{"entity": "researcher", "timestamp": "2026-08-12T17:48:24.493Z", "family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "affiliations": ["Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden.", "Affinity Proteomics, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0"}}, "publications": [{"entity": "publication", "iuid": "01a6b1a78bb54a8f8e4c51b7ca9f3d9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/01a6b1a78bb54a8f8e4c51b7ca9f3d9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/01a6b1a78bb54a8f8e4c51b7ca9f3d9b"}}, "title": "Longitudinal protein profiling of blood during childhood into early adulthood.", "authors": [{"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/648c9ed3483a4eb8a1d228cf7e59f6a7.json"}}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Bueno \u00c1lvez", "given": "Mar\u00eda", "initials": "M", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Kebede Merid", "given": "Simon", "initials": "S"}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Kull", "given": "Inger", "initials": "I", "orcid": "0000-0001-6096-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f248045358c4711b1d10d7b9fe9649c.json"}}, {"family": "Merritt", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Klevebro", "given": "Susanna", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}], "type": "journal article", "published": "2026-04-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Proteomic research enhances our understanding of health- and disease-related biological processes. Protein profiling during healthy childhood provides important insights into normal physiological development. We longitudinally measured 5416 plasma proteins at four follow-ups during childhood (4-, 8-, 16 years) and early adulthood (24 years) in 100 randomly selected subjects participating in a population-based Swedish cohort, using Olink Explore HT. In total, 3509 proteins were included in the analysis. 54% of the proteins were found to be associated with age, and we observed several protein trajectories from childhood to adulthood based on clustering. In addition to proteins involved in bone, teeth and cartilage formation, we identified differences in proteins involved in neural function, drug metabolism, and hormonal control. There were pronounced sex-related differences in protein levels, particularly at follow-ups 16 and 24, characterized by, for example, growth, response to stimuli and regulation of catabolic processes. We demonstrate dynamic age- and sex-related changes in protein levels during the first two decades of life. Our study results may serve as an important resource in understanding human physiological development, disease etiology, and for future protein biomarker research.", "doi": "10.1038/s41467-026-72095-3", "pmid": "42020385", "labels": {"NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13102979"}, {"db": "pii", "key": "10.1038/s41467-026-72095-3"}], "notes": [], "created": "2026-04-28T06:03:05.109Z", "modified": "2026-04-28T06:03:05.659Z"}, {"entity": "publication", "iuid": "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", 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{"href": "https://publications.scilifelab.se/researcher/22a7a44fa1b94d5a87e561442e905432.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N", "orcid": "0000-0002-7835-4357", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1b2d0ce6ea452b82a35c603a073eb1.json"}}, {"family": "Reepalu", "given": "Anton", "initials": "A", "orcid": "0000-0003-1690-8921", "researcher": {"href": "https://publications.scilifelab.se/researcher/18a2d4fc25964bc48bd8d5b3593aab5a.json"}}, {"family": "Roy", "given": "Joy", "initials": "J", "orcid": "0000-0002-5645-1260", "researcher": {"href": "https://publications.scilifelab.se/researcher/d59de368e4784a3cb56dcc634fde37ef.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sen", "given": "Meltem", "initials": "M", "orcid": "0000-0002-6248-7091", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f5b63f920994f81bc6fec1a37105cba.json"}}, {"family": "Siika", "given": "Antti", "initials": "A", "orcid": "0000-0002-2551-2526", "researcher": {"href": "https://publications.scilifelab.se/researcher/596e04ba84e54b188f93ed3e3be94ebf.json"}}, {"family": "Simonson", "given": "Oscar E", "initials": "OE"}, {"family": "Sivertsson", "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": "https://publications.scilifelab.se/researcher/66bfc091e8784259bfbf0f30a996391e.json"}}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A", "orcid": "0000-0001-8928-3374", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b2d7f254c57489da8329627d49bad87.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Str\u00e5lin", "given": "Kristoffer", "initials": "K", "orcid": "0000-0002-8801-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6ffa1185f4142b7ab7c372c0c139df6.json"}}, {"family": "Sund\u00e9n-Cullberg", "given": "Jonas", "initials": "J"}, {"family": "Sundling", "given": "Christopher", "initials": "C", "orcid": "0000-0002-6138-690X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89c1e689a46b4b14adb0dc99e1c0a58c.json"}}, {"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": "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": "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": "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": "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": "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": "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": "c0cca1c6d075493a89f033df6dcecc11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0cca1c6d075493a89f033df6dcecc11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0cca1c6d075493a89f033df6dcecc11"}}, "title": "Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation", "authors": [{"family": "Sparreman Mikus", "given": "Maria", "initials": "M"}, {"family": "Kolmert", "given": "Johan", "initials": "J"}, {"family": "Andersson", "given": "Lars I", "initials": "LI"}, {"family": "\u00d6stling", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Knowles", "given": "Richard G", "initials": "RG"}, {"family": "G\u00f3mez", "given": "Cristina", "initials": "C", "orcid": "0000-0001-8518-0095", "researcher": {"href": "https://publications.scilifelab.se/researcher/be06de557dc94f8db25380f5765eeca4.json"}}, {"family": "Ericsson", "given": "Magnus", "initials": "M"}, {"family": "Th\u00f6rngren", "given": "John Olof", "initials": "JO"}, {"family": "Emami Khoonsari", "given": "Payam", "initials": "P"}, {"family": "Dahl\u00e9n", "given": "Barbro", "initials": "B"}, {"family": "Kupczyk", "given": "Maciej", "initials": "M"}, {"family": "De Meulder", "given": "Bertrand", "initials": "B"}, {"family": "Auffray", "given": "Charles", "initials": "C"}, {"family": "Bakke", "given": "Per S", "initials": "PS"}, {"family": "Beghe", "given": "Bianca", "initials": "B"}, {"family": "Bel", "given": "Elisabeth H", "initials": "EH"}, {"family": "Caruso", "given": "Massimo", "initials": "M", "orcid": "0000-0002-4412-2080", "researcher": {"href": "https://publications.scilifelab.se/researcher/6712f12cc1004b5ba44d2803b9a6fb1b.json"}}, {"family": "Chanez", "given": "Pascal", "initials": "P"}, {"family": "Chawes", "given": "Bo", "initials": "B"}, {"family": "Fowler", "given": "Stephen J", "initials": "SJ", "orcid": "0000-0002-4524-1663", "researcher": {"href": "https://publications.scilifelab.se/researcher/5986cb3bab4b482c831862a85c85b238.json"}}, {"family": "Gaga", "given": "Mina", "initials": "M", "orcid": "0000-0002-9949-6012", "researcher": {"href": "https://publications.scilifelab.se/researcher/124934c35baf4fb89053532fcc354a96.json"}}, {"family": "Geiser", "given": "Thomas", "initials": "T"}, {"family": "Gjomarkaj", "given": "Mark", "initials": "M"}, {"family": "Horv\u00e1th", "given": "Ildik\u00f3", "initials": "I"}, {"family": "Howarth", "given": "Peter H", "initials": "PH", "orcid": "0000-0003-0619-7927", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae17cd831edd48d7b851773eded77345.json"}}, {"family": "Johnston", "given": "Sebastian L", "initials": "SL"}, {"family": "Joos", "given": "Guy", "initials": "G", "orcid": "0000-0002-3149-9444", "researcher": {"href": "https://publications.scilifelab.se/researcher/f324289e94b844c980ff7be24032b9b3.json"}}, {"family": "Krug", "given": "Norbert", "initials": "N"}, {"family": "Montuschi", "given": "Paolo", "initials": "P"}, {"family": "Musial", "given": "Jacek", "initials": "J"}, {"family": "Ni\u017cankowska-Mogilnicka", "given": "Ewa", "initials": "E"}, {"family": "Olsson", "given": "Henric K", "initials": "HK"}, {"family": "Papi", "given": "Alberto", "initials": "A"}, {"family": "Rabe", "given": "Klaus F", "initials": "KF"}, {"family": "Sandstr\u00f6m", "given": "Thomas", "initials": "T"}, {"family": "Shaw", "given": "Dominick E", "initials": "DE", "orcid": "0000-0003-4106-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/56efd0f5f85a478493f8b25d23e371be.json"}}, {"family": "Siafakas", "given": "Nikolaos M", "initials": "NM"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Riley", "given": "John H", "initials": "JH"}, {"family": "Bates", "given": "Stewart", "initials": "S"}, {"family": "Middelveld", "given": "Roelinde J M", "initials": "RJM"}, {"family": "Wheelock", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-8113-0653", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3cd2b99e3e9486ba41030c809a48c51.json"}}, {"family": "Chung", "given": "Kian Fan", "initials": "KF"}, {"family": "Adcock", "given": "Ian M", "initials": "IM", "orcid": "0000-0003-2101-8843", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ed3d714173144fabe2aa61165810992.json"}}, {"family": "Sterk", "given": "Peter J", "initials": "PJ"}, {"family": "Djukanovic", "given": "Ratko", "initials": "R"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Dahl\u00e9n", "given": "Sven Erik", "initials": "SE"}, {"family": "James", "given": "Anna", "initials": "A"}], "type": "journal-article", "published": "2022-02-00", "journal": {"title": "Eur Respir J", "issn": "0903-1936", "issn-l": "0903-1936", "volume": "59", "issue": "2", "pages": "2100142"}, "abstract": "Asthma phenotyping requires novel biomarker discovery.\n\nTo identify plasma biomarkers associated with asthma phenotypes by application of a new proteomic panel to samples from two well-characterised cohorts of severe (SA) and mild-to-moderate (MMA) asthmatics, COPD subjects and healthy controls (HCs).\n\nAn antibody-based array targeting 177 proteins predominantly involved in pathways relevant to inflammation, lipid metabolism, signal transduction and extracellular matrix was applied to plasma from 525 asthmatics and HCs in the U-BIOPRED cohort, and 142 subjects with asthma and COPD from the validation cohort BIOAIR. Effects of oral corticosteroids (OCS) were determined by a 2-week, placebo-controlled OCS trial in BIOAIR, and confirmed by relation to objective OCS measures in U-BIOPRED.\n\nIn U-BIOPRED, 110 proteins were significantly different, mostly elevated, in SA compared to MMA and HCs. 10 proteins were elevated in SA versus MMA in both U-BIOPRED and BIOAIR (alpha-1-antichymotrypsin, apolipoprotein-E, complement component 9, complement factor I, macrophage inflammatory protein-3, interleukin-6, sphingomyelin phosphodiesterase 3, TNF receptor superfamily member 11a, transforming growth factor-\u03b2 and glutathione S-transferase). OCS treatment decreased most proteins, yet differences between SA and MMA remained following correction for OCS use. Consensus clustering of U-BIOPRED protein data yielded six clusters associated with asthma control, quality of life, blood neutrophils, high-sensitivity C-reactive protein and body mass index, but not Type-2 inflammatory biomarkers. The mast cell specific enzyme carboxypeptidase A3 was one major contributor to cluster differentiation.\n\nThe plasma proteomic panel revealed previously unexplored yet potentially useful Type-2-independent biomarkers and validated several proteins with established involvement in the pathophysiology of SA.", "doi": "10.1183/13993003.00142-2021", "pmid": "34737220", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8850689"}, {"db": "pii", "key": "13993003.00142-2021"}], "notes": [], "created": "2021-11-10T10:57:08.791Z", "modified": "2024-01-16T13:48:37.618Z"}, {"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": "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": "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": "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": "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": "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": "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": "5c4e7cd6c6ad47f5bd1054cafd7408a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c4e7cd6c6ad47f5bd1054cafd7408a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c4e7cd6c6ad47f5bd1054cafd7408a0"}}, "title": "Point-of-Care Approaches for Meningitis Diagnosis in a Low-Resource Setting (Southwestern Uganda): Observational Cohort Study Protocol of the \"PI-POC\" Trial.", "authors": [{"family": "Gaudenzi", "given": "Giulia", "initials": "G", "orcid": "0000-0003-4923-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba29165719cb46eba1a62c4c3e9cb232.json"}}, {"family": "Kumbakumba", "given": "Elias", "initials": "E", "orcid": "0000-0001-7206-0609", "researcher": {"href": "https://publications.scilifelab.se/researcher/8395ba3e303747e4ba9cb03c2ce8ef2c.json"}}, {"family": "Rasti", "given": "Reza", "initials": "R", "orcid": "0000-0001-7816-8338", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e28ed799ee044f89513d9bd672e64d9.json"}}, {"family": "Nanjebe", "given": "Deborah", "initials": "D", "orcid": "0000-0002-5440-7100", "researcher": {"href": "https://publications.scilifelab.se/researcher/e436dca4c9844756b2b13205a106296b.json"}}, {"family": "R\u00e9u", "given": "Pedro", "initials": "P", "orcid": "0000-0001-7454-7189", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c6e427a91df4b13b68be281692efc68.json"}}, {"family": "Nyehangane", "given": "Dan", "initials": "D", "orcid": "0000-0002-1898-4162", "researcher": {"href": "https://publications.scilifelab.se/researcher/91b877a3dd1a42828a6133484ef66865.json"}}, {"family": "M\u00e5rtensson", "given": "Andreas", "initials": "A", "orcid": "0000-0001-7504-8365", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a064d85bb8d4da6a4e036fb887da577.json"}}, {"family": "Nassejje", "given": "Milly", "initials": "M", "orcid": "0000-0002-9964-1814", "researcher": {"href": "https://publications.scilifelab.se/researcher/c30c51e8624b45169c006d6617345a21.json"}}, {"family": "Karlsson", "given": "Jens", "initials": "J", "orcid": "0000-0002-8005-9197", "researcher": {"href": "https://publications.scilifelab.se/researcher/a35fef42c1e04345a6a60557f3b770c6.json"}}, {"family": "Mzee", "given": "John", "initials": "J", "orcid": "0000-0002-9932-6953", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4bbfae70cab440da6a098fed5b6b388.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Businge", "given": "Stephen", "initials": "S", "orcid": "0000-0002-7094-1178", "researcher": {"href": "https://publications.scilifelab.se/researcher/949fae87c1124e9a8cfbf67f91397b05.json"}}, {"family": "Loh", "given": "Edmund", "initials": "E", "orcid": "0000-0001-7050-566X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e1fa0e881641c3999c556090a66a90.json"}}, {"family": "Boum Ii", "given": "Yap", "initials": "Y", "orcid": "0000-0002-6823-8539", "researcher": {"href": "https://publications.scilifelab.se/researcher/76ff1244bc9e4a7fb99b821c3598473e.json"}}, {"family": "Andersson-Svahn", "given": "Helene", "initials": "H", "orcid": "0000-0003-3409-276X", "researcher": {"href": "https://publications.scilifelab.se/researcher/608c083d9f924fdd9f3f4948d498f64e.json"}}, {"family": "Gantelius", "given": "Jesper", "initials": "J", "orcid": "0000-0002-2581-1542", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbb1b41e117142d18c0730183dc6eb28.json"}}, {"family": "Mwanga-Amumpaire", "given": "Juliet", "initials": "J", "orcid": "0000-0002-6738-477X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c024f8147ab94837b2344ce9aae0d92b.json"}}, {"family": "Alfv\u00e9n", "given": "Tobias", "initials": "T", "orcid": "0000-0002-2328-3512", "researcher": {"href": "https://publications.scilifelab.se/researcher/d808542ea67e466bbc93802c57574b8c.json"}}], "type": "journal article", "published": "2020-11-04", "journal": {"title": "JMIR Res Protoc", "issn": "1929-0748", "volume": "9", "issue": "11", "pages": "e21430", "issn-l": null}, "abstract": "A timely differential diagnostic is essential to identify the etiology of central nervous system (CNS) infections in children, in order to facilitate targeted treatment, manage patients, and improve clinical outcome.\n\nThe Pediatric Infection-Point-of-Care (PI-POC) trial is investigating novel methods to improve and strengthen the differential diagnostics of suspected childhood CNS infections in low-income health systems such as those in Southwestern Uganda. This will be achieved by evaluating (1) a novel DNA-based diagnostic assay for CNS infections, (2) a commercially available multiplex PCR-based meningitis/encephalitis (ME) panel for clinical use in a facility-limited laboratory setting, (3) proteomics profiling of blood from children with severe CNS infection as compared to outpatient controls with fever yet not severely ill, and (4) Myxovirus resistance protein A (MxA) as a biomarker in blood for viral CNS infection. Further changes in the etiology of childhood CNS infections after the introduction of the pneumococcal conjugate vaccine against Streptococcus pneumoniae will be investigated. In addition, the carriage and invasive rate of Neisseria meningitidis will be recorded and serotyped, and the expression of its major virulence factor (polysaccharide capsule) will be investigated.\n\nThe PI-POC trial is a prospective observational study of children including newborns up to 12 years of age with clinical features of CNS infection, and age-/sex-matched outpatient controls with fever yet not severely ill. Participants are recruited at 2 Pediatric clinics in Mbarara, Uganda. Cerebrospinal fluid (for cases only), blood, and nasopharyngeal (NP) swabs (for both cases and controls) sampled at both clinics are analyzed at the Epicentre Research Laboratory through gold-standard methods for CNS infection diagnosis (microscopy, biochemistry, and culture) and a commercially available ME panel for multiplex PCR analyses of the cerebrospinal fluid. An additional blood sample from cases is collected on day 3 after admission. After initial clinical analyses in Mbarara, samples will be transported to Stockholm, Sweden for (1) validation analyses of a novel nucleic acid-based POC test, (2) biomarker research, and (3) serotyping and molecular characterization of S. pneumoniae and N. meningitidis.\n\nA pilot study was performed from January to April 2019. The PI-POC trial enrollment of patients begun in April 2019 and will continue until September 2020, to include up to 300 cases and controls. Preliminary results from the PI-POC study are expected by the end of 2020.\n\nThe findings from the PI-POC study can potentially facilitate rapid etiological diagnosis of CNS infections in low-resource settings and allow for novel methods for determination of the severity of CNS infection in such environment.\n\nClinicalTrials.gov NCT03900091; https://clinicaltrials.gov/ct2/show/NCT03900091.