Project: PRJNA928413
Gamma delta (γδ) 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 Vδ2- γδ T cells, with equivalent representation of Vδ1+ and Vδ1- cells, that are distinct from γδ T cells found in normal human tissues. These tumor-resident Vδ2- 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 Vδ2- γδ T cells have blunted IL-2 production, they retain expression of cytolytic effector molecules and costimulatory receptors like 4-1BB. Exhausted Vδ2- γδ T cells are comprised of three distinct populations that lack TCF-7, are clonally expanded, express of cytotoxic molecules, and possess multiple Vδ2- TCRs. Human tumor-derived Vδ2- γδ T cells maintain cytotoxic function and pro-inflammatory cytokine secretion in vitro. The transcriptional program of Vδ2- T cells in pre-treatment tumor biopsies predicted subsequent clinical responses to PD-1 blockade in vivo in cancer patients. Thus, Vδ2- γδ 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).
General