", "issue": "1", "pages": "96-98", "issn-l": "0091-6749"}, "abstract": null, "doi": "10.1016/j.jaci.2021.03.034", "pmid": "33892926", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8051851"}, {"db": "pii", "key": "S0091-6749(21)00556-X"}], "notes": [], "created": "2022-11-10T22:49:31.895Z", "modified": "2023-06-19T11:52:47.010Z"}, {"entity": "publication", "iuid": "fb9ccf42f5584a0785bbb5b7c45463e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb9ccf42f5584a0785bbb5b7c45463e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb9ccf42f5584a0785bbb5b7c45463e5"}}, "title": "Symptoms and Functional Impairment Assessed 8 Months After Mild COVID-19 Among Health Care Workers.", "authors": [{"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Rosell", "given": "Axel", "initials": "A"}, {"family": "Phillipson", "given": "Mia", "initials": "M"}, {"family": "Mangsbo", "given": "Sara M", "initials": "SM"}, {"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": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2021-05-18", "journal": {"title": "JAMA", "issn": "1538-3598", "issn-l": "0098-7484", "volume": "325", "issue": "19", "pages": "2015-2016"}, "abstract": null, "doi": "10.1001/jama.2021.5612", "pmid": "33825846", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "2778528"}, {"db": "pmc", "key": "PMC8027932"}], "notes": [], "created": "2021-04-08T05:37:27.638Z", "modified": "2021-12-09T08:39:03.115Z"}, {"entity": "publication", "iuid": "9e59e7c86b544a77ad2dcb68a7cfad1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e59e7c86b544a77ad2dcb68a7cfad1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e59e7c86b544a77ad2dcb68a7cfad1b"}}, "title": "Serine Protease HTRA1 as a Novel Target Antigen in Primary Membranous Nephropathy.", "authors": [{"family": "Al-Rabadi", "given": "Laith Farah", "initials": "LF"}, {"family": "Caza", "given": "Tiffany", "initials": "T"}, {"family": "Trivin-Avillach", "given": "Claire", "initials": "C"}, {"family": "Rodan", "given": "Aylin R", "initials": "AR", "orcid": "0000-0001-9202-2378", "researcher": {"href": "https://publications.scilifelab.se/researcher/c61468ba35da4701beba5615857d05c9.json"}}, {"family": "Andeen", "given": "Nicole", "initials": "N", "orcid": "0000-0002-4882-6640", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e9cad6c9fac42c9a2f81b0b258f7e5a.json"}}, {"family": "Hayashi", "given": "Norifumi", "initials": "N"}, {"family": "Williams", "given": "Brandi", "initials": "B"}, {"family": "Revelo", "given": "Monica P", "initials": "MP"}, {"family": "Clayton", "given": "Fred", "initials": "F"}, {"family": "Abraham", "given": "Jo", "initials": "J"}, {"family": "Lin", "given": "Edwin", "initials": "E"}, {"family": "Liou", "given": "Willisa", "initials": "W", "orcid": "0000-0002-3280-9635", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc5f36e54ef749d8ad87447c9363897e.json"}}, {"family": "Zou", "given": "Chang-Jiang", "initials": "CJ"}, {"family": "Ramkumar", "given": "Nirupama", "initials": "N"}, {"family": "Cummins", "given": "Tim", "initials": "T"}, {"family": "Wilkey", "given": "Daniel W", "initials": "DW"}, {"family": "Kawalit", "given": "Issa", "initials": "I"}, {"family": "Herzog", "given": "Christian", "initials": "C"}, {"family": "Storey", "given": "Aaron", "initials": "A"}, {"family": "Edmondson", "given": "Rick", "initials": "R"}, {"family": "Sjoberg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Yang", "given": "Tianxin", "initials": "T"}, {"family": "Chien", "given": "Jeremy", "initials": "J"}, {"family": "Merchant", "given": "Michael", "initials": "M", "orcid": "0000-0003-4128-4057", "researcher": {"href": "https://publications.scilifelab.se/researcher/46a22dcea21d4a8781a1cd44473af131.json"}}, {"family": "Arthur", "given": "John", "initials": "J"}, {"family": "Klein", "given": "Jon", "initials": "J"}, {"family": "Larsen", "given": "Chris", "initials": "C"}, {"family": "Beck", "given": "Laurence H", "initials": "LH"}], "type": "journal article", "published": "2021-05-05", "journal": {"title": "J. Am. Soc. Nephrol.", "issn": "1533-3450", "volume": "32", "issue": "7", "pages": "1666-1681", "issn-l": "1046-6673"}, "abstract": "Identification of target antigens PLA2R, THSD7A, NELL1, or Semaphorin-3B can explain the majority of cases of primary membranous nephropathy (MN). However, target antigens remain unidentified in 15%-20% of patients.\n\nA multipronged approach, using traditional and modern technologies, converged on a novel target antigen, and capitalized on the temporal variation in autoantibody titer for biomarker discovery. Immunoblotting of human glomerular proteins followed by differential immunoprecipitation and mass spectrometric analysis was complemented by laser-capture microdissection followed by mass spectrometry, elution of immune complexes from renal biopsy specimen tissue, and autoimmune profiling on a protein fragment microarray.\n\nThese approaches identified serine protease HTRA1 as a novel podocyte antigen in a subset of patients with primary MN. Sera from two patients reacted by immunoblotting with a 51-kD protein within glomerular extract and with recombinant human HTRA1, under reducing and nonreducing conditions. Longitudinal serum samples from these patients seemed to correlate with clinical disease activity. As in PLA2R- and THSD7A- associated MN, anti-HTRA1 antibodies were predominantly IgG4, suggesting a primary etiology. Analysis of sera collected during active disease versus remission on protein fragment microarrays detected significantly higher titers of anti-HTRA1 antibody in active disease. HTRA1 was specifically detected within immune deposits of HTRA1-associated MN in 14 patients identified among three cohorts. Screening of 118 \"quadruple-negative\" (PLA2R-, THSD7A-, NELL1-, EXT2-negative) patients in a large repository of MN biopsy specimens revealed a prevalence of 4.2%.\n\nConventional and more modern techniques converged to identify serine protease HTRA1 as a target antigen in MN.", "doi": "10.1681/ASN.2020101395", "pmid": "33952630", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "ASN.2020101395"}], "notes": [], "created": "2021-05-19T07:33:08.735Z", "modified": "2021-11-10T12:25:06.464Z"}, {"entity": "publication", "iuid": "110674e87a0a4e7c91505e34d91e3eba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/110674e87a0a4e7c91505e34d91e3eba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/110674e87a0a4e7c91505e34d91e3eba"}}, "title": "False Positive Results in SARS-CoV-2 Serological Tests for Samples From Patients With Chronic Inflammatory Diseases.", "authors": [{"family": "Kharlamova", "given": "Nastya", "initials": "N"}, {"family": "Dunn", "given": "Nicky", "initials": "N"}, {"family": "Bedri", "given": "Sahl K", "initials": "SK"}, {"family": "Jerling", "given": "Svante", "initials": "S"}, {"family": "Almgren", "given": "Malin", "initials": "M"}, {"family": "Faustini", "given": "Francesca", "initials": "F"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "R\u00f6nnelid", "given": "Johan", "initials": "J"}, {"family": "Pullerits", "given": "Rille", "initials": "R"}, {"family": "Gjertsson", "given": "Inger", "initials": "I"}, {"family": "Lundberg", "given": "Karin", "initials": "K"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"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": "Fink", "given": "Katharina", "initials": "K"}, {"family": "Fogdell-Hahn", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2021-05-03", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "12", "issue": null, "pages": "666114", "issn-l": "1664-3224"}, "abstract": "Patients with chronic inflammatory diseases are often treated with immunosuppressants and therefore are of particular concern during the SARS-CoV-2 pandemic. Serological tests will improve our understanding of the infection and immunity in this population, unless they tests give false positive results. The aim of this study was to evaluate the specificity of SARS-Cov-2 serological assays using samples from patients with chronic inflammatory diseases collected prior to April 2019, thus defined as negative. Samples from patients with multiple sclerosis (MS, n=10), rheumatoid arthritis (RA, n=47) with or without rheumatoid factor (RF) and/or anti-cyclic citrullinated peptide antibodies (anti-CCP2) and systemic lupus erythematosus (SLE, n=10) with or without RF, were analyzed for SARS-CoV-2 antibodies using 17 commercially available lateral flow assays (LFA), two ELISA kits and one in-house developed IgG multiplex bead-based assay. Six LFA and the in-house validated IgG assay correctly produced negative results for all samples. However, the majority of assays (n=13), gave false positive signal for samples from patients with RA and SLE. This was most notable in samples from RF positive RA patients. No false positive samples were detected in any assay using samples from patients with MS. Poor specificity of commercial serological assays could possibly be, at least partly, due to interfering antibodies in samples from patients with chronic inflammatory diseases. For these patients, the risk of false positivity should be considered when interpreting results of the SARS-CoV-2 serological assays.", "doi": "10.3389/fimmu.2021.666114", "pmid": "34012450", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8126683"}], "notes": [], "created": "2021-05-18T10:19:43.536Z", "modified": "2021-11-10T12:25:08.755Z"}, {"entity": "publication", "iuid": "5e5f1508d37040dcb78aba8b44f02efd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e5f1508d37040dcb78aba8b44f02efd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e5f1508d37040dcb78aba8b44f02efd"}}, "title": "Antibodies to SARS-CoV-2 and risk of past or future sick leave.", "authors": [{"family": "Dillner", "given": "Joakim", "initials": "J"}, {"family": "Elfstr\u00f6m", "given": "K Miriam", "initials": "KM"}, {"family": "Blomqvist", "given": "Jonas", "initials": "J"}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Lagheden", "given": "Camilla", "initials": "C"}, {"family": "Nordqvist-Kleppe", "given": "Sara", "initials": "S"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Jernbom Falk", "given": "August", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Hultin", "given": "Emilie", "initials": "E"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "M\u00e5nberg", "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": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Mattsson", "given": "Johan", "initials": "J"}, {"family": "M\u00fchr", "given": "Laila Sara Arroyo", "initials": "LSA"}, {"family": "Conneryd Lundgren", "given": "Kalle", "initials": "K"}], "type": "journal article", "published": "2021-03-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "5160", "issn-l": "2045-2322"}, "abstract": "The extent that antibodies to SARS-CoV-2 may protect against future virus-associated disease is unknown. We invited all employees (n = 15,300) at work at the Karolinska University Hospital, Stockholm, Sweden to participate in a study examining SARS-Cov-2 antibodies in relation to registered sick leave. For consenting 12,928 healthy hospital employees antibodies to SARS-CoV-2 could be determined and compared to participant sick leave records. Subjects with viral serum antibodies were not at excess risk for future sick leave (adjusted odds ratio (OR) controlling for age and sex: 0.85 [95% confidence interval (CI) (0.85 (0.43-1.68)]. By contrast, subjects with antibodies had an excess risk for sick leave in the weeks prior to testing [adjusted OR in multivariate analysis: 3.34 (2.98-3.74)]. Thus, presence of viral antibodies marks past disease and protection against excess risk of future disease. Knowledge of whether exposed subjects have had disease in the past or are at risk for future disease is essential for planning of control measures.Trial registration: First registered on 02/06/20, ClinicalTrials.gov NCT04411576.", "doi": "10.1038/s41598-021-84356-w", "pmid": "33664279", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-84356-w"}, {"db": "pmc", "key": "PMC7933367"}, {"db": "ClinicalTrials.gov", "key": "NCT04411576"}], "notes": [], "created": "2021-03-06T13:49:00.332Z", "modified": "2021-11-10T12:26:31.510Z"}, {"entity": "publication", "iuid": "ee18e674971a4b5f89d31d1203a60cda", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee18e674971a4b5f89d31d1203a60cda.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee18e674971a4b5f89d31d1203a60cda"}}, "title": "Allergome-wide peptide microarrays enable epitope deconvolution in allergen-specific immunotherapy", "authors": [{"family": "Mikus", "given": "Maria", "initials": "M"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Andersson", "given": "Morgan", "initials": "M"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Levin", "given": "Mattias", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "van Hage", "given": "Marianne", "initials": "M"}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}], "type": "journal-article", "published": "2021-03-00", "journal": {"title": "Journal of Allergy and Clinical Immunology", "issn": "1085-8725", "issn-l": "0091-6749", "volume": "147", "issue": "3", "pages": "1077-1086"}, "abstract": "The interaction of allergens and allergen-specific IgE initiates the allergic cascade after crosslinking of receptors on effector cells. Antibodies of other isotypes may modulate such a reaction. Receptor crosslinking requires binding of antibodies to multiple epitopes on the allergen. Limited information is available on the complexity of the epitope structure of most allergens.\n\nWe sought to allow description of the complexity of IgE, IgG4, and IgG epitope recognition at a global, allergome-wide level during allergen-specific immunotherapy (AIT).\n\nWe generated an allergome-wide microarray comprising 731 allergens in the form of more than 172,000 overlapping 16-mer peptides. Allergen recognition by IgE, IgG4, and IgG was examined in serum samples collected from subjects undergoing AIT against pollen allergy.\n\nExtensive induction of linear peptide-specific Phl p 1- and Bet v 1-specific humoral immunity was demonstrated in subjects undergoing a 3-year-long AIT against grass and birch pollen allergy, respectively. Epitope profiles differed between subjects but were largely established already after 1 year of AIT, suggesting that dominant allergen-specific antibody clones remained as important contributors to humoral immunity following their initial establishment during the early phase of AIT. Complex, subject-specific patterns of allergen isoform and group cross-reactivities in the repertoires were observed, patterns that may indicate different levels of protection against different allergen sources.\n\nThe study highlights the complexity and subject-specific nature of allergen epitopes recognized following AIT. We envisage that epitope deconvolution will be an important aspect of future efforts to describe and analyze the outcomes of AIT in a personalized manner.", "doi": "10.1016/j.jaci.2020.08.002", "pmid": "32791163", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0091-6749(20)31108-8"}], "notes": [], "created": "2020-08-20T06:07:25.147Z", "modified": "2023-06-19T11:55:27.568Z"}, {"entity": "publication", "iuid": "c54fad9a92ff45be90b06c461c2854cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c54fad9a92ff45be90b06c461c2854cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c54fad9a92ff45be90b06c461c2854cb"}}, "title": "Exploring autoantibody signatures in brain tissue from patients with severe mental illness.", "authors": [{"family": "Just", "given": "David", "initials": "D", "orcid": "0000-0001-6126-2256", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f687d3a9cf4400932c75510807c764.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d155273b5b54e61b773f263e4f2ce9b.json"}}, {"family": "Mitsios", "given": "Nicholas", "initials": "N", "orcid": "0000-0001-6243-4953", "researcher": {"href": "https://publications.scilifelab.se/researcher/38efa44f5ed64192b432d6384584f00d.json"}}, {"family": "Stockmeier", "given": "Craig A", "initials": "CA", "orcid": "0000-0003-1861-1013", "researcher": {"href": "https://publications.scilifelab.se/researcher/89ebb5b73b9a42498192d35aea2d92c5.json"}}, {"family": "Rajkowska", "given": "Grazyna", "initials": "G", "orcid": "0000-0002-4348-4688", "researcher": {"href": "https://publications.scilifelab.se/researcher/4122635fead74359983624753ee365ff.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Cunningham", "given": "Janet L", "initials": "JL", "orcid": "0000-0001-7876-7779", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab30dd6c6874bc7a227a8699c4a7085.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Carlstr\u00f6m", "given": "Eva Lindholm", "initials": "EL", "orcid": "0000-0001-8055-7826", "researcher": {"href": "https://publications.scilifelab.se/researcher/c433744d926b450097e71784b8bcc27c.json"}}], "type": "journal article", "published": "2020-11-18", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "volume": "10", "issue": "1", "pages": "401", "issn-l": "2158-3188"}, "abstract": "In recent years, studies have shown higher prevalence of autoantibodies in patients with schizophrenia compared to healthy individuals. This study applies an untargeted and a targeted affinity proteomics approach to explore and characterize the autoantibody repertoire in brain tissues from 73 subjects diagnosed with schizophrenia and 52 control subjects with no psychiatric or neurological disorders. Selected brain tissue lysates were first explored for IgG reactivity on planar microarrays composed of 11,520 protein fragments representing 10,820 unique proteins. Based on these results of ours and other previous studies of autoantibodies related to psychosis, we selected 226 fragments with an average length of 80 amino acids, representing 127 unique proteins. Tissue-based analysis of IgG reactivities using antigen suspension bead arrays was performed in a multiplex and parallel fashion for all 125 subjects. Among the detected autoantigens, higher IgG reactivity in subjects with schizophrenia, as compared to psychiatrically healthy subjects, was found against the glutamate ionotropic receptor NMDA type subunit 2D (anti-GluN2D). In a separate cohort with serum samples from 395 young adults with a wider spectrum of psychiatric disorders, higher levels of serum autoantibodies targeting GluN2D were found when compared to 102 control individuals. By further validating GluN2D and additional potential autoantigens, we will seek insights into how these are associated with severe mental illnesses.", "doi": "10.1038/s41398-020-01079-8", "pmid": "33208725", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-020-01079-8"}, {"db": "pmc", "key": "PMC7676257"}], "notes": [], "created": "2020-11-19T10:26:29.658Z", "modified": "2021-11-10T12:45:09.790Z"}, {"entity": "publication", "iuid": "7b76865fb2364e6fa8946090ea425154", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b76865fb2364e6fa8946090ea425154.