Multi-cancer comparative multi-omics approach reveals a permissive tumor microenvironment in renal cell carcinoma through accumulation of exhausted CD8+ and CD4+CD8+ double positive T cells 2661

Abstract Description Introduction Renal cell carcinoma (RCC) is responsive to immunotherapy despite having a low tumor mutational burden. Interestingly, the degree of CD8+ T cell infiltration in RCC negatively correlates with outcomes, suggesting that a deeper understanding of the tumor microenvironment may provide critical insight to help improve clinical outcomes. Methods We conducted a multi-omics approach including flow cytometry, multiplex immunohistochemistry, and single-cell RNA-seq to compare immune cell composition, gene expression, spatial distribution, and cell-cell interactions among a cohort of primary breast cancer, head and neck squamous cell carcinoma, non-small cell lung cancer, and RCC specimens. Results Flow cytometry analysis of tumor-infiltrating lymphocytes (TILs) revealed increased exhausted CD8 + (Tex) and CD4+CD8+ double positive (DP) T cells and decreased CD4+ T cells including regulatory T (Treg) cells in RCC samples compared to other tumor types. scRNA-seq analysis of TILs confirmed these results and showed Tex cells as a major population of CD8+ T cells. Using biomarkers for tumor-reactive cells including 4-1BB, CD39, and CD103 along with a gene signature to identify neo-antigen reactive T cells, we found that the Tex population contained putative tumor-reactive T cells and were not merely bystander cells. Conclusion Exhausted CD8+ and DP T cells in RCC contain tumor-reactive T cells and may represent a novel cell population capable of targeting RCC. Funding Sources Funding: Funding was provided by a sponsored research grant from GlaxoSmithKline, the Providence Portland Medical Foundation, and the M. J. Murdock Charitable Trust. Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)