Paper

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment

Osmaan Shahid, Chow, Melissa, Pauken, Kristen E, Mahuron, Kelly M, Schenkel, Jason M, Delaney, Conor, Long, Jaclyn M, Sharpe, Arlene H, Huang, Linglin, Rosenblum, Michael D, Tsai, Katy K, Kuchroo, Juhi R, Newcomer, Kathleen, Daud, Adil I, Burke, Kelly P, Fung, Megan E, Guinn, Samantha, Lowe, Margaret M, Lagattuta, Kaitlyn A, Luber, Jacob M, Singer, Meromit

2020

Overview

Abstract The ability to monitor anti-tumor CD8+ T cell responses in the blood has tremendous therapeutic potential. Here, we used paired single-cell RNA sequencing and T cell receptor (TCR) sequencing to detect and characterize “tumor matching” (TM) CD8+ T cells in the blood of mice with MC38 tumors and melanoma patients using the TCR as a molecular barcode. TM cells showed increased activation compared to non-matching T cells in blood, and appeared less exhausted than matching counterparts in tumor. Importantly, PD-1, which has been used to identify putative circulating anti-tumor CD8+ T cells, showed poor sensitivity for identifying TM cells. By leveraging the transcriptome we identified candidate cell surface marker panels for TM cells in mice and melanoma patients, and validated NKG2D, CD39, and CX3CR1 in mice. These data demonstrate that the TCR can be used to identify tumor-relevant populations for comprehensive characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells. Summary Using single-cell RNA-sequencing coupled with TCR sequencing, we detected CD8+ T cell clones shared between blood and tumor in mice and melanoma patients, characterized these matching clones in blood and tumor, and identified potential biomarkers for their isolation in blood. Competing Interest Statement The authors declare the enclosed potential conflicts of interest. M.D.R. is a founder of TRex Bio and Sitryx Bio and receives research funding from Abbvie, LEO Pharma, and TRex bio. A.I.D. has funds from Merck, Oncosec, BMS, Roche, Genentech, Pfizer, Incyte, Novartis and Checkmate, is on advisory boards for Xencor, Pfizer, Array, has stock in TRex, SQZ bio., and patents with Oncosec on Gene Therapy of melanoma. A.H.S. has patents on the PD-1 pathway licensed by Roche/Genentech and Novartis, consults for Novartis, is on the scientific advisory boards for Surface Oncology, Sqz Biotech, Elstar Therapeutics, Elpiscience, Selecta and Monopteros, and has research funding from Merck, Novartis, Roche, and Quark Ventures. K.K.T discloses institutional research funding from Array/Pfizer, BMS, Oncosec, Regeneron, and Replimune. From August 4th 2020, MS is an employee of Guardant Health. The authors have no additional financial conflicts of interest to disclose. Footnotes * ↵+ co-first authors

• Publisher: Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
• Subject: Blood / CD8 antigen / Cell activation / Cell surface / Cloning / CX3CR1 protein / Gene expression / Gene therapy / Immunology / Lymphocytes / Lymphocytes T / Melanoma / PD-1 protein / Research funding / Surface markers / T cell receptors / Transcription / Transcriptomes / Tumors