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b76865fb2364e6fa8946090ea425154"}}, "title": "The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19.", "authors": [{"family": "Consiglio", "given": "Camila Rosat", "initials": "CR", "orcid": "0000-0002-8901-2328", "researcher": {"href": "https://publications.scilifelab.se/researcher/7df7044aa718438ca370ed90cdd9c282.json"}}, {"family": "Cotugno", "given": "Nicola", "initials": "N", "orcid": "0000-0002-7748-1581", "researcher": {"href": "https://publications.scilifelab.se/researcher/56dc2dd7b83d4fbd9d20a008f89604da.json"}}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Amodio", "given": "Donato", "initials": "D", "orcid": "0000-0003-4550-3018", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1c02699a9564c09bff0a28036089857.json"}}, {"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f9c2cfec48e4c4d8e9bc528a02d489b.json"}}, {"family": "Tan", "given": "Ziyang", "initials": "Z"}, {"family": "Zicari", "given": "Sonia", "initials": "S", "orcid": "0000-0003-1240-8057", "researcher": {"href": "https://publications.scilifelab.se/researcher/6721817c6fa143d69be06d7bcc960579.json"}}, {"family": "Ruggiero", "given": "Alessandra", "initials": "A", "orcid": "0000-0002-1041-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f80953fcc4f42fabfc21a70d6a39aba.json"}}, {"family": "Pascucci", "given": "Giuseppe Rubens", "initials": "GR", "orcid": "0000-0002-5978-1193", "researcher": {"href": "https://publications.scilifelab.se/researcher/27e5b15541cb4305aacfbcdc76e8070c.json"}}, {"family": "Santilli", "given": "Veronica", "initials": "V"}, {"family": "Campbell", "given": "Tessa", "initials": "T"}, {"family": "Bryceson", "given": "Yenan", "initials": "Y"}, {"family": "Eriksson", "given": "Daniel", "initials": "D"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Marchesi", "given": "Alessandra", "initials": "A"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Campana", "given": "Andrea", "initials": "A"}, {"family": "Villani", "given": "Alberto", "initials": "A", "orcid": "0000-0002-9120-0424", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d74ddfe5709426783a3b9c753cacad3.json"}}, {"family": "Rossi", "given": "Paolo", "initials": "P"}, {"family": "CACTUS Study Team", "given": "", "initials": ""}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Palma", "given": "Paolo", "initials": "P", "orcid": "0000-0002-3066-4719", "researcher": {"href": "https://publications.scilifelab.se/researcher/275341cd978547cfa2aaf179cbd74011.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2020-11-12", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "183", "issue": "4", "pages": "968-981.e7"}, "abstract": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is typically very mild and often asymptomatic in children. A complication is the rare multisystem inflammatory syndrome in children (MIS-C) associated with COVID-19, presenting 4-6 weeks after infection as high fever, organ dysfunction, and strongly elevated markers of inflammation. The pathogenesis is unclear but has overlapping features with Kawasaki disease suggestive of vasculitis and a likely autoimmune etiology. We apply systems-level analyses of blood immune cells, cytokines, and autoantibodies in healthy children, children with Kawasaki disease enrolled prior to COVID-19, children infected with SARS-CoV-2, and children presenting with MIS-C. We find that the inflammatory response in MIS-C differs from the cytokine storm of severe acute COVID-19, shares several features with Kawasaki disease, but also differs from this condition with respect to T cell subsets, interleukin (IL)-17A, and biomarkers associated with arterial damage. Finally, autoantibody profiling suggests multiple autoantibodies that could be involved in the pathogenesis of MIS-C.", "doi": "10.1016/j.cell.2020.09.016", "pmid": "32966765", "labels": {"Autoimmunity and Serology Profiling": "Service", "Affinity Proteomics Stockholm": "Service", "Cellular Immunomonitoring": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(20)31157-0"}, {"db": "pmc", "key": "PMC7474869"}], "notes": [], "created": "2020-09-07T21:59:50.131Z", "modified": "2024-01-16T13:48:41.355Z"}, {"entity": "publication", "iuid": "e173e02b94644b7b8a5040986accb4a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e173e02b94644b7b8a5040986accb4a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e173e02b94644b7b8a5040986accb4a0"}}, "title": "Generation and validation of recombinant antibodies to study human aminoacyl-tRNA synthetases.", "authors": [{"family": "Preger", "given": "Charlotta", "initials": "C"}, {"family": "Wigren", "given": "Edvard", "initials": "E", "orcid": "0000-0002-7933-0939", "researcher": {"href": "https://publications.scilifelab.se/researcher/c844b8d4d0554443b369f6c0f128ea7e.json"}}, {"family": "Ossipova", "given": "Elena", "initials": "E"}, {"family": "Marks", "given": "Carolyn", "initials": "C"}, {"family": "Lengqvist", "given": "Johan", "initials": "J"}, {"family": "Hofstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Andersson", "given": "Oskar", "initials": "O"}, {"family": "Jakobsson", "given": "Per-Johan", "initials": "PJ", "orcid": "0000-0001-7665-9715", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb148e2233b4541bc7c8b340f0cf12c.json"}}, {"family": "Gr\u00e4slund", "given": "Susanne", "initials": "S"}, {"family": "Persson", "given": "Helena", "initials": "H", "orcid": "0000-0002-2965-0395", "researcher": {"href": "https://publications.scilifelab.se/researcher/971d18bca1874c9cb8630c15c530c11d.json"}}], "type": "journal article", "published": "2020-10-09", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "295", "issue": "41", "pages": "13981-13993"}, "abstract": "Aminoacyl-tRNA synthetases (aaRSs) have long been viewed as mere housekeeping proteins and have therefore often been overlooked in drug discovery. However, recent findings have revealed that many aaRSs have noncanonical functions, and several of the aaRSs have been linked to autoimmune diseases, cancer, and neurological disorders. Deciphering these roles has been challenging because of a lack of tools to enable their study. To help solve this problem, we have generated recombinant high-affinity antibodies for a collection of thirteen cytoplasmic and one mitochondrial aaRSs. Selected domains of these proteins were produced recombinantly in Escherichia coli and used as antigens in phage display selections using a synthetic human single-chain fragment variable library. All targets yielded large sets of antibody candidates that were validated through a panel of binding assays against the purified antigen. Furthermore, the top-performing binders were tested in immunoprecipitation followed by MS for their ability to capture the endogenous protein from mammalian cell lysates. For antibodies targeting individual members of the multi-tRNA synthetase complex, we were able to detect all members of the complex, co-immunoprecipitating with the target, in several cell types. The functionality of a subset of binders for each target was also confirmed using immunofluorescence. The sequences of these proteins have been deposited in publicly available databases and repositories. We anticipate that this open source resource, in the form of high-quality recombinant proteins and antibodies, will accelerate and empower future research of the role of aaRSs in health and disease.", "doi": "10.1074/jbc.RA120.012893", "pmid": "32817337", "labels": {"Autoimmunity and Serology Profiling": "Service", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0021-9258(17)49797-3"}, {"db": "pmc", "key": "PMC7549041"}], "notes": [], "created": "2020-12-02T15:16:20.268Z", "modified": "2025-10-17T13:05:07.951Z"}, {"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": "bb0b805b5429464ab0bddbb9a6f7787e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb0b805b5429464ab0bddbb9a6f7787e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb0b805b5429464ab0bddbb9a6f7787e"}}, "title": "Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality.", "authors": [{"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d66c199ece143a6ab15222d8b55e3ea.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Chen", "given": "Xu", "initials": "X"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Lee", "given": "Woojoo", "initials": "W"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications.scilifelab.se/researcher/085cca6e87fb4639b720b0e5c8c1da2a.json"}}, {"family": "Thomas", "given": "Cecilia Engel", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1156f987764218af202efbd76c31fd.json"}}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Silveira", "given": "Angela", "initials": "A", "orcid": "0000-0003-2063-4935", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd1197769804dd48b9de86f11340ef2.json"}}, {"family": "Hall", "given": "Per", "initials": "P", "orcid": "0000-0002-5640-9126", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e177f5d95f34b148064662f34ef6660.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK"}, {"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": "2020-10-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "3", "issue": "10", "pages": "e202000817"}, "abstract": "Despite recognizing aging as a common risk factor of many human diseases, little is known about its molecular traits. To identify age-associated proteins circulating in human blood, we screened 156 individuals aged 50-92 using exploratory and multiplexed affinity proteomics assays. Profiling eight additional study sets (N = 3,987), performing antibody validation, and conducting a meta-analysis revealed a consistent age association (P = 6.61 \u00d7 10-6) for circulating histidine-rich glycoprotein (HRG). Sequence variants of HRG influenced how the protein was recognized in the immunoassays. Indeed, only the HRG profiles affected by rs9898 were associated with age and predicted the risk of mortality (HR = 1.25 per SD; 95% CI = 1.12-1.39; P = 6.45 \u00d7 10-5) during a follow-up period of 8.5 yr after blood sampling (IQR = 7.7-9.3 yr). Our affinity proteomics analysis found associations between the particular molecular traits of circulating HRG with age and all-cause mortality. The distinct profiles of this multipurpose protein could serve as an accessible and informative indicator of the physiological processes related to biological aging.", "doi": "10.26508/lsa.202000817", "pmid": "32737166", "labels": {"Autoimmunity and Serology Profiling": "Service", "Affinity Proteomics Stockholm": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3/10/e202000817"}, {"db": "pmc", "key": "PMC7409555"}], "notes": [], "created": "2020-08-21T08:30:48.217Z", "modified": "2024-01-16T13:48:41.646Z"}, {"entity": "publication", "iuid": "213dcd6a98684a7ea8372fe50ab19850", "links": {"self": {"href": "https://publications.scilifelab.se/publication/213dcd6a98684a7ea8372fe50ab19850.json"}, "display": {"href": "https://publications.scilifelab.se/publication/213dcd6a98684a7ea8372fe50ab19850"}}, "title": "Association of serum anti-centromere protein F antibodies with clinical response to infliximab in patients with rheumatoid arthritis: A prospective study.", "authors": [{"family": "Lourido", "given": "Luc\u00eda", "initials": "L"}, {"family": "Ruiz-Romero", "given": "Cristina", "initials": "C"}, {"family": "Picchi", "given": "Flor", "initials": "F"}, {"family": "Diz-Rosales", "given": "Naomi", "initials": "N"}, {"family": "Vilaboa-Gal\u00e1n", "given": "Sergio", "initials": "S"}, {"family": "Fern\u00e1ndez-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Tasende", "given": "Jos\u00e9 Antonio Pinto", "initials": "JAP"}, {"family": "P\u00e9rez-Pamp\u00edn", "given": "Eva", "initials": "E"}, {"family": "Regueiro", "given": "Cristina", "initials": "C"}, {"family": "Mera-Varela", "given": "Antonio", "initials": "A"}, {"family": "Gonzalez", "given": "Antonio", "initials": "A"}, {"family": "Hambardzumyan", "given": "Karen", "initials": "K"}, {"family": "Saevarsdottir", "given": "Saedis", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Blanco", "given": "Francisco J", "initials": "FJ"}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "Semin. Arthritis Rheum.", "issn": "1532-866X", "volume": "50", "issue": "5", "pages": "1101-1108", "issn-l": "0049-0172"}, "abstract": "One-third of rheumatoid arthritis (RA) patients demonstrate no clinical improvement after receiving tumor necrosis factor inhibitors (TNFi). The presence of serum autoantibodies is a hallmark in RA and may provide information on future response to treatment. The aim of this prospective study was to search for novel serum autoantibodies useful to predict clinical response to TNFi.\n\nThe autoantibody repertoire was profiled on RA patients treated with TNFi as a first line of biologic therapy (N = 185), who were recruited in three independent cohorts. The presence and levels of autoantibodies in serum at baseline were analysed in association with the clinical response after 24 weeks follow-up. A multiplex bead array built using antigens selected from an initial untargeted screening was employed to identify the autoantibodies on a discovery cohort (N = 50) and to verify and validate the results on verification (N = 61) and validation (N = 74) cohorts. Non-parametric tests, meta-analysis and Receiver Operating Curves (ROC) were performed in order to assess the clinical relevance of the observed findings.\n\nNovel autoantibodies were associated with the clinical response to TNFi, showing different reactivity profiles among the different TNFi. The baseline levels of IgG antibodies against Centromere protein F (CENPF), a protein related to cell proliferation, were significantly (p<0.05) increased in responders (N = 111) to infliximab (IFX) compared to non-responders (N = 44). The addition of anti-CENPF antibodies to demographic and clinical variables (age, sex, DAS28-ESR) resulted in the best model to discriminate responders, showing an area under the curve (AUC) of 0.756 (95% CI [0.639-0.874], p = 0.001). A further meta-analysis demonstrated the significant association of anti-CENPF levels with the patient's subsequent response to IFX, showing a standardized mean difference (SMD) of -0.65 (95% CI [-1.02;-0. 27], p = 0.018).\n\nOur study reveals for the first time the potential of circulating anti-CENPF antibodies to predict the clinical response to IFX before starting the treatment. This finding could be potentially useful to guide therapeutic decisions and may lead to further studies focusing on the role of CENPF on RA pathology.", "doi": "10.1016/j.semarthrit.2020.06.010", "pmid": "32920323", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0049-0172(20)30190-6"}], "notes": [], "created": "2020-09-15T12:16:35.815Z", "modified": "2021-11-10T12:50:02.160Z"}, {"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": "84851b50878d4f5b85ea8fb5174a680f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84851b50878d4f5b85ea8fb5174a680f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84851b50878d4f5b85ea8fb5174a680f"}}, "title": "Screening for autoantibody targets in post-vaccination narcolepsy using proteome arrays.", "authors": [{"family": "Lind", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1473-5468", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6124e404ef349dc8d687838cb8eaf92.json"}}, {"family": "Eriksson", "given": "Daniel", "initials": "D"}, {"family": "Akel", "given": "Omar", "initials": "O"}, {"family": "Ramelius", "given": "Anita", "initials": "A"}, {"family": "Palm", "given": "Lars", "initials": "L"}, {"family": "Lernmark", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Elding Larsson", "given": "Helena", "initials": "H"}, {"family": "Landegren", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2020-04-00", "journal": {"volume": "91", "issn": "1365-3083", "issue": "4", "pages": "e12864", "title": "Scand. J. Immunol.", "issn-l": "0300-9475"}, "abstract": "Narcolepsy type 1 (NT1) is a chronic sleep disorder caused by a specific loss of hypocretin-producing neurons. The incidence of NT1 increased in Sweden, Finland and Norway following Pandemrix\u00ae-vaccination, initiated to prevent the 2009 influenza pandemic. The pathogenesis of NT1 is poorly understood, and causal links to vaccination are yet to be clarified. The strong association with Human leukocyte antigen (HLA) DQB1*06:02 suggests an autoimmune pathogenesis, but proposed autoantigens remain controversial. We used a two-step approach to identify autoantigens in patients that acquired NT1 after Pandemrix\u00ae-vaccination. Using arrays of more than 9000 full-length human proteins, we screened the sera of 10 patients and 24 healthy subjects for autoantibodies. Identified candidate antigens were expressed in vitro to enable validation studies with radiobinding assays (RBA). The validation cohort included NT1 patients (n = 39), their first-degree relatives (FDR) (n = 66), population controls (n = 188), and disease controls representing multiple sclerosis (n = 100) and FDR to type 1 diabetes patients (n = 41). Reactivity towards previously suggested NT1 autoantigen candidates including Tribbles homolog 2, Prostaglandin D2 receptor, Hypocretin receptor 2 and \u03b1-MSH/proopiomelanocortin was not replicated in the protein array screen. By comparing case to control signals, three novel candidate autoantigens were identified in the protein array screen; LOC401464, PARP3 and FAM63B. However, the RBA did not confirm elevated reactivity towards either of these proteins. In summary, three putative autoantigens in NT1 were identified by protein array screening. Autoantibodies against these candidates could not be verified with independent methods. Further studies are warranted to identify hypothetical autoantigens related to the pathogenesis of Pandemrix\u00ae-induced NT1.", "doi": "10.1111/sji.12864", "pmid": "32056243", "labels": {"Autoimmunity and Serology Profiling": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-02-21T15:13:34.020Z", "modified": "2024-01-16T13:48:42.689Z"}, {"entity": "publication", "iuid": "6160899370e74e65b1403e1296bad63c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6160899370e74e65b1403e1296bad63c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6160899370e74e65b1403e1296bad63c"}}, "title": "Mining the Proteome Associated with Rheumatic and Autoimmune Diseases.", "authors": [{"family": "Ruiz-Romero", "given": "Cristina", "initials": "C", "orcid": "0000-0001-7649-9803", "researcher": {"href": "https://publications.scilifelab.se/researcher/2eecce47df434f559416e44079b53721.json"}}, {"family": "Lam", "given": "Maggie P Y", "initials": "MPY", "orcid": "0000-0001-9488-8319", "researcher": {"href": "https://publications.scilifelab.se/researcher/707e7d77c065403d9a3e00030ee4e4f9.