{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T20:15:31Z","timestamp":1791404131035,"version":"4.3.3"},"reference-count":109,"publisher":"Elsevier BV","issue":"25","license":[{"start":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,11,2]],"date-time":"2023-11-02T00:00:00Z","timestamp":1698883200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell"],"published-print":{"date-parts":[[2023,12]]},"DOI":"10.1016\/j.cell.2023.10.024","type":"journal-article","created":{"date-parts":[[2023,11,27]],"date-time":"2023-11-27T15:29:31Z","timestamp":1701098971000},"page":"5569-5586.e21","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":58,"title":["TScan-II: A genome-scale platform for the de novo identification of CD4+ T\u00a0cell epitopes"],"prefix":"10.1016","volume":"186","author":[{"given":"Mohammad H.","family":"Dezfulian","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomasz","family":"Kula","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Pranzatelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nolan","family":"Kamitaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingda","family":"Meng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bhuwan","family":"Khatri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paola","family":"Perez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qikai","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aiquan","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayano C.","family":"Kohlgruber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumei","family":"Leng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ananth Aditya","family":"Jupudi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle L.","family":"Joachims","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John A.","family":"Chiorini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher J.","family":"Lessard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. Darise","family":"Farris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Senthil K.","family":"Muthuswamy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Blake M.","family":"Warner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7923-6283","authenticated-orcid":false,"given":"Stephen J.","family":"Elledge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.cell.2023.10.024_bib1","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nrg2703","article-title":"Origin and evolution of the adaptive immune system: genetic events and selective pressures","volume":"11","author":"Flajnik","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.cell.2023.10.024_bib2","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1016\/j.cell.2019.07.009","article-title":"T-scan: A genome-wide method for the systematic discovery of T\u00a0cell epitopes","volume":"178","author":"Kula","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.cell.2023.10.024_bib3","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1016\/j.cell.2014.03.047","article-title":"Deconstructing the peptide-MHC specificity of T\u00a0cell recognition","volume":"157","author":"Birnbaum","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.cell.2023.10.024_bib4","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1038\/s41592-020-0867-z","article-title":"T cell antigen discovery","volume":"18","author":"Joglekar","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2023.10.024_bib5","doi-asserted-by":"crossref","first-page":"4553","DOI":"10.1038\/s41467-019-12444-7","article-title":"Rapid selection and identification of functional CD8+ T\u00a0cell epitopes from large peptide-coding libraries","volume":"10","author":"Sharma","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2023.10.024_bib6","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1126\/science.284.5418.1351","article-title":"Cloning genes encoding MHC class II-restricted antigens: mutated CDC27 as a tumor antigen","volume":"284","author":"Wang","year":"1999","journal-title":"Science"},{"key":"10.1016\/j.cell.2023.10.024_bib7","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/s41592-018-0305-7","article-title":"T cell antigen discovery via trogocytosis","volume":"16","author":"Li","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2023.10.024_bib8","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1038\/s41590-019-0335-z","article-title":"Deciphering CD4+ T\u00a0cell specificity using novel MHC-TCR chimeric receptors","volume":"20","author":"Kisielow","year":"2019","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib9","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abf4001","article-title":"Antigen identification for HLA class I- and HLA class II-restricted T\u00a0cell receptors using cytokine-capturing antigen-presenting cells","volume":"6","author":"Lee","year":"2021","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib10","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1146\/annurev-immunol-032712-095910","article-title":"Pathways of antigen processing","volume":"31","author":"Blum","year":"2013","journal-title":"Annu. Rev. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib11","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/nri3818","article-title":"The ins and outs of MHC class II-mediated antigen processing and presentation","volume":"15","author":"Roche","year":"2015","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib12","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1038\/nri1708","article-title":"Regulation of MHC class II gene expression by the class II transactivator","volume":"5","author":"Reith","year":"2005","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib13","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1111\/j.1749-6632.1995.tb44522.x","article-title":"A review of T-cell receptors in multiple sclerosis: clonal expansion and persistence of human T-cells specific for an immunodominant myelin basic protein peptide","volume":"756","author":"Wucherpfennig","year":"1995","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"10.1016\/j.cell.2023.10.024_bib14","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1016\/j.bbamcr.2016.03.026","article-title":"The multifaceted roles of the invariant chain CD74 \u2014 more than just a chaperone","volume":"1863","author":"Schr\u00f6der","year":"2016","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.cell.2023.10.024_bib15","doi-asserted-by":"crossref","first-page":"2093","DOI":"10.1172\/JCI83792","article-title":"Public T\u00a0cell receptors confer high-avidity CD4 responses to HIV controllers","volume":"126","author":"Benati","year":"2016","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.cell.2023.10.024_bib16","doi-asserted-by":"crossref","first-page":"3338","DOI":"10.1073\/pnas.1502857112","article-title":"Rationally designed fluorogenic protease reporter visualizes spatiotemporal dynamics of apoptosis in\u00a0vivo","volume":"112","author":"To","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2023.10.024_bib17","doi-asserted-by":"crossref","first-page":"eaaw4912","DOI":"10.1126\/science.aaw4912","article-title":"A glycine-specific N-degron pathway mediates the quality control of protein N-myristoylation","volume":"365","author":"Timms","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.cell.2023.10.024_bib18","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1242\/jcs.059758","article-title":"Role of intramembrane charged residues in the quality control of unassembled T-cell receptor \u03b1-chains at the endoplasmic reticulum","volume":"123","author":"Soetandyo","year":"2010","journal-title":"J.\u00a0Cell Sci."},{"key":"10.1016\/j.cell.2023.10.024_bib19","doi-asserted-by":"crossref","first-page":"8878","DOI":"10.1158\/0008-5472.CAN-06-1450","article-title":"Enhanced antitumor activity of murine-human hybrid T-cell receptor (TCR) in human lymphocytes is associated with improved pairing and TCR\/CD3 stability","volume":"66","author":"Cohen","year":"2006","journal-title":"Cancer Res."},{"key":"10.1016\/j.cell.2023.10.024_bib20","doi-asserted-by":"crossref","first-page":"3898","DOI":"10.1158\/0008-5472.CAN-06-3986","article-title":"Enhanced antitumor activity of T\u00a0cells engineered to express T-cell receptors with a second disulfide bond","volume":"67","author":"Cohen","year":"2007","journal-title":"Cancer Res."},{"key":"10.1016\/j.cell.2023.10.024_bib21","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.tibs.2017.11.008","article-title":"TCR signaling: mechanisms of initiation and propagation","volume":"43","author":"Courtney","year":"2018","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.cell.2023.10.024_bib22","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1086\/433188","article-title":"HIV controllers: A homogeneous group of HIV-1-infected patients with spontaneous control of viral replication","volume":"41","author":"Lambotte","year":"2005","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.cell.2023.10.024_bib23","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aat0687","article-title":"CD4+ T cell\u2013mediated HLA class II cross-restriction in HIV controllers","volume":"3","author":"Galperin","year":"2018","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib24","doi-asserted-by":"crossref","first-page":"947","DOI":"10.3389\/fimmu.2018.00947","article-title":"NY-ESO-1 based immunotherapy of cancer: current perspectives","volume":"9","author":"Thomas","year":"2018","journal-title":"Front. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1097\/CJI.0000000000000101","article-title":"Expression of MAGE-A and NY-ESO-1 in primary and metastatic cancers","volume":"39","author":"Park","year":"2016","journal-title":"J.\u00a0Immunother."},{"key":"10.1016\/j.cell.2023.10.024_bib26","doi-asserted-by":"crossref","first-page":"197ra103","DOI":"10.1126\/scitranslmed.3006034","article-title":"Identification of a titin-derived HLA-A1-presented peptide as a cross-reactive target for engineered MAGE A3-directed T\u00a0cells","volume":"5","author":"Cameron","year":"2013","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.cell.2023.10.024_bib27","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1097\/CJI.0b013e3182829903","article-title":"Cancer regression and neurological toxicity following anti-MAGE-A3 TCR gene therapy","volume":"36","author":"Morgan","year":"2013","journal-title":"J.