{"entity": "researcher", "timestamp": "2026-08-09T07:55:15.810Z", "family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "affiliations": ["School of Medical Sciences, \u00d6rebro University, \u00d6rebro, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e"}}, "publications": [{"entity": "publication", "iuid": "8c6967586d3c4def943eaead301e16a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c6967586d3c4def943eaead301e16a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c6967586d3c4def943eaead301e16a6"}}, "title": "Anti-integrin \u03b1v\u03b26 IgG antibody as a diagnostic and prognostic marker in ulcerative colitis: A cross-sectional and longitudinal study defining a specific disease phenotype.", "authors": [{"family": "Pertsinidou", "given": "Eleftheria", "initials": "E", "orcid": "0000-0002-8492-4045", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2d82952fdfe4adfbf152907224cac6a.json"}}, {"family": "Salomon", "given": "Benita", "initials": "B", "orcid": "0009-0002-8951-9839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0b9a6d679bd49e9bc9aa042d46d09c2.json"}}, {"family": "Bergemalm", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1906-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50a7ccd948a492f900b8d44d5fc7f3b.json"}}, {"family": "Salihovic", "given": "Samira", "initials": "S", "orcid": "0000-0001-5752-4196", "researcher": {"href": "https://publications.scilifelab.se/researcher/df1fba46be0541838544241a1e5aeeed.json"}}, {"family": "Hedin", "given": "Charlotte R H", "initials": "CRH", "orcid": "0000-0002-4921-8516", "researcher": {"href": "https://publications.scilifelab.se/researcher/d451be670f7f456ebca935690af79076.json"}}, {"family": "Ling Lundstr\u00f6m", "given": "Maria", "initials": "M", "orcid": "0000-0001-5518-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9c830b64f10403896bf3fd32c8e0afc.json"}}, {"family": "Keita", "given": "\u00c5sa V", "initials": "\u00c5V", "orcid": "0000-0002-6820-0215", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f0a7516d7104295be67073e6d5c04af.json"}}, {"family": "Magnusson", "given": "Maria K", "initials": "MK", "orcid": "0000-0002-8888-4968", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa4ee61498234362819679d3c13745a3.json"}}, {"family": "Eriksson", "given": "Carl", "initials": "C", "orcid": "0000-0002-1046-383X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf81d9aaa93645ae91dc40ebe9151b0d.json"}}, {"family": "Bengtson", "given": "May-Bente", "initials": "MB", "orcid": "0000-0002-5615-7141", "researcher": {"href": "https://publications.scilifelab.se/researcher/bae2f822ebea4830a0222ea80e16abd4.json"}}, {"family": "Gr\u00e4nn\u00f6", "given": "Olle", "initials": "O", "orcid": "0000-0002-4329-1659", "researcher": {"href": "https://publications.scilifelab.se/researcher/927332e01b4f44bbb588b3e52ddbd9af.json"}}, {"family": "Aabrekk", "given": "Tone B", "initials": "TB"}, {"family": "Mov\u00e9rare", "given": "Robert", "initials": "R", "orcid": "0000-0001-6611-5036", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef0011b9d8494f2694be45235a3dcc5f.json"}}, {"family": "Rydell", "given": "Niclas", "initials": "N", "orcid": "0000-0001-5661-1343", "researcher": {"href": "https://publications.scilifelab.se/researcher/23740102f75e4bde928938135eee6a08.json"}}, {"family": "Ekoff", "given": "Helena", "initials": "H", "orcid": "0000-0002-9746-114X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd1fd7f42ee44dcc86abe80f4877d89c.json"}}, {"family": "R\u00f6nnelid", "given": "Johan", "initials": "J", "orcid": "0000-0003-1186-3226", "researcher": {"href": "https://publications.scilifelab.se/researcher/25d1ba81c51a4bca974e84c9ea117cbe.json"}}, {"family": "BIO-IBD consortium\n", "given": "", "initials": ""}, {"family": "D'Amato", "given": "Mauro", "initials": "M", "orcid": "0000-0003-2743-5197", "researcher": {"href": "https://publications.scilifelab.se/researcher/538f828b3e61418fad903e0184c545cd.json"}}, {"family": "Detlie", "given": "Trond E", "initials": "TE", "orcid": "0000-0002-1576-5298", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd4da2d237d418cbf2b33851424fac6.json"}}, {"family": "Huppertz-Hauss", "given": "Gert", "initials": "G", "orcid": "0000-0002-5693-8773", "researcher": {"href": "https://publications.scilifelab.se/researcher/98caba3288924613b0a082f77783b174.json"}}, {"family": "Opheim", "given": "Randi", "initials": "R", "orcid": "0000-0002-0513-1435", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba159aa19a24409b8581a3f07af9943.json"}}, {"family": "Ricanek", "given": "Petr", "initials": "P", "orcid": "0000-0003-2454-7388", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d60d0651fa645189b12695cff6686cd.json"}}, {"family": "Kristensen", "given": "Vendel