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "\u00d6nnerfjord", "given": "Patrik", "initials": "P"}, {"family": "Utz", "given": "Paul J", "initials": "PJ"}, {"family": "Van Eyk", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0001-9050-148X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e860403a0224d588958a9c588688ff6.json"}}, {"family": "Venkatraman", "given": "Vidya", "initials": "V"}, {"family": "Fert-Bober", "given": "Justyna", "initials": "J", "orcid": "0000-0002-2824-5056", "researcher": {"href": "https://publications.scilifelab.se/researcher/3736463bff894b4bbf54ea57e14efce5.json"}}, {"family": "Watt", "given": "Fiona E", "initials": "FE"}, {"family": "Blanco", "given": "Francisco J", "initials": "FJ", "orcid": "0000-0001-9821-7635", "researcher": {"href": "https://publications.scilifelab.se/researcher/5673a00f769049b68c2a0d41c8eacac2.json"}}], "type": "journal article", "published": "2019-12-06", "journal": {"volume": "18", "issn": "1535-3907", "issue": "12", "pages": "4231-4239", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "A steady increase in the incidence of osteoarthritis and other rheumatic diseases has been observed in recent decades, including autoimmune conditions such as rheumatoid arthritis, spondyloarthropathies, systemic lupus erythematosus, systemic sclerosis, and Sj\u00f6gren's syndrome. Rheumatic and autoimmune diseases (RADs) are characterized by the inflammation of joints, muscles, or other connective tissues. In addition to often experiencing debilitating mobility and pain, RAD patients are also at a higher risk of suffering comorbidities such as cardiovascular or infectious events. Given the socioeconomic impact of RADs, broad research efforts have been dedicated to these diseases worldwide. In the present work, we applied literature mining platforms to identify \"popular\" proteins closely related to RADs. The platform is based on publicly available literature. The results not only will enable the systematic prioritization of candidates to perform targeted proteomics studies but also may lead to a greater insight into the key pathogenic processes of these disorders.", "doi": "10.1021/acs.jproteome.9b00360", "pmid": "31599600", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-11-06T15:11:34.786Z", "modified": "2021-07-07T15:50:03.161Z"}, {"entity": "publication", "iuid": "2f1000dd88294e998e0791c5f66afd42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f1000dd88294e998e0791c5f66afd42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f1000dd88294e998e0791c5f66afd42"}}, "title": "The autoantibody response to cyclic citrullinated collagen type II peptides in rheumatoid arthritis.", "authors": [{"family": "Liang", "given": "Bibo", "initials": "B"}, {"family": "Ge", "given": "Changrong", "initials": "C"}, {"family": "L\u00f6nnblom", "given": "Erik", "initials": "E"}, {"family": "Lin", "given": "Xiaoyin", "initials": "X"}, {"family": "Feng", "given": "Hui", "initials": "H"}, {"family": "Xiao", "given": "Lianbo", "initials": "L"}, {"family": "Bai", "given": "Jing'an", "initials": "J"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Nandakumar", "given": "Kutty Selva", "initials": "KS"}, {"family": "Zhao", "given": "Ming", "initials": "M"}, {"family": "Holmdahl", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2019-09-01", "journal": {"volume": "58", "issn": "1462-0332", "issue": "9", "pages": "1623-1633", "title": "Rheumatology (Oxford)", "issn-l": "1462-0324"}, "abstract": "The detection of anti-citrullinated peptide antibodies (ACPAs) is a serological hallmark of RA. Autoantibodies reactive with collagen type II (CII) are present in RA sera and synovial fluid and are potentially pathogenic. Here, we investigate the prevalence and specificity of the autoantibody responses to defined citrullinated cyclic peptides derived from CII in a China RA cohort.\n\nUsing bead-based multiplex assay, we examined the presence of autoantibodies binding to 54 cyclic 17-mer citrullinated CII peptides, encompassing all citrullinate epitopes in CII, and the corresponding unmodified peptides in 415 RA patients, in addition to 304 patients with OA. Furthermore, the autoantibody responses to a selected set of 10 cyclic citrullinated peptides were also examined in 203 healthy individuals.\n\nAutoantibody responses to cyclic citrullinated CII peptides were higher in RA patients as compared with OA patients or healthy individuals, whereas little or negligible antibody responses to cyclic unmodified CII peptides were observed. Interestingly, several novel citrullinated CII epitopes were identified. Antibodies to these novel citrullinated CII epitopes showed not only substantial overlapping reactivities but also had unique specificities.\n\nWe found a high prevalence of autoantibodies against cyclic citrullinated CII in the sera of patients in a China RA cohort. The present study revealed heterogeneous binding patterns against novel citrullinated CII epitopes, which may help to stratify RA patients into different subgroups.", "doi": "10.1093/rheumatology/kez073", "pmid": "30892636", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "5396722"}], "notes": [], "created": "2019-11-06T15:11:33.129Z", "modified": "2021-07-07T15:50:03.030Z"}, {"entity": "publication", "iuid": "d7fdfd620a754dffb5455e4782d7c3ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7fdfd620a754dffb5455e4782d7c3ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7fdfd620a754dffb5455e4782d7c3ec"}}, "title": "Array-Based Profiling of Proteins and Autoantibody Repertoires in CSF.", "authors": [{"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": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Jernbom Falk", "given": "August", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-08-23", "journal": {"volume": "2044", "issn": "1940-6029", "issue": null, "pages": "303-318", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Protein profiling enabled through affinity proteomics represents a powerful strategy for analysis of complex samples such as human body fluids. Cerebrospinal fluid (CSF) is the proximal fluid of the central nervous system and is commonly analyzed in the context of neurological diseases. Through the presence of brain-derived proteins, this fluid can offer insight into the physiological state of the brain. Here, we describe multiplex and flexible protein and autoantibody profiling approaches using suspension bead arrays. Through minimal sample processing, these methods enable high-throughput analysis of hundreds of samples and proteins in one single assay and thereby provide powerful approaches for discovery of disease-associated proteins and autoantigens.", "doi": "10.1007/978-1-4939-9706-0_19", "pmid": "31432421", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-11-06T15:11:34.083Z", "modified": "2021-07-07T15:55:21.138Z"}, {"entity": "publication", "iuid": "8aad6ceb7086447cb14545d9433c1791", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8aad6ceb7086447cb14545d9433c1791.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8aad6ceb7086447cb14545d9433c1791"}}, "title": "Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk.", "authors": [{"family": "Tengvall", "given": "Katarina", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Huang", "given": "Jesse", "initials": "J"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Kammer", "given": "Patrick", "initials": "P"}, {"family": "Bistr\u00f6m", "given": "Martin", "initials": "M"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Lima Bomfim", "given": "Izaura", "initials": "I"}, {"family": "Stridh", "given": "Pernilla", "initials": "P"}, {"family": "Butt", "given": "Julia", "initials": "J"}, {"family": "Brenner", "given": "Nicole", "initials": "N"}, {"family": "Michel", "given": "Angelika", "initials": "A"}, {"family": "Lundberg", "given": "Karin", "initials": "K"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Ernberg", "given": "Ingemar", "initials": "I"}, {"family": "Olafsson", "given": "Sigurgeir", "initials": "S"}, {"family": "Dilthey", "given": "Alexander T", "initials": "AT"}, {"family": "Hillert", "given": "Jan", "initials": "J"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Sundstr\u00f6m", "given": "Peter", "initials": "P"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Waterboer", "given": "Tim", "initials": "T"}, {"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"}}], "type": "clinical trial", "published": "2019-08-20", "journal": {"volume": "116", "issn": "1091-6490", "issue": "34", "pages": "16955-16960", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Multiple sclerosis (MS) is a chronic inflammatory, likely autoimmune disease of the central nervous system with a combination of genetic and environmental risk factors, among which Epstein-Barr virus (EBV) infection is a strong suspect. We have previously identified increased autoantibody levels toward the chloride-channel protein Anoctamin 2 (ANO2) in MS. Here, IgG antibody reactivity toward ANO2 and EBV nuclear antigen 1 (EBNA1) was measured using bead-based multiplex serology in plasma samples from 8,746 MS cases and 7,228 controls. We detected increased anti-ANO2 antibody levels in MS (P = 3.5 \u00d7 10-36) with 14.6% of cases and 7.8% of controls being ANO2 seropositive (odds ratio [OR] = 1.6; 95% confidence intervals [95%CI]: 1.5 to 1.8). The MS risk increase in ANO2-seropositive individuals was dramatic when also exposed to 3 known risk factors for MS: HLA-DRB1*15:01 carriage, absence of HLA-A*02:01, and high anti-EBNA1 antibody levels (OR = 24.9; 95%CI: 17.9 to 34.8). Reciprocal blocking experiments with ANO2 and EBNA1 peptides demonstrated antibody cross-reactivity, mapping to ANO2 [aa 140 to 149] and EBNA1 [aa 431 to 440]. HLA gene region was associated with anti-ANO2 antibody levels and HLA-DRB1*04:01 haplotype was negatively associated with ANO2 seropositivity (OR = 0.6; 95%CI: 0.5 to 0.7). Anti-ANO2 antibody levels were not increased in patients from 3 other inflammatory disease cohorts. The HLA influence and the fact that specific IgG production usually needs T cell help provides indirect evidence for a T cell ANO2 autoreactivity in MS. We propose a hypothesis where immune reactivity toward EBNA1 through molecular mimicry with ANO2 contributes to the etiopathogenesis of MS.", "doi": "10.1073/pnas.1902623116", "pmid": "31375628", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1902623116"}, {"db": "pmc", "key": "PMC6708327"}], "notes": [], "created": "2019-11-06T15:11:35.887Z", "modified": "2021-07-06T15:13:37.900Z"}, {"entity": "publication", "iuid": "bd5799ffebf94e4e8814aabb13c7c7be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd5799ffebf94e4e8814aabb13c7c7be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd5799ffebf94e4e8814aabb13c7c7be"}}, "title": "The autoimmune targets in IPEX are dominated by gut epithelial proteins.", "authors": [{"family": "Eriksson", "given": "Daniel", "initials": "D"}, {"family": "Bacchetta", "given": "Rosa", "initials": "R"}, {"family": "Gunnarsson", "given": "H\u00f6r\u00f0ur Ingi", "initials": "HI"}, {"family": "Chan", "given": "Alice", "initials": "A"}, {"family": "Barzaghi", "given": "Federica", "initials": "F"}, {"family": "Ehl", "given": "Stephan", "initials": "S"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "van Gool", "given": "Frederic", "initials": "F"}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Lundqvist", "given": "Christina", "initials": "C"}, {"family": "Laakso", "given": "Saila M", "initials": "SM"}, {"family": "R\u00f6nnblom", "given": "Anders", "initials": "A"}, {"family": "Ekwall", "given": "Olov", "initials": "O"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "Bensing", "given": "Sophie", "initials": "S"}, {"family": "Husebye", "given": "Eystein S", "initials": "ES"}, {"family": "Anderson", "given": "Mark", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Landegren", "given": "Nils", "initials": "N"}], "type": "letter", "published": "2019-07-00", "journal": {"volume": "144", "issn": "1097-6825", "issue": "1", "pages": "327-330.e8", "title": "J. Allergy Clin. Immunol.", "issn-l": "0091-6749"}, "abstract": null, "doi": "10.1016/j.jaci.2019.02.031", "pmid": "31027649", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "S0091-6749(19)30387-2"}], "notes": [], "created": "2020-02-21T10:25:19.472Z", "modified": "2025-12-03T09:48:04.559Z"}, {"entity": "publication", "iuid": "b47eaaf183d04aac8512a94a34b8cdcd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b47eaaf183d04aac8512a94a34b8cdcd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b47eaaf183d04aac8512a94a34b8cdcd"}}, "title": "Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'.", "authors": [{"family": "Landegren", "given": "Nils", "initials": "N", "orcid": "0000-0002-6163-9540", "researcher": {"href": "https://publications.scilifelab.se/researcher/13ceacb17b7448709f9bfcd593bec1e2.json"}}, {"family": "Rosen", "given": "Lindsey B", "initials": "LB", "orcid": "0000-0001-5894-3878", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ee4a40ef9343a9af897979b0e8e2dc.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Smith", "given": "Gustav", "initials": "G"}, {"family": "Ferre", "given": "Elise M N", "initials": "EMN", "orcid": "0000-0002-3285-7768", "researcher": {"href": "https://publications.scilifelab.se/researcher/41ec8466cb88424fb1d29e07c63df47c.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Sharon", "given": "Donald", "initials": "D"}, {"family": "Snyder", "given": "Michael", "initials": "M", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2594af48f3d45e68983030873c06cf5.json"}}, {"family": "Lionakis", "given": "Michail", "initials": "M"}, {"family": "Anderson", "given": "Mark", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}], "type": "journal article", "published": "2019-06-27", "journal": {"volume": "8", "issn": "2050-084X", "issue": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "The AIRE gene plays a key role in the development of central immune tolerance by promoting thymic presentation of tissue-specific molecules. Patients with AIRE-deficiency develop multiple autoimmune manifestations and display autoantibodies against the affected tissues. In 2016 it was reported that: i) the spectrum of autoantibodies in patients with AIRE-deficiency is much broader than previously appreciated; ii) neutralizing autoantibodies to type I interferons (IFNs) could provide protection against type 1 diabetes in these patients (Meyer et al., 2016). We attempted to replicate these new findings using a similar experimental approach in an independent patient cohort, and found no evidence for either conclusion.", "doi": "10.7554/eLife.43578", "pmid": "31244471", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Autoimmunity and Serology Profiling": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6597240"}, {"db": "pii", "key": "43578"}], "notes": [], "created": "2019-06-30T19:14:13.830Z", "modified": "2023-06-19T12:50:16.488Z"}, {"entity": "publication", "iuid": "d81332752ac544d4a3f4e26a9be1bf56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d81332752ac544d4a3f4e26a9be1bf56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d81332752ac544d4a3f4e26a9be1bf56"}}, "title": "Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.", "authors": [{"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Ioannou", "given": "Marina", "initials": "M"}, {"family": "Tamburro", "given": "Davide", "initials": "D"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Branca", "given": "Rui M", "initials": "RM"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.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": "2019-06-06", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "8324", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "There is a strong need for procedures that enable context and application dependent validation of antibodies. Here, we applied a magnetic bead assisted workflow and immunoprecipitation mass spectrometry (IP-MS/MS) to assess antibody selectivity for the detection of proteins in human plasma. A resource was built on 414 IP experiments using 157 antibodies (targeting 120 unique proteins) in assays with heat-treated or untreated EDTA plasma. For each protein we determined their antibody related degrees of enrichment using z-scores and their frequencies of identification across all IP assays. Out of 1,313 unique endogenous proteins, 426 proteins (33%) were detected in >20% of IPs, and these background components were mainly comprised of proteins from the complement system. For 45% (70/157) of the tested antibodies, the expected target proteins were enriched (z-score \u2265 3). Among these 70 antibodies, 59 (84%) co-enriched other proteins beside the intended target and mainly due to sequence homology or protein abundance. We also detected protein interactions in plasma, and for IGFBP2 confirmed these using several antibodies and sandwich immunoassays. The protein enrichment data with plasma provide a very useful and yet lacking resource for the assessment of antibody selectivity. Our insights will contribute to a more informed use of affinity reagents for plasma proteomics assays.", "doi": "10.1038/s41598-019-43552-5", "pmid": "31171813", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-43552-5"}, {"db": "pmc", "key": "PMC6554399"}], "notes": [], "created": "2019-11-06T15:11:37.992Z", "modified": "2024-01-16T13:48:44.259Z"}, {"entity": "publication", "iuid": "51dc68d4f49f42b1b70a0d6b09444fbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51dc68d4f49f42b1b70a0d6b09444fbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51dc68d4f49f42b1b70a0d6b09444fbb"}}, "title": "Recognition of Amino Acid Motifs, Rather Than Specific Proteins, by Human Plasma Cell-Derived Monoclonal Antibodies to Posttranslationally Modified Proteins in Rheumatoid Arthritis.", "authors": [{"family": "Steen", "given": "Johanna", "initials": "J"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sahlstr\u00f6m", "given": "Peter", "initials": "P"}, {"family": "Odowd", "given": "Victoria", "initials": "V"}, {"family": "Israelsson", "given": "Lena", "initials": "L"}, {"family": "Krishnamurthy", "given": "Akilan", "initials": "A"}, {"family": "Badreh", "given": "Sara", "initials": "S"}, {"family": "Mathsson Alm", "given": "Linda", "initials": "L"}, {"family": "Compson", "given": "Joanne", "initials": "J"}, {"family": "Ramsk\u00f6ld", "given": "Daniel", "initials": "D"}, {"family": "Ndlovu", "given": "Welcome", "initials": "W"}, {"family": "Rapecki", "given": "Stephen", "initials": "S"}, {"family": "Hansson", "given": "Monika", "initials": "M"}, {"family": "Titcombe", "given": "Philip J", "initials": "PJ"}, {"family": "Bang", "given": "Holger", "initials": "H"}, {"family": "Mueller", "given": "Daniel L", "initials": "DL"}, {"family": "Catrina", "given": "Anca I", "initials": "AI"}, {"family": "Gr\u00f6nwall", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9111-5537", "researcher": {"href": "https://publications.scilifelab.se/researcher/39191966104a46c89bd5512298e7541e.json"}}, {"family": "Skriner", "given": "Karl", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Lightwood", "given": "Daniel", "initials": "D"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V", "orcid": "0000-0001-9251-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027fbf97444632a470b33e446d4d67.json"}}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "71", "issn": "2326-5205", "issue": "2", "title": "Arthritis & rheumatology (Hoboken, N.J.)", "pages": "196-209", "issn-l": "2326-5191"}, "abstract": "Antibodies against posttranslationally modified proteins are a hallmark of rheumatoid arthritis (RA), but the emergence and pathogenicity of these autoantibodies are still incompletely understood. The aim of this study was to analyze the antigen specificities and mutation patterns of monoclonal antibodies (mAb) derived from RA synovial plasma cells and address the question of antigen cross-reactivity.\n\nIgG-secreting cells were isolated from RA synovial fluid, and the variable regions of the immunoglobulins were sequenced (n = 182) and expressed in full-length mAb (n = 93) and also as germline-reverted versions. The patterns of reactivity with 53,019 citrullinated peptides and 49,211 carbamylated peptides and the potential of the mAb to promote osteoclastogenesis were investigated.\n\nFour unrelated anti-citrullinated protein autoantibodies (ACPAs), of which one was clonally expanded, were identified and found to be highly somatically mutated in the synovial fluid of a patient with RA. The ACPAs recognized >3,000 unique peptides modified by either citrullination or carbamylation. This highly multireactive autoantibody feature was replicated for Ig sequences derived from B cells from the peripheral blood of other RA patients. The plasma cell-derived mAb were found to target distinct amino acid motifs and partially overlapping protein targets. They also conveyed different effector functions as revealed in an osteoclast activation assay.\n\nThese findings suggest that the high level of cross-reactivity among RA autoreactive B cells is the result of different antigen encounters, possibly at different sites and at different time points. This is consistent with the notion that RA is initiated in one context, such as in the mucosal organs, and thereafter targets other sites, such as the joints.", "doi": "10.1002/art.40699", "pmid": "30152202", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6563427"}], "notes": [], "created": "2018-09-11T08:00:34.082Z", "modified": "2024-01-16T13:48:44.747Z"}, {"entity": "publication", "iuid": "ff283a0beebc45f2932247fe9c082748", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff283a0beebc45f2932247fe9c082748.