\u00a0Immunother."},{"key":"10.1016\/j.cell.2023.10.024_bib28","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1182\/blood-2013-03-490565","article-title":"Cardiovascular toxicity and titin cross-reactivity of affinity-enhanced T\u00a0cells in myeloma and melanoma","volume":"122","author":"Linette","year":"2013","journal-title":"Blood"},{"key":"10.1016\/j.cell.2023.10.024_bib29","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1172\/JCI120391","article-title":"Effective NY-ESO-1-specific MHC II-restricted T\u00a0cell receptors from antigen-negative hosts enhance tumor regression","volume":"129","author":"Poncette","year":"2019","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.cell.2023.10.024_bib30","doi-asserted-by":"crossref","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2023.10.024_bib31","article-title":"Empirical identification and validation of tumor-targeting T\u00a0cell receptors from circulation using autologous pancreatic tumor organoids","volume":"9","author":"Meng","year":"2021","journal-title":"J.\u00a0Immunother. Cancer"},{"key":"10.1016\/j.cell.2023.10.024_bib32","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1038\/s41467-020-14968-9","article-title":"Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes","volume":"11","author":"Chong","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2023.10.024_bib33","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1158\/2326-6066.CIR-19-0541","article-title":"Proteogenomics uncovers a vast repertoire of shared tumor-specific antigens in ovarian cancer","volume":"8","author":"Zhao","year":"2020","journal-title":"Cancer Immunol. Res."},{"key":"10.1016\/j.cell.2023.10.024_bib34","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/s41587-021-01021-3","article-title":"Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer","volume":"40","author":"Ouspenskaia","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2023.10.024_bib35","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/s42003-021-02007-2","article-title":"Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens","volume":"4","author":"Xiang","year":"2021","journal-title":"Commun. Biol."},{"key":"10.1016\/j.cell.2023.10.024_bib36","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1007\/s00018-011-0655-0","article-title":"Non-conventional sources of peptides presented by MHC class I","volume":"68","author":"Starck","year":"2011","journal-title":"Cell. Mol. Life Sci."},{"key":"10.1016\/j.cell.2023.10.024_bib37","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/s41392-019-0092-3","article-title":"Peptides encoded by noncoding genes: challenges and perspectives","volume":"4","author":"Wang","year":"2019","journal-title":"Signal Transduct. Target. Ther."},{"key":"10.1016\/j.cell.2023.10.024_bib38","doi-asserted-by":"crossref","first-page":"D413","DOI":"10.1093\/nar\/gkab847","article-title":"TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome","volume":"50","author":"Lv","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2023.10.024_bib39","doi-asserted-by":"crossref","first-page":"128","DOI":"10.6026\/97320630006128","article-title":"A database of six eukaryotic hypothetical genes and proteins","volume":"6","author":"Adinarayana","year":"2011","journal-title":"Bioinformation"},{"key":"10.1016\/j.cell.2023.10.024_bib40","first-page":"D783","article-title":"Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools","volume":"48","author":"Gonzalez-Galarza","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2023.10.024_bib41","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1056\/NEJM200103013440907","article-title":"Tolerance and autoimmunity","volume":"344","author":"Kamradt","year":"2001","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.cell.2023.10.024_bib42","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1097\/00005792-196505000-00001","article-title":"Sjoegren\u2019s syndrome. A clinical, pathological, and serological study of sixty-two cases","volume":"44","author":"Bloch","year":"1965","journal-title":"Med. (Baltim.)"},{"key":"10.1016\/j.cell.2023.10.024_bib43","doi-asserted-by":"crossref","first-page":"203","DOI":"10.4049\/jimmunol.130.1.203","article-title":"Immunohistologic analysis of lymphoid infiltrates in primary Sjogren\u2019s syndrome using monoclonal antibodies","volume":"130","author":"Adamson","year":"1983","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib44","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.jaut.2009.10.004","article-title":"Characteristics of the minor salivary gland infiltrates in Sj\u00f6gren\u2019s syndrome","volume":"34","author":"Christodoulou","year":"2010","journal-title":"J.\u00a0Autoimmun."