A", "initials": "VA", "orcid": "0000-0002-0876-8634", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ae40659dd99447f9b445b650d6890e5.json"}}, {"family": "\u00d6hman", "given": "Lena", "initials": "L", "orcid": "0000-0001-8142-2106", "researcher": {"href": "https://publications.scilifelab.se/researcher/79239c8719b24eba951c4e1702952d5e.json"}}, {"family": "S\u00f6derholm", "given": "Johan D", "initials": "JD", "orcid": "0000-0002-3250-5367", "researcher": {"href": "https://publications.scilifelab.se/researcher/24c3e1f92a7449caa5db6e47e9d7bca7.json"}}, {"family": "Kruse", "given": "Robert", "initials": "R", "orcid": "0000-0003-1785-8540", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad3ea1c83bcf4ee0b7f1af08206f8c9a.json"}}, {"family": "Lindqvist", "given": "Carl M", "initials": "CM", "orcid": "0000-0003-3887-9519", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc425582c7134cfaa889ad4fd117a573.json"}}, {"family": "Carlson", "given": "Marie", "initials": "M", "orcid": "0000-0002-3762-8489", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e51ed20d984b688456dd957e1eda32.json"}}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "H\u00f8ivik", "given": "Marte L", "initials": "ML", "orcid": "0000-0002-0104-465X", "researcher": {"href": "https://publications.scilifelab.se/researcher/874d02c909b44d88bafd0f3ee8b8d945.json"}}, {"family": "Halfvarson", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0122-7234", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c18b8a6cc54dfa8ad14b0c97261bfa.json"}}], "type": "journal article", "published": "2025-05-08", "journal": {"title": "J Crohns Colitis", "issn": "1876-4479", "volume": "19", "issue": "5", "issn-l": null}, "abstract": "The diagnostic and prognostic properties of anti-integrin \u03b1v\u03b26 immunoglobulin G (IgG) autoantibodies in ulcerative colitis (UC) are poorly understood. We aimed to assess the diagnostic performance of anti-integrin \u03b1v\u03b26 autoantibodies and examine their association with disease outcomes.\n\nSerum samples from a Swedish inception cohort of patients with suspected inflammatory bowel disease (IBD, n = 473) were analyzed using an in-house fluorescence enzyme immunoassay based on EliA technology. Findings were validated in a Norwegian population-based inception cohort (n = 570). Diagnostic performance was assessed by calculating the area under the curve (AUC) with 95% confidence intervals and determining sensitivity and specificity. Reclassification was evaluated using the net reclassification index.\n\nIn the discovery cohort, patients with UC, IBD-unclassified, or colonic Crohn's disease exhibited higher median autoantibody levels compared to symptomatic and healthy controls. In the validation cohort, the autoantibody demonstrated 79% sensitivity and 94% specificity for UC vs symptomatic controls at a cut-off of 400 UA/l. Its diagnostic performance (AUC = 0.92, 95% CI, 0.89-0.95) was superior to hs-CRP (AUC = 0.65, 95% CI, 0.60-0.70, P < .001) and faecal calprotectin (fcalpro) (AUC = 0.88, 95% CI, 0.84-0.92, P = .09). Combining the autoantibody with fcalpro further improved diagnostic accuracy (AUC = 0.97, 95% CI, 0.95-0.98) and patient reclassification (P < .001). Autoantibody positivity was associated with a severe phenotype of UC, characterised by increased inflammatory activity and higher IL-17A and granzyme B levels. Higher autoantibody levels were linked to an aggressive disease course, remaining stable in aggressive UC but decreasing in indolent disease (P = .003).\n\nAnti-integrin \u03b1v\u03b26 is a reliable diagnostic and prognostic marker for UC, with potential clinical implementation.", "doi": "10.1093/ecco-jcc/jjaf062", "pmid": "40251889", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12086997"}, {"db": "pii", "key": "8116397"}], "notes": [], "created": "2025-11-25T19:22:40.889Z", "modified": "2025-11-25T19:22:42.026Z"}, {"entity": "publication", "iuid": "53004388459e465ab3c59b47d352f040", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53004388459e465ab3c59b47d352f040.