Single Cell Analyses Reveal a Functionally Heterogeneous Exhausted CD8+ T Cell Subpopulation that is Correlated with Response to Checkpoint Therapy in Melanoma

Abstract

PD-1 pathway inhibitors have revolutionized cancer therapy. However, most patients do not durably benefit, highlighting the need for biomarkers to stratify patients as responders or non-responders. While CD8+ tumor infiltrating lymphocytes (TILs) have been associated with immune checkpoint therapy response, there is not a consensus on which CD8+ TIL subpopulations have the most prognostic value. Preclinical studies have focused on progenitor-like exhausted CD8+ T cells (TPEX), since TPEX proliferate more in response to PD-1 inhibitors than other exhausted T cell (TEX) subpopulations. However, immune checkpoint inhibitor (ICI) treatment drives TPEX differentiation into other TEX populations that can mediate anti-tumor immunity. These data complicate the ability to identify prognostically important T cell populations in patients that predict ICI treatment response. In this study, we found that advanced melanoma patients with ≥20% of CD8+ TILs co-expressing PD-1 and CTLA-4 (termed CPHi TILs) had better objective response rates and survival following PD-1 monotherapy than those below this threshold. Characterization of the CPHi TIL subset using bulk and single cell RNA sequencing showed that while TPEX-like cells were present within the CPHi subset, they were in the minority of these cells. Rather, the CPHi population was numerically dominated by other subsets, including cycling, terminally exhausted, cytotoxic-like, and/or resident memory-like TEX populations, and a subset enriched for glycolytic genes. Collectively, these data show that CPHi TILs correlate with response in melanoma, but this TIL subset is a heterogenous mix of different subpopulations that may differentially contribute to anti-tumor immunity following checkpoint blockade.