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff283a0beebc45f2932247fe9c082748"}}, "title": "Individual and stable autoantibody repertoires in healthy individuals.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Sallinen", "given": "Riitta", "initials": "R"}, {"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"}}], "type": "clinical trial", "published": "2019-02-00", "journal": {"title": "Autoimmunity", "issn": "1607-842X", "volume": "52", "issue": "1", "pages": "1-11", "issn-l": "0891-6934"}, "abstract": "In the era towards precision medicine, we here present the individual specific autoantibody signatures of 193 healthy individuals. The self-reactive IgG signatures are stable over time in a way that each individual profile is recognized in longitudinal sampling. The IgG autoantibody reactivity towards an antigen array comprising 335 protein fragments, representing 204 human proteins with potential relevance to autoimmune disorders, was measured in longitudinal plasma samples from 193 healthy individuals. This analysis resulted in unique autoantibody barcodes for each individual that were maintained over one year's time. The reactivity profiles, or signatures, are person specific in regards to the number of reactivities and antigen specificity. Two independent data sets were consistent in that each healthy individual displayed reactivity towards 0-16 antigens, with a median of six. Subsequently, four selected individuals were profiled on in-house produced high-density protein arrays containing 23,000 protein fragments representing 14,000 unique protein coding genes. Based on a unique, broad and deep longitudinal profiling of autoantibody reactivities, our results demonstrate a unique autoreactive profile in each analyzed healthy individual. The need and interest for broad-ranged and high-resolution molecular profiling of healthy individuals is rising. We have here generated and assessed an initial perspective on the global distribution of the self-reactive IgG repertoire in healthy individuals, by investigating 193 well-characterized healthy individuals. Highlights A unique longitudinal profiling of autoantibody repertoires in healthy individuals Autoantibody profiles are highly individual and stable over time All individuals display IgG binding to human protein fragments The specificity of disease associated autoantigens needs to be thoroughly characterized The identification of a small set of highly reactive autoantigens Importance of stringent antigen and sample specific cut-offs for defining reactivity.", "doi": "10.1080/08916934.2019.1581774", "pmid": "30835561", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-03-15T14:31:46.423Z", "modified": "2021-07-08T13:44:33.785Z"}, {"entity": "publication", "iuid": "fa29854dfdb74e01917b77d3a808c4c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa29854dfdb74e01917b77d3a808c4c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa29854dfdb74e01917b77d3a808c4c6"}}, "title": "The antimicrobial protein S100A12 identified as a potential autoantigen in a subgroup of atopic dermatitis patients.", "authors": [{"family": "Mikus", "given": "Maria", "initials": "M", "orcid": "0000-0001-6560-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/f569884286e147a18003426c423ec63c.json"}}, {"family": "Johansson", "given": "Catharina", "initials": "C", "orcid": "0000-0003-1303-3795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d22c4c4377ec43d899a5e49e26ab611f.json"}}, {"family": "Acevedo", "given": "Nathalie", "initials": "N"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Scheynius", "given": "Annika", "initials": "A", "orcid": "0000-0001-5520-990X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bab97d838e044d79bd32a1c207eca96.json"}}], "type": "journal article", "published": "2019-01-31", "journal": {"volume": "9", "issn": "2045-7022", "issue": null, "pages": "6", "title": "Clin Transl Allergy", "issn-l": "2045-7022"}, "abstract": "Atopic dermatitis (AD) is a complex heterogeneous chronic inflammatory skin disease. Specific IgE antibodies against autoantigens have been observed in a subgroup of AD patients, however, little is known about IgG-auto-reactivity in AD. To investigate the presence of autoreactive IgG antibodies, we performed autoantibody profiling of IgG in patients with AD of different severities and in healthy controls (HC).\n\nFirst, we performed an untargeted screening in plasma samples from 40 severe AD (sAD) patients and 40 HC towards 1152 protein fragments on planar antigen microarrays. Next, based on the findings and addition of more fragments, a targeted antigen suspension bead array was designed to profile a cohort of 50 sAD patients, 123 patients with moderate AD (mAD), and 84 HC against 148 protein fragments representing 96 unique proteins.\n\nForty-nine percent of the AD patients showed increased IgG-reactivity to any of the four antigens representing keratin associated protein 17-1 (KRTAP17-1), heat shock protein family A (Hsp70) member 4 (HSPA4), S100 calcium binding proteins A12 (S100A12), and Z (S100Z). The reactivity was more frequent in the sAD patients (66%) than in those with mAD (41%), whereas only present in 25% of the HC. IgG-reactivity to S100A12, a protein including an antimicrobial peptide, was only observed in AD patients (13/173).\n\nAutoantibody profiling of IgG-reactivity using microarray technology revealed an autoantibody-based subgroup in patients with AD. The four identified autoantigens and especially S100A12 could, if characterized further, increase the understanding of different pathogenic mechanisms behind AD and thereby enable better treatment.", "doi": "10.1186/s13601-019-0240-4", "pmid": "30728947", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "240"}, {"db": "pmc", "key": "PMC6354350"}], "notes": [], "created": "2019-03-15T14:32:29.742Z", "modified": "2024-01-16T13:48:44.779Z"}, {"entity": "publication", "iuid": "2da1046f242b46f1b8d0c059c2531df1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2da1046f242b46f1b8d0c059c2531df1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2da1046f242b46f1b8d0c059c2531df1"}}, "title": "Detection of autoantibodies against cancer-testis antigens in non-small cell lung cancer.", "authors": [{"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Holgersson", "given": "Georg", "initials": "G"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Mattsson", "given": "Johanna S M", "initials": "JSM"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "St\u00e5hle", "given": "Elisabeth", "initials": "E"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2018-11-00", "journal": {"volume": "125", "issn": "1872-8332", "issue": null, "pages": "157-163", "title": "Lung Cancer", "issn-l": "0169-5002"}, "abstract": "Cancer-testis antigens (CTAs) are defined as proteins that are specifically expressed in testis or placenta and their expression is frequently activated in cancer. Due to their ability to induce an immune response, CTAs may serve as suitable targets for immunotherapy. The aim of this study was to evaluate if there is reactivity against CTAs in the plasma of non-small cell lung cancer (NSCLC) patients through the detection of circulating antibodies.\n\nTo comprehensively analyze autoantibodies against CTAs the multiplexing capacities of suspension bead array technology was used. Bead arrays were created with 120 protein fragments, representing 112 CTAs. Reactivity profiles were measured in plasma samples from 133 NSCLC patients and 57 cases with benign lung diseases.\n\nAltogether reactivity against 69 antigens, representing 81 CTAs, was demonstrated in at least one of the analyzed samples. Twenty-nine of the antigens (45 CTAs) demonstrated exclusive reactivity in NSCLC samples. Reactivity against cancer-testis antigen family 47; member A (CT47A) genes, P antigen family member 3 (PAGE3), variable charge X-linked (VCX), melanoma antigen family B1 (MAGEB1), lin-28 homolog B (LIN28B) and chromosome 12 open reading frame 54 (C12orf54) were only found in NSCLC patients at a frequency of 1%-4%. The presence of autoantibodies towards these six antigens was confirmed in an independent group of 34 NSCLC patients.\n\nWe identified autoantibodies against CTAs in the plasma of lung cancer patients. The reactivity pattern of autoantibodies was higher in cancer patients compared to the benign group, stable over time, but low in frequency of occurrence. The findings suggest that some CTAs are immunogenic and that these properties can be utilized as immune targets.", "doi": "10.1016/j.lungcan.2018.09.012", "pmid": "30429015", "labels": {"Autoimmunity and Serology Profiling": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0169-5002(18)30571-3"}], "notes": [], "created": "2018-09-27T10:09:23.485Z", "modified": "2024-01-16T13:48:45.262Z"}, {"entity": "publication", "iuid": "dbb7100176834f25a78cb9c51629e5e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbb7100176834f25a78cb9c51629e5e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbb7100176834f25a78cb9c51629e5e7"}}, "title": "Autoantibody profiling reveals four protein candidate autoantigens associated with systemic lupus erythematosus.", "authors": [{"family": "Frosteg\u00e5rd", "given": "J", "initials": "J"}, {"family": "Hellstr\u00f6m", "given": "C", "initials": "C"}, {"family": "Nilsson", "given": "P", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Frosteg\u00e5rd", "given": "A G", "initials": "AG"}, {"family": "Ajeganova", "given": "S", "initials": "S"}], "type": "journal article", "published": "2018-09-00", "journal": {"title": "Lupus", "issn": "1477-0962", "volume": "27", "issue": "10", "pages": "1670-1678", "issn-l": "0961-2033"}, "abstract": "Objectives In systemic lupus erythematosus (SLE) there are typically many autoantibodies. The disease heterogeneity could be better understood with discovery of phenotype-specific antigens targeted by autoantibodies. We here aimed to identify novel autoantigens potentially related to SLE disease and a major complication, atherosclerosis. Methods Antigen microarrays were used to profile IgG autoantibody reactivity against 77 protein fragments (20-140 amino acids (aa) long, median 89 aa) produced within the Human Protein Atlas project, in serum samples from SLE patients ( n = 107) and age- and sex-matched population-based controls ( n = 107). Common carotid intima-media thickness, plaque occurrence and echogenicity were determined by B-mode ultrasound. Results We determined significant differences between patients and controls in IgG reactivity against four proteins. In patients compared to controls, there was an increase of IgG reactivity against zinc finger protein 688 (ZNF688), early B cell factor 2 (EBF2), crystallin, alpha B (CRYAB) and tumor necrosis factor receptor superfamily member 13C (TNFRSF13C). Of these four antigens, only anti-ZNF688 was associated with carotid atherosclerosis (plaque occurrence) and vulnerable plaques in SLE. There was a weak association between anti-EBF2 and SLE disease activity but no significant associations were determined for other measured IgG reactivity. Conclusions In this discovery screening we here demonstrate new candidate autoantigens with differential reactivity (reflecting autoantibody levels) in SLE patients and in controls and in relation to atherosclerosis in SLE.", "doi": "10.1177/0961203318788153", "pmid": "30041579", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-11T08:03:22.586Z", "modified": "2021-07-07T15:50:03.355Z"}, {"entity": "publication", "iuid": "aa58c6b3b5294ad7879ee9e7314b39be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa58c6b3b5294ad7879ee9e7314b39be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa58c6b3b5294ad7879ee9e7314b39be"}}, "title": "SURGE complex of Plasmodium falciparum in the rhoptry-neck (SURFIN4.2-RON4-GLURP) contributes to merozoite invasion.", "authors": [{"family": "Quintana", "given": "Maria Del Pilar", "initials": "MDP"}, {"family": "Ch'ng", "given": "Jun-Hong", "initials": "JH"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Imam", "given": "Maryam", "initials": "M"}, {"family": "Hultenby", "given": "Kjell", "initials": "K"}, {"family": "Theisen", "given": "Michael", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Chan", "given": "Sherwin", "initials": "S"}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2018-08-09", "journal": {"volume": "13", "issn": "1932-6203", "issue": "8", "pages": "e0201669", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Plasmodium falciparum invasion into red blood cells (RBCs) is a complex process engaging proteins on the merozoite surface and those contained and sequentially released from the apical organelles (micronemes and rhoptries). Fundamental to invasion is the formation of a moving junction (MJ), a region of close apposition of the merozoite and the RBC plasma membranes, through which the merozoite draws itself before settling into a newly formed parasitophorous vacuole (PV). SURFIN4.2 was identified at the surface of the parasitized RBCs (pRBCs) but was also found apically associated with the merozoite. Using antibodies against the N-terminus of the protein we show the presence of SURFIN4.2 in the neck of the rhoptries, its secretion into the PV and shedding into the culture supernatant upon schizont rupture. Using immunoprecipitation followed by mass spectrometry we describe here a novel protein complex we have named SURGE where SURFIN4.2 forms interacts with the rhoptry neck protein 4 (RON4) and the Glutamate Rich Protein (GLURP). The N-terminal cysteine-rich-domain (CRD) of SURFIN4.2 mediates binding to the RBC membrane and its interaction with RON4 suggests its involvement in the contact between the merozoite apex and the RBC at the MJ. Supporting this suggestion, we also found that polyclonal antibodies to the extracellular domain (including the CRD) of SURFIN4.2 partially inhibit merozoite invasion. We propose that the formation of the SURGE complex participates in the establishment of parasite infection within the PV and the RBCs.", "doi": "10.1371/journal.pone.0201669", "pmid": "30092030", "labels": {"Autoimmunity and Serology Profiling": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-10007"}, {"db": "pmc", "key": "PMC6084945"}], "notes": [], "created": "2018-09-11T08:02:06.055Z", "modified": "2024-01-16T13:48:45.764Z"}, {"entity": "publication", "iuid": "a50bb36d96474125b75d2ea90439aca6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a50bb36d96474125b75d2ea90439aca6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a50bb36d96474125b75d2ea90439aca6"}}, "title": "Autoantibody profiling in intraocular fluid of patients with uveitis.", "authors": [{"family": "Ten Berge", "given": "Josianne C", "initials": "JC"}, {"family": "Schreurs", "given": "Marco Wj", "initials": "MW"}, {"family": "van Rosmalen", "given": "Joost", "initials": "J"}, {"family": "Rothova", "given": "Aniki", "initials": "A"}], "type": "journal article", "published": "2018-07-10", "journal": {"title": "Exp. Eye Res.", "issn": "1096-0007", "volume": "176", "issue": null, "pages": "141-146", "issn-l": "0014-4835"}, "abstract": "A high prevalence of serum antiretinal antibodies (ARAs) in patients with uveitis has been previously described, though their clinical role remains elusive. Assessment of intraocular ARAs may provide further insight into the pathogenesis of diverse uveitis entities. In this study we investigate the prevalence of multiple specific anti-ocular antibodies (AOcAs), including ARAs, in intraocular fluid of patients with uveitis. Autoantibody profiling with 188 different ocular antigens was performed by a multiplex immunoassay with intraocular fluid samples of 76 patients with uveitis. Clinical data from uveitis patients were collected and statistical analyses were executed to evaluate associations between intraocular AOcAs and clinical characteristics. Controls consisted of 19 intraocular fluid samples from cataract patients. A spectrum of 22 different AOcAs was present in higher levels in patients with uveitis than in controls (p\u202f<\u202f0.05), but in moderately elevated titers (<2x). High elevations of intraocular AOcAs in uveitis (>5x compared to cataract) were observed in varicella zoster virus-induced uveitis, multiple sclerosis-associated uveitis and patients with unexplained uveitis but positive quantiferon test. Presence of macular edema was associated with increased intraocular levels of tyrosinase antibodies. Our results show that patients with uveitis are characterized by the presence of a broad spectrum of moderately elevated levels of intraocular AOcAs, and high intraocular AOcA levels were found in several specific uveitis entities. This study favors secondary production of AOcAs and not their inciting role.", "doi": "10.1016/j.exer.2018.07.012", "pmid": "30006272", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-4835(18)30007-1"}], "notes": [], "created": "2018-09-11T08:12:48.253Z", "modified": "2021-03-05T08:22:49.705Z"}, {"entity": "publication", "iuid": "0919104287de4c74b1a57916ead0298b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0919104287de4c74b1a57916ead0298b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0919104287de4c74b1a57916ead0298b"}}, "title": "Multiplexed Antigen Bead Arrays for the Assessment of Antibody Selectivity and Epitope Mapping.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.