Single-Cell Modeling of CD8+ T Cell Exhaustion Predicts Response to Cancer Immunotherapy

Abstract

Accurate prediction of response to immune checkpoint blockade (ICB) and simultaneous development of new efficacious ICB strategy are unmet needs for cancer immunotherapy1-5. Despite the advance of existing clinical or computational biomarkers6-10, it is very limited in explicating phenotypic variability of tumor-infiltrating CD8+ T lymphocytes (TILs) at the single-cell level, including tumor-specificity11,12 and distinct exhaustion profiles13-16, that are crucial for the responsiveness to ICB. Here we show that a quantitative criterion, D value, for evaluating tumor-specific TIL exhaustion, identified by our new high-dimensional single-cell-based computational method, called HD-scMed, accurately predicts response to the ICB, i.e., PD-1, CTLA-4, and PD-1+CTLA-4, with the performance of AUC=100% in human tumors. D-value is the Euclidean distance from a subset of exhausted CD8+ TILs, identified as Pareto Front (PF)18-21 by HD-scMed within the high-dimensional expression space of a variety of exhaustion markers, to the baseline TILs excluded by the PF. We phenotypically distinguished two types of TIL \"exhaustion\" by the D value, namely \"D Extremely-high\" in non-responders, associating with high tumor-specificity imprinted with enhanced exhaustion and inactivated effector and cytotoxic signatures; and \"D low\" specific to responders, alternatively enriched with T cell activation and cytolytic effector T cell signatures. We also observed a large portion of \"D negative\" bystander T cells irrelevant to response. Notably, D-low TILs in clinical responders display very low LAG3 expression. To reverse the functionality of the LAG3-high TILs after receiving PD-1+CTLA-4, we combined LAG3 with PD-1+CTLA-4 in treating a murine tumor model. Remarkably, LAG3+PD-1+CTLA-4 displays extraordinary antitumor efficacy to eradicate advanced tumors, which is associated with burst GZMBhi TIL populations; whereas PD-1+CTLA-4 or PD-1+CTLA-4 plus other ICBs as control only induce moderate tumor growth inhibition. Our study has important implications for cancer immunotherapy as providing both accurate predictions of ICB response and alternative strategy to reverse ICB resistance.