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53004388459e465ab3c59b47d352f040"}}, "title": "Systems-level immunomonitoring in children with solid tumors to enable precision medicine.", "authors": [{"family": "Chen", "given": "Qi", "initials": "Q", "orcid": "0000-0002-5864-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a.json"}}, {"family": "Zhao", "given": "Binbin", "initials": "B", "orcid": "0000-0002-5560-6750", "researcher": {"href": "https://publications.scilifelab.se/researcher/22329dc812fc4684acce02c18ae6fa18.json"}}, {"family": "Tan", "given": "Ziyang", "initials": "Z", "orcid": "0000-0001-5958-2584", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd87015d70fb4f71a9c5c40a22b84d4e.json"}}, {"family": "Hedberg", "given": "Gustav", "initials": "G"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Negrini", "given": "Erika", "initials": "E"}, {"family": "P\u00e1ez", "given": "Laura Pi\u00f1ero", "initials": "LP"}, {"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f9c2cfec48e4c4d8e9bc528a02d489b.json"}}, {"family": "James", "given": "Anna", "initials": "A"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mike\u0161", "given": "Jarom\u00edr", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Bernhardsson", "given": "Anna Karin", "initials": "AK"}, {"family": "Reitzner", "given": "Stefan Markus", "initials": "SM", "orcid": "0000-0003-0151-2780", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ca59c30b2e45459eb3638c65b452b3.json"}}, {"family": "von Walden", "given": "Ferdinand", "initials": "F"}, {"family": "O'Neill", "given": "Olivia", "initials": "O"}, {"family": "Barcenilla", "given": "Hugo", "initials": "H", "orcid": "0000-0002-7255-362X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0f0d6085e774a0fbdc1ad8d6eea3c23.json"}}, {"family": "Wang", "given": "Chunlin", "initials": "C"}, {"family": "Davis", "given": "Mark M", "initials": "MM"}, {"family": "Carlson", "given": "Lena-Maria", "initials": "LM"}, {"family": "Pal", "given": "Niklas", "initials": "N"}, {"family": "Blomgren", "given": "Klas", "initials": "K", "orcid": "0000-0002-0476-7271", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb3b554177d481ebc9d4aa0f3b1fbc4.json"}}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "Herold", "given": "Nikolas", "initials": "N", "orcid": "0000-0001-9468-4543", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2af6f17f76457680908c36693f2de5.json"}}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Kogner", "given": "Per", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications.scilifelab.se/researcher/e963274b921a4a2c8263f509334d4e22.json"}}, {"family": "Ljungblad", "given": "Linda", "initials": "L"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2025-03-06", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "188", "issue": "5", "pages": "1425-1440.e11", "issn-l": "0092-8674"}, "abstract": "Cancer is the leading cause of death from disease in children. Survival depends not only on surgery, cytostatic drugs, and radiation but also on systemic immune responses. Factors influencing these immune responses in children of different ages and tumor types are unknown. Novel immunotherapies can enhance anti-tumor immune responses, but few children have benefited, and markers of effective responses are lacking. Here, we present a systems-level analysis of immune responses in 191 children within a population-based cohort with diverse tumors and reveal that age and tumor type shape immune responses differently. Systemic inflammation and cytotoxic T cell responses correlate with tumor mutation rates and immune cell infiltration. Clonally expanded T cell responses are rarely detected in blood or tumors at diagnosis but are sometimes elicited during treatment. Expanded T cells are similarly regulated in children and adults with more immunogenic cancers. This research aims to facilitate the development of precision immunotherapies for children with cancer.", "doi": "10.1016/j.cell.2024.12.014", "pmid": "39837329", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Affinity Proteomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(24)01427-2"}], "notes": [], "created": "2025-01-30T10:50:10.864Z", "modified": "2025-11-28T10:42:05.786Z"}, {"entity": "publication", "iuid": "066cfae0c81d420a8e8a1191c72d3ace", "links": {"self": {"href": "https://publications.scilifelab.se/publication/066cfae0c81d420a8e8a1191c72d3ace.json"}, "display": {"href": "https://publications.scilifelab.se/publication/066cfae0c81d420a8e8a1191c72d3ace"}}, "title": "Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method.", "authors": [{"family": "Rajan", "given": "Sukithar