\n\nDERR1-10.2196/21430.", "doi": "10.2196/21430", "pmid": "33146628", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "v9i11e21430"}, {"db": "pmc", "key": "PMC7690656"}, {"db": "ClinicalTrials.gov", "key": "NCT03900091"}], "notes": [], "created": "2020-12-07T16:38:28.050Z", "modified": "2021-11-10T12:45:31.567Z"}, {"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": "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": "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": "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": "d64c9f1bb86044c88061329283767e2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d64c9f1bb86044c88061329283767e2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d64c9f1bb86044c88061329283767e2e"}}, "title": "Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers.", "authors": [{"family": "Remnest\u00e5l", "given": "Julia", "initials": "J", "orcid": "0000-0002-3908-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/00a88350afba45fb8200786904bf51ca.json"}}, {"family": "\u00d6ijerstedt", "given": "Linn", "initials": "L"}, {"family": "Ullgren", "given": "Abbe", "initials": "A"}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Graff", "given": "Caroline", "initials": "C"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2020-06-23", "journal": {"title": "Transl Neurodegener", "issn": "2047-9158", "volume": "9", "issue": "1", "pages": "27", "issn-l": null}, "abstract": "The clinical presentations of frontotemporal dementia (FTD) are diverse and overlap with other neurological disorders. There are, as of today, no biomarkers in clinical practice for diagnosing the disorders. Here, we aimed to find protein markers in cerebrospinal fluid (CSF) from patients with FTD, presymptomatic mutation carriers and non-carriers.\n\nAntibody suspension bead arrays were used to analyse 328 proteins in CSF from patients with behavioural variant FTD (bvFTD, n = 16) and progressive primary aphasia (PPA, n = 13), as well as presymptomatic mutation carriers (PMC, n = 16) and non-carriers (NC, n = 8). A total of 492 antibodies were used to measure protein levels by direct labelling of the CSF samples. The findings were further examined in an independent cohort including 13 FTD patients, 79 patients with Alzheimer's disease and 18 healthy controls.\n\nWe found significantly altered protein levels in CSF from FTD patients compared to unaffected individuals (PMC and NC) for 26 proteins. The analysis show patterns of separation between unaffected individuals and FTD patients, especially for those with a clinical diagnosis of bvFTD. The most statistically significant differences in protein levels were found for VGF, TN-R, NPTXR, TMEM132D, PDYN and NF-M. Patients with FTD were found to have higher levels of TN-R and NF-M, and lower levels of VGF, NPTXR, TMEM132D and PDYN, compared to unaffected individuals. The main findings were reproduced in the independent cohort.\n\nIn this pilot study, we show a separation of FTD patients from unaffected individuals based on protein levels in CSF. Further investigation is required to explore the CSF profiles in larger cohorts, but the results presented here has the potential to enable future clinical utilization of these potential biomarkers within FTD.", "doi": "10.1186/s40035-020-00198-y", "pmid": "32576262", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40035-020-00198-y"}, {"db": "pmc", "key": "PMC7310563"}], "notes": [], "created": "2021-01-08T16:29:12.262Z", "modified": "2024-01-16T13:48:42.365Z"}, {"entity": "publication", "iuid": "8e603d87758a42abbfab399d8aae90a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e603d87758a42abbfab399d8aae90a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e603d87758a42abbfab399d8aae90a8"}}, "title": "Newborn Screening for Presymptomatic Diagnosis of Complement and Phagocyte Deficiencies.", "authors": [{"family": "Dezfouli", "given": "Mahya", "initials": "M"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Skattum", "given": "Lillemor", "initials": "L"}, {"family": "Abolhassani", "given": "Hassan", "initials": "H"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Torabi-Rahvar", "given": "Monireh", "initials": "M"}, {"family": "Franco Jarava", "given": "Clara", "initials": "C"}, {"family": "Martin-Nalda", "given": "Andrea", "initials": "A"}, {"family": "Ferrer Balaguer", "given": "Juana M", "initials": "JM"}, {"family": "Slade", "given": "Charlotte A", "initials": "CA"}, {"family": "Roos", "given": "Anja", "initials": "A"}, {"family": "Fernandez Pereira", "given": "Luis M", "initials": "LM"}, {"family": "L\u00f3pez-Trascasa", "given": "Margarita", "initials": "M"}, {"family": "Gonzalez-Granado", "given": "Luis I", "initials": "LI"}, {"family": "Allende-Martinez", "given": "Luis M", "initials": "LM"}, {"family": "Mizuno", "given": "Yumi", "initials": "Y"}, {"family": "Yoshida", "given": "Yusuke", "initials": "Y"}, {"family": "Friman", "given": "Vanda", "initials": "V"}, {"family": "Lundgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Aghamohammadi", "given": "Asghar", "initials": "A"}, {"family": "Rezaei", "given": "Nima", "initials": "N"}, {"family": "Hern\u00e1ndez-Gonzalez", "given": "Manuel", "initials": "M"}, {"family": "von D\u00f6beln", "given": "Ulrika", "initials": "U"}, {"family": "Truedsson", "given": "Lennart", "initials": "L"}, {"family": "Hara", "given": "Toshiro", "initials": "T"}, {"family": "Nonoyama", "given": "Shigeaki", "initials": "S"}, {"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": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}], "type": "journal article", "published": "2020-03-17", "journal": {"title": "Front Immunol", "issn": "1664-3224", "issn-l": "1664-3224", "volume": "11", "issue": null, "pages": "455"}, "abstract": "The clinical outcomes of primary immunodeficiencies (PIDs) are greatly improved by accurate diagnosis early in life. However, it is not common to consider PIDs before the manifestation of severe clinical symptoms. Including PIDs in the nation-wide newborn screening programs will potentially improve survival and provide better disease management and preventive care in PID patients. This calls for the detection of disease biomarkers in blood and the use of dried blood spot samples, which is a part of routine newborn screening programs worldwide. Here, we developed a newborn screening method based on multiplex protein profiling for parallel diagnosis of 22 innate immunodeficiencies affecting the complement system and respiratory burst function in phagocytosis. The proposed method uses a small fraction of eluted blood from dried blood spots and is applicable for population-scale performance. The diagnosis method is validated through a retrospective screening of immunodeficient patient samples. This diagnostic approach can pave the way for an earlier, more comprehensive and accurate diagnosis of complement and phagocytic disorders, which ultimately lead to a healthy and active life for the PID patients.", "doi": "10.3389/fimmu.2020.00455", "pmid": "32256498", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7090021"}], "notes": [], "created": "2020-12-10T19:03:49.605Z", "modified": "2021-11-10T12:52:59.137Z"}, {"entity": "publication", "iuid": "a5ffc222ff2f4848955dbd9ffdb38a85", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5ffc222ff2f4848955dbd9ffdb38a85.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5ffc222ff2f4848955dbd9ffdb38a85"}}, "title": "Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length.", "authors": [{"family": "Li", "given": "Chen", "initials": "C"}, {"family": "Stoma", "given": "Svetlana", "initials": "S"}, {"family": "Lotta", "given": "Luca A", "initials": "LA"}, {"family": "Warner", "given": "Sophie", "initials": "S"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Allione", "given": "Alessandra", "initials": "A"}, {"family": "Arp", "given": "Pascal P", "initials": "PP"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Buxton", "given": "Jessica L", "initials": "JL"}, {"family": "Da Silva Couto Alves", "given": "Alexessander", "initials": "A"}, {"family": "Deelen", "given": "Joris", "initials": "J"}, {"family": "Fedko", "given": "Iryna O", "initials": "IO"}, {"family": "Gordon", "given": "Scott D", "initials": "SD"}, {"family": "Jiang", "given": "Tao", "initials": "T"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Kerrison", "given": "Nicola", "initials": "N"}, {"family": "Loe", "given": "Taylor K", "initials": "TK"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Miraglio", "given": "Benjamin", "initials": "B"}, {"family": "Pervjakova", "given": "Natalia", "initials": "N"}, {"family": "Russo", "given": "Alessia", "initials": "A"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "van der Spek", "given": "Ashley", "initials": "A"}, {"family": "Verhoeven", "given": "Josine E", "initials": "JE"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Beekman", "given": "Marian", "initials": "M"}, {"family": "Blakemore", "given": "Alexandra I", "initials": "AI"}, {"family": "Canzian", "given": "Federico", "initials": "F"}, {"family": "Hamby", "given": "Stephen E", "initials": "SE"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Jones", "given": "Peter D", "initials": "PD"}, {"family": "Jousilahti", "given": "Pekka", "initials": "P"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Sillanp\u00e4\u00e4", "given": "Elina", "initials": "E"}, {"family": "Suchiman", "given": "H Eka", "initials": "HE"}, {"family": "van Heemst", "given": "Diana", "initials": "D"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Agudo", "given": "Antonio", "initials": "A"}, {"family": "Boeing", "given": "Heiner", "initials": "H"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Chirlaque", "given": "Maria-Dolores", "initials": "MD"}, {"family": "Fagherazzi", "given": "Guy", "initials": "G"}, {"family": "Ferrari", "given": "Pietro", "initials": "P"}, {"family": "Franks", "given": "Paul", "initials": "P"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Eriksson", "given": "Johan Gunnar", "initials": "JG"}, {"family": "Gunter", "given": "Marc", "initials": "M"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Hovatta", "given": "Iiris", "initials": "I"}, {"family": "Imaz", "given": "Liher", "initials": "L"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Kaaks", "given": "Rudolf", "initials": "R"}, {"family": "Key", "given": "Timothy", "initials": "T"}, {"family": "Krogh", "given": "Vittorio", "initials": "V"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Moreno", "given": "Concha", "initials": "C"}, {"family": "Onland-Moret", "given": "N Charlotte", "initials": "NC"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Overvad", "given": "Kim", "initials": "K"}, {"family": "Palli", "given": "Domenico", "initials": "D"}, {"family": "Panico", "given": "Salvatore", "initials": "S"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Quir\u00f3s", "given": "J Ram\u00f3n", "initials": "JR"}, {"family": "Jarvelin", "given": "Marjo Riitta", "initials": "MR"}, {"family": "Rodr\u00edguez-Barranco", "given": "Miguel", "initials": "M"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Severi", "given": "Gianluca", "initials": "G"}, {"family": "Slagboom", "given": "P Eline", "initials": "PE"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Tjonneland", "given": "Anne", "initials": "A"}, {"family": "Trichopoulou", "given": "Antonia", "initials": "A"}, {"family": "Tumino", "given": "Rosario", "initials": "R"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van der Schouw", "given": "Yvonne T", "initials": "YT"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Weiderpass", "given": "Elisabete", "initials": "E"}, {"family": "Denchi", "given": "Eros Lazzerini", "initials": "EL"}, {"family": "Matullo", "given": "Giuseppe", "initials": "G"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Codd", "given": "Veryan", "initials": "V"}], "type": "journal article", "published": "2020-03-05", "journal": {"title": "Am. J. Hum. Genet.", "issn": "1537-6605", "volume": "106", "issue": "3", "pages": "389-404", "issn-l": "0002-9297"}, "abstract": "Leukocyte telomere length (LTL) is a heritable biomarker of genomic aging. In this study, we perform a genome-wide meta-analysis of LTL by pooling densely genotyped and imputed association results across large-scale European-descent studies including up to 78,592 individuals. We identify 49 genomic regions at a false dicovery rate (FDR) < 0.05 threshold and prioritize genes at 31, with five highlighting nucleotide metabolism as an important regulator of LTL. We report six genome-wide significant loci in or near SENP7, MOB1B, CARMIL1, PRRC2A, TERF2, and RFWD3, and our results support recently identified PARP1, POT1, ATM, and MPHOSPH6 loci. Phenome-wide analyses in >350,000 UK Biobank participants suggest that genetically shorter telomere length increases the risk of hypothyroidism and decreases the risk of thyroid cancer, lymphoma, and a range of proliferative conditions. Our results replicate previously reported associations with increased risk of coronary artery disease and lower risk for multiple cancer types. Our findings substantially expand current knowledge on genes that regulate LTL and their impact on human health and disease.", "doi": "10.1016/j.ajhg.2020.02.006", "pmid": "32109421", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(20)30048-3"}, {"db": "pmc", "key": "PMC7058826"}], "notes": [], "created": "2020-03-03T12:57:27.050Z", "modified": "2021-11-10T12:53:17.953Z"}, {"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": "3e566b52c0814a2186badf96a7dcb3be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e566b52c0814a2186badf96a7dcb3be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e566b52c0814a2186badf96a7dcb3be"}}, "title": "The human secretome", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Svensson", "given": "Anne Sophie", "initials": "AS"}, {"family": "Scheffel", "given": "Julia", "initials": "J"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Ekblad", "given": "Siri", "initials": "S"}, {"family": "Dannemeyer", "given": "Melanie", "initials": "M"}, {"family": "Kanje", "given": "Sara", "initials": "S"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Volk", "given": "Anna Luisa", "initials": "AL"}, {"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"}, {"family": "Dodig-Crnkovic", "given": "Tea", "initials": "T"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS"}, {"family": "Hong", "given": "Mun Gwan", "initials": "MG"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Vuu", "given": "Jimmy", "initials": "J"}, {"family": "Lindstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Robinson", "given": "Jonathan", "initials": "J"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Sullivan", "given": "Devin", "initials": "D"}, {"family": "Thul", "given": "Peter", "initials": "P"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"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": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Voldborg", "given": "Bj\u00f8rn G", "initials": "BG"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"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": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal-article", "published": "2019-11-26", "journal": {"title": "Sci. Signal.", "issn": "1945-0877", "issn-l": "1945-0877", "volume": "12", "issue": "609", "pages": "eaaz0274"}, "abstract": "The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immunoassays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.", "doi": "10.1126/scisignal.aaz0274", "pmid": "31772123", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Spatial Proteomics": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-03T08:34:48.430Z", "modified": "2021-12-09T13:59:58.034Z"}, {"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": "9dbe3bf19fd34984889399769e724b95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9dbe3bf19fd34984889399769e724b95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9dbe3bf19fd34984889399769e724b95"}}, "title": "Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Bostr\u00f6m", "given": "Tove", "initials": "T"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"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": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2019-07-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "18", "issue": "7", "pages": "2706-2718", "issn-l": "1535-3893"}, "abstract": "The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (\u226460 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.", "doi": "10.1021/acs.jproteome.8b00924", "pmid": "31094526", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-08T14:57:52.618Z", "modified": "2021-07-08T13:44:33.481Z"}, {"entity": "publication", "iuid": "cca3260cc4224306b9f2b254e6b95349", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cca3260cc4224306b9f2b254e6b95349.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cca3260cc4224306b9f2b254e6b95349"}}, "title": "Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease.", "authors": [{"family": "Andersson", "given": "Annika", "initials": "A"}, {"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Nellg\u00e5rd", "given": "Bengt", "initials": "B"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Edfors", "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"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ilag", "given": "Leopold L", "initials": "LL"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"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": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"title": "Clin. Chim. Acta", "issn": "1873-3492", "volume": "494", "issue": null, "pages": "79-93", "issn-l": "0009-8981"}, "abstract": "Detailed knowledge of protein changes in cerebrospinal fluid (CSF) across healthy and diseased individuals would provide a better understanding of the onset and progression of neurodegenerative disorders. In this study, we selected 20 brain-enriched proteins previously identified in CSF by antibody suspension bead arrays (SBA) to be potentially biomarkers for Alzheimer's disease (AD) and verified these using an orthogonal approach. We examined the same set of 94 CSF samples from patients affected by AD (including preclinical and prodromal), mild cognitive impairment (MCI), non-AD dementia and healthy individuals, which had previously been analyzed by SBA. Twenty-eight parallel reaction monitoring (PRM) assays were developed and 13 of them could be validated for protein quantification. Antibody profiles were verified by PRM. For seven proteins, the antibody profiles were highly correlated with the PRM results (r > 0.7) and GAP43, VCAM1 and PSAP were identified as potential markers of preclinical AD. In conclusion, we demonstrate the usefulness of targeted mass spectrometry as a tool for the orthogonal verification of antibody profiling data, suggesting that these complementary methods can be successfully applied for comprehensive exploration of CSF protein levels in neurodegenerative disorders.", "doi": "10.1016/j.cca.2019.03.243", "pmid": "30858094", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0009-8981(19)30348-1"}], "notes": [], "created": "2020-01-08T10:40:27.440Z", "modified": "2021-07-08T13:44:33.634Z"}, {"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": "4e3ef82c1f734edf960e6e4199afa5d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e3ef82c1f734edf960e6e4199afa5d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e3ef82c1f734edf960e6e4199afa5d2"}}, "title": "Plasma protein profiling reveals candidate biomarkers for multiple sclerosis treatment.", "authors": [{"family": "Bedri", "given": "Sahl Khalid", "initials": "SK", "orcid": "0000-0002-7750-5723", "researcher": {"href": "https://publications.scilifelab.se/researcher/9663f8ac6fd74c7f97aab4120d05d1d4.json"}}, {"family": "Nilsson", "given": "Ola B", "initials": "OB"}, {"family": "Fink", "given": "Katharina", "initials": "K"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Manouchehrinia", "given": "Ali", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Hillert", "given": "Jan", "initials": "J"}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H"}, {"family": "Glaser", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-05-29", "journal": {"volume": "14", "issn": "1932-6203", "issue": "5", "pages": "e0217208", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Multiple sclerosis (MS) treatment options have improved significantly over the past decades, but the consequences of MS can still be devastating and the needs for monitoring treatment surveillance are considerable. In the current study we used affinity proteomics technology to identify potential biomarkers which could ultimately be used to as facilitate treatment decisions. We profiled the intra-individual changes in the levels of 59 target proteins using an antibody suspension bead array in serial plasma samples from 44 MS patients during treatment with