Exhausted intratumoral Vd2- ?d T cells in human kidney cancer retain effector function [bulk RNA-seq]

Gamma delta (?d) T cells reside within human tissues including tumors, but their role in mediating anti-tumor response with immune checkpoint inhibition is unknown. Using single-cell approaches, we found that kidney cancers are infiltrated by diverse Vd2- ?d T cells, with equivalent representation of Vd1+ and Vd1- cells, that are distinct from ?d T cells found in normal human tissues. These tumor-resident Vd2- T cells can express the transcriptional program of exhausted alpha beta (ab) CD8+ T cells as well as canonical markers of terminal T cell exhaustion including PD-1, TIGIT and TIM-3. While Vd2- ?d T cells have blunted IL-2 production, they retain expression of cytolytic effector molecules and costimulatory receptors like 4-1BB. Exhausted Vd2- ?d T cells are comprised of three distinct populations that lack TCF-7, are clonally expanded, express of cytotoxic molecules, and possess multiple Vd2- TCRs. Human tumor-derived Vd2- ?d T cells maintain cytotoxic function and pro-inflammatory cytokine secretion in vitro. The transcriptional program of Vd2- T cells in pre-treatment tumor biopsies predicted subsequent clinical responses to PD-1 blockade in vivo in cancer patients. Thus, Vd2- ?d T cells within the tumor microenvironment can contribute to anti-tumor efficacy. Overall design: Tumor samples were obtained from resection surgery from 6 adult patients with histologically confirmed renal cell carcinoma (RCC). Samples were minced and digested, then FACS-sorted for live gd, CD4, and CD8 T cells. Bulk RNA libraries were constructed using the Smart-seq2 protocol and sequenced on an Illumina HiSeq 4000. The sequenced data was used to generate a variant call format (VCF) file containing single-nucleotide polymorphism (SNP) data for each patient (used later by Demuxlet to demultiplex pooled scRNA data generated from the same tumor samples).