K", "initials": "SK"}, {"family": "Lindqvist", "given": "M\u00e5rten", "initials": "M"}, {"family": "Brummer", "given": "Robert Jan", "initials": "RJ"}, {"family": "Schoultz", "given": "Ida", "initials": "I"}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}], "type": "journal article", "published": "2019-09-17", "journal": {"volume": "14", "issn": "1932-6203", "issue": "9", "pages": "e0222171", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The human gut microbiota is well established as an important factor in health and disease. Fecal sample microbiota are often analyzed as a proxy for gut microbiota, and characterized with respect to their composition profiles. Modern approaches employ whole genome shotgun next-generation sequencing as the basis for these analyses. Sequencing depth as well as choice of next-generation sequencing data analysis method constitute two main interacting methodological factors for such an approach. In this study, we used 200 million sequence read pairs from one fecal sample for comparing different taxonomy classification methods, using default and custom-made reference databases, at different sequencing depths. A mock community data set with known composition was used for validating the classification methods. Results suggest that sequencing beyond 60 million read pairs does not seem to improve classification. The phylogeny prediction pattern, when using the default databases and the consensus database, appeared to be similar for all three methods. Moreover, these methods predicted rather different species. We conclude that the choice of sequencing depth and classification method has important implications for taxonomy composition prediction. A multi-method-consensus approach for robust gut microbiota NGS analysis is recommended.", "doi": "10.1371/journal.pone.0222171", "pmid": "31527871", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-19-08745"}, {"db": "pmc", "key": "PMC6748435"}], "notes": [], "created": "2019-12-03T10:46:32.234Z", "modified": "2021-06-18T14:06:50.523Z"}, {"entity": "publication", "iuid": "1db8dc97446746fb82180569ebc97fac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1db8dc97446746fb82180569ebc97fac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1db8dc97446746fb82180569ebc97fac"}}, "title": "Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci.", "authors": [{"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Assadi", "given": "Ghazaleh", "initials": "G"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Reznichenko", "given": "Anna", "initials": "A"}, {"family": "Akhter", "given": "Tahmina", "initials": "T"}, {"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Bonfiglio", "given": "Ferdinando", "initials": "F"}, {"family": "Hansen", "given": "Mark Berner", "initials": "MB"}, {"family": "Sandberg", "given": "Kristian", "initials": "K", "orcid": "0000-0002-6395-6590", "researcher": {"href": "https://publications.scilifelab.se/researcher/2747d3fe7810406fafc429d9e66225ef.json"}}, {"family": "Greco", "given": "Dario", "initials": "D"}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2019-01-10", "journal": {"volume": "25", "issn": "1536-4844", "issue": "2", "pages": "306-316", "title": "Inflamm Bowel Dis", "issn-l": null}, "abstract": "Few studies have investigated the blood proteome of inflammatory bowel disease (IBD). We characterized the serum abundance of proteins encoded at 163 known IBD risk loci and tested these proteins for their biomarker discovery potential.\n\nBased on the Human Protein Atlas (HPA) antibody availability, 218 proteins from genes mapping at 163 IBD risk loci were selected. Targeted serum protein profiles from 49 Crohn's disease (CD) patients, 51 ulcerative colitis (UC) patients, and 50 sex- and age-matched healthy individuals were obtained using multiplexed antibody suspension bead array assays. Differences in relative serum abundance levels between disease groups and controls were examined. Replication was attempted for CD-UC comparisons (including disease subtypes) by including 64 additional patients (33 CD and 31 UC). Antibodies targeting a potentially novel risk protein were validated by paired antibodies, Western blot, immuno-capture mass spectrometry, and epitope mapping.