natalizumab followed by fingolimod. Nine proteins showed decreasing plasma levels during natalizumab treatment, with PEBP1 and RTN3 displaying the most significant changes. Protein levels remained stable during fingolimod treatment for both proteins. The decreasing PEBP1 levels during natalizumab treatment could be validated using ELISA and replicated in an independent cohort. These results support the use of this technology as a high throughput method of identifying potentially useful biomarkers of MS treatment.", "doi": "10.1371/journal.pone.0217208", "pmid": "31141529", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-30095"}, {"db": "pmc", "key": "PMC6541274"}], "notes": [], "created": "2020-01-08T10:33:44.382Z", "modified": "2021-07-07T15:50:03.117Z"}, {"entity": "publication", "iuid": "560d795f2669408a8ca8d5fcc2a2c7f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/560d795f2669408a8ca8d5fcc2a2c7f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/560d795f2669408a8ca8d5fcc2a2c7f8"}}, "title": "Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients.", "authors": [{"family": "Idborg", "given": "Helena", "initials": "H"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Ossipova", "given": "Elena", "initials": "E"}, {"family": "Wigren", "given": "Edvard", "initials": "E"}, {"family": "Preger", "given": "Charlotta", "initials": "C"}, {"family": "Mobarrez", "given": "Fariborz", "initials": "F"}, {"family": "Checa", "given": "Antonio", "initials": "A"}, {"family": "Sohrabian", "given": "Azita", "initials": "A"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Fernandes-Cerqueira", "given": "C\u00e1tia", "initials": "C"}, {"family": "R\u00f6nnelid", "given": "Johan", "initials": "J"}, {"family": "Oke", "given": "Vilija", "initials": "V"}, {"family": "Grosso", "given": "Giorgia", "initials": "G"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Wheelock", "given": "Craig E", "initials": "CE"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Gr\u00e4slund", "given": "Susanne", "initials": "S"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Jakobsson", "given": "Per-Johan", "initials": "PJ"}], "type": "journal article", "published": "2019-05-17", "journal": {"volume": "10", "issn": "1664-3224", "issue": null, "pages": "1029", "title": "Front Immunol", "issn-l": "1664-3224"}, "abstract": "Systemic Lupus Erythematosus (SLE) is a heterogeneous autoimmune disease, which currently lacks specific diagnostic biomarkers. The diversity within the patients obstructs clinical trials but may also reflect differences in underlying pathogenesis. Our objective was to obtain protein profiles to identify potential general biomarkers of SLE and to determine molecular subgroups within SLE for patient stratification. Plasma samples from a cross-sectional study of well-characterized SLE patients (n = 379) and matched population controls (n = 316) were analyzed by antibody suspension bead array targeting 281 proteins. To investigate the differences between SLE and controls, Mann-Whitney U-test with Bonferroni correction, generalized linear modeling and receiver operating characteristics (ROC) analysis were performed. K-means clustering was used to identify molecular SLE subgroups. We identified Interferon regulating factor 5 (IRF5), solute carrier family 22 member 2 (SLC22A2) and S100 calcium binding protein A12 (S100A12) as the three proteins with the largest fold change between SLE patients and controls (SLE/Control = 1.4, 1.4, and 1.2 respectively). The lowest p-values comparing SLE patients and controls were obtained for S100A12, Matrix metalloproteinase-1 (MMP1) and SLC22A2 (padjusted = 3 \u00d7 10-9, 3 \u00d7 10-6, and 5 \u00d7 10-6 respectively). In a set of 15 potential biomarkers differentiating SLE patients and controls, two of the proteins were transcription factors, i.e., IRF5 and SAM pointed domain containing ETS transcription factor (SPDEF). IRF5 was up-regulated while SPDEF was found to be down-regulated in SLE patients. Unsupervised clustering of all investigated proteins identified three molecular subgroups among SLE patients, characterized by (1) high levels of rheumatoid factor-IgM, (2) low IRF5, and (3) high IRF5. IRF5 expressing microparticles were analyzed by flow cytometry in a subset of patients to confirm the presence of IRF5 in plasma and detection of extracellular IRF5 was further confirmed by immunoprecipitation-mass spectrometry (IP-MS). Interestingly IRF5, a known genetic risk factor for SLE, was detected extracellularly and suggested by unsupervised clustering analysis to differentiate between SLE subgroups. Our results imply a set of circulating molecules as markers of possible pathogenic importance in SLE. We believe that these findings could be of relevance for understanding the pathogenesis and diversity of SLE, as well as for selection of patients in clinical trials.", "doi": "10.3389/fimmu.2019.01029", "pmid": "31156624", "labels": {"Affinity Proteomics Stockholm": "Collaborative", "Protein Science Facility (PSF)": "Service", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6533644"}], "notes": [], "created": "2020-01-07T14:14:18.374Z", "modified": "2025-10-17T13:05:08.213Z"}, {"entity": "publication", "iuid": "d67b5e82a7544296a879c586809375f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d67b5e82a7544296a879c586809375f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d67b5e82a7544296a879c586809375f8"}}, "title": "A High-throughput Bead-based Affinity Assay Enables Analysis of Genital Protein Signatures in Women At Risk of HIV Infection.", "authors": [{"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Bradley", "given": "Frideborg", "initials": "F"}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Guthrie", "given": "Brandon L", "initials": "BL"}, {"family": "Birse", "given": "Kenzie", "initials": "K"}, {"family": "No\u00ebl-Romas", "given": "Laura", "initials": "L"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Bosire", "given": "Rose", "initials": "R"}, {"family": "Kiarie", "given": "James", "initials": "J"}, {"family": "Farquhar", "given": "Carey", "initials": "C"}, {"family": "Burgener", "given": "Adam D", "initials": "AD"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Broliden", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "18", "issn": "1535-9484", "issue": "3", "pages": "461-476", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Women at high risk of HIV infection, including sex workers and those with active genital inflammation, have molecular signatures of immune activation and epithelial barrier remodeling in samples of their genital mucosa. These alterations in the local immunological milieu are likely to impact HIV susceptibility. We here analyze host genital protein signatures in HIV uninfected women, with high frequency of condom use, living in HIV-serodiscordant relationships. Cervicovaginal secretions from women living in HIV-serodiscordant relationships ( n = 62) were collected at three time points over 12 months. Women living in HIV-negative seroconcordant relationships (controls, n = 25) were sampled at one time point. All study subjects were examined for demographic parameters associated with susceptibility to HIV infection. The cervicovaginal samples were analyzed using a high-throughput bead-based affinity assay. Proteins involved in epithelial barrier function and inflammation were increased in HIV-serodiscordant women. By combining several methods of analysis, a total of five proteins (CAPG, KLK10, SPRR3, elafin/PI3, CSTB) were consistently associated with this study group. Proteins analyzed using the affinity set-up were further validated by label-free tandem mass spectrometry in a partially overlapping cohort with concordant results. Women living in HIV-serodiscordant relationships thus had elevated levels of proteins involved in epithelial barrier function and inflammation despite low prevalence of sexually transmitted infections and a high frequency of safe sex practices. The identified proteins are important markers to follow during assessment of mucosal HIV susceptibility factors and a high-throughput bead-based affinity set-up could be a suitable method for such evaluation.", "doi": "10.1074/mcp.RA118.000757", "pmid": "30504243", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "RA118.000757"}, {"db": "pmc", "key": "PMC6398207"}], "notes": [], "created": "2020-01-08T13:20:33.442Z", "modified": "2021-07-07T15:50:03.340Z"}, {"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": "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": "0b7149b563544ff390db27e0229d0286", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b7149b563544ff390db27e0229d0286.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b7149b563544ff390db27e0229d0286"}}, "title": "Multi-ethnic genome-wide association study for atrial fibrillation.", "authors": [{"family": "Roselli", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5267-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dd28aad250f42719d505c21ed76013b.json"}}, {"family": "Chaffin", "given": "Mark D", "initials": "MD", "orcid": "0000-0002-1234-5562", "researcher": {"href": "https://publications.scilifelab.se/researcher/c73477de5ca0468ab051fd6eab7bad81.json"}}, {"family": "Weng", "given": "Lu-Chen", "initials": "LC"}, {"family": "Aeschbacher", "given": "Stefanie", "initials": "S"}, {"family": "Ahlberg", "given": "Gustav", "initials": "G"}, {"family": "Albert", "given": "Christine M", "initials": "CM"}, {"family": "Almgren", "given": "Peter", "initials": "P", "orcid": "0000-0002-0473-0241", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1a61189c4846eaa1de74d1fd79c8bb.json"}}, {"family": "Alonso", "given": "Alvaro", "initials": "A", "orcid": "0000-0002-2225-8323", "researcher": {"href": "https://publications.scilifelab.se/researcher/5213f2852c3e4ebb9a2c77883f46a04d.json"}}, {"family": "Anderson", "given": "Christopher D", "initials": "CD"}, {"family": "Aragam", "given": "Krishna G", "initials": "KG"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Barnard", "given": "John", "initials": "J", "orcid": "0000-0003-2403-8268", "researcher": {"href": "https://publications.scilifelab.se/researcher/93c6ec0bcbe54cc6b139f96adc40d4f4.json"}}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Benjamin", "given": "Emelia J", "initials": "EJ", "orcid": "0000-0003-4076-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/31c69bdf118d4b36ad65a6c4f780bab2.json"}}, {"family": "Bihlmeyer", "given": "Nathan A", "initials": "NA"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Bloom", "given": "Heather L", "initials": "HL"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bottinger", "given": "Erwin B", "initials": "EB"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0001-8509-148X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e137fc0192e4fa295a88589d57e3498.json"}}, {"family": "Calkins", "given": "Hugh", "initials": "H"}, {"family": "Campbell", "given": "Archie", "initials": "A", "orcid": "0000-0003-0198-5078", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d6b9cb975246e5aa97c60035e2fdcc.json"}}, {"family": "Cappola", "given": "Thomas P", "initials": "TP"}, {"family": "Carlquist", "given": "John", "initials": "J"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chen", "given": "Lin Y", "initials": "LY"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Choi", "given": "Eue-Keun", "initials": "EK"}, {"family": "Choi", "given": "Seung Hoan", "initials": "SH"}, {"family": "Christophersen", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6141-4712", "researcher": {"href": "https://publications.scilifelab.se/researcher/6430b9a129c1433a8e883a16a174b7a1.json"}}, {"family": "Chung", "given": "Mina K", "initials": "MK"}, {"family": "Cole", "given": "John W", "initials": "JW"}, {"family": "Conen", "given": "David", "initials": "D"}, {"family": "Cook", "given": "James", "initials": "J"}, {"family": "Crijns", "given": "Harry J", "initials": "HJ"}, {"family": "Cutler", "given": "Michael J", "initials": "MJ"}, {"family": "Damrauer", "given": "Scott M", "initials": "SM"}, {"family": "Daniels", "given": "Brian R", "initials": "BR"}, {"family": "Darbar", "given": "Dawood", "initials": "D"}, {"family": "Delgado", "given": "Graciela", "initials": "G"}, {"family": "Denny", "given": "Joshua C", "initials": "JC"}, {"family": "Dichgans", "given": "Martin", "initials": "M", "orcid": "0000-0002-0654-387X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f41f224e973440f6a78a49b54ca35e3a.json"}}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Dudink", "given": "Elton A", "initials": "EA", "orcid": "0000-0003-4572-3969", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f18954644f14b83b72172e03c2fc0d9.json"}}, {"family": "Dudley", "given": "Samuel C", "initials": "SC"}, {"family": "Esa", "given": "Nada", "initials": "N"}, {"family": "Esko", "given": "Tonu", "initials": "T", "orcid": "0000-0003-1982-6569", "researcher": {"href": "https://publications.scilifelab.se/researcher/d72619c1e29d44e8b8454902d2af8d9e.json"}}, {"family": "Eskola", "given": "Markku", "initials": "M"}, {"family": "Fatkin", "given": "Diane", "initials": "D"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Geelhoed", "given": "Bastiaan", "initials": "B"}, {"family": "Grewal", "given": "Raji P", "initials": "RP"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Gupta", "given": "Namrata", "initials": "N"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5894-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a0552f8a6514baa9bdb6809148aaddc.json"}}, {"family": "Gutmann", "given": "Rebecca", "initials": "R"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Hernesniemi", "given": "Jussi", "initials": "J"}, {"family": "Hocking", "given": "Lynne J", "initials": "LJ"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Horimoto", "given": "Andrea R V R", "initials": "ARVR"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Huang", "given": "Paul L", "initials": "PL"}, {"family": "Huffman", "given": "Jennifer", "initials": "J", "orcid": "0000-0002-9672-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa4efb5afae47528265d8be0d5e67fd.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Ipek", "given": "Esra Gucuk", "initials": "EG"}, {"family": "Ito", "given": "Kaoru", "initials": "K"}, {"family": "Jimenez-Conde", "given": "Jordi", "initials": "J"}, {"family": "Johnson", "given": "Renee", "initials": "R"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW", "orcid": "0000-0002-3246-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479b794031d4df7bed96340b3470c19.json"}}, {"family": "K\u00e4\u00e4b", "given": "Stefan", "initials": "S"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y", "orcid": "0000-0001-8748-5597", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf00b09991c4b40bd77a4f2c5bfad97.json"}}, {"family": "Kane", "given": "John P", "initials": "JP"}, {"family": "Kastrati", "given": "Adnan", "initials": "A"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S", "orcid": "0000-0002-6724-032X", "researcher": {"href": "https://publications.scilifelab.se/researcher/90e1dbf77e38479780a7fd6d5b0a34ee.json"}}, {"family": "Katschnig-Winter", "given": "Petra", "initials": "P"}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Kietselaer", "given": "Bas L", "initials": "BL"}, {"family": "Kirchhof", "given": "Paulus", "initials": "P"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME", "orcid": "0000-0003-0663-7275", "researcher": {"href": 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"initials": "U"}, {"family": "Wang", "given": "Biqi", "initials": "B"}, {"family": "Weeke", "given": "Peter E", "initials": "PE"}, {"family": "Weijs", "given": "Bob", "initials": "B", "orcid": "0000-0003-3202-4931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5f4a2e7a32d45a1843f130d3dd2cbfa.json"}}, {"family": "Weiss", "given": "Raul", "initials": "R"}, {"family": "Weiss", "given": "Stefan", "initials": "S", "orcid": "0000-0002-3553-4315", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a7c021b692c4fc1b2468c63fd0b2c43.json"}}, {"family": "Wells", "given": "Quinn S", "initials": "QS"}, {"family": "Wiggins", "given": "Kerri L", "initials": "KL", "orcid": "0000-0003-2749-1279", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9d1f9cb10ef4038abb10fb6ee289504.json"}}, {"family": "Wong", "given": "Jorge A", "initials": "JA"}, {"family": "Woo", "given": "Daniel", "initials": "D"}, {"family": "Worrall", "given": "Bradford B", "initials": "BB"}, {"family": "Yang", "given": "Pil-Sung", "initials": "PS"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Yoneda", "given": "Zachary T", "initials": "ZT"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA", "orcid": "0000-0002-9599-4866", "researcher": {"href": "https://publications.scilifelab.se/researcher/25bb007311104c92983dbcce80f72260.json"}}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd513dc49e0945bc8298f72d1244648d.json"}}], "type": "journal article", "published": "2018-06-11", "journal": {"volume": "50", "issn": "1546-1718", "issue": "9", "pages": "1225-1233", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Atrial fibrillation (AF) affects more than 33 million individuals worldwide1 and has a complex heritability2. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF. We also performed transcriptome-wide analyses that identified 57 AF-associated genes, 42 of which overlap with GWAS loci. The identified loci implicate genes enriched within cardiac developmental, electrophysiological, contractile and structural pathways. These results extend our understanding of the biological pathways underlying AF and may facilitate the development of therapeutics for AF.", "doi": "10.1038/s41588-018-0133-9", "pmid": "29892015", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0133-9"}, {"db": "pmc", "key": "PMC6136836"}, {"db": "mid", "key": "NIHMS986675"}], "notes": [], "created": "2019-01-09T07:22:19.148Z", "modified": "2021-07-07T15:50:02.934Z"}, {"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": "fba60e30a15c48deb80ae21f3fffe15d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fba60e30a15c48deb80ae21f3fffe15d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fba60e30a15c48deb80ae21f3fffe15d"}}, "title": "Protein profiling in serum after traumatic brain injury in rats reveals potential injury markers.", "authors": [{"family": "Thelin", "given": "Eric Peter", "initials": "EP"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Frostell", "given": "Arvid", "initials": "A"}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Risling", "given": "M\u00e5rten", "initials": "M"}, {"family": "Svensson", "given": "Mikael", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Bellander", "given": "Bo-Michael", "initials": "BM"}], "type": "journal article", "published": "2018-03-15", "journal": {"volume": "340", "issn": "1872-7549", "issue": null, "title": "Behav. Brain Res.", "pages": "71-80", "issn-l": "0166-4328"}, "abstract": "The serum proteome following traumatic brain injury (TBI) could provide information for outcome prediction and injury monitoring. The aim with this affinity proteomic study was to identify serum proteins over time and between normoxic and hypoxic conditions in focal TBI.\n\nSprague Dawley rats (n=73) received a 3mm deep controlled cortical impact (\"severe injury\"). Following injury, the rats inhaled either a normoxic (22% O2) or hypoxic (11% O2) air mixture for 30min before resuscitation. The rats were sacrificed at day 1, 3, 7, 14 and 28 after trauma. A total of 204 antibodies targeting 143 unique proteins of interest in TBI research, were selected. The sample proteome was analyzed in a suspension bead array set-up. Comparative statistics and factor analysis were used to detect differences as well as variance in the data.\n\nWe found that complement factor 9 (C9), complement factor B (CFB) and aldolase c (ALDOC) were detected at higher levels the first days after trauma. In contrast, hypoxia inducing factor (HIF)1\u03b1, amyloid precursor protein (APP) and WBSCR17 increased over the subsequent weeks. S100A9 levels were higher in hypoxic-compared to normoxic rats, together with a majority of the analyzed proteins, albeit few reached statistical significance. The principal component analysis revealed a variance in the data, highlighting clusters of proteins.