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": "2018-05-02", "journal": {"volume": "1785", "issn": "1940-6029", "issue": null, "pages": "239-248", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "With the increasing number of binding reagents for affinity-based investigations of the human proteome, high-throughput tools for the characterization of the used reagents become essential. For the analysis of binding selectivity, bead-based antigen arrays offer a miniaturized and parallelized assay platform to meet such needs, as they enable two-dimensional multiplexing to analyze up to 384 samples against up to 500 analytes in a single round of analysis. In this chapter, we describe our protocols for the generation of multiplex bead arrays built on immobilized protein fragments, as well as biotinylated peptides. Combined together, these two versions of antigen arrays offer a versatile approach for multiplexed characterization of antibody binding selectivity, off-target interactions, as well as mapping for the amino acids of epitopes involved in antibody binding.", "doi": "10.1007/978-1-4939-7841-0_16", "pmid": "29714023", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2018-09-11T08:04:59.257Z", "modified": "2021-07-08T12:07:33.951Z"}, {"entity": "publication", "iuid": "fbf86430359d4c0da55f59a2a1c70d6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbf86430359d4c0da55f59a2a1c70d6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbf86430359d4c0da55f59a2a1c70d6a"}}, "title": "High-Density Antigen Microarrays for the Assessment of Antibody Selectivity and Off-Target Binding.", "authors": [{"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"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": "Ayoglu", "given": "Burcu", "initials": "B"}], "type": "journal article", "published": "2018-05-02", "journal": {"volume": "1785", "issn": "1940-6029", "issue": null, "pages": "231-238", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "With the increasing availability of collections of antibodies, their evaluation in terms of binding selectivity becomes an important but challenging task. Planar antigen microarrays are very suitable tools to address this task and provide a powerful proteomics platform for the characterization of the binding selectivity of antibodies toward thousands of antigens in parallel. In this chapter, we describe our in-house developed procedures for the generation of high-density planar antigen microarrays with over 21,000 features. We also provide the details of the assay protocol, which we routinely use for the assessment of binding selectivity of the polyclonal antibodies generated within the Human Protein Atlas.", "doi": "10.1007/978-1-4939-7841-0_15", "pmid": "29714022", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-11T08:04:14.919Z", "modified": "2024-01-16T13:48:46.345Z"}, {"entity": "publication", "iuid": "393b99fadee3457f861d2abb322eb0a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/393b99fadee3457f861d2abb322eb0a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/393b99fadee3457f861d2abb322eb0a1"}}, "title": "ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease.", "authors": [{"family": "Bremer", "given": "Hanna D", "initials": "HD"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Renneker", "given": "Stefanie", "initials": "S"}, {"family": "Lattwein", "given": "Erik", "initials": "E"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Lillieh\u00f6\u00f6k", "given": "Inger", "initials": "I"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Hansson-Hamlin", "given": "Helene", "initials": "H"}], "type": "journal article", "published": "2018-03-19", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "4852", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Dogs can spontaneously develop complex systemic autoimmune disorders, with similarities to human autoimmune disease. Autoantibodies directed at self-antigens are a key feature of these autoimmune diseases. Here we report the identification of interleukin enhancer-binding factors 2 and 3 (ILF2 and ILF3) as autoantigens in canine immune-mediated rheumatic disease. The ILF2 autoantibodies were discovered in a small, selected canine cohort through the use of human protein arrays; a method not previously described in dogs. Subsequently, ILF3 autoantibodies were also identified in the same cohort. The results were validated with an independent method in a larger cohort of dogs. ILF2 and ILF3 autoantibodies were found exclusively, and at a high frequency, in dogs that showed a speckled pattern of antinuclear antibodies on immunofluorescence. ILF2 and ILF3 autoantibodies were also found at low frequency in human patients with SLE and Sj\u00f6gren's syndrome. These autoantibodies have the potential to be used as diagnostic biomarkers for canine, and possibly also human, autoimmune disease.", "doi": "10.1038/s41598-018-23034-w", "pmid": "29556082", "labels": {"Autoimmunity and Serology Profiling": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-23034-w"}, {"db": "pmc", "key": "PMC5859008"}], "notes": [], "created": "2018-09-11T08:06:07.439Z", "modified": "2024-01-16T13:48:46.724Z"}, {"entity": "publication", "iuid": "fffb461dc95c4148b32555dcc16d46db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fffb461dc95c4148b32555dcc16d46db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fffb461dc95c4148b32555dcc16d46db"}}, "title": "Antibodies in children with malaria to PfEMP1, RIFIN and SURFIN expressed at the Plasmodium falciparum parasitized red blood cell surface.", "authors": [{"family": "Quintana", "given": "Maria Del Pilar", "initials": "MDP"}, {"family": "Ch'ng", "given": "Jun-Hong", "initials": "JH"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Idris", "given": "Zulkarnain Md", "initials": "ZM"}, {"family": "Saiwaew", "given": "Somporn", "initials": "S"}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2018-02-19", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "3262", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Naturally acquired antibodies to proteins expressed on the Plasmodium falciparum parasitized red blood cell (pRBC) surface steer the course of a malaria infection by reducing sequestration and stimulating phagocytosis of pRBC. Here we have studied a selection of proteins representing three different parasite gene families employing a well-characterized parasite with a severe malaria phenotype (FCR3S1.2). The presence of naturally acquired antibodies, impact on rosetting rate, surface reactivity and opsonization for phagocytosis in relation to different blood groups of the ABO system were assessed in a set of sera from children with mild or complicated malaria from an endemic area. We show that the naturally acquired immune responses, developed during malaria natural infection, have limited access to the pRBCs inside a blood group A rosette. The data also indicate that SURFIN", "doi": "10.1038/s41598-018-21026-4", "pmid": "29459776", "labels": {"Autoimmunity and Serology Profiling": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-21026-4"}, {"db": "pmc", "key": "PMC5818650"}], "notes": [], "created": "2018-09-11T08:08:52.221Z", "modified": "2024-01-16T13:48:46.915Z"}, {"entity": "publication", "iuid": "34f2371179704c95b05bc42435907de7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34f2371179704c95b05bc42435907de7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34f2371179704c95b05bc42435907de7"}}, "title": "Thiol-ene-epoxy thermoset for low-temperature bonding to biofunctionalized microarray surfaces.", "authors": [{"family": "Zhou", "given": "Xiamo C", "initials": "XC"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Druet", "given": "Amaury", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "van der Wijngaart", "given": "Wouter", "initials": "W"}, {"family": "Haraldsson", "given": "Tommy", "initials": "T"}, {"family": "Carlborg", "given": "Carl Fredrik", "initials": "CF"}], "type": "journal article", "published": "2017-10-25", "journal": {"volume": "17", "issn": "1473-0189", "issue": "21", "pages": "3672-3681", "title": "Lab Chip", "issn-l": null}, "abstract": "One way to improve the sensitivity and throughput of miniaturized biomolecular assays is to integrate microfluidics to enhance the transport efficiency of biomolecules to the reaction sites. Such microfluidic integration requires bonding of a prefabricated microfluidic gasket to an assay surface without destroying its biological activity. In this paper we address the largely unmet challenge to accomplish a proper seal between a microfluidic gasket and a protein surface, with maintained biological activity and without contaminating the surface or blocking the microfluidic channels. We introduce a novel dual cure polymer resin for the formation of microfluidic gaskets that can be room-temperature bonded to a range of substrates using only UVA light. This polymer is the first polymer that features over a month of shelf life between the structure formation and the bonding, moreover the fully cured polymer gaskets feature the following set of properties suitable for microfluidics: high stiffness, which prevents microfluidic channel collapse during handling; very limited absorption of biomolecules; and no significant leaching of uncured monomers. We describe the novel polymer resin and its characteristics, study through FT-IR, and demonstrate its use as microfluidic well-arrays bonded onto protein array slides at room temperature followed by multiplexed immunoassays. The results confirm maintained biological activity and show high repeatability between protein arrays. This new approach for integrating microfluidic gaskets to biofunctionalised surfaces has the potential to improve sample throughput and decrease manufacturing costs for miniaturized biomolecular systems.", "doi": "10.1039/c7lc00652g", "pmid": "28975170", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T12:13:55.170Z", "modified": "2021-07-08T12:07:34.033Z"}, {"entity": "publication", "iuid": "5b8b687aecf24e9eba5daa40a6545bc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b8b687aecf24e9eba5daa40a6545bc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b8b687aecf24e9eba5daa40a6545bc9"}}, "title": "Clonal Evolution of Autoreactive Germinal Centers.", "authors": [{"family": "Degn", "given": "S\u00f8ren E", "initials": "SE"}, {"family": "van der Poel", "given": "Cees E", "initials": "CE"}, {"family": "Firl", "given": "Daniel J", "initials": "DJ"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Al Qureshah", "given": "Fahd A", "initials": "FA"}, {"family": "Bajic", "given": "Goran", "initials": "G"}, {"family": "Mesin", "given": "Luka", "initials": "L"}, {"family": "Reynaud", "given": "Claude-Agn\u00e8s", "initials": "CA"}, {"family": "Weill", "given": "Jean-Claude", "initials": "JC"}, {"family": "Utz", "given": "Paul J", "initials": "PJ"}, {"family": "Victora", "given": "Gabriel D", "initials": "GD"}, {"family": "Carroll", "given": "Michael C", "initials": "MC"}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "170", "issn": "1097-4172", "issue": "5", "pages": "913-926.e19", "title": "Cell", "issn-l": "0092-8674"}, "abstract": "Germinal centers (GCs) are the primary sites of clonal B cell expansion and affinity maturation, directing the production of high-affinity antibodies. This response is a central driver of pathogenesis in autoimmune diseases, such as systemic lupus erythematosus (SLE), but the natural history of autoreactive GCs remains unclear. Here, we present a novel mouse model where the presence of a single autoreactive B cell clone drives the TLR7-dependent activation, expansion, and differentiation of other autoreactive B\u00a0cells in spontaneous GCs. Once tolerance was broken for one self-antigen, autoreactive GCs generated B cells targeting other self-antigens. GCs became independent of the initial clone and evolved toward dominance of individual clonal lineages, indicating affinity maturation. This process produced serum autoantibodies to a breadth of self-antigens, leading to antibody deposition in the kidneys. Our data provide insight into the maturation of the self-reactive B cell response, contextualizing the epitope spreading observed in autoimmune disease.", "doi": "10.1016/j.cell.2017.07.026", "pmid": "28841417", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(17)30833-4"}], "notes": [], "created": "2017-12-19T15:31:50.567Z", "modified": "2021-03-05T08:22:49.621Z"}, {"entity": "publication", "iuid": "216ae64b6c9f43328ad351f4c4320330", "links": {"self": {"href": "https://publications.scilifelab.se/publication/216ae64b6c9f43328ad351f4c4320330.json"}, "display": {"href": "https://publications.scilifelab.se/publication/216ae64b6c9f43328ad351f4c4320330"}}, "title": "Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis.", "authors": [{"family": "Zandian", "given": "A", "initials": "A"}, {"family": "Wing\u00e5rd", "given": "L", "initials": "L"}, {"family": "Nilsson", "given": "H", "initials": "H"}, {"family": "Sj\u00f6stedt", "given": "E", "initials": "E"}, {"family": "Johansson", "given": "D X", "initials": "DX"}, {"family": "Just", "given": "D", "initials": "D"}, {"family": "Hellstr\u00f6m", "given": "C", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "M", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "J M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "A", "initials": "A"}, {"family": "Norbeck", "given": "O", "initials": "O"}, {"family": "Owe-Larsson", "given": "B", "initials": "B"}, {"family": "Nilsson", "given": "P", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Persson", "given": "M A A", "initials": "MAA"}], "type": "journal article", "published": "2017-07-25", "journal": {"volume": "7", "issn": "2158-3188", "issue": "7", "pages": "e1177", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": "Immunological and inflammatory reactions have been suggested to have a role in the development of schizophrenia, a hypothesis that has recently been supported by genetic data. The aim of our study was to perform an unbiased search for autoantibodies in patients with a first psychotic episode, and to explore the association between any seroreactivity and the development of a Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM-IV) disorder characterized by chronic or relapsing psychotic symptoms. We collected plasma samples from 53 patients when they were treated for their first-episode psychosis, and 41 non-psychotic controls, after which the patients were followed for a mean duration of 7 years. Thirty patients were diagnosed with schizophrenia, delusional disorder, schizoaffective disorder, bipolar disorder or a long-term unspecified nonorganic psychosis during follow-up, whereas 23 patients achieved complete remission. At the end of follow-up, plasma samples were analyzed for IgG reactivity to 2304 fragments of human proteins using a multiplexed affinity proteomic technique. Eight patient samples showed autoreactivity to the N-terminal fragment of the PAGE (P antigen) protein family (PAGE2B/PAGE2/PAGE5), whereas no such autoreactivity was seen among the controls. PAGE autoreactivity was associated with a significantly increased risk of being diagnosed with schizophrenia during follow-up (odds ratio 6.7, relative risk 4.6). An immunohistochemistry analysis using antisera raised against the N-terminal fragment stained an unknown extracellular target in human cortical brain tissue. Our findings suggest that autoreactivity to the N-terminal portion of the PAGE protein family is associated with schizophrenia in a subset of patients with first-episode psychosis.", "doi": "10.1038/tp.2017.160", "pmid": "28742074", "labels": {"Tissue Profiling": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "tp2017160"}, {"db": "pmc", "key": "PMC5538130"}], "notes": [], "created": "2017-11-02T11:35:53.436Z", "modified": "2021-07-08T13:44:33.083Z"}, {"entity": "publication", "iuid": "abdbca126350420e9b7f8ebdea2f3541", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abdbca126350420e9b7f8ebdea2f3541.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abdbca126350420e9b7f8ebdea2f3541"}}, "title": "Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage.", "authors": [{"family": "Ge", "given": "Changrong", "initials": "C"}, {"family": "Tong", "given": "Dongmei", "initials": "D"}, {"family": "Liang", "given": "Bibo", "initials": "B"}, {"family": "L\u00f6nnblom", "given": "Erik", "initials": "E"}, {"family": "Schneider", "given": "Nadine", "initials": "N"}, {"family": "Hagert", "given": "Cecilia", "initials": "C"}, {"family": "Viljanen", "given": "Johan", "initials": "J"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Stawikowska", "given": "Roma", "initials": "R"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Fields", "given": "Gregg B", "initials": "GB"}, {"family": "Skogh", "given": "Thomas", "initials": "T"}, {"family": "Kastbom", "given": "Alf", "initials": "A"}, {"family": "Kihlberg", "given": "Jan", "initials": "J"}, {"family": "Burkhardt", "given": "Harald", "initials": "H"}, {"family": "Dobritzsch", "given": "Doreen", "initials": "D"}, {"family": "Holmdahl", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2017-07-06", "journal": {"volume": "2", "issn": "2379-3708", "issue": "13", "pages": null, "title": "JCI Insight", "issn-l": "2379-3708"}, "abstract": "Today, it is known that autoimmune diseases start a long time before clinical symptoms appear. Anti-citrullinated protein antibodies (ACPAs) appear many years before the clinical onset of rheumatoid arthritis (RA). However, it is still unclear if and how ACPAs are arthritogenic. To better understand the molecular basis of pathogenicity of ACPAs, we investigated autoantibodies reactive against the C1 epitope of collagen type II (CII) and its citrullinated variants. We found that these antibodies are commonly occurring in RA. A mAb (ACC1) against citrullinated C1 was found to cross-react with several noncitrullinated epitopes on native CII, causing proteoglycan depletion of cartilage and severe arthritis in mice. Structural studies by X-ray crystallography showed that such recognition is governed by a shared structural motif \"RG-TG\" within all the epitopes, including electrostatic potential-controlled citrulline specificity. Overall, we have demonstrated a molecular mechanism that explains how ACPAs trigger arthritis.", "doi": "10.1172/jci.insight.93688", "pmid": "28679953", "labels": {"Protein Science Facility (PSF)": "Service", "Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "93688"}, {"db": "pmc", "key": "PMC5499374"}], "notes": [], "created": "2017-10-05T06:44:19.600Z", "modified": "2021-07-07T15:50:03.269Z"}, {"entity": "publication", "iuid": "1fbfeb18c3aa4a91b322f65e6504dbe5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fbfeb18c3aa4a91b322f65e6504dbe5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fbfeb18c3aa4a91b322f65e6504dbe5"}}, "title": "High-Density Serum/Plasma Reverse Phase Protein Arrays.", "authors": [{"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"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": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}], "type": "journal article", "published": "2017-07-05", "journal": {"volume": "1619", "issn": "1940-6029", "issue": null, "pages": "229-238", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "In-depth exploration and characterization of human serum and plasma proteomes is an attractive strategy for the identification of potential prognostic or diagnostic biomarkers. The possibility of analyzing larger numbers of samples in a high-throughput fashion has markedly increased with affinity-based microarrays, thus providing higher statistical power to these biomarker studies. Here, we describe a protocol for high-density serum and plasma reverse phase protein arrays (RPPAs). We demonstrate how a biobank of 12,392 samples was immobilized and analyzed on a single microarray slide, allowing high-quality profiling of abundant target proteins across all samples in one assay.", "doi": "10.1007/978-1-4939-7057-5_18", "pmid": "28674890", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:36:59.288Z", "modified": "2021-07-08T12:07:33.995Z"}, {"entity": "publication", "iuid": "38aaed196e084a14b7adad22ab9523a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38aaed196e084a14b7adad22ab9523a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38aaed196e084a14b7adad22ab9523a9"}}, "title": "Neuroproteomic Profiling of Cerebrospinal Fluid (CSF) by Multiplexed Affinity Arrays.", "authors": [{"family": "H\u00e4ggmark-M\u00e5nberg", "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": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2017-05-17", "journal": {"volume": "1598", "issn": "1940-6029", "issue": null, "pages": "247-254", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Protein profiling through affinity proteomic approaches represents a powerful strategy for the analysis of human body fluids. Cerebrospinal fluid (CSF), being the fluid proximal to the central nervous system, is commonly analyzed in the context of neurological diseases, and can offer novel insights into the physiological state of the brain. Ultimately, and by analyzing the presence of brain-derived proteins in larger sets of samples that represent different phenotypes, profiling of CSF may serve as an important source to discover and verify disease-associated markers. Here, we describe a multiplexed and flexible protein profiling approach using antibody-based assays on suspension bead arrays. Through streamlined sample processing, protein biotinylation, and single-binder assay readout, this method enables high-throughput neuroproteomic analysis of up to 384 proteins in 384 samples.", "doi": "10.1007/978-1-4939-6952-4_11", "pmid": "28508365", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:18:02.763Z", "modified": "2021-07-08T12:07:34.045Z"}, {"entity": "publication", "iuid": "60f106fef94544f29aab7a81662a8624", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60f106fef94544f29aab7a81662a8624.