},{"key":"10.1016\/j.cell.2023.10.024_bib45","doi-asserted-by":"crossref","first-page":"1566","DOI":"10.3899\/jrheum.130256","article-title":"Minor salivary gland inflammatory lesions in Sj\u00f6gren syndrome: do they evolve?","volume":"40","author":"Kapsogeorgou","year":"2013","journal-title":"J.\u00a0Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib46","first-page":"210","article-title":"T cell subpopulations in the labial minor\u00a0salivary gland histopathologic lesion of Sj\u00f6gren\u2019s syndrome","volume":"18","author":"Skopouli","year":"1991","journal-title":"J.\u00a0Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib47","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1016\/j.jaci.2016.01.024","article-title":"Cytometry by time-of-flight immunophenotyping identifies a blood Sj\u00f6gren\u2019s signature correlating with disease activity and glandular inflammation","volume":"137","author":"Mingueneau","year":"2016","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib48","doi-asserted-by":"crossref","DOI":"10.1172\/jci.insight.85609","article-title":"Single-cell analysis of glandular T\u00a0cell receptors in Sj\u00f6gren\u2019s syndrome","volume":"1","author":"Joachims","year":"2016","journal-title":"JCI Insight"},{"key":"10.1016\/j.cell.2023.10.024_bib49","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1136\/ard.45.8.677","article-title":"HLA-DR expression by labial minor salivary gland tissues in Sj\u00f6gren\u2019s syndrome","volume":"45","author":"Moutsopoulos","year":"1986","journal-title":"Ann. Rheum. Dis."},{"key":"10.1016\/j.cell.2023.10.024_bib50","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1002\/art.1780290908","article-title":"Expression of histocompatibility antigen HLA-DR by salivary gland epithelial cells in Sj\u00f6gren\u2019s syndrome","volume":"29","author":"Fox","year":"1986","journal-title":"Arthritis Rheum."},{"key":"10.1016\/j.cell.2023.10.024_bib51","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1111\/j.1365-2249.1993.tb03389.x","article-title":"Increased epithelial expression of HLA-DQ and HLA-DP molecules in salivary glands from patients with Sj\u00f6gren\u2019s syndrome compared with obstructive sialadenitis","volume":"92","author":"Thrane","year":"1993","journal-title":"Clin. Exp. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib52","first-page":"1884","article-title":"Possible function of salivary gland epithelial cells as nonprofessional antigen-presenting cells in the development of Sj\u00f6gren\u2019s syndrome","volume":"29","author":"Tsunawaki","year":"2002","journal-title":"J.\u00a0Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib53","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1136\/ard.2004.033837","article-title":"Basal lamina disorganisation of the acini and ducts of labial salivary glands from patients with Sj\u00f6gren\u2019s syndrome: association with mononuclear cell infiltration","volume":"65","author":"Molina","year":"2006","journal-title":"Ann. Rheum. Dis."},{"key":"10.1016\/j.cell.2023.10.024_bib54","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1002\/1529-0131(199902)42:2<229::AID-ANR4>3.0.CO;2-X","article-title":"Expression of B7 costimulatory molecules by salivary gland epithelial cells in patients with Sj\u00f6gren\u2019s syndrome","volume":"42","author":"Manoussakis","year":"1999","journal-title":"Arthritis Rheum."},{"key":"10.1016\/j.cell.2023.10.024_bib55","doi-asserted-by":"crossref","first-page":"3107","DOI":"10.4049\/jimmunol.166.5.3107","article-title":"Functional expression of a costimulatory B7.2 (CD86) protein on human salivary gland epithelial cells that interacts with the CD28 receptor, but has reduced binding to CTLA4","volume":"166","author":"Kapsogeorgou","year":"2001","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib56","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1002\/art.20789","article-title":"Novel role of CD40 in Fas-dependent apoptosis of cultured salivary epithelial cells from patients with Sj\u00f6gren\u2019s syndrome","volume":"52","author":"Ping","year":"2005","journal-title":"Arthritis Rheum."},{"key":"10.1016\/j.cell.2023.10.024_bib57","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.jaut.2013.11.003","article-title":"Differentiation of follicular helper T\u00a0cells by salivary gland epithelial cells in primary Sj\u00f6gren\u2019s syndrome","volume":"51","author":"Gong","year":"2014","journal-title":"J.\u00a0Autoimmun."},{"key":"10.1016\/j.cell.2023.10.024_bib58","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1002\/art.1780210308","article-title":"Relationship of Hla-Dw3 and Hla-B8 to Sj\u00f6gren\u2019s syndrome","volume":"21","author":"Fye","year":"1978","journal-title":"Arthritis Rheum."