\n\nProtein profiling of serum following TBI using an antibody based microarray revealed temporal changes of several proteins over an extended period of up to four weeks. Further studies are warranted to confirm our findings.", "doi": "10.1016/j.bbr.2016.08.058", "pmid": "27591967", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0166-4328(16)30576-9"}], "notes": [], "created": "2017-05-03T12:59:06.280Z", "modified": "2021-07-07T15:50:03.418Z"}, {"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": "9a66e1ee51af4d9dacf0840a88138663", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663"}}, "title": "A pathology atlas of the human cancer transcriptome.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G", "orcid": "0000-0001-5232-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/c76df55999a74ebfaada13e0cc775de8.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca09f57bdc44e7fa33a472f04859a4d.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Liu", "given": "Zhengtao", "initials": "Z", "orcid": "0000-0001-7803-6044", "researcher": {"href": "https://publications.scilifelab.se/researcher/53a62a58b12f4f4c87ebe4135826c91a.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e79e661083f49bf90cbbfc19670f404.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Djureinovic", "given": "Dijana", "initials": "D", "orcid": "0000-0002-1852-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/17058abc202c4da794e35722c1f234df.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}], "type": "journal article", "published": "2017-08-18", "journal": {"volume": "357", "issn": "1095-9203", "issue": "6352", "title": "Science", "pages": "eaan2507", "issn-l": "0036-8075"}, "abstract": "Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.", "doi": "10.1126/science.aan2507", "pmid": "28818916", "labels": {"National Genomics Infrastructure": "Service", "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "357/6352/eaan2507"}], "notes": [], "created": "2017-11-03T16:19:27.334Z", "modified": "2024-01-16T13:48:47.600Z"}, {"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": "11cec8cacdd44603bc2ae2054cc21468", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11cec8cacdd44603bc2ae2054cc21468.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11cec8cacdd44603bc2ae2054cc21468"}}, "title": "A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.", "authors": [{"family": "Manning", "given": "Alisa", "initials": "A"}, {"family": "Highland", "given": "Heather M", "initials": "HM"}, {"family": "Gasser", "given": "Jessica", "initials": "J"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Tukiainen", "given": "Taru", "initials": "T"}, {"family": "Fontanillas", "given": "Pierre", "initials": "P"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Rivas", "given": "Manuel A", "initials": "MA"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Locke", "given": "Adam E", "initials": "AE"}, {"family": "Cingolani", "given": "Pablo", "initials": "P"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Vi\u00f1uela", "given": "Ana", "initials": "A"}, {"family": "Brown", "given": "Andrew A", "initials": "AA"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Flannick", "given": "Jason", "initials": "J"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Gamazon", "given": "Eric R", "initials": "ER"}, {"family": "Gaulton", "given": "Kyle J", "initials": "KJ"}, {"family": "Im", "given": "Hae Kyung", "initials": "HK"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Blackwell", "given": "Thomas W", "initials": "TW"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Burtt", "given": "No\u00ebl P", "initials": "NP"}, {"family": "Chen", "given": "Yuhui", "initials": "Y"}, {"family": "Green", "given": "Todd", "initials": "T"}, {"family": "Hartl", "given": "Christopher", "initials": "C"}, {"family": "Kang", "given": "Hyun Min", "initials": "HM"}, {"family": "Kumar", "given": "Ashish", "initials": "A"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Ma", "given": "Clement", "initials": "C"}, {"family": "Moutsianas", "given": "Loukas", "initials": "L"}, {"family": "Pearson", "given": "Richard D", "initials": "RD"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Rayner", "given": "N William", "initials": "NW"}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "van de Bunt", "given": "Martijn", "initials": "M"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Koskinen", "given": "Seppo", "initials": "S"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Jacobs", "given": "Suzanne B R", "initials": "SBR"}, {"family": "Wessel", "given": "Jennifer", "initials": "J"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}, {"family": "Blancher", "given": "Christine", "initials": "C"}, {"family": "Buck", "given": "Gemma", "initials": "G"}, {"family": "Buck", "given": "David", "initials": "D"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Gabriel", "given": "Stacey", "initials": "S"}, {"family": "Gjesing", "given": "Anette P", "initials": "AP"}, {"family": "Groves", "given": "Christopher J", "initials": "CJ"}, {"family": "Hollensted", "given": "Mette", "initials": "M"}, {"family": "Huyghe", "given": "Jeroen R", "initials": "JR"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Jun", "given": "Goo", "initials": "G"}, {"family": "Justesen", "given": "Johanne Marie", "initials": "JM"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Murphy", "given": "Jacquelyn", "initials": "J"}, {"family": "Neville", "given": "Matt", "initials": "M"}, {"family": "Onofrio", "given": "Robert", "initials": "R"}, {"family": "Small", "given": "Kerrin S", "initials": "KS"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Trakalo", "given": "Joseph", "initials": "J"}, {"family": "Banks", "given": "Eric", "initials": "E"}, {"family": "Carey", "given": "Jason", "initials": "J"}, {"family": "Carneiro", "given": "Mauricio O", "initials": "MO"}, {"family": "DePristo", "given": "Mark", "initials": "M"}, {"family": "Farjoun", "given": "Yossi", "initials": "Y"}, {"family": "Fennell", "given": "Timothy", "initials": "T"}, {"family": "Goldstein", "given": "Jacqueline I", "initials": "JI"}, {"family": "Grant", "given": "George", "initials": "G"}, {"family": "Hrab\u00e9 de Angelis", "given": "Martin", "initials": "M"}, {"family": "Maguire", "given": "Jared", "initials": "J"}, {"family": "Neale", "given": "Benjamin M", "initials": "BM"}, {"family": "Poplin", "given": "Ryan", "initials": "R"}, {"family": "Purcell", "given": "Shaun", "initials": "S"}, {"family": "Schwarzmayr", "given": "Thomas", "initials": "T"}, {"family": "Shakir", "given": "Khalid", "initials": "K"}, {"family": "Smith", "given": "Joshua D", "initials": "JD"}, {"family": "Strom", "given": "Tim M", "initials": "TM"}, {"family": "Wieland", "given": "Thomas", "initials": "T"}, {"family": "Lindstrom", "given": "Jaana", "initials": "J"}, {"family": "Brandslund", "given": "Ivan", "initials": "I"}, {"family": "Christensen", "given": "Cramer", "initials": "C"}, {"family": "Surdulescu", "given": "Gabriela L", "initials": "GL"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Doney", "given": "Alex S F", "initials": "ASF"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Rolandsson", "given": "Olov", "initials": "O"}, {"family": "Rosengren", "given": "Anders H", "initials": "AH"}, {"family": "Farook", "given": "Vidya S", "initials": "VS"}, {"family": "Thameem", "given": "Farook", "initials": "F"}, {"family": "Puppala", "given": "Sobha", "initials": "S"}, {"family": "Kumar", "given": "Satish", "initials": "S"}, {"family": "Lehman", "given": "Donna M", "initials": "DM"}, {"family": "Jenkinson", "given": "Christopher P", "initials": "CP"}, {"family": "Curran", "given": "Joanne E", "initials": "JE"}, {"family": "Hale", "given": "Daniel Esten", "initials": "DE"}, {"family": "Fowler", "given": "Sharon P", "initials": "SP"}, {"family": "Arya", "given": "Rector", "initials": "R"}, {"family": "DeFronzo", "given": "Ralph A", "initials": "RA"}, {"family": "Abboud", "given": "Hanna E", "initials": "HE"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Hicks", "given": "Pamela J", "initials": "PJ"}, {"family": "Palmer", "given": "Nicholette D", "initials": "ND"}, {"family": "Ng", "given": "Maggie C Y", "initials": "MCY"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "Freedman", "given": "Barry I", "initials": "BI"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "Kinnunen", "given": "Leena", "initials": "L"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Swift", "given": "Amy", "initials": "A"}, {"family": "Pasko", "given": "Dorota", "initials": "D"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Fadista", "given": "Jo\u00e3o", "initials": "J"}, {"family": "Pollin", "given": "Toni I", "initials": "TI"}, {"family": "Barzilai", "given": "Nir", "initials": "N"}, {"family": "Atzmon", "given": "Gil", "initials": "G"}, {"family": "Glaser", "given": "Benjamin", "initials": "B"}, {"family": "Thorand", "given": "Barbara", "initials": "B"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Roden", "given": "Michael", "initials": "M"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Kriebel", "given": "Jennifer", "initials": "J"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Griswold", "given": "Michael", "initials": "M"}, {"family": "Taylor", "given": "Herman A", "initials": "HA"}, {"family": "Wilson", "given": "Gregory", "initials": "G"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Oksa", "given": "Heikki", "initials": "H"}, {"family": "Scott", "given": "William R", "initials": "WR"}, {"family": "Afzal", "given": "Uzma", "initials": "U"}, {"family": "Tan", "given": "Sian-Tsung", "initials": "ST"}, {"family": "Loh", "given": "Marie", "initials": "M"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Sehmi", "given": "Jobanpreet", "initials": "J"}, {"family": "Kooner", "given": "Jaspal Singh", "initials": "JS"}, {"family": "Lehne", "given": "Benjamin", "initials": "B"}, {"family": "Cho", "given": "Yoon Shin", "initials": "YS"}, {"family": "Lee", "given": "Jong-Young", "initials": "JY"}, {"family": "Han", "given": "Bok-Ghee", "initials": "BG"}, {"family": "K\u00e4r\u00e4j\u00e4m\u00e4ki", "given": "Annemari", "initials": "A"}, {"family": "Qi", "given": "Qibin", "initials": "Q"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Huang", "given": "Jinyan", "initials": "J"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Below", "given": "Jennifer E", "initials": "JE"}, {"family": "Aguilar", "given": "David", "initials": "D"}, {"family": "Wong", "given": "Tien Yin", "initials": "TY"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Khor", "given": "Chiea-Chuen", "initials": "CC"}, {"family": "Chia", "given": "Kee Seng", "initials": "KS"}, {"family": "Lim", "given": "Wei Yen", "initials": "WY"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Chan", "given": "Edmund", "initials": "E"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Aung", "given": "Tin", "initials": "T"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Hakaste", "given": "Liisa", "initials": "L"}, {"family": "Kravic", "given": "Jasmina", "initials": "J"}, {"family": "J\u00f8rgensen", "given": "Marit E", "initials": "ME"}, {"family": "Lauritzen", "given": "Torsten", "initials": "T"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Stirrups", "given": "Kathleen E", "initials": "KE"}, {"family": "Owen", "given": "Katharine R", "initials": "KR"}, {"family": "Farmer", "given": "Andrew J", "initials": "AJ"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "O'Rahilly", "given": "Stephen P", 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{"family": "Hu", "given": "Cheng", "initials": "C"}, {"family": "Jia", "given": "Weiping", "initials": "W"}, {"family": "Ma", "given": "Ronald C W", "initials": "RCW"}, {"family": "McVean", "given": "Gilean", "initials": "G"}, {"family": "Park", "given": "Taesung", "initials": "T"}, {"family": "Prabhakaran", "given": "Dorairaj", "initials": "D"}, {"family": "Sandhu", "given": "Manjinder", "initials": "M"}, {"family": "Scott", "given": "James", "initials": "J"}, {"family": "Sladek", "given": "Rob", "initials": "R"}, {"family": "Tandon", "given": "Nikhil", "initials": "N"}, {"family": "Teo", "given": "Yik Ying", "initials": "YY"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA"}, {"family": "Kesaniemi", "given": "Y Antero", "initials": "YA"}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Abecasis", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Bell", "given": "Graeme I", "initials": "GI"}, {"family": "Blangero", "given": "John", "initials": "J"}, {"family": "Cox", "given": "Nancy J", "initials": "NJ"}, {"family": "Duggirala", "given": "Ravindranath", "initials": "R"}, {"family": "Seielstad", "given": "Mark", "initials": "M"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Dupuis", "given": "Josee", "initials": "J"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Hanis", "given": "Craig L", "initials": "CL"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Gloyn", "given": "Anna L", "initials": "AL"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "66", "issn": "1939-327X", "issue": "7", "pages": "2019-2032", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "To identify novel coding association signals and facilitate characterization of mechanisms influencing glycemic traits and type 2 diabetes risk, we analyzed 109,215 variants derived from exome array genotyping together with an additional 390,225 variants from exome sequence in up to 39,339 normoglycemic individuals from five ancestry groups. We identified a novel association between the coding variant (p.Pro50Thr) in AKT2 and fasting plasma insulin (FI), a gene in which rare fully penetrant mutations are causal for monogenic glycemic disorders. The low-frequency allele is associated with a 12% increase in FI levels. This variant is present at 1.1% frequency in Finns but virtually absent in individuals from other ancestries. Carriers of the FI-increasing allele had increased 2-h insulin values, decreased insulin sensitivity, and increased risk of type 2 diabetes (odds ratio 1.05). In cellular studies, the AKT2-Thr50 protein exhibited a partial loss of function. We extend the allelic spectrum for coding variants in AKT2 associated with disorders of glucose homeostasis and demonstrate bidirectional effects of variants within the pleckstrin homology domain of AKT2.", "doi": "10.2337/db16-1329", "pmid": "28341696", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "db16-1329"}, {"db": "pmc", "key": "PMC5482074"}, {"db": "mid", "key": "EMS72347"}], "notes": [], "created": "2017-10-25T15:18:19.643Z", "modified": "2024-01-16T13:48:47.816Z"}, {"entity": "publication", "iuid": "9ffdf7a669174f9b940bb01c93fab8a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9"}}, "title": "A subcellular map of the human proteome.", "authors": [{"family": "Thul", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1441c2fca5d4946987ec975986fcfa2.json"}}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L", "orcid": "0000-0002-2387-3491", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b0ca6c2a8f64be89222a6029885b08c.json"}}, {"family": "Wiking", "given": "Mikaela", "initials": "M", "orcid": "0000-0002-6368-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/b69baef540a14859a7b4fd966c3b9245.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc22f13eb21a4c75a6e7cad7686bcc8a.json"}}, {"family": "Geladaki", "given": "Aikaterini", "initials": "A", "orcid": "0000-0002-0530-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/28081295132343c5bfc4b1e9bcfb8201.json"}}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Alm", "given": "Tove", "initials": "T", "orcid": "0000-0002-2643-8241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a0b5ee89148475581faf42ea53d61bd.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rk", "given": "Lars", "initials": "L", "orcid": "0000-0002-8116-882X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1092280955d44d1f99258f4f812fb6c7.json"}}, {"family": "Breckels", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-8918-7171", "researcher": {"href": "https://publications.scilifelab.se/researcher/3efbca65f39d4f7aa8df049a39e0c8a9.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Fall", "given": "Jenny", "initials": "J"}, {"family": "Gatto", "given": "Laurent", "initials": "L", "orcid": "0000-0002-1520-2268", "researcher": {"href": "https://publications.scilifelab.se/researcher/242f5219a40547439c0cc4b07e26e71d.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications.scilifelab.se/researcher/80019f26676347d5b6c4124d63eeaf86.json"}}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Mulvey", "given": "Claire M", "initials": "CM", "orcid": "0000-0002-2989-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc08b919bd8a423f8a6df8b880979045.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ad1d3b1313460583a16329a0143a1d.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R", "orcid": "0000-0001-8787-8868", "researcher": {"href": "https://publications.scilifelab.se/researcher/83314cf7a93543bf9cd6f68f9657e99e.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a96138841741f9acff4a50100c2a25.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Winsnes", "given": "Casper", "initials": "C", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a64c707c8b54b6bbd31dae6485a1392.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2017-05-26", "journal": {"volume": "356", "issn": "1095-9203", "issue": "6340", "pages": null, "title": "Science", "issn-l": "0036-8075"}, "abstract": "Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.", "doi": "10.1126/science.aal3321", "pmid": "28495876", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Spatial Proteomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "science.aal3321"}], "notes": [], "created": "2017-10-31T15:27:28.787Z", "modified": "2024-01-16T13:48:47.941Z"}, {"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": "4e03b1140bb94f24a5dfc579a2902505", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e03b1140bb94f24a5dfc579a2902505.