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60f106fef94544f29aab7a81662a8624"}}, "title": "Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies.", "authors": [{"family": "Sierra-S\u00e1nchez", "given": "\u00c1lvaro", "initials": "\u00c1"}, {"family": "Garrido-Mart\u00edn", "given": "Diego", "initials": "D"}, {"family": "Lourido", "given": "Luc\u00eda", "initials": "L"}, {"family": "Gonz\u00e1lez-Gonz\u00e1lez", "given": "Mar\u00eda", "initials": "M"}, {"family": "D\u00edez", "given": "Paula", "initials": "P"}, {"family": "Ruiz-Romero", "given": "Cristina", "initials": "C"}, {"family": "Sj\u00f6ber", "given": "Ronald", "initials": "R"}, {"family": "Droste", "given": "Conrad", "initials": "C"}, {"family": "De Las Rivas", "given": "Javier", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Blanco", "given": "Francisco", "initials": "F"}, {"family": "Fuentes", "given": "Manuel", "initials": "M"}], "type": "journal article", "published": "2017-05-05", "journal": {"volume": "16", "issn": "1535-3907", "issue": "5", "pages": "1890-1899", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Osteoarthritis (OA) is one of the most prevalent articular diseases. The identification of proteins closely associated with the diagnosis, progression, prognosis, and treatment response is dramatically required for this pathology. In this work, differential serum protein profiles have been identified in OA and rheumatoid arthritis (RA) by antibody arrays containing 151 antibodies against 121 antigens in a cohort of 36 samples. Then the identified differential serum protein profiles have been validated in a larger cohort of 282 samples. The overall immunoreactivity is higher in the pathological situations in comparison with the controls. Several proteins have been identified as biomarker candidates for OA and RA. Most of these biomarker candidates are proteins related to inflammatory response, lipid metabolism, or bone and extracellular matrix formation, degradation, or remodeling.", "doi": "10.1021/acs.jproteome.6b00980", "pmid": "28379711", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:37:51.039Z", "modified": "2021-07-07T15:50:03.155Z"}, {"entity": "publication", "iuid": "ffaed83ff04c4f058b2fb20f13022ba5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffaed83ff04c4f058b2fb20f13022ba5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffaed83ff04c4f058b2fb20f13022ba5"}}, "title": "A Preliminary Report: Radical Surgery and Stem Cell Transplantation for the Treatment of Patients With Pancreatic Cancer.", "authors": [{"family": "Omazic", "given": "Brigitta", "initials": "B"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "L\u00f6hr", "given": "Matthias", "initials": "M"}, {"family": "Segersv\u00e4rd", "given": "Ralf", "initials": "R"}, {"family": "Verbeke", "given": "Caroline", "initials": "C"}, {"family": "Magalhaes", "given": "Isabelle", "initials": "I"}, {"family": "Potacova", "given": "Zuzana", "initials": "Z"}, {"family": "Mattsson", "given": "Jonas", "initials": "J"}, {"family": "Terman", "given": "Alexei", "initials": "A"}, {"family": "Ghazi", "given": "Sam", "initials": "S"}, {"family": "Albiin", "given": "Nils", "initials": "N"}, {"family": "Kartalis", "given": "Nikolaos", "initials": "N"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Poiret", "given": "Thomas", "initials": "T"}, {"family": "Zhenjiang", "given": "Liu", "initials": "L"}, {"family": "Heuchel", "given": "Rainer", "initials": "R"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Permert", "given": "Johan", "initials": "J"}, {"family": "Maeurer", "given": "Markus J", "initials": "MJ"}, {"family": "Ringden", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "40", "issn": "1537-4513", "issue": "4", "title": "J. Immunother.", "pages": "132-139", "issn-l": "1524-9557"}, "abstract": "We examined the immunologic effects of allogeneic hematopoietic stem cell transplantation (HSCT) in the treatment of pancreatic ductal adenocarcinoma, a deadly disease with a median survival of 24 months for resected tumors and a 5-year survival rate of 6%. After adjuvant chemotherapy, 2 patients with resected pancreatic ductal adenocarcinoma underwent HSCT with HLA-identical sibling donors. Comparable patients who underwent radical surgery, but did not have a donor, served as controls (n=6). Both patients developed humoral and cellular (ie, HLA-A*01:01-restricted) immune responses directed against 2 novel tumor-associated antigens (TAAs), INO80E and UCLH3 after HSCT. Both TAAs were highly expressed in the original tumor tissue suggesting that HSCT promoted a clinically relevant, long-lasting cellular immune response. In contrast to untreated controls, who succumbed to progressive disease, both patients are tumor-free 9 years after diagnosis. Radical surgery combined with HSCT may cure pancreatic adenocarcinoma and change the cellular immune repertoire capable of responding to clinically and biologically relevant TAAs.", "doi": "10.1097/CJI.0000000000000164", "pmid": "28338506", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:39:38.489Z", "modified": "2021-07-08T12:07:34.361Z"}, {"entity": "publication", "iuid": "442e355248544b87a31a6f4208cade10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/442e355248544b87a31a6f4208cade10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/442e355248544b87a31a6f4208cade10"}}, "title": "Whole-Proteome Peptide Microarrays for Profiling Autoantibody Repertoires within Multiple Sclerosis and Narcolepsy.", "authors": [{"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"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": "Ayoglu", "given": "Burcu", "initials": "B"}], "type": "journal article", "published": "2017-03-03", "journal": {"volume": "16", "issn": "1535-3907", "issue": "3", "pages": "1300-1314", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "The underlying molecular mechanisms of autoimmune diseases are poorly understood. To unravel the autoimmune processes across diseases, comprehensive and unbiased analyses of proteins targets recognized by the adaptive immune system are needed. Here we present an approach starting from high-density peptide arrays to characterize autoantibody repertoires and to identify new autoantigens. A set of ten plasma and serum samples from subjects with multiple sclerosis, narcolepsy, and without any disease diagnosis were profiled on a peptide array representing the whole proteome, hosting 2.2 million 12-mer peptides with a six amino acid lateral shift. On the basis of the IgG reactivities found on these whole-proteome peptide microarrays, a set of 23 samples was then studied on a targeted array with 174\u202f000 12-mer peptides of single amino acid lateral shift. Finally, verification of IgG reactivities was conducted with a larger sample set (n = 448) using the bead-based peptide microarrays. The presented workflow employed three different peptide microarray formats to discover and resolve the epitopes of human autoantibodies and revealed two potentially new autoantigens: MAP3K7 in multiple sclerosis and NRXN1 in narcolepsy. The presented strategy provides insights into antibody repertoire reactivity at a peptide level and may accelerate the discovery and validation of autoantigens in human diseases.", "doi": "10.1021/acs.jproteome.6b00916", "pmid": "28121444", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:40:32.221Z", "modified": "2021-07-08T13:44:33.196Z"}, {"entity": "publication", "iuid": "4463761683c544979c68bd54d04d4690", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4463761683c544979c68bd54d04d4690.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4463761683c544979c68bd54d04d4690"}}, "title": "Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing.", "authors": [{"family": "Ch'ng", "given": "Jun-Hong", "initials": "JH"}, {"family": "Sirel", "given": "Madle", "initials": "M"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Del Pilar Quintana", "given": "Maria", "initials": "M"}, {"family": "Chun Leung Chan", "given": "Sherwin", "initials": "S"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Tellgren-Roth", "given": "Asa", "initials": "A"}, {"family": "Nilsson", "given": "IngMarie", "initials": "I"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2017-02-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43190", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Variable surface antigens of Plasmodium falciparum have been a major research focus since they facilitate parasite sequestration and give rise to deadly malaria complications. Coupled with its potential use as a vaccine candidate, the recent suggestion that the repetitive interspersed families of polypeptides (RIFINs) mediate blood group A rosetting and influence blood group distribution has raised the research profile of these adhesins. Nevertheless, detailed investigations into the functions of this highly diverse multigene family remain hampered by the limited number of validated reagents. In this study, we assess the specificities of three promising polyclonal anti-RIFIN antibodies that were IgG-purified from sera of immunized animals. Their epitope regions were mapped using a 175,000-peptide microarray holding overlapping peptides of the P. falciparum variable surface antigens. Through immunoblotting and immunofluorescence imaging, we show that different antibodies give varying results in different applications/assays. Finally, we authenticate the antibody-based detection of RIFINs in two previously uncharacterized non-rosetting parasite lines by identifying the dominant rif transcripts using RNA sequencing.", "doi": "10.1038/srep43190", "pmid": "28233866", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "srep43190"}, {"db": "pmc", "key": "PMC5324397"}], "notes": [], "created": "2017-11-02T11:40:03.653Z", "modified": "2021-07-07T15:50:03.085Z"}, {"entity": "publication", "iuid": "77013ba616c2495e8f68bf6a247e26f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77013ba616c2495e8f68bf6a247e26f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77013ba616c2495e8f68bf6a247e26f2"}}, "title": "Towards encoded particles for highly multiplexed colorimetric point of care autoantibody detection.", "authors": [{"family": "Svedberg", "given": "Gustav", "initials": "G"}, {"family": "Jeong", "given": "Yunjin", "initials": "Y"}, {"family": "Na", "given": "Hunjong", "initials": "H"}, {"family": "Jang", "given": "Jisung", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Kwon", "given": "Sunghoon", "initials": "S"}, {"family": "Gantelius", "given": "Jesper", "initials": "J"}, {"family": "Svahn", "given": "Helene Andersson", "initials": "HA"}], "type": "journal article", "published": "2017-01-31", "journal": {"volume": "17", "issn": "1473-0189", "issue": "3", "pages": "549-556", "title": "Lab Chip", "issn-l": null}, "abstract": "Highly multiplexed point of care tests could improve diagnostic accuracy and differential diagnostic capacity in for instance emergency medicine and low resource environments. Available technology platforms for POC biomarker detection are typically simplex or low-plexed, whereas common lab-based microarray systems allow for the simultaneous detection of thousands of DNA or protein biomarkers. In this study, we demonstrate a novel suspension particle array platform that utilizes 900 \u03bcm bricks for POC amenable colorimetric biomarker detection with an encoding capacity of over two million. Due to the mm-scale size, both the lithographic codes and colorimetric signals of individual particles can be visualized using a consumer grade office flatbed scanner, with a potential for simultaneous imaging of around 19\u2009000 particles per scan. The analytical sensitivity of the assay was determined to be 4 ng ml(-1) using an antibody model system. As a proof of concept, autoantibodies toward anoctamin 2 were detected in order to discriminate between multiple sclerosis plasma samples and healthy controls with p < 0.0001 and an inter-assay % CV of 9.44%.", "doi": "10.1039/c6lc01358a", "pmid": "28102419", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:41:16.257Z", "modified": "2021-07-07T15:50:03.198Z"}, {"entity": "publication", "iuid": "3d0cc871ee8644d1b9ecf349a1eb0965", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d0cc871ee8644d1b9ecf349a1eb0965.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d0cc871ee8644d1b9ecf349a1eb0965"}}, "title": "Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer.", "authors": [{"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Henjes", "given": "Frauke", "initials": "F"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Magnusson", "given": "Patrik", "initials": "P"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"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": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2017-01-06", "journal": {"volume": "16", "issn": "1535-3907", "issue": "1", "pages": "204-216", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "There is a demand for novel targets and approaches to diagnose and treat prostate cancer (PCA). In this context, serum and plasma samples from a total of 609 individuals from two independent patient cohorts were screened for IgG reactivity against a sum of 3833 human protein fragments. Starting from planar protein arrays with 3786 protein fragments to screen 80 patients with and without PCA diagnosis, 161 fragments (4%) were chosen for further analysis based on their reactivity profiles. Adding 71 antigens from literature, the selection of antigens was corroborated for their reactivity in a set of 550 samples using suspension bead arrays. The antigens prostein (SLC45A3), TATA-box binding protein (TBP), and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) showed higher reactivity in PCA patients with late disease compared with early disease. Because of its prostate tissue specificity, we focused on prostein and continued with mapping epitopes of the 66-mer protein fragment using patient samples. Using bead-based assays and 15-mer peptides, a minimal peptide epitope was identified and refined by alanine scanning to the KPxAPFP. Further sequence alignment of this motif revealed homology to transmembrane protein 79 (TMEM79) and TGF-beta-induced factor 2 (TGIF2), thus providing a reasoning for cross-reactivity found in females. A comprehensive workflow to discover and validate IgG reactivity against prostein and homologous targets in human serum and plasma was applied. This study provides useful information when searching for novel biomarkers or drug targets that are guided by the reactivity of the immune system against autoantigens.", "doi": "10.1021/acs.jproteome.6b00620", "pmid": "27700103", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:14.584Z", "modified": "2021-07-08T13:44:33.168Z"}, {"entity": "publication", "iuid": "6d4051df52d54ba9bfd4f813cd64f9d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d4051df52d54ba9bfd4f813cd64f9d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d4051df52d54ba9bfd4f813cd64f9d5"}}, "title": "Serum Autoantibody Profiling of Patients with Paraneoplastic and Non-Paraneoplastic Autoimmune Retinopathy.", "authors": [{"family": "Ten Berge", "given": "Josianne C", "initials": "JC"}, {"family": "van Rosmalen", "given": "Joost", "initials": "J"}, {"family": "Vermeer", "given": "Jacolien", "initials": "J"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Rothova", "given": "Aniki", "initials": "A"}, {"family": "Schreurs", "given": "Marco W J", "initials": "MW"}], "type": "journal article", "published": "2016-12-08", "journal": {"volume": "11", "issn": "1932-6203", "issue": "12", "pages": "e0167909", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Although multiple serum antiretinal autoantibodies (ARAs) have been reported in patients with paraneoplastic and non-paraneoplastic autoimmune retinopathy ((n)pAIR), not all retinal antigens involved in (n)pAIR are specified. This study aims to serologically identify patients with presumed (n)pAIR through determination of both known and unknown ARAs by autoantibody profiling.\n\nAn antigen suspension bead array using 188 different antigens representing 97 ocular proteins was performed to detect ARAs in serum samples of patients with presumed (n)pAIR (n = 24), uveitis (n = 151) and cataract (n = 21). Logistic regressions were used to estimate the associations between ocular antigens and diagnosis. Validation of interphotoreceptor matrix proteoglycan 2 (IMPG2) and recoverin antigens was performed by immunohistochemistry and immunoblot, respectively.\n\nSamples of patients with presumed (n)pAIR exhibited a broad spectrum of ARAs. We identified retinal antigens that have already been described previously (e.g. recoverin), but also identified novel ARA targets. Most ARAs were not specific for (n)pAIR since their presence was also observed in patients with cataract or uveitis. High titers of autoantibodies directed against photoreceptor-specific nuclear receptor and retinol-binding protein 3 were more common in patients with presumed (n)pAIR compared to uveitis (p = 0.015 and p = 0.018, respectively). The presence of all other ARAs did not significantly differ between groups. In patients with presumed (n)pAIR, anti-recoverin autoantibodies were the most prevalent ARAs. Validation of bead array results by immunohistochemistry (anti-IMPG2) and immunoblot (anti-recoverin) showed concordant results in (n)pAIR patients.