\n\nBy univariate analysis, 13 proteins mostly related to neutrophil, T-cell, and B-cell activation and function were differentially expressed in IBD patients vs healthy controls, 3 in CD patients vs healthy controls and 2 in UC patients vs healthy controls (q < 0.01). Multivariate analyses further differentiated disease groups from healthy controls and CD subtypes from UC (P < 0.05). Extended characterization of an antibody targeting a novel, discriminative serum marker, the laccase (multicopper oxidoreductase) domain containing 1 (LACC1) protein, provided evidence for antibody on-target specificity.\n\nUsing affinity proteomics, we identified a set of IBD-associated serum proteins encoded at IBD risk loci. These candidate proteins hold the potential to be exploited as diagnostic biomarkers of IBD.", "doi": "10.1093/ibd/izy326", "pmid": "30358838", "labels": {"Affinity Proteomics Stockholm": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5144272"}, {"db": "pmc", "key": "PMC6327232"}], "notes": [], "created": "2018-10-26T06:07:49.951Z", "modified": "2025-10-17T13:05:08.266Z"}, {"entity": "publication", "iuid": "0622ae34d9a6494b8e6514e89b1099e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0622ae34d9a6494b8e6514e89b1099e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0622ae34d9a6494b8e6514e89b1099e2"}}, "title": "Subphenotypes of inflammatory bowel disease are characterized by specific serum protein profiles.", "authors": [{"family": "Andersson", "given": "Erik", "initials": "E", "orcid": "0000-0002-6598-1984", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b4b839a52be43a3a71123736c4c01af.json"}}, {"family": "Bergemalm", "given": "Daniel", "initials": "D"}, {"family": "Kruse", "given": "Robert", "initials": "R"}, {"family": "Neumann", "given": "Gunter", "initials": "G"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2017-10-05", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "12", "issue": "10", "pages": "e0186142"}, "abstract": "Genetic and immunological data indicate that inflammatory bowel disease (IBD) are characterized by specific inflammatory protein profiles. However, the serum proteome of IBD is still to be defined. We aimed to characterize the inflammatory serum protein profiles of Crohn's disease (CD) and ulcerative colitis (UC), using the novel proximity extension assay.\n\nA panel of 91 inflammatory proteins were quantified in a discovery cohort of CD (n = 54), UC patients (n = 54), and healthy controls (HCs; n = 54). We performed univariate analyses by t-test, with false discovery rate correction. A sparse partial least-squares (sPLS) approach was used to identify additional discriminative proteins. The results were validated in a replication cohort.\n\nBy univariate analysis, 17 proteins were identified with significantly different abundances in CD and HCs, and 12 when comparing UC and HCs. Additionally, 64 and 45 discriminant candidate proteins, respectively, were identified with the multivariate approach. Correspondingly, significant cross-validation error rates of 0.12 and 0.19 were observed in the discovery cohort. Only FGF-19 was identified from univariate comparisons of CD and UC, but 37 additional discriminant candidates were identified using the multivariate approach. The observed cross-validation error rate for CD vs. UC remained significant when restricting the analyses to patients in clinical remission. Using univariate comparisons, 16 of 17 CD-associated proteins and 8 of 12 UC-associated proteins were validated in the replication cohort. The area under the curve for CD and UC was 0.96 and 0.92, respectively, when the sPLS model from the discovery cohort was applied to the replication cohort.\n\nBy using the novel PEA method and a panel of inflammatory proteins, we identified proteins with significantly different quantities in CD patients and UC patients compared to HCs. Our data highlight the potential of the serum IBD proteome as a source for identification of future diagnostic biomarkers.", "doi": "10.1371/journal.pone.0186142", "pmid": "28982144", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-13227"}, {"db": "pmc", "key": "PMC5628935"}], "notes": [], "created": "2020-01-23T15:08:28.310Z", "modified": "2023-04-14T13:56:09.416Z"}]}