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e03b1140bb94f24a5dfc579a2902505"}}, "title": "Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function", "authors": [{"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Felix", "given": "Janine F", "initials": "JF"}, {"family": "Schillert", "given": "Arne", "initials": "A"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Chen", "given": "Ming Huei", "initials": "MH"}, {"family": "Leening", "given": "Maarten J G", "initials": "MJG"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Gro\u00dfmann", "given": "Vera", "initials": "V"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Shah", "given": "Sanjiv J", "initials": "SJ"}, {"family": "Pramana", "given": "Setia", "initials": "S"}, {"family": "Lieb", "given": "Wolfgang", "initials": "W"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Stanton", "given": "Alice V", "initials": "AV"}, {"family": "Malzahn", "given": "D\u00f6rthe", "initials": "D"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Minelli", "given": "Cosetta", "initials": "C"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Lyytik\u00e4inen", "given": "Leo Pekka", "initials": "LP"}, {"family": "Tiller", "given": "Daniel", "initials": "D"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Monnereau", "given": "Claire", "initials": "C"}, {"family": "Di Tullio", "given": "Marco R", "initials": "MR"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Morley", "given": "Michael", "initials": "M"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Aragam", "given": "Jayashri", "initials": "J"}, {"family": "Benjamin", "given": "Emelia J", "initials": "EJ"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Bisping", "given": "Egbert", "initials": "E"}, {"family": "Broeckel", "given": "Ulrich", "initials": "U"}, {"family": "Cheng", "given": "Susan", "initials": "S"}, {"family": "Deckers", "given": "Jaap W", "initials": "JW"}, {"family": "Del Greco M", "given": "Fabiola", "initials": "F"}, {"family": "Edelmann", "given": "Frank", "initials": "F"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Friedrich", "given": "Nele", "initials": "N"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Hughes", "given": "Alun D", "initials": "AD"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "investigators", "given": "KNHI", "initials": "K"}, {"family": "Kruppa", "given": "Jochen", "initials": "J"}, {"family": "Lackner", "given": "Karl J", "initials": "KJ"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Laskowski", "given": "Rafael", "initials": "R"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Leosdottir", "given": "Margr\u00e9t", "initials": "M"}, {"family": "Lin", "given": "Honghuang", "initials": "H"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Loley", "given": "Christina", "initials": "C"}, {"family": "MacRae", "given": "Calum A", "initials": "CA"}, {"family": "Mascalzoni", "given": "Deborah", "initials": "D"}, {"family": "Mayet", "given": "Jamil", "initials": "J"}, {"family": "Medenwald", "given": "Daniel", "initials": "D"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "M\u00fcller", "given": "Christian", "initials": "C"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Nappo", "given": "Stefania", "initials": "S"}, {"family": "Nilsson", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Nuding", "given": "Sebastian", "initials": "S"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Pfeufer", "given": "Arne", "initials": "A"}, {"family": "Pietzner", "given": "Diana", "initials": "D"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Ruohonen", "given": "Saku T", "initials": "ST"}, {"family": "Sacco", "given": "Ralph L", "initials": "RL"}, {"family": "Samdarshi", "given": "Tandaw E", "initials": "TE"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Sharp", "given": "Andrew S P", "initials": "ASP"}, {"family": "Shields", "given": "Denis C", "initials": "DC"}, {"family": "Sorice", "given": "Rossella", "initials": "R"}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Surendran", "given": "Praveen", "initials": "P"}, {"family": "Thom", "given": "Simon", "initials": "S"}, {"family": "T\u00f6glhofer", "given": "Anna M", "initials": "AM"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Wachter", "given": "Rolf", "initials": "R"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Ziegler", "given": "Andreas", "initials": "A"}, {"family": "M\u00fcnzel", "given": "Thomas", "initials": "T"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Cappola", "given": "Thomas P", "initials": "TP"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Mitchell", "given": "Gary F", "initials": "GF"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Dueker", "given": "Nicole D", "initials": "ND"}, {"family": "Jaddoe", "given": "Vincent W V", "initials": "VWV"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Russ", "given": "Martin", "initials": "M"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Pieske", "given": "Burkert", "initials": "B"}, {"family": "Barron", "given": "Anthony J", "initials": "AJ"}, {"family": "Zweiker", "given": "Robert", "initials": "R"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Liu", "given": "Kiang", "initials": "K"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Blankenberg", "given": "Stefan", "initials": "S"}, {"family": "Larson", "given": "Martin G", "initials": "MG"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}], "type": "journal-article", "published": "2017-04-10", "journal": {"volume": "127", "issn": "0021-9738", "issue": "5", "pages": "1798-1812", "title": "J Clin Invest.", "issn-l": null}, "abstract": null, "doi": "10.1172/jci84840", "pmid": "28394258", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:35.302Z", "modified": "2021-07-07T15:50:03.445Z"}, {"entity": "publication", "iuid": "d2131eeeed404689b6cf4dba0f546d6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2131eeeed404689b6cf4dba0f546d6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2131eeeed404689b6cf4dba0f546d6e"}}, "title": "Discovery of circulating proteins associated to knee radiographic osteoarthritis.", "authors": [{"family": "Lourido", "given": "Luc\u00eda", "initials": "L"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Fern\u00e1ndez-Tajes", "given": "Juan", "initials": "J"}, {"family": "Oreiro", "given": "Natividad", "initials": "N"}, {"family": "Henjes", "given": "Frauke", "initials": "F"}, {"family": "Hellstr\u00f6m", "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": "Ruiz-Romero", "given": "Cristina", "initials": "C"}, {"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": "2017-03-09", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "137", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Currently there are no sufficiently sensitive biomarkers able to reflect changes in joint remodelling during osteoarthritis (OA). In this work, we took an affinity proteomic approach to profile serum samples for proteins that could serve as indicators for the diagnosis of radiographic knee OA. Antibody suspension bead arrays were applied to analyze serum samples from patients with OA (n\u2009=\u2009273), control subjects (n\u2009=\u200976) and patients with rheumatoid arthritis (RA, n\u2009=\u2009244). For verification, a focused bead array was built and applied to an independent set of serum samples from patients with OA (n\u2009=\u2009188), control individuals (n\u2009=\u200983) and RA (n\u2009=\u2009168) patients. A linear regression analysis adjusting for sex, age and body mass index (BMI) revealed that three proteins were significantly elevated (P\u2009<\u20090.05) in serum from OA patients compared to controls: C3, ITIH1 and S100A6. A panel consisting of these three proteins had an area under the curve of 0.82 for the classification of OA and control samples. Moreover, C3 and ITIH1 levels were also found to be significantly elevated (P\u2009<\u20090.05) in OA patients compared to RA patients. Upon validation in additional study sets, the alterations of these three candidate serum biomarker proteins could support the diagnosis of radiographic knee OA.", "doi": "10.1038/s41598-017-00195-8", "pmid": "28273936", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-00195-8"}, {"db": "pmc", "key": "PMC5427840"}], "notes": [], "created": "2017-10-30T10:15:33.970Z", "modified": "2021-07-08T12:07:34.275Z"}, {"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": "bb9d97d33bd445a488b6c9a31e179703", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb9d97d33bd445a488b6c9a31e179703.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb9d97d33bd445a488b6c9a31e179703"}}, "title": "Elevated levels of circulating CDH5 and FABP1 in association with human drug-induced liver injury.", "authors": [{"family": "Mikus", "given": "Maria", "initials": "M"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Gry", "given": "Marcus", "initials": "M"}, {"family": "Bachmann", "given": "Julie", "initials": "J"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Yimer", "given": "Getnet", "initials": "G"}, {"family": "Aklillu", "given": "Eleni", "initials": "E"}, {"family": "Makonnen", "given": "Eyasu", "initials": "E"}, {"family": "Aderaye", "given": "Getachew", "initials": "G"}, {"family": "Roach", "given": "James", "initials": "J"}, {"family": "Fier", "given": "Ian", "initials": "I"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "G\u00f6pfert", "given": "Jens", "initials": "J"}, {"family": "Perazzo", "given": "Hugo", "initials": "H"}, {"family": "Poynard", "given": "Thierry", "initials": "T"}, {"family": "Stephens", "given": "Camilla", "initials": "C"}, {"family": "Andrade", "given": "Ra\u00fal J", "initials": "RJ"}, {"family": "Lucena", "given": "M Isabel", "initials": "MI"}, {"family": "Arber", "given": "Nadir", "initials": "N"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Watkins", "given": "Paul B", "initials": "PB"}, {"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": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "37", "issn": "1478-3231", "issue": "1", "pages": "132-140", "title": "Liver Int.", "issn-l": "1478-3223"}, "abstract": "The occurrence of drug-induced liver injury (DILI) is a major issue in all phases of drug development. To identify novel biomarker candidates associated with DILI, we utilised an affinity proteomics strategy, where antibody suspension bead arrays were applied to profile plasma and serum samples from human DILI cases and controls.\n\nAn initial screening was performed using 4594 randomly selected antibodies, representing 3450 human proteins. Resulting candidate proteins together with proposed DILI biomarker candidates generated a DILI array of 251 proteins for subsequent target analysis and verifications. In total, 1196 samples from 241 individuals across four independent cohorts were profiled: healthy volunteers receiving acetaminophen, patients with human immunodeficiency virus and/or tuberculosis receiving treatment, DILI cases originating from a wide spectrum of drugs, and healthy volunteers receiving heparins.\n\nWe observed elevated levels of cadherin 5, type 2 (CDH5) and fatty acid-binding protein 1 (FABP1) in DILI cases. In the two longitudinal cohorts, CDH5 was elevated already at baseline. FABP1 was elevated after treatment initiation and seemed to respond more rapidly than alanine aminotransferase (ALT). The elevations were verified in the DILI cases treated with various drugs. In the heparin cohort, CDH5 was stable over time whereas FABP1 was elevated.\n\nThese results suggest that CDH5 may have value as a susceptibility marker for DILI. FABP1 was identified as a biomarker candidate with superior characteristics regarding tissue distribution and kinetics compared to ALT but likely with limited predictive value for the development of severe DILI. Further studies are needed to determine the clinical utility of the proposed markers.", "doi": "10.1111/liv.13174", "pmid": "27224670", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5215406"}], "notes": [], "created": "2017-05-03T12:59:07.167Z", "modified": "2021-07-08T13:44:33.558Z"}, {"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": "7362064a1f044c14a2e50a26392e171a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7362064a1f044c14a2e50a26392e171a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7362064a1f044c14a2e50a26392e171a"}}, "title": "CSF profiling of the human brain enriched proteome reveals associations of neuromodulin and neurogranin to Alzheimer's disease.", "authors": [{"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"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": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Nellg\u00e5rd", "given": "Bengt", "initials": "B"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "10", "issn": "1862-8354", "issue": "12", "pages": "1242-1253", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "This study is part of a larger effort aiming to expand the knowledge of brain-enriched proteins in human cerebrospinal fluid (CSF) and to provide novel insight into the relation between such proteins and different neurodegenerative diseases.\n\nHere 280 brain-enriched proteins in CSF from patients with Alzheimer's disease (AD), Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are profiled. In total, 441 human samples of ventricular CSF collected post mortem and lumbar CSF collected ante mortem are analyzed using 376 antibodies in a suspension bead array setup, utilizing a direct labelling approach.\n\nAmong several proteins displaying differentiated profiles between sample groups, we focus here on two synaptic proteins, neuromodulin (GAP43) and neurogranin (NRGN). They are both found at elevated levels in CSF from AD patients in two independent cohorts, providing disease-associated profiles in addition to verifying and strengthening previously observed patterns. Increased levels are also observed for patients for whom the AD diagnosis was not established at the time of sampling.\n\nThese findings indicate that analyzing the brain-enriched proteins in CSF is of particular interest to increase the understanding of the CSF proteome and its relation to neurodegenerative disorders. In addition, this study lends support to the notion that measurements of these synaptic proteins could potentially be of great relevance in future diagnostic tests for AD.", "doi": "10.1002/prca.201500150", "pmid": "27604409", "labels": {"Fluorescence Tissue Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5157753"}], "notes": [], "created": "2017-05-03T12:59:05.983Z", "modified": "2021-07-08T13:44:33.352Z"}, {"entity": "publication", "iuid": "f8be8649e5f64414a6f83831d43ee7fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8be8649e5f64414a6f83831d43ee7fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8be8649e5f64414a6f83831d43ee7fa"}}, "title": "Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data.", "authors": [{"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Lee", "given": "Woojoo", "initials": "W"}, {"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": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2016-10-07", "journal": {"volume": "15", "issn": "1535-3907", "issue": "10", "pages": "3473-3480", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Enhanced by the growing number of biobanks, biomarker studies can now be performed with reasonable statistical power by using large sets of samples. Antibody-based proteomics by means of suspension bead arrays offers one attractive approach to analyze serum, plasma, or CSF samples for such studies in microtiter plates. To expand measurements beyond single batches, with either 96 or 384 samples per plate, suitable normalization methods are required to minimize the variation between plates. Here we propose two normalization approaches utilizing MA coordinates. The multidimensional MA (multi-MA) and MA-loess both consider all samples of a microtiter plate per suspension bead array assay and thus do not require any external reference samples. We demonstrate the performance of the two MA normalization methods with data obtained from the analysis of 384 samples including both serum and plasma. Samples were randomized across 96-well sample plates, processed, and analyzed in assay plates, respectively. Using principal component analysis (PCA), we could show that plate-wise clusters found in the first two components were eliminated by multi-MA normalization as compared with other normalization methods. Furthermore, we studied the correlation profiles between random pairs of antibodies and found that both MA normalization methods substantially reduced the inflated correlation introduced by plate effects. Normalization approaches using multi-MA and MA-loess minimized batch effects arising from the analysis of several assay plates with antibody suspension bead arrays. In a simulated biomarker study, multi-MA restored associations lost due to plate effects. Our normalization approaches, which are available as R package MDimNormn, could also be useful in studies using other types of high-throughput assay data.", "doi": "10.1021/acs.jproteome.5b01131", "pmid": "27570895", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:06.576Z", "modified": "2021-07-08T12:07:34.332Z"}, {"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": "02d76cd334a44d96af295cc57d1d359a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02d76cd334a44d96af295cc57d1d359a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02d76cd334a44d96af295cc57d1d359a"}}, "title": "Protein profiles of CCL5, HPGDS, and NPSR1 in plasma reveal association with childhood asthma.", "authors": [{"family": "Hamsten", "given": "C", "initials": "C"}, {"family": "H\u00e4ggmark", "given": "A", "initials": "A"}, {"family": "Grundstr\u00f6m", "given": "J", "initials": "J"}, {"family": "Mikus", "given": "M", "initials": "M"}, {"family": "Lindskog", "given": "C", "initials": "C"}, {"family": "Konradsen", "given": "J R", "initials": "JR"}, {"family": "Eklund", "given": "A", "initials": "A"}, {"family": "Pershagen", "given": "G", "initials": "G"}, {"family": "Wickman", "given": "M", "initials": "M"}, {"family": "Grunewald", "given": "J", "initials": "J"}, {"family": "Mel\u00e9n", "given": "E", "initials": "E"}, {"family": "Hedlin", "given": "G", "initials": "G"}, {"family": "Nilsson", "given": "P", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "van Hage", "given": "M", "initials": "M"}], "type": "journal article", "published": "2016-09-00", "journal": {"volume": "71", "issn": "1398-9995", "issue": "9", "pages": "1357-1361", "title": "Allergy", "issn-l": "0105-4538"}, "abstract": "Asthma is a common chronic childhood disease with many different phenotypes that need to be identified. We analyzed a broad range of plasma proteins in children with well-characterized asthma phenotypes to identify potential markers of childhood asthma. Using an affinity proteomics approach, plasma levels of 362 proteins covered by antibodies from the Human Protein Atlas were investigated in a total of 154 children with persistent or intermittent asthma and controls. After screening, chemokine ligand 5 (CCL5) hematopoietic prostaglandin D synthase (HPGDS) and neuropeptide S receptor 1 (NPSR1) were selected for further investigation. Significantly lower levels of both CCL5 and HPGDS were found in children with persistent asthma, while NPSR1 was found at higher levels in children with mild intermittent asthma compared to healthy controls. In addition, the protein levels were investigated in another respiratory disease, sarcoidosis, showing significantly higher NPSR1 levels in sera from sarcoidosis patients compared to healthy controls. Immunohistochemical staining of healthy tissues revealed high cytoplasmic expression of HPGDS in mast cells, present in stroma of both airway epithelia, lung as well as in other organs. High expression of NPSR1 was observed in neuroendocrine tissues, while no expression was observed in airway epithelia or lung. In conclusion, we have utilized a broad-scaled affinity proteomics approach to identify three proteins with altered plasma levels in asthmatic children, representing one of the first evaluations of HPGDS and NPSR1 protein levels in plasma.", "doi": "10.1111/all.12927", "pmid": "27145233", "labels": {"Tissue Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:06.869Z", "modified": "2021-07-07T15:50:02.902Z"}, {"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": "dd6d859f676b4de796fcf2fd433aa840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd6d859f676b4de796fcf2fd433aa840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd6d859f676b4de796fcf2fd433aa840"}}, "title": "Elevated levels of FN1 and CCL2 in bronchoalveolar lavage fluid from sarcoidosis patients.", "authors": [{"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Wiklundh", "given": "Emil", "initials": "E"}, {"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": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Eklund", "given": "Anders", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2016-06-04", "journal": {"volume": "17", "issn": "1465-993X", "issue": "1", "pages": "69", "title": "Respir. Res.", "issn-l": "1465-9921"}, "abstract": "Sarcoidosis is a granulomatous systemic inflammatory disease in which more than 90\u00a0% of all patients develop pulmonary manifestations. Several gene associations have previously been described, but established and clinically useful biomarkers are still absent. This study aimed to find proteins in bronchoalveolar lavage (BAL) fluid that can be associated with the disease.\n\nWe developed and performed profiling of 94 selected proteins in BAL fluid and serum samples obtained from newly diagnosed and non-treated patients with sarcoidosis. Using multiplexed immunoassays, a total of 317 BAL and 217 serum samples were analyzed, including asthmatic patients and healthy individuals as controls.\n\nOur analyses revealed increased levels of eight proteins in sarcoidosis patients compared to controls. Out of these, fibronectin (FN1) and C-C motif chemokine 2 (CCL2) revealed the strongest associations. In addition, cadherin 5 (CDH5) was found to correlate positively with lymphocyte cell numbers in BAL fluid.