},{"key":"10.1016\/j.cell.2023.10.024_bib59","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1056\/NEJM197704212961602","article-title":"Sj\u00f6gren\u2019s syndrome associated with HLA-Dw3","volume":"296","author":"Chused","year":"1977","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.cell.2023.10.024_bib60","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1126\/science.3458307","article-title":"Gene interaction at HLA-DQ enhances autoantibody production in primary Sj\u00f6gren\u2019s syndrome","volume":"232","author":"Harley","year":"1986","journal-title":"Science"},{"key":"10.1016\/j.cell.2023.10.024_bib61","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1038\/ng.2792","article-title":"Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sj\u00f6gren\u2019s syndrome","volume":"45","author":"Lessard","year":"2013","journal-title":"Nat. Genet."},{"key":"10.1016\/j.cell.2023.10.024_bib62","doi-asserted-by":"crossref","first-page":"4287","DOI":"10.1038\/s41467-022-30773-y","article-title":"Genome-wide association study identifies Sj\u00f6gren\u2019s risk loci with functional implications in immune and glandular cells","volume":"13","author":"Khatri","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2023.10.024_bib63","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1084\/jem.182.4.953","article-title":"Dual T\u00a0cell receptor alpha chain T\u00a0cells in autoimmunity","volume":"182","author":"Elliott","year":"1995","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.cell.2023.10.024_bib64","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1159\/000053792","article-title":"Dual TCR-expressing T lymphocytes in health and disease","volume":"125","author":"Hinz","year":"2001","journal-title":"Int. Arch. Allergy Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib65","doi-asserted-by":"crossref","first-page":"637","DOI":"10.4049\/jimmunol.1800904","article-title":"Dual TCR T\u00a0cells: identity crisis or multitaskers?","volume":"202","author":"Schuldt","year":"2019","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib66","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/icb.1997.16","article-title":"Molecular mimicry: can epitope mimicry induce autoimmune disease?","volume":"75","author":"Davies","year":"1997","journal-title":"Immunol. Cell Biol."},{"key":"10.1016\/j.cell.2023.10.024_bib67","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1007\/s12016-011-8294-7","article-title":"Molecular mimicry as a mechanism of autoimmune disease","volume":"42","author":"Cusick","year":"2012","journal-title":"Clin. Rev. Allergy Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib68","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1136\/adc.79.5.448","article-title":"Molecular mimicry in autoimmune disease","volume":"79","author":"Leech","year":"1998","journal-title":"Arch. Dis. Child."},{"key":"10.1016\/j.cell.2023.10.024_bib69","first-page":"4895","article-title":"Oral microbial flora of patients with Sicca syndrome","volume":"18","author":"Zhou","year":"2018","journal-title":"Mol. Med. Rep."},{"key":"10.1016\/j.cell.2023.10.024_bib70","doi-asserted-by":"crossref","first-page":"3088","DOI":"10.1093\/rheumatology\/kez004","article-title":"T cells in primary Sj\u00f6gren\u2019s syndrome: targets for early intervention","volume":"60","author":"Verstappen","year":"2021","journal-title":"Rheumatology (Oxford)"},{"key":"10.1016\/j.cell.2023.10.024_bib71","doi-asserted-by":"crossref","first-page":"R238","DOI":"10.1186\/ar4081","article-title":"Systems analysis of primary Sj\u00f6gren\u2019s syndrome pathogenesis in salivary glands identifies shared pathways in human and a mouse model","volume":"14","author":"Horvath","year":"2012","journal-title":"Arthritis Res. Ther."},{"key":"10.1016\/j.cell.2023.10.024_bib72","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1038\/s41591-021-01296-8","article-title":"SARS-CoV-2 infection of the oral cavity and saliva","volume":"27","author":"Huang","year":"2021","journal-title":"Nat. Med."},{"key":"10.1016\/j.cell.2023.10.024_bib73","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/s41584-021-00605-2","article-title":"Epithelial\u2013immune cell interplay in primary Sj\u00f6gren syndrome salivary gland pathogenesis","volume":"17","author":"Verstappen","year":"2021","journal-title":"Nat. Rev. Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib74","doi-asserted-by":"crossref","first-page":"D409","DOI":"10.1093\/nar\/gkac776","article-title":"IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions","volume":"51","author":"Cai","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2023.10.024_bib75","article-title":"HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy","volume":"9","author":"Marcu","year":"2021","journal-title":"J.\u00a0Immunother. Cancer"},{"key":"10.1016\/j.cell.2023.10.024_bib76","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1038\/88694","article-title":"Structure of a human insulin peptide\u2013HLA-DQ8 complex and susceptibility to type 1 diabetes","volume":"2","author":"Lee","year":"2001","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib77","first-page":"1134","article-title":"The role of HLA class II genes in insulin-dependent diabetes mellitus: molecular analysis of 180 Caucasian, multiplex families","volume":"59","author":"Noble","year":"1996","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.cell.2023.10.024_bib78","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1038\/ng.3353","article-title":"Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk","volume":"47","author":"Hu","year":"2015","journal-title":"Nat. Genet."