Abstract CD8+ T cell infiltration into solid tumors has been shown to correlate with patient prognosis in numerous carcinomas. Furthermore, response to checkpoint blockade therapies has been linked to an induction of T cell function and rescue of T cell exhaustion in patients. Expression of both PD-1 and CD39 on exhausted CD8+ T cells has been described in murine models of chronic disease and recently human carcinomas. Here we profile breast tumor, melanoma, and chronic lymphocytic leukemia (CLL) for the frequency and phenotype of exhausted CD8+ T cells. We find that the frequency of exhausted CD8+ T cells is highest in melanoma among these tumor types which may suggest correlation with mutational burden. Functional analysis of PD-1+ CD39+ cells in human tumors shows significant reduction of IFNγ, TNFα, and IL-2 production as assessed by intracellular flow cytometry. Further phenotyping of exhausted CD8+ T cells revealed a loss of expression of both the IL-7 receptor alpha (CD127) and KLRG1, suggesting terminal differentiation of these cells. PD-1+ CD39+ T cells also expressed CD103 suggesting potential similarities with differentiation into a peripheral resident memory phenotype. Indeed PD-1+ CD39+ exhausted T cells were only identified in peripheral tissues where cancer cells were present, such as solid tumors, tumor positive tumor draining lymph nodes, and one CLL patient, but not identified in the circulation or tumor negative tumor draining lymph nodes of patients. Finally, single cell and T cell receptor sequencing revealed distinct transcriptional and clonal signatures of PD-1+ CD39+ CD8+ T cells suggesting them to be a unique population in response to tumor antigen.
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