\n\nPatients with (n)pAIR are characterized by the presence of a broad spectrum of ARAs. The diagnosis of (n)pAIR cannot be based on the mere presence of serum ARAs, as these are also commonly present in uveitis as well as in age-related cataract patients.", "doi": "10.1371/journal.pone.0167909", "pmid": "27930731", "labels": {"Tissue Profiling": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-31043"}, {"db": "pmc", "key": "PMC5145218"}], "notes": [], "created": "2017-05-03T12:59:15.494Z", "modified": "2021-07-07T15:50:03.173Z"}, {"entity": "publication", "iuid": "fa3ef484e6d748b4966432d39d1173e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa3ef484e6d748b4966432d39d1173e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa3ef484e6d748b4966432d39d1173e0"}}, "title": "Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling.", "authors": [{"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2016-09-25", "journal": {"volume": "33", "issn": "1876-4347", "issue": "5 Pt A", "pages": "582-592", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "High-density protein microarrays of recombinant human protein fragments, representing 12,412 unique Ensembl Gene IDs, have here been produced and explored. These protein microarrays were used to analyse antibody off-target interactions, as well as for profiling the human autoantibody repertoire in plasma against the antigens represented by the protein fragments. Affinity-purified polyclonal antibodies produced within the Human Protein Atlas (HPA) were analysed on microarrays of three different sizes, ranging from 384 antigens to 21,120 antigens, for evaluation of the antibody validation criteria in the HPA. Plasma samples from secondary progressive multiple sclerosis patients were also screened in order to explore the feasibility of these arrays for broad-scale profiling of autoantibody reactivity. Furthermore, analysis on these near proteome-wide microarrays was complemented with analysis on HuProt\u2122 Human Proteome protein microarrays. The HPA recombinant protein microarray with 21,120 antigens and the HuProt\u2122 Human Proteome protein microarray are currently the largest protein microarray platforms available to date. The results on these arrays show that the Human Protein Atlas antibodies have few off-target interactions if the antibody validation criteria are kept stringent and demonstrate that the HPA-produced high-density recombinant protein fragment microarrays allow for a high-throughput analysis of plasma for identification of possible autoantibody targets in the context of various autoimmune conditions.", "doi": "10.1016/j.nbt.2015.09.002", "pmid": "26417875", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(15)00154-5"}], "notes": [], "created": "2017-05-02T12:58:25.314Z", "modified": "2021-07-08T13:44:33.755Z"}, {"entity": "publication", "iuid": "cec0e6d64af84e8a85d94a5a36393b4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cec0e6d64af84e8a85d94a5a36393b4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cec0e6d64af84e8a85d94a5a36393b4b"}}, "title": "Autoantibody targets in vaccine-associated narcolepsy.", "authors": [{"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Lima Bomfim", "given": "Izaura", "initials": "I"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Arnheim-Dahlstr\u00f6m", "given": "Lisen", "initials": "L"}, {"family": "Hallb\u00f6\u00f6k", "given": "Tove", "initials": "T"}, {"family": "Darin", "given": "Niklas", "initials": "N"}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Partinen", "given": "Markku", "initials": "M"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2016-09-00", "journal": {"volume": "49", "issn": "1607-842X", "issue": "6", "pages": "421-433", "title": "Autoimmunity", "issn-l": "0891-6934"}, "abstract": "Narcolepsy is a chronic sleep disorder with a yet unknown cause, but the specific loss of hypocretin-producing neurons together with a strong human leukocyte antigen (HLA) association has led to the hypothesis that autoimmune mechanisms might be involved. Here, we describe an extensive effort to profile autoimmunity repertoires in serum with the aim to find disease-related autoantigens. Initially, 57 serum samples from vaccine-associated and sporadic narcolepsy patients and controls were screened for IgG reactivity towards 10 846 fragments of human proteins using planar microarrays. The discovered differential reactivities were verified on suspension bead arrays in the same sample collection followed by further investigation of 14 antigens in 176 independent samples, including 57 narcolepsy patients. Among these 14 antigens, methyltransferase-like 22 (METTL22) and 5'-nucleotidase cytosolic IA (NT5C1A) were recognized at a higher frequency in narcolepsy patients of both sample sets. Upon sequence analysis of the 14 proteins, polymerase family, member 3 (PARP3), acyl-CoA-binding domain containing 7 (ARID4B), glutaminase 2 (GLS2) and cyclin-dependent kinase-like 1 (CDKL1) were found to contain amino acid sequences with homology to proteins found in the H1N1 vaccine. These findings could become useful elements of further clinical assays that aim towards a better phenotypic understanding of narcolepsy and its triggers.", "doi": "10.1080/08916934.2016.1183655", "pmid": "27206786", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:15.201Z", "modified": "2021-07-08T13:44:33.640Z"}, {"entity": "publication", "iuid": "d3e71dbad2824161ac09fe05702d8d67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3e71dbad2824161ac09fe05702d8d67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3e71dbad2824161ac09fe05702d8d67"}}, "title": "Antigen arrays for profiling autoantibody repertoires.", "authors": [{"family": "Ayoglu", "given": "Burcu", "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"}}], "type": "journal article", "published": "2016-05-00", "journal": {"volume": "8", "issn": "1757-6199", "issue": "10", "pages": "1105-1126", "title": "Bioanalysis", "issn-l": "1757-6180"}, "abstract": "Autoantibodies are a key component for the diagnosis, prognosis and monitoring of various diseases. In order to discover novel autoantibody targets, highly multiplexed assays based on antigen arrays hold a great potential and provide possibilities to analyze hundreds of body fluid samples for their reactivity pattern against thousands of antigens in parallel. Here, we provide an overview of the available technologies for producing antigen arrays, highlight some of the technical and methodological considerations and discuss their applications as discovery tools. Together with recent studies utilizing antigen arrays, we give an overview on how the different types of antigen arrays have and will continue to deliver novel insights into autoimmune diseases among several others.", "doi": "10.4155/bio.16.31", "pmid": "27097564", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:15.784Z", "modified": "2021-07-08T12:07:34.287Z"}, {"entity": "publication", "iuid": "90b020cf6aaf415fbd5f81ac9c8c3fc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90b020cf6aaf415fbd5f81ac9c8c3fc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90b020cf6aaf415fbd5f81ac9c8c3fc8"}}, "title": "Neuroproteomic profiling of human body fluids.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"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"}}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "10", "issn": "1862-8354", "issue": "4", "pages": "485-502", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "Analysis of protein expression and abundance provides a possibility to extend the current knowledge on disease-associated processes and pathways. The human brain is a complex organ and dysfunction or damage can give rise to a variety of neurological diseases. Although many proteins potentially reflecting disease progress are originating from brain, the scarce availability of human tissue material has lead to utilization of body fluids such as cerebrospinal fluid and blood in disease-related research. Within the most common neurological disorders, much effort has been spent on studying the role of a few hallmark proteins in disease pathogenesis but despite extensive investigation, the signatures they provide seem insufficient to fully understand and predict disease progress. In order to expand the view the field of neuroproteomics has lately emerged alongside developing technologies, such as affinity proteomics and mass spectrometry, for multiplexed and high-throughput protein profiling. Here, we provide an overview of how such technologies have been applied to study neurological disease and we also discuss some important considerations concerning discovery of disease-associated profiles.", "doi": "10.1002/prca.201500065", "pmid": "26286680", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:42:43.819Z", "modified": "2021-07-08T12:07:34.180Z"}, {"entity": "publication", "iuid": "1fc2070f62c74b61866aa02ca06f973e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fc2070f62c74b61866aa02ca06f973e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fc2070f62c74b61866aa02ca06f973e"}}, "title": "Anoctamin 2 identified as an autoimmune target in multiple sclerosis.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bredenberg", "given": "Johan", "initials": "J"}, {"family": "Lima Bomfim", "given": "Izaura", "initials": "I"}, {"family": "Holmgren", "given": "Erik", "initials": "E"}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H"}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO"}, {"family": "Abdelmagid", "given": "Nada", "initials": "N"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Waterboer", "given": "Tim", "initials": "T"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2016-02-23", "journal": {"volume": "113", "issn": "1091-6490", "issue": "8", "pages": "2188-2193", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Multiple sclerosis (MS) is the most common chronic inflammatory disease of the central nervous system and also is regarded as an autoimmune condition. However, the antigenic targets of the autoimmune response in MS have not yet been deciphered. In an effort to mine the autoantibody repertoire within MS, we profiled 2,169 plasma samples from MS cases and population-based controls using bead arrays built with 384 human protein fragments selected from an initial screening with 11,520 antigens. Our data revealed prominently increased autoantibody reactivity against the chloride-channel protein anoctamin 2 (ANO2) in MS cases compared with controls. This finding was corroborated in independent assays with alternative protein constructs and by epitope mapping with peptides covering the identified region of ANO2. Additionally, we found a strong interaction between the presence of ANO2 autoantibodies and the HLA complex MS-associated DRB1*15 allele, reinforcing a potential role for ANO2 autoreactivity in MS etiopathogenesis. Furthermore, immunofluorescence analysis in human MS brain tissue showed ANO2 expression as small cellular aggregates near and inside MS lesions. Thus this study represents one of the largest efforts to characterize the autoantibody repertoire within MS. The findings presented here demonstrate that an ANO2 autoimmune subphenotype may exist in MS and lay the groundwork for further studies focusing on the pathogenic role of ANO2 autoantibodies in MS.", "doi": "10.1073/pnas.1518553113", "pmid": "26862169", "labels": {"Fluorescence Tissue Profiling": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1518553113"}, {"db": "pmc", "key": "PMC4776531"}], "notes": [], "created": "2017-05-03T12:59:10.751Z", "modified": "2021-07-08T13:44:33.077Z"}, {"entity": "publication", "iuid": "110f4581854a476b9c6f6e1d9b01a259", "links": {"self": {"href": "https://publications.scilifelab.se/publication/110f4581854a476b9c6f6e1d9b01a259.json"}, "display": {"href": "https://publications.scilifelab.se/publication/110f4581854a476b9c6f6e1d9b01a259"}}, "title": "Transglutaminase 4 as a prostate autoantigen in male subfertility", "authors": [{"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Sharon", "given": "Donald", "initials": "D"}, {"family": "Shum", "given": "Anthony K", "initials": "AK"}, {"family": "Khan", "given": "Imran S", "initials": "IS"}, {"family": "Fasano", "given": "Kayla J", "initials": "KJ"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Ardesj\u00f6-Lundgren", "given": "Brita", "initials": "B"}, {"family": "Alimohammadi", "given": "Mohammad", "initials": "M"}, {"family": "Rathsman", "given": "Sandra", "initials": "S"}, {"family": "Ludvigsson", "given": "Jonas F", "initials": "JF"}, {"family": "Lundh", "given": "Dan", "initials": "D"}, {"family": "Motrich", "given": "Ruben", "initials": "R"}, {"family": "Rivero", "given": "Virginia", "initials": "V"}, {"family": "Fong", "given": "Lawrence", "initials": "L"}, {"family": "Giwercman", "given": "Aleksander", "initials": "A"}, {"family": "Gustafsson", "given": "Jan", "initials": "J"}, {"family": "Perheentupa", "given": "Jaakko", "initials": "J"}, {"family": "Husebye", "given": "Eystein S", "initials": "ES"}, {"family": "Anderson", "given": "Mark S", "initials": "MS"}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}], "type": "journal-article", "published": "2015-06-17", "journal": {"volume": "7", "issn": "1946-6234", "issue": "292", "pages": "292ra101", "title": "Sci. Transl. Med.", "issn-l": "1946-6234"}, "abstract": "Autoimmune polyendocrine syndrome type 1 (APS1), a monogenic disorder caused by AIRE gene mutations, features multiple autoimmune disease components. Infertility is common in both males and females with APS1. Although female infertility can be explained by autoimmune ovarian failure, the mechanisms underlying male infertility have remained poorly understood. We performed a proteome-wide autoantibody screen in APS1 patient sera to assess the autoimmune response against the male reproductive organs. By screening human protein arrays with male and female patient sera and by selecting for gender-imbalanced autoantibody signals, we identified transglutaminase 4 (TGM4) as a male-specific autoantigen. Notably, TGM4 is a prostatic secretory molecule with critical role in male reproduction. TGM4 autoantibodies were detected in most of the adult male APS1 patients but were absent in all the young males. Consecutive serum samples further revealed that TGM4 autoantibodies first presented during pubertal age and subsequent to prostate maturation. We assessed the animal model for APS1, the Aire-deficient mouse, and found spontaneous development of TGM4 autoantibodies specifically in males. Aire-deficient mice failed to present TGM4 in the thymus, consistent with a defect in central tolerance for TGM4. In the mouse, we further link TGM4 immunity with a destructive prostatitis and compromised secretion of TGM4. Collectively, our findings in APS1 patients and Aire-deficient mice reveal prostate autoimmunity as a major manifestation of APS1 with potential role in male subfertility.", "doi": "10.1126/scitranslmed.aaa9186", "pmid": "26084804", "labels": {"Bioinformatics Support and Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "Autoimmunity and Serology Profiling": "Service", "PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "7/292/292ra101"}], "notes": [], "created": "2017-05-02T12:57:44.848Z", "modified": "2023-06-19T09:06:56.580Z"}, {"entity": "publication", "iuid": "7e7dd1c9a9e64925b730afad2cc79c29", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e7dd1c9a9e64925b730afad2cc79c29.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e7dd1c9a9e64925b730afad2cc79c29"}}, "title": "Proteomic profiling reveals autoimmune targets in sarcoidosis.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Wiklundh", "given": "Emil", "initials": "E"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE"}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Eklund", "given": "Anders", "initials": "A"}, {"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2015-03-01", "journal": {"volume": "191", "issn": "1535-4970", "issue": "5", "pages": "574-583", "title": "Am. J. Respir. Crit. Care Med.", "issn-l": "1073-449X"}, "abstract": "There is a need to further characterize the antibody repertoire in relation to sarcoidosis and potentially related autoantigens.\n\nWe investigated bronchoalveolar lavage (BAL) and serum samples from patients with sarcoidosis and healthy and diseased control subjects to discover sarcoidosis-associated autoantigens.\n\nAntigen microarrays built on 3,072 protein fragments were used to screen for IgG reactivity in 73 BAL samples from subjects with sarcoidosis, subjects with asthma, and healthy subjects. A set of 131 targets were selected for subsequent verification on suspension bead arrays using 272 additional BAL samples and 141 paired sera. Reactivity to four antigens was furthermore analyzed in 22 unprocessed BAL samples from patients with fibrosis and 269 plasma samples from patients diagnosed with myositis.\n\nReactivity toward zinc finger protein 688 and mitochondrial ribosomal protein L43 were discovered with higher frequencies in patients with sarcoidosis, for mitochondrial ribosomal protein L43 especially in patients with non-L\u00f6fgren syndrome. Increased reactivity toward nuclear receptor coactivator 2 was also observed in patients with non-L\u00f6fgren syndrome as compared with patients with L\u00f6fgren syndrome. The antigen representing adenosine diphosphate-ribosylation factor GTPase activating protein 1 revealed high reactivity frequency in all sample groups but with significantly higher level of IgG reactivities in patients with sarcoidosis.\n\nAutoantigen reactivity was present in most BAL and serum samples analyzed, and the results revealed high interindividual heterogeneity, with most of the reactivities observed in single individuals only. Four proteins are here proposed as sarcoidosis-associated autoimmune targets and of interest for further validation in independent cohorts.", "doi": "10.1164/rccm.201407-1341OC", "pmid": "25608002", "labels": {"Tissue Profiling": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:43:12.854Z", "modified": "2021-07-08T12:07:34.150Z"}, {"entity": "publication", "iuid": "fb59553b95b94e188d2b737b4ecd2221", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb59553b95b94e188d2b737b4ecd2221.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb59553b95b94e188d2b737b4ecd2221"}}, "title": "Analysis of autoantibody profiles in osteoarthritis using comprehensive protein array concepts.", "authors": [{"family": "Henjes", "given": "Frauke", "initials": "F"}, {"family": "Lourido", "given": "Luc\u00eda", "initials": "L"}, {"family": "Ruiz-Romero", "given": "Cristina", "initials": "C"}, {"family": "Fern\u00e1ndez-Tajes", "given": "Juan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Gonzalez-Gonzalez", "given": "Mar\u00eda", "initials": "M"}, {"family": "Blanco", "given": "Francisco J", "initials": "FJ"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Fuentes", "given": "Manuel", "initials": "M"}], "type": "journal article", "published": "2014-11-07", "journal": {"volume": "13", "issn": "1535-3907", "issue": "11", "pages": "5218-5229", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Osteoarthritis (OA) is the most common rheumatic disease and one of the most disabling pathologies worldwide. To date, the diagnostic methods of OA are very limited, and there are no available medications capable of halting its characteristic cartilage degeneration. Therefore, there is a significant interest in new biomarkers useful for the early diagnosis, prognosis, and therapeutic monitoring. In the recent years, protein microarrays have emerged as a powerful proteomic tool to search for new biomarkers. In this study, we have used two concepts for generating protein arrays, antigen microarrays, and NAPPA (nucleic acid programmable protein arrays), to characterize differential autoantibody profiles in a set of 62 samples from OA, rheumatoid arthritis (RA), and healthy controls. An untargeted screen was performed on 3840 protein fragments spotted on planar antigen arrays, and 373 antigens were selected for validation on bead-based arrays. In the NAPPA approach, a targeted screening was performed on 80 preselected proteins. The autoantibody targeting CHST14 was validated by ELISA in the same set of patients. Altogether, nine and seven disease related autoantibody target candidates were identified, and this work demonstrates a combination of these two array concepts for biomarker discovery and their usefulness for characterizing disease-specific autoantibody profiles.", "doi": "10.1021/pr500775a", "pmid": "25227461", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:44:05.600Z", "modified": "2021-07-08T12:07:34.343Z"}, {"entity": "publication", "iuid": "6435089b8b354ebf812b692036692fab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6435089b8b354ebf812b692036692fab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6435089b8b354ebf812b692036692fab"}}, "title": "Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays.", "authors": [{"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Axn\u00e4s", "given": "Barbara Bis\u0142awska", "initials": "BB"}, {"family": "Stengele", "given": "Klaus-Peter", "initials": "K"}, {"family": "B\u00fchler", "given": "Jochen", "initials": "J"}, {"family": "Albert", "given": "Thomas J", "initials": "TJ"}, {"family": "Richmond", "given": "Todd A", "initials": "TA"}, {"family": "Hu", "given": "Francis Jingxin", "initials": "FJ"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "13", "issn": "1535-9484", "issue": "6", "pages": "1585-1597", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Antibodies are of importance for the field of proteomics, both as reagents for imaging cells, tissues, and organs and as capturing agents for affinity enrichment in mass-spectrometry-based techniques. It is important to gain basic insights regarding the binding sites (epitopes) of antibodies and potential cross-reactivity to nontarget proteins. Knowledge about an antibody's linear epitopes is also useful in, for instance, developing assays involving the capture of peptides obtained from trypsin cleavage of samples prior to mass spectrometry analysis. Here, we describe, for the first time, the design and use of peptide arrays covering all human proteins for the analysis of antibody specificity, based on parallel in situ photolithic synthesis of a total of 2.1 million overlapping peptides. This has allowed analysis of on- and off-target binding of both monoclonal and polyclonal antibodies, complemented with precise mapping of epitopes based on full amino acid substitution scans. The analysis suggests that linear epitopes are relatively short, confined to five to seven residues, resulting in apparent off-target binding to peptides corresponding to a large number of unrelated human proteins. However, subsequent analysis using recombinant proteins suggests that these linear epitopes have a strict conformational component, thus giving us new insights regarding how antibodies bind to their antigens.", "doi": "10.1074/mcp.M113.033308", "pmid": "24705123", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "M113.033308"}, {"db": "pmc", "key": "PMC4047477"}], "notes": [], "created": "2017-05-04T14:55:39.895Z", "modified": "2021-07-08T13:44:33.318Z"}, {"entity": "publication", "iuid": "759e422202f44866bfaa57c67d40af2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/759e422202f44866bfaa57c67d40af2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/759e422202f44866bfaa57c67d40af2b"}}, "title": "Bead arrays for antibody and complement profiling reveal joint contribution of antibody isotypes to C3 deposition.