{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T09:50:13Z","timestamp":1782121813340,"version":"3.54.5"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T00:00:00Z","timestamp":1782086400000},"content-version":"vor","delay-in-days":87,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-23-CE17-0011-01"],"award-info":[{"award-number":["ANR-23-CE17-0011-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-23-CE17-0011-03"],"award-info":[{"award-number":["ANR-23-CE17-0011-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-23-IAHU-0007"],"award-info":[{"award-number":["ANR-23-IAHU-0007"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Shared epitopes pose safety and efficacy issues for T-cell immunotherapy. To characterize the extent of this problem, we performed a computational analysis establishing a complete atlas of shared identical sequences across the human and murine proteomes. Unlike bacterial or viral antigens, self-antigens, including tumor-associated antigens (TAAs), frequently contain sequences of sufficient length to generate identical epitopes in other self-proteins. Epitopes from these shared sequences can theoretically reduce target specificity, confound immunomonitoring studies, and contribute to pre-existing immune tolerance toward TAAs. Notably, a subset of TAAs identified in this atlas is free of this drawback, providing a new criterion for antigen prioritization in cancer immunotherapy. To facilitate the detection of shared sequences, a web server has been made available at https:\/\/epitopemapper.ircan.org\/ and the open-source code at https:\/\/github.com\/IRCAN\/EpitopeMapper.<\/jats:p>","DOI":"10.1093\/nargab\/lqag060","type":"journal-article","created":{"date-parts":[[2026,6,7]],"date-time":"2026-06-07T11:34:46Z","timestamp":1780832086000},"source":"Crossref","is-referenced-by-count":0,"title":["Comprehensive mapping of identical sequences across human proteins emphasizes the widespread issue of shared epitopes in self-antigens"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-4047-6476","authenticated-orcid":false,"given":"Guillaume","family":"Kellermann","sequence":"first","affiliation":[{"name":"Telomium SAS , Ivry-sur-Seine 94200 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7342-3157","authenticated-orcid":false,"given":"Olivier","family":"Croce","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre national de la recherche scientifique (CNRS), Institut national de la sant\u00e9 et de la recherche m\u00e9dicale (INSERM), Institut Hospitalo-Universitaire (IHU) RespirERA, F\u00e9d\u00e9ration Hospitalo-Universitaire (FHU) OncoAge , Nice ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1025-3429","authenticated-orcid":false,"given":"Baharia","family":"Mograbi","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre national de la recherche scientifique (CNRS), Institut national de la sant\u00e9 et de la recherche m\u00e9dicale (INSERM), Institut Hospitalo-Universitaire (IHU) RespirERA, F\u00e9d\u00e9ration Hospitalo-Universitaire (FHU) OncoAge , Nice ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0431-9353","authenticated-orcid":false,"given":"Paul","family":"Hofman","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre national de la recherche scientifique (CNRS), Institut national de la sant\u00e9 et de la recherche m\u00e9dicale (INSERM), Institut Hospitalo-Universitaire (IHU) RespirERA, F\u00e9d\u00e9ration Hospitalo-Universitaire (FHU) OncoAge , Nice ,","place":["France"]},{"name":"Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire (CHU) de Nice , IHU RespirERA, FHU OncoAge, Biobank BB-0033-00025, Nice ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1252-4747","authenticated-orcid":false,"given":"Patrick","family":"Brest","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre national de la recherche scientifique (CNRS), Institut national de la sant\u00e9 et de la recherche m\u00e9dicale (INSERM), Institut Hospitalo-Universitaire (IHU) RespirERA, F\u00e9d\u00e9ration Hospitalo-Universitaire (FHU) OncoAge , Nice ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,22]]},"reference":[{"key":"2026062205180038800_B1","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1093\/bioinformatics\/btw567","article-title":"Assessment of cancer and virus antigens for cross-reactivity in human tissues","volume":"33","author":"Jaravine","year":"2017","journal-title":"Bioinforma Oxf Engl"},{"key":"2026062205180038800_B2","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1186\/s12859-023-05606-4","article-title":"PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins","volume":"24","author":"Marrama","year":"2023","journal-title":"BMC Bioinformatics"},{"key":"2026062205180038800_B3","doi-asserted-by":"publisher","first-page":"e012217","DOI":"10.1136\/jitc-2025-012217","article-title":"Shared epitopes create safety and efficacy concerns in several cancer vaccines","volume":"13","author":"Kellermann","year":"2025","journal-title":"J Immunother Cancer"},{"key":"2026062205180038800_B4","doi-asserted-by":"publisher","first-page":"1677","DOI":"10.4049\/jimmunol.2200798","article-title":"Presentation of human neural stem cell antigens drives regulatory T cell induction","volume":"210","author":"Greilach","year":"2023","journal-title":"J Immunol Baltim Md 1950"},{"key":"2026062205180038800_B5","doi-asserted-by":"publisher","first-page":"111","DOI":"10.4049\/jimmunol.1002612","article-title":"Minimal tolerance to a tumor antigen encoded by a cancer-germline gene","volume":"188","author":"Huijbers","year":"2012","journal-title":"J Immunol Baltim Md 1950"},{"key":"2026062205180038800_B6","doi-asserted-by":"publisher","first-page":"739","DOI":"10.4049\/jimmunol.169.2.739","article-title":"The