\n\nApplying a high throughput proteomics screening technique, we found proteins of potential clinical relevance in the context of sarcoidosis.", "doi": "10.1186/s12931-016-0381-0", "pmid": "27259755", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12931-016-0381-0"}, {"db": "pmc", "key": "PMC4893268"}], "notes": [], "created": "2017-05-03T12:59:07.765Z", "modified": "2021-07-08T13:44:33.690Z"}, {"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": "51d03343148f40518927bc37a26e37cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51d03343148f40518927bc37a26e37cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51d03343148f40518927bc37a26e37cd"}}, "title": "Multiplexed protein profiling by sequential affinity capture.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Mezger", "given": "Anja", "initials": "A", "orcid": "0000-0002-7337-9547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebf61fe41e6f43e4aec2be101de688d4.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.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": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "16", "issn": "1615-9861", "issue": "8", "pages": "1251-1256", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Antibody microarrays enable parallelized and miniaturized analysis of clinical samples, and have proven to provide novel insights for the analysis of different proteomes. However, there are concerns that the performance of such direct labeling and single antibody assays are prone to off-target binding due to the sample context. To improve selectivity and sensitivity while maintaining the possibility to conduct multiplexed protein profiling, we developed a multiplexed and semi-automated sequential capture assay. This novel bead-based procedure encompasses a first antigen capture, labeling of captured protein targets on magnetic particles, combinatorial target elution and a read-out by a secondary capture bead array. We demonstrate in a proof-of-concept setting that target detection via two sequential affinity interactions reduced off-target contribution, while lowered background and noise levels, improved correlation to clinical values compared to single binder assays. We also compared sensitivity levels with single binder and classical sandwich assays, explored the possibility for DNA-based signal amplification, and demonstrate the applicability of the dual capture bead-based antibody microarray for biomarker analysis. Hence, the described concept enhances the possibilities for antibody array assays to be utilized for protein profiling in body fluids and beyond.", "doi": "10.1002/pmic.201500398", "pmid": "26935855", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC5071697"}], "notes": [], "created": "2017-05-03T12:59:05.678Z", "modified": "2021-07-08T13:44:33.244Z"}, {"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": "42fa216cd2dd4477bc402023faa67a7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42fa216cd2dd4477bc402023faa67a7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42fa216cd2dd4477bc402023faa67a7b"}}, "title": "Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease.", "authors": [{"family": "Khoonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "L\u00f6nnberg", "given": "Maria", "initials": "M"}, {"family": "Mikus", "given": "Maria", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Shevchenko", "given": "Ganna", "initials": "G"}], "type": "journal article", "published": "2016-03-07", "journal": {"volume": "11", "issn": "1932-6203", "issue": "3", "pages": "e0150672", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Alzheimer's disease is a neurodegenerative disorder accounting for more than 50% of cases of dementia. Diagnosis of Alzheimer's disease relies on cognitive tests and analysis of amyloid beta, protein tau, and hyperphosphorylated tau in cerebrospinal fluid. Although these markers provide relatively high sensitivity and specificity for early disease detection, they are not suitable for monitor of disease progression. In the present study, we used label-free shotgun mass spectrometry to analyse the cerebrospinal fluid proteome of Alzheimer's disease patients and non-demented controls to identify potential biomarkers for Alzheimer's disease. We processed the data using five programs (DecyderMS, Maxquant, OpenMS, PEAKS, and Sieve) and compared their results by means of reproducibility and peptide identification, including three different normalization methods. After depletion of high abundant proteins we found that Alzheimer's disease patients had lower fraction of low-abundance proteins in cerebrospinal fluid compared to healthy controls (p<0.05). Consequently, global normalization was found to be less accurate compared to using spiked-in chicken ovalbumin for normalization. In addition, we determined that Sieve and OpenMS resulted in the highest reproducibility and PEAKS was the programs with the highest identification performance. Finally, we successfully verified significantly lower levels (p<0.05) of eight proteins (A2GL, APOM, C1QB, C1QC, C1S, FBLN3, PTPRZ, and SEZ6) in Alzheimer's disease compared to controls using an antibody-based detection method. These proteins are involved in different biological roles spanning from cell adhesion and migration, to regulation of the synapse and the immune system.", "doi": "10.1371/journal.pone.0150672", "pmid": "26950848", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-15-44118"}, {"db": "pmc", "key": "PMC4780771"}], "notes": [], "created": "2017-05-03T12:59:08.060Z", "modified": "2021-07-07T15:50:03.072Z"}, {"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": "042bd68daa014d59b178e63954eac1ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/042bd68daa014d59b178e63954eac1ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/042bd68daa014d59b178e63954eac1ad"}}, "title": "Immunocapture strategies in translational proteomics.", "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": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Tamburro", "given": "Davide", "initials": "D"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Uhlen", "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": "2015-11-11", "journal": {"volume": "13", "issn": "1744-8387", "issue": "1", "pages": "83-98", "title": "Expert Rev Proteomics", "issn-l": "1478-9450"}, "abstract": "Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.", "doi": "10.1586/14789450.2016.1111141", "pmid": "26558424", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4732419"}], "notes": [], "created": "2017-05-02T12:56:45.584Z", "modified": "2021-07-08T13:44:32.996Z"}, {"entity": "publication", "iuid": "a17590f906c24e878725bc0543917772", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a17590f906c24e878725bc0543917772.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a17590f906c24e878725bc0543917772"}}, "title": "Heat differentiated complement factor profiling.", "authors": [{"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Skattum", "given": "Lillemor", "initials": "L"}, {"family": "Truedsson", "given": "Lennart", "initials": "L"}, {"family": "von D\u00f6beln", "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": "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"}}, {"family": "Neiman", "given": "Maja", "initials": "M"}], "type": "journal article", "published": "2015-08-03", "journal": {"volume": "126", "issn": "1876-7737", "issue": null, "pages": "155-162", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Complement components and their cascade of reactions are important defense mechanisms within both innate and adaptive immunity. Many complement deficient patients still remain undiagnosed because of a lack of high throughput screening tools. Aiming towards neonatal proteome screening for immunodeficiencies, we used a multiplex profiling approach with antibody bead arrays to measure 9 complement proteins in serum and dried blood spots. Several complement components have been described as heat sensitive, thus their heat-dependent detectability was investigated. Using sera from 16 patients with complement deficiencies and 23 controls, we confirmed that the proteins C1q, C2, C3, C6, C9 and factor H were positively affected by heating, thus the identification of deficient patients was improved when preheating samples. Measurements of C7, C8 and factor I were negatively affected by heating and non-heated samples should be used in analysis of these components. In addition, a proof of concept study demonstrated the feasibility of labeling eluates from dried blood spots to perform a subsequent correct classification of C2-deficiencies. Our study demonstrates the potential of using multiplexed single binder assays for screening of complement components that open possibilities to expand such analysis to other forms of deficiencies.", "doi": "10.1016/j.jprot.2015.05.027", "pmid": "26047714", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1874-3919(15)30029-4"}], "notes": [], "created": "2017-05-02T12:56:42.050Z", "modified": "2021-07-08T13:44:33.492Z"}, {"entity": "publication", "iuid": "b019e78a23ef453e9060d6188198a6c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b019e78a23ef453e9060d6188198a6c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b019e78a23ef453e9060d6188198a6c2"}}, "title": "Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex.", "authors": [{"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "H\u00f6kfelt", "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": "Mulder", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2015-06-15", "journal": {"volume": "10", "issn": "1932-6203", "issue": "6", "pages": "e0130028", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The mammalian brain is a complex organ composed of many specialized cells, harboring sets of both common, widely distributed, as well as specialized and discretely localized proteins. Here we focus on the human brain, utilizing transcriptomics and public available Human Protein Atlas (HPA) data to analyze brain-enriched (frontal cortex) polyadenylated messenger RNA and long non-coding RNA and generate a genome-wide draft of global and cellular expression patterns of the brain. Based on transcriptomics analysis of altogether 27 tissues, we have estimated that approximately 3% (n=571) of all protein coding genes and 13% (n=87) of the long non-coding genes expressed in the human brain are enriched, having at least five times higher expression levels in brain as compared to any of the other analyzed peripheral tissues. Based on gene ontology analysis and detailed annotation using antibody-based tissue micro array analysis of the corresponding proteins, we found the majority of brain-enriched protein coding genes to be expressed in astrocytes, oligodendrocytes or in neurons with molecular properties linked to synaptic transmission and brain development. Detailed analysis of the transcripts and the genetic landscape of brain-enriched coding and non-coding genes revealed brain-enriched splice variants. Several clusters of neighboring brain-enriched genes were also identified, suggesting regulation of gene expression on the chromatin level. This multi-angle approach uncovered the brain-enriched transcriptome and linked genes to cell types and functions, providing novel insights into the molecular foundation of this highly specialized organ.", "doi": "10.1371/journal.pone.0130028", "pmid": "26076492", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-15-09576"}, {"db": "pmc", "key": "PMC4468152"}, {"db": "ArrayExpress", "description": "sequences", "key": "E-MTAB-1733"}], "notes": [], "created": "2017-05-02T12:58:34.528Z", "modified": "2021-07-08T13:44:33.530Z"}, {"entity": "publication", "iuid": "4ae59f5aa7af43cb83377b7e1b1a82b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ae59f5aa7af43cb83377b7e1b1a82b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ae59f5aa7af43cb83377b7e1b1a82b5"}}, "title": "Circulating carnosine dipeptidase 1 associates with weight loss and poor prognosis in gastrointestinal cancer.", "authors": [{"family": "Arner", "given": "Peter", "initials": "P"}, {"family": "Henjes", "given": "Frauke", "initials": "F"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Darmanis", "given": "Spyros", "initials": "S"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Iresj\u00f6", "given": "Britt-Marie", "initials": "BM"}, {"family": "Naredi", "given": "Peter", "initials": "P"}, {"family": "Agustsson", "given": "Thorhallur", "initials": "T"}, {"family": "Lundholm", "given": "Kent", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2015-04-21", "journal": {"volume": "10", "issn": "1932-6203", "issue": "4", "pages": "e0123566", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Cancer cachexia (CC) is linked to poor prognosis. Although the mechanisms promoting this condition are not known, several circulating proteins have been proposed to contribute. We analyzed the plasma proteome in cancer subjects in order to identify factors associated with cachexia.\n\nPlasma was obtained from a screening cohort of 59 patients, newly diagnosed with suspected gastrointestinal cancer, with (n = 32) or without (n = 27) cachexia. Samples were subjected to proteomic profiling using 760 antibodies (targeting 698 individual proteins) from the Human Protein Atlas project. The main findings were validated in a cohort of 93 patients with verified and advanced pancreas cancer.\n\nOnly six proteins displayed differential plasma levels in the screening cohort. Among these, Carnosine Dipeptidase 1 (CNDP1) was confirmed by sandwich immunoassay to be lower in CC (p = 0.008). In both cohorts, low CNDP1 levels were associated with markers of poor prognosis including weight loss, malnutrition, lipid breakdown, low circulating albumin/IGF1 levels and poor quality of life. Eleven of the subjects in the discovery cohort were finally diagnosed with non-malignant disease but omitting these subjects from the analyses did not have any major influence on the results.\n\nIn gastrointestinal cancer, reduced plasma levels of CNDP1 associate with signs of catabolism and poor outcome. These results, together with recently published data demonstrating lower circulating CNDP1 in subjects with glioblastoma and metastatic prostate cancer, suggest that CNDP1 may constitute a marker of aggressive cancer and CC.", "doi": "10.1371/journal.pone.0123566", "pmid": "25898255", "labels": {"Affinity Proteomics Stockholm": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-54419"}, {"db": "pmc", "key": "PMC4405487"}], "notes": [], "created": "2017-05-02T12:58:17.348Z", "modified": "2021-07-08T12:07:34.102Z"}, {"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": "3777a5cd8954424fb426f5163d4d01bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3777a5cd8954424fb426f5163d4d01bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3777a5cd8954424fb426f5163d4d01bf"}}, "title": "Proteomics. Tissue-based map of the human proteome.", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Olsson", "given": "IngMarie", "initials": "I"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Takanen", "given": "Jenny Ottosson", "initials": "JO"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Alm", "given": "Tove", "initials": "T"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Berling", "given": "Holger", "initials": "H"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Rockberg", "given": "Johan", "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": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Persson", "given": "Lukas", "initials": "L"}, {"family": "Johansson", "given": "Fredric", "initials": "F"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f663c0a9e9e1455cbbf8e6aea13af4a9.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-01-23", "journal": {"volume": "347", "issn": "1095-9203", "issue": "6220", "pages": "1260419", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.", "doi": "10.1126/science.1260419", "pmid": "25613900", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "347/6220/1260419"}], "notes": [], "created": "2017-05-02T12:58:49.180Z", "modified": "2023-11-21T16:24:57.712Z"}, {"entity": "publication", "iuid": "d25e8eeba2b9401a99f09ce2238e2a9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d25e8eeba2b9401a99f09ce2238e2a9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d25e8eeba2b9401a99f09ce2238e2a9f"}}, "title": "Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis.", "authors": [{"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Amor", "given": "Sandra", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"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"}}], "type": "journal article", "published": "2014-11-07", "journal": {"volume": "13", "issn": "1535-3907", "issue": "11", "pages": "4607-4619", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "The brain is a vital organ and because it is well shielded from the outside environment, possibilities for noninvasive analysis are often limited. Instead, fluids taken from the spinal cord or circulatory system are preferred sources for the discovery of candidate markers within neurological diseases. In the context of multiple sclerosis (MS), we applied an affinity proteomic strategy and screened 22 plasma samples with 4595 antibodies (3450 genes) on bead arrays, then defined 375 antibodies (334 genes) for targeted analysis in a set of 172 samples and finally used 101 antibodies (43 genes) on 443 plasma as well as 573 cerebrospinal spinal fluid (CSF) samples. This revealed alteration of protein profiles in relation to MS subtypes for IRF8, IL7, METTL14, SLC30A7, and GAP43. Respective antibodies were subsequently used for immunofluorescence on human post-mortem brain tissue with MS pathology for expression and association analysis. There, antibodies for IRF8, IL7, and METTL14 stained neurons in proximity of lesions, which highlighted these candidate protein targets for further studies within MS and brain tissue. The affinity proteomic translation of profiles discovered by profiling human body fluids and tissue provides a powerful strategy to suggest additional candidates to studies of neurological disorders.", "doi": "10.1021/pr500609e", "pmid": "25231264", "labels": {"Fluorescence Tissue Profiling": null, "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:19.857Z", "modified": "2021-07-08T13:44:33.645Z"}, {"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": "7667c1109ce844e994cca622ff027fa5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7667c1109ce844e994cca622ff027fa5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7667c1109ce844e994cca622ff027fa5"}}, "title": "Plasma profiling reveals three proteins associated to amyotrophic lateral sclerosis.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Mikus", "given": "Maria", "initials": "M"}, {"family": "Mohsenchian", "given": "Atefeh", "initials": "A"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Gajewska", "given": "Beata", "initials": "B"}, {"family": "Bara\u0144czyk-Ku\u017ama", "given": "Anna", "initials": "A"}, {"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": "Ku\u017ama-Kozakiewicz", "given": "Magdalena", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2014-08-00", "journal": {"volume": "1", "issn": "2328-9503", "issue": "8", "pages": "544-553", "title": "Ann Clin Transl Neurol", "issn-l": "2328-9503"}, "abstract": "Amyotrophic lateral sclerosis (ALS) is the most common adult motor neuron disease leading to muscular paralysis and death within 3-5 years from onset. Currently, there are no reliable and sensitive markers able to substantially shorten the diagnosis delay. The objective of the study was to analyze a large number of proteins in plasma from patients with various clinical phenotypes of ALS in search for novel proteins or protein profiles that could serve as potential indicators of disease.\r\n\r\nAffinity proteomics in the form of antibody suspension bead arrays were applied to profile plasma samples from 367 ALS patients and 101 controls. The plasma protein content was directly labeled and protein profiles obtained using 352 antibodies from the Human Protein Atlas targeting 278 proteins. A focused bead array was then built to further profile eight selected protein targets in all available samples.