Abstract IA-02: The tumor-reactive CD8+ T-cell repertoire in pancreatic cancer as revealed by single-cell sequencing

Abstract We recently reported on the analysis of the tumor-infiltrating T-cell repertoire in human pancreatic cancer by means of single cell RNA-sequencing (scRNA-seq), demonstrating the presence of expanded tumor-reactive CD8+ TCR clonotypes in these tumors (Sci Transl Med 2023 Nov 15;15 (722): eadh9562). In view of the low numbers of somatic mutations in pancreatic cancer, we chose to perform an unbiased screening against autologous tumor cells rather than against predicted mutanome-encoded neoepitopes as performed in other recent studies. Systematical testing of tumor-reactive TCRs against predicted neoepitopes thus far did not result in hits, suggesting that linear, mutanome-encoded peptides may not represent the immunodominant T cell epitopes targeted by the natural T-cell response. In parallel, we conducted a similar analysis of the tumor-infiltrating T-cell repertoire in two distinct syngeneic mouse models for pancreatic cancer from which we isolated 100 tumor-reactive TCRs. While some of these TCRs were exclusively reactive against the tumor of origin, we found most to react against recurrent tumor antigens. By means of immunopeptidome analyses, we identified a number of T-cell epitopes that reflect this reactivity pattern: a ‘private’ mutanome-encoded neoepitope and several epitopes derived from over-expressed tumor-associated autoantigens. In a third, complementary study, we addressed the question whether T-cell receptors (TCRs) raised through immunization with tumor-specific neoepitopes, as identified by mutanome analysis and HLA-peptide binding algorithms in human pancreatic cancer, would duly mediate T-cell reactivity against the autologous tumors in which the epitope-encoding mutations were identified. We therefore immunized humanized (human TCR-locus, HLA-transgenic) mice with synthetic peptides representing 18 carefully selected candidate neoepitopes. For 4 of these epitopes, we successfully isolated fully human TCRs that specifically recognize naturally processed neoepitopes on tumor cells. Taken together, our studies demonstrate that pancreatic cancer can be targeted by T-cells directed against neoepitopes and tumor-associated autoantigens, but also raise important questions concerning the pros and cons of these options. Citation Format: Rienk Offringa. The tumor-reactive CD8+ T-cell repertoire in pancreatic cancer as revealed by single-cell sequencing abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84 (17 Suppl₂): Abstract nr IA-02.