{"entity": "journal", "iuid": "be3ec4bdf7f841b2a4b08bd8b1b80af4", "timestamp": "2026-07-12T18:13:39.635Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Sci.%20Transl.%20Med..json"}, "display": {"href": "https://publications.scilifelab.se/journal/Sci.%20Transl.%20Med."}}, "title": "Sci. Transl. Med.", "issn": "1946-6234", "issn-l": "1946-6234", "publications_count": 2, "publications": [{"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", 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"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": "110f4581854a476b9c6f6e1d9b01a259", "links": {"self": {"href": "https://publications.scilifelab.se/publication/110f4581854a476b9c6f6e1d9b01a259.json"}, "display": {"href": "https://publications.scilifelab.se/publication/110f4581854a476b9c6f6e1d9b01a259"}}, "title": "Transglutaminase 4 as a prostate autoantigen in male subfertility", "authors": [{"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Sharon", "given": "Donald", "initials": "D"}, {"family": "Shum", "given": "Anthony K", "initials": "AK"}, {"family": "Khan", "given": "Imran S", "initials": "IS"}, {"family": "Fasano", "given": "Kayla J", "initials": "KJ"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Ardesj\u00f6-Lundgren", "given": "Brita", "initials": "B"}, {"family": "Alimohammadi", "given": "Mohammad", "initials": "M"}, {"family": "Rathsman", "given": "Sandra", "initials": "S"}, {"family": "Ludvigsson", "given": "Jonas F", "initials": "JF"}, {"family": "Lundh", "given": "Dan", "initials": "D"}, {"family": "Motrich", "given": "Ruben", "initials": "R"}, {"family": "Rivero", "given": "Virginia", "initials": "V"}, {"family": "Fong", "given": "Lawrence", "initials": "L"}, {"family": "Giwercman", "given": "Aleksander", "initials": "A"}, {"family": "Gustafsson", "given": "Jan", "initials": "J"}, {"family": "Perheentupa", "given": "Jaakko", "initials": "J"}, {"family": "Husebye", "given": "Eystein S", "initials": "ES"}, {"family": "Anderson", "given": "Mark S", "initials": "MS"}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}], "type": "journal-article", "published": "2015-06-17", "journal": {"volume": "7", "issn": "1946-6234", "issue": "292", "pages": "292ra101", "title": "Sci. Transl. Med.", "issn-l": "1946-6234"}, "abstract": "Autoimmune polyendocrine syndrome type 1 (APS1), a monogenic disorder caused by AIRE gene mutations, features multiple autoimmune disease components. Infertility is common in both males and females with APS1. Although female infertility can be explained by autoimmune ovarian failure, the mechanisms underlying male infertility have remained poorly understood. We performed a proteome-wide autoantibody screen in APS1 patient sera to assess the autoimmune response against the male reproductive organs. By screening human protein arrays with male and female patient sera and by selecting for gender-imbalanced autoantibody signals, we identified transglutaminase 4 (TGM4) as a male-specific autoantigen. Notably, TGM4 is a prostatic secretory molecule with critical role in male reproduction. TGM4 autoantibodies were detected in most of the adult male APS1 patients but were absent in all the young males. Consecutive serum samples further revealed that TGM4 autoantibodies first presented during pubertal age and subsequent to prostate maturation. We assessed the animal model for APS1, the Aire-deficient mouse, and found spontaneous development of TGM4 autoantibodies specifically in males. Aire-deficient mice failed to present TGM4 in the thymus, consistent with a defect in central tolerance for TGM4. In the mouse, we further link TGM4 immunity with a destructive prostatitis and compromised secretion of TGM4. Collectively, our findings in APS1 patients and Aire-deficient mice reveal prostate autoimmunity as a major manifestation of APS1 with potential role in male subfertility.", "doi": "10.1126/scitranslmed.aaa9186", "pmid": "26084804", "labels": {"Bioinformatics Support and Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "Autoimmunity and Serology Profiling": "Service", "PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "7/292/292ra101"}], "notes": [], "created": "2017-05-02T12:57:44.848Z", "modified": "2023-06-19T09:06:56.580Z"}], "created": "2020-01-27T10:00:04.991Z", "modified": "2020-11-27T13:14:08.432Z"}