Qualitative Analysis of Tumor-Infiltrating Lymphocytes across Human Tumor Types Reveals a Higher Proportion of Bystander CD8(+) T Cells in Non-Melanoma Cancers Compared to Melanoma

SIMPLE SUMMARY: Human tumors are often infiltrated by T cells; however, it remains unclear what proportion of T cells infiltrating tumors are bystander and non-tumor specific. We have investigated qualitative characteristics of these tumor-infiltrating lymphocytes (TILs) based on their gene-expression in the tumor-microenvironment or on their response to autologous tumor cells in vitro. Despite a considerable inter-sample variability, we found the overall proportion of bystander (non-tumor reactive) TILs to be remarkably high. Importantly, we observed a higher proportion of bystander TILs in non-melanoma tumors, compared to melanoma. This study suggests that immunotherapeutic strategies, especially when applied to non-melanoma tumors, should be tailored to reinvigorate the small proportion of tumor-reactive T cells infiltrating the tumor-microenvironment. ABSTRACT: Background: Human intratumoral T cell infiltrates can be defined by quantitative or qualitative features, such as their ability to recognize autologous tumor antigens. In this study, we reproduced the tumor-T cell interactions of individual patients to determine and compared the qualitative characteristics of intratumoral T cell infiltrates across multiple tumor types. Methods: We employed 187 pairs of unselected tumor-infiltrating lymphocytes (TILs) and autologous tumor cells from patients with melanoma, renal-, ovarian-cancer or sarcoma, and single-cell RNA sequencing data from a pooled cohort of 93 patients with melanoma or epithelial cancers. Measures of TIL quality including the proportion of tumor-reactive CD8(+) and CD4(+) TILs, and TIL response polyfunctionality were determined. Results: Tumor-specific CD8(+) and CD4(+) TIL responses were detected in over half of the patients in vitro, and greater CD8(+) TIL responses were observed in melanoma, regardless of previous anti-PD-1 treatment, compared to renal cancer, ovarian cancer and sarcoma. The proportion of tumor-reactive CD4(+) TILs was on average lower and the differences less pronounced across tumor types. Overall, the proportion of tumor-reactive TILs in vitro was remarkably low, implying a high fraction of TILs to be bystanders, and highly variable within the same tumor type. In situ analyses, based on eight single-cell RNA-sequencing datasets encompassing melanoma and five epithelial cancers types, corroborated the results obtained in vitro. Strikingly, no strong correlation between the proportion of CD8(+) and CD4(+) tumor-reactive TILs was detected, suggesting the accumulation of these responses in the tumor microenvironment to follow non-overlapping biological pathways. Additionally, no strong correlation between TIL responses and tumor mutational burden (TMB) in melanoma was observed, indicating that TMB was not a major driving force of response. No substantial differences in polyfunctionality across tumor types were observed. Conclusions: These analyses shed light on the functional features defining the quality of TIL infiltrates in cancer. A significant proportion of TILs across tumor types, especially non-melanoma, are bystander T cells. These results highlight the need to develop strategies focused on the tumor-reactive TIL subpopulation.