{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T02:08:52Z","timestamp":1780106932342,"version":"3.54.0"},"posted":{"date-parts":[[2026,5,22]]},"group-title":"Cancer Biology","reference-count":60,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T00:00:00Z","timestamp":1779408000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,5,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Immune checkpoint inhibition (ICI) is clinically active against multiple cancers, including urothelial cancer at the non-muscle invasive, muscle-invasive, and metastatic stages. Despite this, large numbers of patients experience disease progression and relapse after treatment with ICI-containing regimens. Tumor antigen-specific T cells are critical to ICI response, however few studies have evaluated the breadth and magnitude of tumor antigen-specific T cell responses with ICI therapy. In this study, we mapped the tumor antigen immunodominance hierarchy in the BBN963 model of murine basal-like bladder cancer for endogenous tumor neoantigens expressed physiologically. We used a high-throughput matrixed ELISpot assay to detect CD8\n                  <jats:sup>+<\/jats:sup>\n                  T cell responses to predicted BBN963 tumor antigens derived from multiple mutational genomic sources. We found CD8+ T cell responses were directed against a subset of tumor antigens forming a stable and reproducible immunodominance hierarchy across individual mice. Treatment with anti-PD-1 or anti-CTLA-4 did not substantially reshape this hierarchy or broadly shift dominant responses to previously defined subdominant epitopes. Predicted peptide MHC binding stability and affinity was associated with antigen immunogenicity. Cancer-testis antigens, endogenous retroviral antigens, and SNV-derived tumor antigens that were immunogenic were found across tumor subclones. By diversifying the immunogenic antigen repertoire beyond SNVs, we achieved nearly 100% tumor subclone coverage, suggesting that broader antigen selection could help immunotherapy target more tumor subclones. In conclusion, this study supports the stability of the immunodominance hierarchy under ICI therapy and a role for broadening antigen discovery to multiple expressional sources in immunotherapy design.\n                <\/jats:p>","DOI":"10.64898\/2026.05.20.726664","type":"posted-content","created":{"date-parts":[[2026,5,23]],"date-time":"2026-05-23T06:05:16Z","timestamp":1779516316000},"source":"Crossref","is-referenced-by-count":0,"title":["Immunodominance Hierarchy of Endogenous BBN963 Bladder Cancer Antigens Remains Stable Under Anti-PD1 and Anti-CTLA4 Immunotherapy"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3063-6064","authenticated-orcid":false,"given":"Misha S.","family":"Fini","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA, 27514"},{"name":"Lineberger Comprehensive Cancer Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA, 27514"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica R.","family":"Alley","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA, 27514"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9399-5999","authenticated-orcid":false,"given":"Steven P.","family":"Vensko","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA, 27514"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5819-7561","authenticated-orcid":false,"given":"Dhuvarakesh","family":"Karthikeyan","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA, 27514"},{"name":"Department of Bioinformatics and Computational Biology, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA, 27514"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4120-8708","authenticated-orcid":false,"given":"Jin Seok","family":"Lee","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA, 27514"},{"name":"Department of Bioinformatics and Computational Biology, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA, 27514"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason A.","family":"Garness","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA, 27514"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-8420-4766","authenticated-orcid":false,"given":"Emily","family":"Paul","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, Moffitt 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