},{"key":"10.1016\/j.cell.2023.10.024_bib79","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/ng.1076","article-title":"Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis","volume":"44","author":"Raychaudhuri","year":"2012","journal-title":"Nat. Genet."},{"key":"10.1016\/j.cell.2023.10.024_bib80","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1002\/art.40040","article-title":"Genome-wide association analysis reveals genetic heterogeneity of Sj\u00f6gren\u2019s syndrome according to ancestry","volume":"69","author":"Taylor","year":"2017","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib81","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1038\/ng.2779","article-title":"A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sj\u00f6gren\u2019s syndrome at 7q11.23","volume":"45","author":"Li","year":"2013","journal-title":"Nat. Genet."},{"key":"10.1016\/j.cell.2023.10.024_bib82","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1038\/s41586-020-2277-x","article-title":"Complement genes contribute sex-biased vulnerability in diverse disorders","volume":"582","author":"Kamitaki","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.cell.2023.10.024_bib83","doi-asserted-by":"crossref","first-page":"1440","DOI":"10.1002\/art.42122","article-title":"Complement C4 copy number variation is linked to SSA\/Ro and SSB\/la autoantibodies in systemic inflammatory autoimmune diseases","volume":"74","author":"Lundtoft","year":"2022","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib84","doi-asserted-by":"crossref","first-page":"1842","DOI":"10.1002\/art.42270","article-title":"Strong association of combined genetic deficiencies in the classical complement pathway with risk of systemic lupus erythematosus and primary Sj\u00f6gren\u2019s syndrome","volume":"74","author":"Lundtoft","year":"2022","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib85","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1002\/art.1780291014","article-title":"A strong association between null alleles at the C4A locus in the major histocompatibility complex and systemic sclerosis","volume":"29","author":"Briggs","year":"1986","journal-title":"Arthritis Rheum."},{"key":"10.1016\/j.cell.2023.10.024_bib86","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/0090-1229(91)90111-M","article-title":"DR3 and nonDR3 associated complement component C4A deficiency in systemic lupus erythematosus","volume":"60","author":"Kumar","year":"1991","journal-title":"Clin. Immunol. Immunopathol."},{"key":"10.1016\/j.cell.2023.10.024_bib87","doi-asserted-by":"crossref","first-page":"16021","DOI":"10.1038\/ncomms16021","article-title":"Transancestral mapping and genetic load in systemic lupus erythematosus","volume":"8","author":"Langefeld","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2023.10.024_bib88","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1136\/ard.57.8.503","article-title":"A study of the association of HLA DR, DQ, and complement C4 alleles with systemic lupus erythematosus in Iceland","volume":"57","author":"Steinsson","year":"1998","journal-title":"Ann. Rheum. Dis."},{"key":"10.1016\/j.cell.2023.10.024_bib89","first-page":"2590","article-title":"A study of C4AQ0 and MHC haplotypes in Icelandic multicase families with systemic lupus erythematosus","volume":"27","author":"Kristj\u00e1nsd\u00f3ttir","year":"2000","journal-title":"J.\u00a0Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib90","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1038\/nri1456","article-title":"A protective role for innate immunity in systemic lupus erythematosus","volume":"4","author":"Carroll","year":"2004","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib91","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1097\/00002281-200309000-00006","article-title":"Apoptosis in systemic lupus erythematosus","volume":"15","author":"White","year":"2003","journal-title":"Curr. Opin. Rheumatol."},{"issue":"Suppl 3","key":"10.1016\/j.cell.2023.10.024_bib92","first-page":"S95","article-title":"Complement deficiency: predisposing factor to autoimmune syndromes","volume":"7","author":"Atkinson","year":"1989","journal-title":"Clin. Exp. Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib93","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.108330","article-title":"Complement C4A regulates autoreactive B cells in murine lupus","volume":"33","author":"Simoni","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.cell.2023.10.024_bib94","doi-asserted-by":"crossref","first-page":"18435","DOI":"10.1074\/jbc.M601298200","article-title":"The human major histocompatibility complex class II HLA-DRB1 and HLA-DQA1 genes are separated by a CTCF-binding enhancer-blocking element","volume":"281","author":"Majumder","year":"2006","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.cell.2023.10.024_bib95","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.12089","article-title":"Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity","volume":"5","author":"Raj","year":"2016","journal-title":"eLife"},{"key":"10.1016\/j.cell.2023.10.024_bib96","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1002\/art.42119","article-title":"Complement C4, the major histocompatibility complex, and autoimmunity","volume":"74","author":"Vyse","year":"2022","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib97","doi-asserted-by":"crossref","DOI":"10.1136\/rmdopen-2023-003214","article-title":"Genetic dissection of HLA-DRB1\u221715:01 and XL9 region variants in Japanese patients with systemic lupus erythematosus: primary role for HLA-DRB1\u221715:01","volume":"9","author":"Kawasaki","year":"2023","journal-title":"RMD Open"},{"key":"10.1016\/j.cell.2023.10.024_bib98","doi-asserted-by":"crossref","DOI":"10.1016\/j.clim.2022.108953","article-title":"Systemic lupus erythematosus as a genetic disease","volume":"236","author":"Harley","year":"2022","journal-title":"Clin. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib99","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.699722","article-title":"Sclerosing Sialadenitis Is Associated With Salivary Gland Hypofunction and a Unique Gene Expression Profile in Sj\u00f6gren\u2019s Syndrome","volume":"12","author":"Yin","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.cell.2023.10.024_bib100","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"10.1016\/j.cell.2023.10.024_bib101","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. journal"},{"key":"10.1016\/j.cell.2023.10.024_bib102","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis.","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol."},{"key":"10.1016\/j.cell.2023.10.024_bib103","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.3192","article-title":"Spatial reconstruction of single-cell gene expression data.","volume":"33","author":"Satija","year":"2015","journal-title":"Nat Biotechnol."},{"key":"10.1016\/j.cell.2023.10.024_bib104","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1634\/theoncologist.2018-0823","article-title":"Sicca syndrome associated with immune checkpoint inhibitor therapy","volume":"24","author":"Warner","year":"2019","journal-title":"Oncologist"},{"key":"10.1016\/j.cell.2023.10.024_bib105","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1002\/art.39859","article-title":"2016 American College of Rheumatology\/European League Against Rheumatism classification criteria for primary Sj\u00f6gren\u2019s syndrome: A consensus and data-driven methodology involving three international patient cohorts","volume":"69","author":"Shiboski","year":"2017","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.cell.2023.10.024_bib106","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1136\/annrheumdis-2016-210571","article-title":"2016 American College of Rheumatology\/European League Against Rheumatism classification criteria for primary Sj\u00f6gren\u2019s syndrome: A consensus and data-driven methodology involving three international patient cohorts","volume":"76","author":"Shiboski","year":"2017","journal-title":"Ann. Rheum. Dis."},{"key":"10.1016\/j.cell.2023.10.024_bib107","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1038\/nm.3973","article-title":"Ductal pancreatic cancer modeling and drug screening using human pluripotent stem cell- and patient-derived tumor organoids","volume":"21","author":"Huang","year":"2015","journal-title":"Nat. Med."},{"key":"10.1016\/j.cell.2023.10.024_bib108","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1038\/s41587-020-0505-4","article-title":"Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening","volume":"38","author":"Huang","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2023.10.024_bib109","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. Biotechnol."}],"container-title":["Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0092867423011753?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0092867423011753?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,11,21]],"date-time":"2024-11-21T05:29:09Z","timestamp":1732166949000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0092867423011753"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12]]},"references-count":109,"journal-issue":{"issue":"25","published-print":{"date-parts":[[2023,12]]}},"alternative-id":["S0092867423011753"],"URL":"https:\/\/doi.org\/10.1016\/j.cell.2023.10.024","relation":{},"ISSN":["0092-8674"],"issn-type":[{"value":"0092-8674","type":"print"}],"subject":[],"published":{"date-parts":[[2023,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"TScan-II: A genome-scale platform for the de novo identification of CD4+ T\u00a0cell epitopes","name":"articletitle","label":"Article Title"},{"value":"Cell","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cell.2023.10.024","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}