\r\n\r\nDisease-associated significant differences were observed and replicated for profiles from antibodies targeting the proteins: neurofilament medium polypeptide (NEFM), solute carrier family 25 (SLC25A20), and regulator of G-protein signaling 18 (RGS18).\r\n\r\nUpon further validation in several independent cohorts with inclusion of a broad range of other neurological disorders as controls, the alterations of these three protein profiles in plasma could potentially provide new molecular markers of disease that contribute to the quest of understanding ALS pathology.", "doi": "10.1002/acn3.83", "pmid": "25356426", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC4184557"}], "notes": [], "created": "2017-05-04T14:55:39.286Z", "modified": "2021-07-08T13:44:33.363Z"}, {"entity": "publication", "iuid": "c2f170156b274272b4560b2dc5dc14b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2f170156b274272b4560b2dc5dc14b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2f170156b274272b4560b2dc5dc14b1"}}, "title": "Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Chaouch", "given": "Amina", "initials": "A"}, {"family": "Lochm\u00fcller", "given": "Hanns", "initials": "H"}, {"family": "Politano", "given": "Luisa", "initials": "L"}, {"family": "Bertini", "given": "Enrico", "initials": "E"}, {"family": "Spitali", "given": "Pietro", "initials": "P"}, {"family": "Hiller", "given": "Monika", "initials": "M"}, {"family": "Niks", "given": "Eric H", "initials": "EH"}, {"family": "Gualandi", "given": "Francesca", "initials": "F"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Bushby", "given": "Kate", "initials": "K"}, {"family": "Aartsma-Rus", "given": "Annemieke", "initials": "A"}, {"family": "Schwartz", "given": "Elena", "initials": "E"}, {"family": "Le Priol", "given": "Yannick", "initials": "Y"}, {"family": "Straub", "given": "Volker", "initials": "V"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Cirak", "given": "Sebahattin", "initials": "S"}, {"family": "'t Hoen", "given": "Peter A C", "initials": "PAC"}, {"family": "Muntoni", "given": "Francesco", "initials": "F"}, {"family": "Ferlini", "given": "Alessandra", "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"}}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C"}], "type": "journal article", "published": "2014-07-00", "journal": {"volume": "6", "issn": "1757-4684", "issue": "7", "pages": "918-936", "title": "EMBO Mol Med", "issn-l": "1757-4676"}, "abstract": "Despite the recent progress in the broad-scaled analysis of proteins in body fluids, there is still a lack in protein profiling approaches for biomarkers of rare diseases. Scarcity of samples is the main obstacle hindering attempts to apply discovery driven protein profiling in rare diseases. We addressed this challenge by combining samples collected within the BIO-NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies. Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we identified eleven proteins associated with muscular dystrophy, among which four proteins were elevated in blood from muscular dystrophy patients: carbonic anhydrase III (CA3) and myosin light chain 3 (MYL3), both specifically expressed in slow-twitch muscle fibers and mitochondrial malate dehydrogenase 2 (MDH2) and electron transfer flavoprotein A (ETFA). Using age-matched sub-cohorts, 9 protein profiles correlating with disease progression and severity were identified, which hold promise for the development of new clinical tools for management of dystrophinopathies.", "doi": "10.15252/emmm.201303724", "pmid": "24920607", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "emmm.201303724"}, {"db": "pmc", "key": "PMC4119355"}], "notes": [], "created": "2017-05-04T14:55:39.591Z", "modified": "2021-07-08T13:44:33.596Z"}, {"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": "f368c76367db4f02886060683e16b0dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f368c76367db4f02886060683e16b0dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f368c76367db4f02886060683e16b0dc"}}, "title": "Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria.", "authors": [{"family": "Bachmann", "given": "Julie", "initials": "J"}, {"family": "Burt\u00e9", "given": "Florence", "initials": "F"}, {"family": "Pramana", "given": "Setia", "initials": "S"}, {"family": "Conte", "given": "Ianina", "initials": "I"}, {"family": "Brown", "given": "Biobele J", "initials": "BJ"}, {"family": "Orimadegun", "given": "Adebola E", "initials": "AE"}, {"family": "Ajetunmobi", "given": "Wasiu A", "initials": "WA"}, {"family": "Afolabi", "given": "Nathaniel K", "initials": "NK"}, {"family": "Akinkunmi", "given": "Francis", "initials": "F"}, {"family": "Omokhodion", "given": "Samuel", "initials": "S"}, {"family": "Akinbami", "given": "Felix O", "initials": "FO"}, {"family": "Shokunbi", "given": "Wuraola A", "initials": "WA"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"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": "Sodeinde", "given": "Olugbemiro", "initials": "O"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}, {"family": "Fernandez-Reyes", "given": "Delmiro", "initials": "D"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2014-04-00", "journal": {"volume": "10", "issn": "1553-7374", "issue": "4", "pages": "e1004038", "title": "PLoS Pathog.", "issn-l": "1553-7366"}, "abstract": "Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria.", "doi": "10.1371/journal.ppat.1004038", "pmid": "24743550", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PPATHOGENS-D-13-01973"}, {"db": "pmc", "key": "PMC3990714"}], "notes": [], "created": "2017-05-04T14:55:40.729Z", "modified": "2021-07-08T13:44:33.732Z"}, {"entity": "publication", "iuid": "c0034e9a600646e7ae016f0897affcba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0034e9a600646e7ae016f0897affcba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0034e9a600646e7ae016f0897affcba"}}, "title": "Antibody performance in western blot applications is context-dependent.", "authors": [{"family": "Algen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Agaton", "given": "Charlotta", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rling", "given": "Lisa", "initials": "L"}, {"family": "Bj\u00f6rling", "given": "Erik", "initials": "E"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Persson", "given": "Anja", "initials": "A"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Wern\u00e9rus", "given": "Henrik", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ottosson Takanen", "given": "Jenny", "initials": "J"}, {"family": "Hober", "given": "Sophia", "initials": "S"}], "type": "journal article", "published": "2014-03-00", "journal": {"volume": "9", "issn": "1860-7314", "issue": "3", "pages": "435-445", "title": "Biotechnol J", "issn-l": "1860-6768"}, "abstract": "An important concern for the use of antibodies in various applications, such as western blot (WB) or immunohistochemistry (IHC), is specificity. This calls for systematic validations using well-designed conditions. Here, we have analyzed 13\u2009000 antibodies using western blot with lysates from human cell lines, tissues, and plasma. Standardized stratification showed that 45% of the antibodies yielded supportive staining, and the rest either no staining (12%) or protein bands of wrong size (43%). A comparative study of WB and IHC showed that the performance of antibodies is application-specific, although a correlation between no WB staining and weak IHC staining could be seen. To investigate the influence of protein abundance on the apparent specificity of the antibody, new WB analyses were performed for 1369 genes that gave unsupportive WBs in the initial screening using cell lysates with overexpressed full-length proteins. Then, more than 82% of the antibodies yielded a specific band corresponding to the full-length protein. Hence, the vast majority of the antibodies (90%) used in this study specifically recognize the target protein when present at sufficiently high levels. This demonstrates the context- and application-dependence of antibody validation and emphasizes that caution is needed when annotating binding reagents as specific or cross-reactive. WB is one of the most commonly used methods for validation of antibodies. Our data implicate that solely using one platform for antibody validation might give misleading information and therefore at least one additional method should be used to verify the achieved data.", "doi": "10.1002/biot.201300341", "pmid": "24403002", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:15.317Z", "modified": "2021-07-08T13:44:33.580Z"}, {"entity": "publication", "iuid": "ef02a7c09ee04259ad9d5d188407e72e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef02a7c09ee04259ad9d5d188407e72e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef02a7c09ee04259ad9d5d188407e72e"}}, "title": "Analysis of plasma from prostate cancer patients links decreased carnosine dipeptidase 1 levels to lymph node metastasis", "authors": [{"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "O\u2019Hurley", "given": "Gillian", "initials": "G"}, {"family": "Branca", "given": "Rui", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Bjartell", "given": "Anders", "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": "2014-03-00", "journal": {"volume": "2", "issn": "2212-9626", "issue": null, "pages": "14-24", "title": "Translational Proteomics", "issn-l": null}, "abstract": null, "doi": "10.1016/j.trprot.2013.12.001", "pmid": null, "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:41.613Z", "modified": "2021-07-08T12:12:51.627Z"}, {"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": "4a97b8bf12f54a8690d0d5080224dd19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a97b8bf12f54a8690d0d5080224dd19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a97b8bf12f54a8690d0d5080224dd19"}}, "title": "Magnetic bead assisted labeling of antibodies at nanogram scale.", "authors": [{"family": "Dezfouli", "given": "Mahya", "initials": "M"}, {"family": "Vickovic", "given": "Sanja", "initials": "S"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"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": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2014-01-00", "journal": {"volume": "14", "issn": "1615-9861", "issue": "1", "pages": "14-18", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "There are currently several initiatives that aim to produce binding reagents for proteome-wide analysis. To enable protein detection, visualization, and target quantification, covalent coupling of reporter molecules to antibodies is essential. However, current labeling protocols recommend considerable amount of antibodies, require antibody purity and are not designed for automation. Given that small amounts of antibodies are often sufficient for downstream analysis, we developed a labeling protocol that combines purification and modification of antibodies at submicrogram quantities. With the support of magnetic microspheres, automated labeling of antibodies in parallel using biotin or fluorescent dyes was achieved.", "doi": "10.1002/pmic.201300283", "pmid": "24307663", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:41.037Z", "modified": "2021-07-08T12:07:34.096Z"}, {"entity": "publication", "iuid": "e2c12498a4ee40849faac3f32a0dfe51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2c12498a4ee40849faac3f32a0dfe51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2c12498a4ee40849faac3f32a0dfe51"}}, "title": "Profiling post-centrifugation delay of serum and plasma with antibody bead arrays.", "authors": [{"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Tybring", "given": "Gunnel", "initials": "G"}, {"family": "Divers", "given": "Mark", "initials": "M"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Uhlen", "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": "clinical trial", "published": "2013-12-16", "journal": {"volume": "95", "issn": "1876-7737", "issue": null, "pages": "46-54", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Several biobanking initiatives have emerged to create extensive collections of specimen for biomedical studies and various analytical platforms. An affinity proteomic analysis with antibody suspension bead arrays was conducted to investigate the influence of the pre-analytical time and temperature conditions on blood derived samples. Serum and EDTA plasma prepared from 16 individuals was centrifuged and aliquots were kept either at 4\u00b0C or in ambient temperature for 1h and up to 36h prior to first storage. Multiplexed protein profiles of post-centrifugation delay were generated in 384 biotinylated samples using 373 antibodies that targeted 343 unique proteins. Very few profiles were observed as significantly altered by the studied temperature and time intervals. Single binder and sandwich assays revealed decreasing levels of caldesmon 1 (CALD1) related to EDTA standard tubes and prolonged post-centrifugation delay of 36h. Indications from changes in CALD1 levels require further confirmation in independent material, but the current data suggests that samples should preferentially be frozen during the day of collection when to be profiled with antibody arrays selected for this study.\r\n\r\nAffinity-based profiling of serum and plasma by microarray assays can provide unique opportunities for the discovery of biomarkers. It is though often not known how differences in sample handling after collection influence the downstream analysis. By profiling three types of blood preparations for alterations in protein profiles with respect to time and temperature post centrifugation, we addressed an important component in the analysis and of such specimen. We believe that this analysis adds valuable information to be considered when biobanking blood derived samples. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.", "doi": "10.1016/j.jprot.2013.04.020", "pmid": "23631827", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1874-3919(13)00209-1"}], "notes": [], "created": "2017-05-04T14:55:37.485Z", "modified": "2021-07-08T13:44:33.695Z"}, {"entity": "publication", "iuid": "87e3d2bb0d5442fe9c4911cc26f86f2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f"}}, "title": "Selectivity analysis of single binder assays used in plasma protein profiling.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Nygren", "given": "Per-\u00c5ke", "initials": "P"}, {"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": "2013-12-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "23-24", "pages": "3406-3410", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "The increasing availability of antibodies toward human proteins enables broad explorations of the proteomic landscape in cells, tissues, and body fluids. This includes assays with antibody suspension bead arrays that generate protein profiles of plasma samples by flow cytometer analysis. However, antibody selectivity is context dependent so it is necessary to corroborate on-target detection over off-target binding. To address this, we describe a concept to directly verify interactions from antibody-coupled beads by analysis of their eluates by Western blots and MS. We demonstrate selective antibody binding in complex samples with antibodies toward a set of chosen proteins with different abundance in plasma and serum, and illustrate the need to adjust sample and bead concentrations accordingly. The presented approach will serve as an important tool for resolving differential protein profiles from antibody arrays within plasma biomarker discoveries.", "doi": "10.1002/pmic.201300030", "pmid": "24151238", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4265267"}], "notes": [], "created": "2017-05-04T14:55:38.987Z", "modified": "2021-07-08T13:44:33.385Z"}, {"entity": "publication", "iuid": "8f37c309a6f64a31b226eebe05a10d7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f37c309a6f64a31b226eebe05a10d7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f37c309a6f64a31b226eebe05a10d7c"}}, "title": "Identification of candidate serum proteins for classifying well-differentiated small intestinal neuroendocrine tumors.", "authors": [{"family": "Darmanis", "given": "Spyros", "initials": "S"}, {"family": "Cui", "given": "Tao", "initials": "T"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Li", "given": "Su-Chen", "initials": "S"}, {"family": "\u00d6berg", "given": "Kjell", "initials": "K"}, {"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": "Giandomenico", "given": "Valeria", "initials": "V"}], "type": "journal article", "published": "2013-11-25", "journal": {"volume": "8", "issn": "1932-6203", "issue": "11", "pages": "e81712", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Patients with well-differentiated small intestine neuroendocrine tumors (WD-SI-NETs) are most often diagnosed at a metastatic stage of disease, which reduces possibilities for a curative treatment. Thus new approaches for earlier detection and improved monitoring of the disease are required.\r\n\r\nSuspension bead arrays targeting 124 unique proteins with antibodies from the Human Protein Atlas were used to profile biotinylated serum samples. Discoveries from a cohort of 77 individuals were followed up in a cohort of 132 individuals both including healthy controls as well as patients with untreated primary WD-SI-NETs, lymph node metastases and liver metastases.\r\n\r\nA set of 20 antibodies suggested promising proteins for further verification based on technically verified statistical significance. Proceeding, we assessed the classification performance in an independent cohort of patient serum, achieving, classification accuracy of up to 85% with different subsets of antibodies in respective pairwise group comparisons. The protein profiles of nine targets, namely IGFBP2, IGF1, SHKBP1, ETS1, IL1\u03b1, STX2, MAML3, EGR3 and XIAP were verified as significant contributors to tumor classification.\r\n\r\nWe propose new potential protein biomarker candidates for classifying WD-SI-NETs at different stage of disease. Further evaluation of these proteins in larger sample sets and with alternative approaches is needed in order to further improve our understanding of their functional relation to WD-SI-NETs and their eventual use in diagnostics.", "doi": "10.1371/journal.pone.0081712", "pmid": "24282616", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-13-03665"}, {"db": "pmc", "key": "PMC3839889"}], "notes": [], "created": "2017-05-04T14:55:38.382Z", "modified": "2021-07-08T12:07:34.174Z"}, {"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": "135f821176884e3480bb7c2a8062b568", "links": {"self": {"href": "https://publications.scilifelab.se/publication/135f821176884e3480bb7c2a8062b568.json"}, "display": {"href": "https://publications.scilifelab.se/publication/135f821176884e3480bb7c2a8062b568"}}, "title": "Antibody-based profiling of cerebrospinal fluid within multiple sclerosis.