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Szarka", "given": "Eszter", "initials": "E"}, {"family": "Huber", "given": "Krisztina", "initials": "K"}, {"family": "Orosz", "given": "Anita", "initials": "A"}, {"family": "Babos", "given": "Fruzsina", "initials": "F"}, {"family": "Magyar", "given": "Anna", "initials": "A"}, {"family": "Hudecz", "given": "Ferenc", "initials": "F"}, {"family": "Rojkovich", "given": "Bernadette", "initials": "B"}, {"family": "G\u00e1ti", "given": "Tam\u00e1s", "initials": "T"}, {"family": "Nagy", "given": "Gy\u00f6rgy", "initials": "G"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "S\u00e1rmay", "given": "Gabriella", "initials": "G"}, {"family": "Prechl", "given": "J\u00f3zsef", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Papp", "given": "Kriszti\u00e1n", "initials": "K"}], "type": "journal article", "published": "2014-05-05", "journal": {"volume": "9", "issn": "1932-6203", "issue": "5", "pages": "e96403", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The development of antigen arrays has provided researchers with great tools to identify reactivities against self or foreign antigens from body fluids. Yet, these approaches mostly do not address antibody isotypes and their effector functions even though these are key points for a more detailed understanding of disease processes. Here, we present a bead array-based assay for a multiplexed determination of antigen-specific antibody levels in parallel with their properties for complement activation. We measured the deposition of C3 fragments from serum samples to reflect the degree of complement activation via all three complement activation pathways. We utilized the assay on a bead array containing native and citrullinated peptide antigens to investigate the levels of IgG, IgM and IgA autoantibodies along with their complement activating properties in serum samples of 41 rheumatoid arthritis patients and 40 controls. Our analysis revealed significantly higher IgG reactivity against the citrullinated fibrinogen \u03b2 and filaggrin peptides as well as an IgA reactivity that was exclusive for citrullinated fibrinogen \u03b2 peptide and C3 deposition in rheumatoid arthritis patients. In addition, we characterized the humoral immune response against the viral EBNA-1 antigen to demonstrate the applicability of this assay beyond autoimmune conditions. We observed that particular buffer compositions were demanded for separate measurement of antibody reactivity and complement activation, as detection of antigen-antibody complexes appeared to be masked due to C3 deposition. We also found that rheumatoid factors of IgM isotype altered C3 deposition and introduced false-positive reactivities against EBNA-1 antigen. In conclusion, the presented bead-based assay setup can be utilized to profile antibody reactivities and immune-complex induced complement activation in a high-throughput manner and could facilitate the understanding and diagnosis of several diseases where complement activation plays role in the pathomechanism.", "doi": "10.1371/journal.pone.0096403", "pmid": "24797804", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-14-03336"}, {"db": "pmc", "key": "PMC4010547"}], "notes": [], "created": "2017-05-04T14:55:40.421Z", "modified": "2021-07-08T12:07:34.138Z"}, {"entity": "publication", "iuid": "25fee1b507254b40b328c5dd1a7f3ce2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25fee1b507254b40b328c5dd1a7f3ce2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25fee1b507254b40b328c5dd1a7f3ce2"}}, "title": "Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.", "authors": [{"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Habuka", "given": "Masato", "initials": "M"}, {"family": "Tahmasebpoor", "given": "Simin", "initials": "S"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Takanen", "given": "Jenny Ottosson", "initials": "JO"}, {"family": "Berling", "given": "Holger", "initials": "H"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Sivertsson", "given": "Asa", "initials": "A"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Olsson", "given": "IngMarie", "initials": "I"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"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": "2014-02-00", "journal": {"volume": "13", "issn": "1535-9484", "issue": "2", "pages": "397-406", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to \u223c80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.", "doi": "10.1074/mcp.M113.035600", "pmid": "24309898", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Autoimmunity and Serology Profiling": "Technology development", "Spatial Proteomics": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "M113.035600"}, {"db": "pmc", "key": "PMC3916642"}], "notes": [], "created": "2017-05-04T14:55:17.424Z", "modified": "2021-07-08T13:44:33.111Z"}, {"entity": "publication", "iuid": "0d26cf1338444ca88be5a65923130cb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d26cf1338444ca88be5a65923130cb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d26cf1338444ca88be5a65923130cb5"}}, "title": "Autoantibody profiling in multiple sclerosis using arrays of human protein fragments.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"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"}}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "12", "issn": "1535-9484", "issue": "9", "pages": "2657-2672", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Profiling the autoantibody repertoire with large antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis related diagnoses. Reactivity pattern of 11,520 protein fragments (representing \u223c38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. For more than 2,000 antigens IgG reactivity was observed, among which 64% were found only in single individuals. We used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, which were then re-evaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n = 376) and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, using protein fragments and complementary high-throughput protein array platforms facilitated an alternative route to discovery and verification of potentially disease-associated autoimmunity signatures, that are now proposed as additional antigens for large-scale validation studies across multiple sclerosis biobanks.", "doi": "10.1074/mcp.M112.026757", "pmid": "23732997", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "M112.026757"}, {"db": "pmc", "key": "PMC3769337"}], "notes": [], "created": "2017-05-04T14:55:38.084Z", "modified": "2021-07-08T13:44:33.014Z"}, {"entity": "publication", "iuid": "504f7661fda94a749fe7d389d0bb14fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/504f7661fda94a749fe7d389d0bb14fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/504f7661fda94a749fe7d389d0bb14fe"}}, "title": "High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays.", "authors": [{"family": "Buus", "given": "S\u00f8ren", "initials": "S"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schafer-Nielsen", "given": "Claus", "initials": "C"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "12", "pages": "1790-1800", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Antibodies empower numerous important scientific, clinical, diagnostic, and industrial applications. Ideally, the epitope(s) targeted by an antibody should be identified and characterized, thereby establishing antibody reactivity, highlighting possible cross-reactivities, and perhaps even warning against unwanted (e.g. autoimmune) reactivities. Antibodies target proteins as either conformational or linear epitopes. The latter are typically probed with peptides, but the cost of peptide screening programs tends to prohibit comprehensive specificity analysis. To perform high-throughput, high-resolution mapping of linear antibody epitopes, we have used ultrahigh-density peptide microarrays generating several hundred thousand different peptides per array. Using exhaustive length and substitution analysis, we have successfully examined the specificity of a panel of polyclonal antibodies raised against linear epitopes of the human proteome and obtained very detailed descriptions of the involved specificities. The epitopes identified ranged from 4 to 12 amino acids in size. In general, the antibodies were of exquisite specificity, frequently disallowing even single conservative substitutions. In several cases, multiple distinct epitopes could be identified for the same target protein, suggesting an efficient approach to the generation of paired antibodies. Two alternative epitope mapping approaches identified similar, although not necessarily identical, epitopes. These results show that ultrahigh-density peptide microarrays can be used for linear epitope mapping. With an upper theoretical limit of 2,000,000 individual peptides per array, these peptide microarrays may even be used for a systematic validation of antibodies at the proteomic level.", "doi": "10.1074/mcp.M112.020800", "pmid": "22984286", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "M112.020800"}, {"db": "pmc", "key": "PMC3518105"}], "notes": [], "created": "2017-05-04T14:55:36.590Z", "modified": "2021-07-08T13:44:33.228Z"}, {"entity": "publication", "iuid": "1c65428b58d9411b8a95e81e4cab18b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c65428b58d9411b8a95e81e4cab18b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c65428b58d9411b8a95e81e4cab18b5"}}, "title": "Validation of affinity reagents using antigen microarrays.", "authors": [{"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Sundberg", "given": "M\u00e5rten", "initials": "M"}, {"family": "Gundberg", "given": "Anna", "initials": "A"}, {"family": "Sivertsson", "given": "Asa", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"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"}}], "type": "journal article", "published": "2012-06-15", "journal": {"volume": "29", "issn": "1876-4347", "issue": "5", "pages": "555-563", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "There is a need for standardised validation of affinity reagents to determine their binding selectivity and specificity. This is of particular importance for systematic efforts that aim to cover the human proteome with different types of binding reagents. One such international program is the SH2-consortium, which was formed to generate a complete set of renewable affinity reagents to the SH2-domain containing human proteins. Here, we describe a microarray strategy to validate various affinity reagents, such as recombinant single-chain antibodies, mouse monoclonal antibodies and antigen-purified polyclonal antibodies using a highly multiplexed approach. An SH2-specific antigen microarray was designed and generated, containing more than 6000 spots displayed by 14 identical subarrays each with 406 antigens, where 105 of them represented SH2-domain containing proteins. Approximately 400 different affinity reagents of various types were analysed on these antigen microarrays carrying antigens of different types. The microarrays revealed not only very detailed specificity profiles for all the binders, but also showed that overlapping target sequences of spotted antigens were detected by off-target interactions. The presented study illustrates the feasibility of using antigen microarrays for integrative, high-throughput validation of various types of binders and antigens.", "doi": "10.1016/j.nbt.2011.11.009", "pmid": "22134247", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(11)00257-3"}], "notes": [], "created": "2017-05-04T14:55:37.189Z", "modified": "2021-07-08T13:44:33.060Z"}, {"entity": "publication", "iuid": "5ee700805e74435b81a690144c426c34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ee700805e74435b81a690144c426c34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ee700805e74435b81a690144c426c34"}}, "title": "Biosensor Based Protein Profiling on Reverse Phase Serum Microarray", "authors": [{"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal-article", "published": "2012-00-00", "journal": {"title": "JPB", "issn": "0974-276X", "issn-l": "0974-276X", "volume": "05", "issue": "08", "pages": null}, "abstract": null, "doi": "10.4172/jpb.1000233", "pmid": null, "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:36.331Z", "modified": "2021-07-07T15:55:05.825Z"}, {"entity": "publication", "iuid": "f1401f1407364e189b734a9b3e1582c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1401f1407364e189b734a9b3e1582c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1401f1407364e189b734a9b3e1582c0"}}, "title": "Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.", "authors": [{"family": "Hjelm", "given": "Barbara", "initials": "B"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Sj\u00f6berg", "given": "Anna", "initials": "A"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"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": "Johansson", "given": "Christine", "initials": "C"}, {"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": "2011-11-00", "journal": {"volume": "20", "issn": "1469-896X", "issue": "11", "pages": "1824-1835", "title": "Protein Sci.", "issn-l": "0961-8368"}, "abstract": "A method is described to generate and validate antibodies based on mapping the linear epitopes of a polyclonal antibody followed by sequential epitope-specific capture using synthetic peptides. Polyclonal antibodies directed towards four proteins RBM3, SATB2, ANLN, and CNDP1, potentially involved in human cancers, were selected and antibodies to several non-overlapping epitopes were generated and subsequently validated by Western blot, immunohistochemistry, and immunofluorescence. For all four proteins, a dramatic difference in functionality could be observed for these monospecific antibodies directed to the different epitopes. In each case, at least one antibody was obtained with full functionality across all applications, while other epitope-specific fractions showed no or little functionality. These results present a path forward to use the mapped binding sites of polyclonal antibodies to generate epitope-specific antibodies, providing an attractive approach for large-scale efforts to characterize the human proteome by antibodies.", "doi": "10.1002/pro.716", "pmid": "21898641", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Spatial Proteomics": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC3267947"}], "notes": [], "created": "2017-05-04T14:55:09.271Z", "modified": "2021-07-08T13:44:33.721Z"}, {"entity": "publication", "iuid": "4f647b0a384344e581a7383c15fa9006", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f647b0a384344e581a7383c15fa9006.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f647b0a384344e581a7383c15fa9006"}}, "title": "A roadmap to generate renewable protein binders to the human proteome.", "authors": [{"family": "Colwill", "given": "Karen", "initials": "K"}, {"family": "Renewable Protein Binder Working Group", "given": "", "initials": ""}, {"family": "Gr\u00e4slund", "given": "Susanne", "initials": "S"}], "type": "journal article", "published": "2011-05-15", "journal": {"volume": "8", "issn": "1548-7105", "issue": "7", "pages": "551-558", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": "Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein binders. We report a multicenter study to assess the potential of hybridoma and phage-display technologies in a coordinated large-scale antibody generation and validation effort. We produced over 1,000 antibodies targeting 20 SH2 domain proteins and evaluated them for potency and specificity by enzyme-linked immunosorbent assay (ELISA), protein microarray and surface plasmon resonance (SPR). We also tested selected antibodies in immunoprecipitation, immunoblotting and immunofluorescence assays. Our results show that high-affinity, high-specificity renewable antibodies generated by different technologies can be produced quickly and efficiently. We believe that this work serves as a foundation and template for future larger-scale studies to create renewable protein binders.", "doi": "10.1038/nmeth.1607", "pmid": "21572409", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "nmeth.1607"}], "notes": [], "created": "2017-10-30T10:38:36.549Z", "modified": "2021-05-24T15:27:28.238Z"}, {"entity": "publication", "iuid": "afa95f4100dc4c0da07afa5c8d24a1b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afa95f4100dc4c0da07afa5c8d24a1b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afa95f4100dc4c0da07afa5c8d24a1b6"}}, "title": "Systematic antibody and antigen-based proteomic profiling with microarrays.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"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"}}], "type": "journal article", "published": "2011-03-00", "journal": {"volume": "11", "issn": "1744-8352", "issue": "2", "pages": "219-234", "title": "Expert Rev. Mol. Diagn.", "issn-l": "1473-7159"}, "abstract": "Current approaches within affinity-based proteomics are driven both by the accessibility and availability of antigens and capture reagents, and by suitable multiplexed technologies onto which these are implemented. By combining planar microarrays and other multiparallel systems with sets of reagents, possibilities to discover new and unpredicted protein-disease associations, either via directed hypothesis-driven or via undirected hypothesis-generating target selection, can be created. In the following stages, the discoveries made during these screening phases have to be verified for potential clinical relevance based on both technical and biological aspects. The use of affinity tools throughout discovery and verification has the potential to streamline the introduction of new markers, as transition into clinically required assay formats appears straightforward. In this article, we summarize some of the current building blocks within array- and affinity-based proteomic profiling with a focus on body fluids, by giving a perspective on how current and upcoming developments in this bioscience could enable a path of pursuit for biomarker discovery.", "doi": "10.1586/erm.10.110", "pmid": "21405972", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:29.977Z", "modified": "2021-07-08T13:44:33.525Z"}]}