majority of immunogenic epitopes generate CD4+ T cells that are dependent on MHC class II-bound peptide-flanking residues","volume":"169","author":"Arnold","year":"2002","journal-title":"J Immunol Baltim Md 1950"},{"key":"2026062205180038800_B7","doi-asserted-by":"publisher","first-page":"112827","DOI":"10.1016\/j.celrep.2023.112827","article-title":"Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4+ T cell immunity","volume":"42","author":"Chen","year":"2023","journal-title":"Cell Rep"},{"key":"2026062205180038800_B8","doi-asserted-by":"publisher","first-page":"e129152","DOI":"10.1172\/jci.insight.129152","article-title":"Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection","volume":"4","author":"Ebrahimi-Nik","year":"2019","journal-title":"JCI Insight"},{"key":"2026062205180038800_B9","doi-asserted-by":"publisher","first-page":"e142823","DOI":"10.1172\/JCI142823","article-title":"An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection","volume":"131","author":"Brennick","year":"2021","journal-title":"J Clin Invest"},{"key":"2026062205180038800_B10","doi-asserted-by":"publisher","first-page":"e176740","DOI":"10.1172\/JCI176740","article-title":"Cancer neoepitopes viewed through negative selection and peripheral tolerance: a new path to cancer vaccines","volume":"134","author":"Srivastava","year":"2024","journal-title":"J Clin Invest"},{"key":"2026062205180038800_B11","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1074\/mcp.M600310-MCP200","article-title":"Distorted relation between mRNA copy number and corresponding major histocompatibility complex ligand density on the cell surface","volume":"6","author":"Weinzierl","year":"2007","journal-title":"Mol Cell Proteomics"},{"key":"2026062205180038800_B12","doi-asserted-by":"publisher","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 Immunother Hagerstown Md"},{"key":"2026062205180038800_B13","doi-asserted-by":"publisher","first-page":"e36634","DOI":"10.1371\/journal.pone.0036634","article-title":"Do natural proteins differ from random sequences polypeptides? Natural vs. random proteins classification using an evolutionary neural network","volume":"7","author":"De\u00a0Lucrezia","year":"2012","journal-title":"PLoS One"},{"key":"2026062205180038800_B14","doi-asserted-by":"publisher","first-page":"29419","DOI":"10.1038\/srep29419","article-title":"Exploring the induction of preproinsulin-specific Foxp3(+) CD4(+) Treg cells that inhibit CD8(+) T cell-mediated autoimmune diabetes by DNA vaccination","volume":"6","author":"Stifter","year":"2016","journal-title":"Sci Rep"},{"key":"2026062205180038800_B15","doi-asserted-by":"publisher","first-page":"3122","DOI":"10.4049\/jimmunol.180.5.3122","article-title":"Tumor-specific CD4+ T cells render the tumor environment permissive for infiltration by low-avidity CD8+ T cells","volume":"180","author":"Wong","year":"2008","journal-title":"J Immunol Baltim Md 1950"},{"key":"2026062205180038800_B16","doi-asserted-by":"publisher","first-page":"4","DOI":"10.32607\/20758251-2019-11-4-4-12","article-title":"The contribution of major histocompatibility complex class ii genes to an association with autoimmune diseases","volume":"11","author":"Zakharova","year":"2019","journal-title":"Acta Naturae"},{"key":"2026062205180038800_B17","doi-asserted-by":"publisher","first-page":"2460276","DOI":"10.1080\/2162402X.2025.2460276","article-title":"Identification of TTLL8, POTEE, and PKMYT1 as immunogenic cancer-associated antigens and potential immunotherapy targets in ovarian cancer","volume":"14","author":"Bassoy","year":"2025","journal-title":"OncoImmunology"},{"key":"2026062205180038800_B18","doi-asserted-by":"publisher","first-page":"5323","DOI":"10.1158\/1078-0432.CCR-09-0737","article-title":"The prioritization of cancer antigens: a National Cancer Institute pilot project for the acceleration of translational research","volume":"15","author":"Cheever","year":"2009","journal-title":"Clin Cancer Res Off J Am Assoc Cancer Res"},{"key":"2026062205180038800_B19","doi-asserted-by":"publisher","first-page":"2425","DOI":"10.1093\/jimmun\/vkaf090","article-title":"Defining key parameters of therapeutic activity using mouse cancer neoepitopes","volume":"214","author":"Singhaviranon","year":"2025","journal-title":"J Immunol"},{"key":"2026062205180038800_B20","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1038\/s41586-020-2537-9","article-title":"An RNA vaccine drives immunity in checkpoint-inhibitor-treated melanoma","volume":"585","author":"Sahin","year":"2020","journal-title":"Nature"},{"key":"2026062205180038800_B21","doi-asserted-by":"publisher","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 cells","volume":"5","author":"Cameron","year":"2013","journal-title":"Sci Transl Med"},{"key":"2026062205180038800_B22","doi-asserted-by":"publisher","first-page":"100946","DOI":"10.1016\/j.xgen.2025.100946","article-title":"Benchmarking of T cell receptor-epitope predictors with ePytope-TCR","volume":"5","author":"Drost","year":"2025","journal-title":"Cell Genomics"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/2\/lqag060\/68569236\/lqag060.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/2\/lqag060\/68569236\/lqag060.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T09:18:12Z","timestamp":1782119892000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqag060\/8712973"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,27]]},"references-count":22,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,3,27]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqag060","relation":{},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,6]]},"published":{"date-parts":[[2026,3,27]]},"article-number":"lqag060"}}