Lung tumor–infiltrating T_reghave divergent transcriptional profiles and function linked to checkpoint blockade response

Abstract

Regulatory T cells (T_reg) are conventionally viewed as suppressors of endogenous and therapy-induced antitumor immunity; however, their role in modulating responses to immune checkpoint blockade (ICB) is unclear. In this study, we integrated single-cell RNA-seq/T cell receptor sequencing (TCRseq) of >73,000 tumor-infiltrating T_reg (TIL-T_reg) from anti-PD-1-treated and treatment-naive non-small cell lung cancers (NSCLC) with single-cell analysis of tumor-associated antigen (TAA)-specific T_reg derived from a murine tumor model. We identified 10 subsets of human TIL-T_reg, most of which have high concordance with murine TIL-T_reg subsets. Only one subset selectively expresses high levels of <i>TNFRSF4</i> (OX40) and <i>TNFRSF18</i> (GITR), whose engangement by cognate ligand mediated proliferative programs and NF-κB activation, as well as multiple genes involved in T_reg suppression, including <i>LAG3</i>. Functionally, the OX40^hiGITR^hi subset is the most highly suppressive ex vivo, and its higher representation among total TIL-T_reg correlated with resistance to PD-1 blockade. Unexpectedly, in the murine tumor model, we found that virtually all TIL-T_reg-expressing T cell receptors that are specific for TAA fully develop a distinct T_H1-like signature over a 2-week period after entry into the tumor, down-regulating <i>FoxP3</i> and up-regulating expression of <i>TBX21 (</i>Tbet)<i>, IFNG</i>, and certain proinflammatory granzymes. Transfer learning of a gene score from the murine TAA-specific T_H1-like T_reg subset to the human single-cell dataset revealed a highly analogous subcluster that was enriched in anti-PD-1-responding tumors. These findings demonstrate that TIL-T_reg partition into multiple distinct transcriptionally defined subsets with potentially opposing effects on ICB-induced antitumor immunity and suggest that TAA-specific TIL-T_reg may positively contribute to antitumor responses.