Functional Deorphanization of Tumor-reactive TCRs Uncovers a Landscape of Shared, Immune Dominant Antigens across Cancers

Abstract

Single-cell sequencing has charted the clonal landscape of tumor-infiltrating T cells, but the antigens that drive these responses remain largely undefined, limiting rational immunotherapy design. Here, we introduce TWISTAR, a platform that systematically deorphanizes single-cell-derived TCRs against tumor transcriptomes. By directly validating TCR engagement, TWISTAR exclusively recovers functionally immunogenic antigens. Applying TWISTAR to melanoma, breast, and hepatocellular carcinoma patients responding to immune checkpoint blockade, we uncover that tumor-reactive TCRs recognize a broad repertoire of immunogenic targets beyond neoantigens, including peptides derived from unannotated coding sequences and novel transcripts. Many of these antigens are shared across patients and cancer types, revealing communal targets. Furthermore, we observe immune dominance, consisting of multiple clones converging on few immune dominant epitopes. Together, these findings reveal an unexpectedly broad landscape of tumor immunogenicity, expanding opportunities for the development of pan-cancer vaccines.