Multi-dimensional analysis of tumor-specific and bystander CD8+ tumor infiltrating lymphocytes with TetTCR-SeqHD

Abstract

Abstract Objective Antigen specific CD8+ T cells were isolated from primary tumor tissue and analyzed for on the single cell level to determine tumor-specific signatures for further study. Methods Primary tumor, metastatic lesions, adjacent healthy tissue and peripheral blood were from collected from patients at Dell Seton Medical Center at the University of Texas. Matched tumor and healthy samples underwent exome and RNA sequencing to allow prediction of tumor-specific epitopes. We then synthesized DNA-barcoded tetramers for all predicted tumor associated-epitopes and an HLA-matched library of exogenous epitopes. Tetramer stained CD8+ T cells were then sorted and analyzed by TetTCR-SeqHD, a technology that we recently developed to link TCR antigen specificity, TCR sequence, gene expression, and phenotype of single T cells. Results We analyzed ~2900 tumor infiltrating lymphocytes (TILs) and T cells from adjacent healthy tissue and observed enrichment for cytotoxic effector and tissue resident memory cells within the tumor versus the healthy tissues. We also note an enrichment of bystander cells, specifically those reactive to Epstein Barr Virus epitopes, within the cytotoxic cluster. Finally, we analyze the distribution and differential expression between tumor-specific lymphocytes and bystander T cells, noting reduced expression of CD57 and CD49d in the tumor-specific TILs, as previously described. Conclusions We validate the use of TetTCR-SeqHD for gaining insight into phenotypic and gene expression differences between bystander and tumor-specific TILs. We identified markers for future exploration and demonstrate key differences between shared clonal populations within healthy and cancerous tissues.