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Qundos", "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": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"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": "2013-08-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "15", "pages": "2256-2267", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Antibody suspension bead arrays have proven to enable multiplexed and high-throughput protein profiling in unfractionated plasma and serum samples through a direct labeling approach. We here describe the development and application of an assay for protein profiling of cerebrospinal fluid (CSF). While setting up the assay, systematic intensity differences between sample groups were observed that reflected inherent sample specific total protein amounts. Supplementing the labeling reaction with BSA and IgG diminished these differences without impairing the apparent sensitivity of the assay. We also assessed the effects of heat treatment on the analysis of CSF proteins and applied the assay to profile 43 selected proteins by 101 antibodies in 339 CSF samples from a multiple sclerosis (MS) cohort. Two proteins, GAP43 and SERPINA3 were found to have a discriminating potential with altered intensity levels between sample groups. GAP43 was detected at significantly lower levels in secondary progressive MS compared to early stages of MS and the control group of other neurological diseases. SERPINA3 instead was detected at higher levels in all MS patients compared to controls. The developed assay procedure now offers new possibilities for broad-scale protein profiling of CSF within neurological disorders.", "doi": "10.1002/pmic.201200580", "pmid": "23696371", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:38.686Z", "modified": "2021-07-08T13:44:33.026Z"}, {"entity": "publication", "iuid": "f1a748adc53d487b9c3cf711b8237af8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1a748adc53d487b9c3cf711b8237af8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1a748adc53d487b9c3cf711b8237af8"}}, "title": "Highly multiplexed antibody suspension bead arrays for plasma protein profiling.", "authors": [{"family": "Drobin", "given": "Kimi", "initials": "K"}, {"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": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "137-145", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Alongside the increasing availability of affinity reagents, antibody microarrays have become a powerful tool to screen for target proteins in complex samples. Applying directly labeled samples onto arrays instead of using sandwich assays offers an approach to facilitate a systematic, high-throughput, and flexible exploration of protein profiles in body fluids such as serum or plasma. As an alternative to planar arrays, a system based on color-coded beads for the creation of antibody arrays in suspension has become available to offer a microtiter plate-based option for screening larger number of samples with variable sets of capture reagents. A procedure was established for analyzing biotinylated samples without the necessity to remove excess labeling substance. We have shown that this assay system allows detecting proteins down into lower pico-molar and higher pg/ml levels with dynamic ranges over three orders of magnitude. Presently, this workflow enables the profiling of 384 samples for up to 384 proteins per assay.", "doi": "10.1007/978-1-4614-7209-4_8", "pmid": "23765623", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:37.784Z", "modified": "2021-07-08T12:07:34.315Z"}, {"entity": "publication", "iuid": "46fcccfe99494658bf5552e1a28e8a73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46fcccfe99494658bf5552e1a28e8a73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46fcccfe99494658bf5552e1a28e8a73"}}, "title": "Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).", "authors": [{"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Algen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Sivertsson", "given": "Asa", "initials": "A"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Olsson", "given": "Ingmarie", "initials": "I"}, {"family": "Rydberg", "given": "Urban", "initials": "U"}, {"family": "Hudson", "given": "Paul", "initials": "P"}, {"family": "Ottosson Takanen", "given": "Jenny", "initials": "J"}, {"family": "Berling", "given": "Holger", "initials": "H"}, {"family": "Bj\u00f6rling", "given": "Lisa", "initials": "L"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"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": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"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": "2013-06-07", "journal": {"volume": "12", "issn": "1535-3907", "issue": "6", "pages": "2439-2448", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few tissue-specific proteins and approximately half of the genes expressed in all the analyzed cells. The status for each gene with regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas ( www.proteinatlas.org ).", "doi": "10.1021/pr300924j", "pmid": "23276153", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:13.479Z", "modified": "2021-07-08T13:44:33.207Z"}, {"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": "2e8a48c6bcb0435e81f13645120db225", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e8a48c6bcb0435e81f13645120db225.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e8a48c6bcb0435e81f13645120db225"}}, "title": "Proteomic screen reveals Fbw7 as a modulator of the NF-\u03baB pathway.", "authors": [{"family": "Arabi", "given": "Azadeh", "initials": "A"}, {"family": "Ullah", "given": "Karim", "initials": "K"}, {"family": "Branca", "given": "Rui M M", "initials": "RM"}, {"family": "Johansson", "given": "Johan", "initials": "J"}, {"family": "Bandarra", "given": "Daniel", "initials": "D"}, {"family": "Haneklaus", "given": "Moritz", "initials": "M"}, {"family": "Fu", "given": "Jing", "initials": "J"}, {"family": "Ari\u00ebs", "given": "Ingrid", "initials": "I"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Den Boer", "given": "Monique L", "initials": "ML"}, {"family": "Pokrovskaja", "given": "Katja", "initials": "K"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "Xiao", "given": "Gutian", "initials": "G"}, {"family": "Rocha", "given": "Sonia", "initials": "S"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Sangfelt", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2012-08-07", "journal": {"volume": "3", "issn": "2041-1723", "issue": null, "pages": "976", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Fbw7 is a ubiquitin-ligase that targets several oncoproteins for proteolysis, but the full range of Fbw7 substrates is not known. Here we show that by performing quantitative proteomics combined with degron motif searches, we effectively screened for a more complete set of Fbw7 targets. We identify 89 putative Fbw7 substrates, including several disease-associated proteins. The transcription factor NF-\u03baB2 (p100/p52) is one of the candidate Fbw7 substrates. We show that Fbw7 interacts with p100 via a conserved degron and that it promotes degradation of p100 in a GSK3\u03b2 phosphorylation-dependent manner. Fbw7 inactivation increases p100 levels, which in the presence of NF-\u03baB pathway stimuli, leads to increased p52 levels and activity. Accordingly, the apoptotic threshold can be increased by loss of Fbw7 in a p100-dependent manner. In conclusion, Fbw7-mediated destruction of p100 is a regulatory component restricting the response to NF-\u03baB2 pathway stimulation.", "doi": "10.1038/ncomms1975", "pmid": "22864569", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "ncomms1975"}, {"db": "pmc", "key": "PMC4354031"}], "notes": [], "created": "2017-05-04T14:56:18.815Z", "modified": "2021-07-08T11:36:15.152Z"}, {"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": "5baa7889c10943b3a05a955706c46c32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5baa7889c10943b3a05a955706c46c32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5baa7889c10943b3a05a955706c46c32"}}, "title": "Classification of protein profiles from antibody microarrays using heat and detergent treatment.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"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": "2012-06-15", "journal": {"volume": "29", "issn": "1876-4347", "issue": "5", "pages": "564-570", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "Antibody microarrays offer new opportunities for exploring the proteome and to identify biomarker candidates in human serum and plasma. Here, we have investigated the effect of heat and detergents on an antibody-based suspension bead array (SBA) assay using polyclonal antibodies and biotinylated plasma samples. With protein profiles from more than 2300 antibodies generated in 384-plex antibody SBAs, three major classes of heat and detergent susceptibility could be described. The results show that washing of the beads with SDS (rather than Tween) after target binding lowered intensity levels of basically all profiles and that about 50% of the profiles appeared to be lowered to a similar extent by heating of the sample. About 33% of the profiles appeared to be insensitive to heat treatment while another 17% showed a positive influence of heat to yield elevated profiles. The results suggest that the classification of antibodies is driven by the molecular properties of the antibody-antigen interaction and can generally not be predicted based on protein class or Western blot data. The experimental scheme presented here can be used to systematically categorize antibodies and thereby combine antibodies with similar properties into targeted arrays for analysis of plasma and serum.", "doi": "10.1016/j.nbt.2011.10.005", "pmid": "22023822", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(11)00225-1"}], "notes": [], "created": "2017-05-04T14:55:36.890Z", "modified": "2021-07-08T13:44:33.296Z"}, {"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": "c2e9c06ba1ef4c7882ff2869b01abad4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2e9c06ba1ef4c7882ff2869b01abad4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2e9c06ba1ef4c7882ff2869b01abad4"}}, "title": "Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model.", "authors": [{"family": "Kato", "given": "Bernet S", "initials": "BS"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Holmes", "given": "Chris C", "initials": "CC"}, {"family": "Barrett", "given": "Amy", "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": "Spector", "given": "Tim D", "initials": "TD"}, {"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": "2011-11-17", "journal": {"volume": "9", "issn": "1477-5956", "issue": null, "pages": "73", "title": "Proteome Sci", "issn-l": "1477-5956"}, "abstract": "The advent of affinity-based proteomics technologies for global protein profiling provides the prospect of finding new molecular biomarkers for common, multifactorial disorders. The molecular phenotypes obtained from studies on such platforms are driven by multiple sources, including genetic, environmental, and experimental components. In characterizing the contribution of different sources of variation to the measured phenotypes, the aim is to facilitate the design and interpretation of future biomedical studies employing exploratory and multiplexed technologies. Thus, biometrical genetic modelling of twin or other family data can be used to decompose the variation underlying a phenotype into biological and experimental components.\n\nUsing antibody suspension bead arrays and antibodies from the Human Protein Atlas, we study unfractionated serum from a longitudinal study on 154 twins. In this study, we provide a detailed description of how the variation in a molecular phenotype in terms of protein profile can be decomposed into familial i.e. genetic and common environmental; individual environmental, short-term biological and experimental components. The results show that across 69 antibodies analyzed in the study, the median proportion of the total variation explained by familial sources is 12% (IQR 1-22%), and the median proportion of the total variation attributable to experimental sources is 63% (IQR 53-72%).\n\nThe variability analysis of antibody arrays highlights the importance to consider variability components and their relative contributions when designing and evaluating studies for biomarker discoveries with exploratory, high-throughput and multiplexed methods.", "doi": "10.1186/1477-5956-9-73", "pmid": "22093360", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1477-5956-9-73"}, {"db": "pmc", "key": "PMC3247853"}], "notes": [], "created": "2017-10-30T10:37:06.896Z", "modified": "2021-07-08T13:44:33.591Z"}, {"entity": "publication", "iuid": "46874109988f4ab68218f77bac6175fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46874109988f4ab68218f77bac6175fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46874109988f4ab68218f77bac6175fb"}}, "title": "Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Hedberg", "given": "Jesper J", "initials": "JJ"}, {"family": "D\u00f6nnes", "given": "Pierre R", "initials": "PR"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Hanschke", "given": "Stephan", "initials": "S"}, {"family": "Schindler", "given": "Ralf", "initials": "R"}, {"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": "2011-11-04", "journal": {"volume": "10", "issn": "1535-3907", "issue": "11", "pages": "4925-4934", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "There is a need for reliable and sensitive biomarkers for renal impairments to detect early signs of kidney toxicity and to monitor progression of disease. Here, antibody suspension bead arrays were applied to profile plasma samples from patients with four types of kidney disorders: glomerulonephritis, diabetic nephropathy, obstructive uropathy, and analgesic abuse. In total, 200 clinical renal-associated cases and control plasma samples from different cohorts were profiled. Parallel plasma protein profiles were obtained using biotinylated and nonfractionated samples and a selected set of 94 proteins targeted by 129 antigen-purified polyclonal antibodies. Out of the analyzed target proteins, human fibulin-1 was detected at significantly higher levels in the glomerulonephritis patient group compared to the controls and with elevated levels in patient samples for all other renal disorders investigated. Two polyclonal antibodies and one monoclonal antibody directed toward separate, nonoverlapping epitopes showed the same trend in the discovery cohorts. A technical verification using Western blot analysis of selected patient plasma confirmed the trends toward higher abundance of the target protein in disease samples. Furthermore, a verification study was carried out in the context of glomerulonephritis using an independent case and control cohort, and this confirmed the results from the discovery cohort, suggesting that plasma levels of fibulin-1 could serve as a potential indicator to monitor kidney malfunction or kidney damage.", "doi": "10.1021/pr200286c", "pmid": "21888404", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:36:18.646Z", "modified": "2021-07-08T13:44:33.201Z"}, {"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": "2759f61b2b44435d8c551e4ed8476e7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2759f61b2b44435d8c551e4ed8476e7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2759f61b2b44435d8c551e4ed8476e7b"}}, "title": "Antibody suspension bead arrays.", "authors": [{"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": "2011-03-04", "journal": {"volume": "723", "issn": "1940-6029", "issue": null, "pages": "29-36", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Alongside the increasing availability of affinity reagents, antibody microarrays have been developed to become a powerful tool to screen for target proteins in complex samples. Besides multiplexed sandwich immunoassays, the application of directly applying labeled sample onto arrays with immobilized capture reagents offers an approach to facilitate a systematic, high-throughput analysis of body fluids such as serum or plasma. An alternative to commonly used planar arrays has become available in form of a system based on color-coded beads for the creation of antibody arrays in suspension. The assay procedure offers an uncomplicated option to screen larger numbers of serum or plasma samples with variable sets of capture reagents. In addition, the established procedure of whole sample biotinylation circumvents the purification steps, which are generally required to remove excess labeling substance. We have shown that this assay system allows detecting proteins down into lower pico-molar and higher picogram per milliliter levels with dynamic ranges over three orders of magnitude. Presently, this workflow enables the profiling of 384 clinical samples for up to 100 proteins per assay.", "doi": "10.1007/978-1-61779-043-0_3", "pmid": "21370057", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:37:50.048Z", "modified": "2021-07-08T12:07:34.021Z"}, {"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"}, {"entity": "publication", "iuid": "9972459d788b4187a2c11c60c744ce88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9972459d788b4187a2c11c60c744ce88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9972459d788b4187a2c11c60c744ce88"}}, "title": "Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Langen", "given": "Hanno", "initials": "H"}, {"family": "Becker", "given": "Charlotte", "initials": "C"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"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"}}], "type": "evaluation studies", "published": "2010-11-00", "journal": {"volume": "9", "issn": "1535-9484", "issue": "11", "pages": "2497-2507", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "There is a need for high throughput methods for screening patient samples in the quest for potential biomarkers for diagnostics and patient care. Here, we used a combination of undirected target selection, antibody suspension bead arrays, and heat-induced epitope retrieval to allow for protein profiling of human plasma in a novel and systematic manner. Several antibodies were found to reveal altered protein profiles upon epitope retrieval at elevated temperatures with limits of detection improving into lower ng/ml ranges. In a study based on prostate cancer patients, several proteins with differential profiles were discovered and subsequently validated in an independent cohort. For one of the potential biomarkers, the human carnosine dipeptidase 1 protein (CNDP1), the differences were determined to be related to the glycosylation status of the targeted protein. The study shows a path of pursuit for large scale screening of biobank repositories in a flexible and proteome-wide fashion by utilizing heat-induced epitope retrieval and using an antibody suspension bead array format.", "doi": "10.1074/mcp.M110.001560", "pmid": "20682762", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "M110.001560"}, {"db": "pmc", "key": "PMC2984230"}], "notes": [], "created": "2017-05-04T14:55:29.167Z", "modified": "2021-07-08T13:44:33.459Z"}, {"entity": "publication", "iuid": "948787308e4448c8b8ce4ef0438881e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/948787308e4448c8b8ce4ef0438881e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/948787308e4448c8b8ce4ef0438881e2"}}, "title": "Comparative protein profiling of serum and plasma using an antibody suspension bead array approach.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Kato", "given": "Bernet S", "initials": "BS"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Karpe", "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"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "comparative study", "published": "2010-02-00", "journal": {"volume": "10", "issn": "1615-9861", "issue": "3", "pages": "532-540", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "In the pursuit towards a systematic analysis of human diseases, array-based approaches within antibody proteomics offer high-throughput strategies to discover protein biomarkers in serum and plasma. To investigate the influence of sample preparation on such discovery attempts, we report on a systematic effort to compare serum and plasma protein profiles determined with an antibody suspension bead array. The intensity levels were used to define protein profiles and no significant differences between serum and plasma were observed for 79% of the 174 antibodies (targeting 156 proteins). By excluding 36 antibodies giving rise to differential intensity levels, cluster analysis revealed donor-specific rather than preparation-dependent grouping. With a cohort from a clinically relevant medical condition, the metabolic syndrome, the influence of the sample type on a multiplexed biomarker discovery approach was further investigated. Independent comparisons of protein profiles in serum and plasma revealed an antibody targeting ADAMTSL-4, a protein that would qualify to be studied further in association with the condition. In general, the preparation type had an impact on the results of the applied antibody suspension bead array, and while the technical variability was equal, plasma offered a greater biological variability and allowed to give rise to more discoveries than serum.", "doi": "10.1002/pmic.200900657", "pmid": "19953555", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:29.681Z", "modified": "2021-07-08T13:44:33.443Z"}]}