Epigenetic Determinants of CD8+ T Cell Exhaustion

Abstract

T cell exhaustion describes an acquired dysfunction common in settings of chronic viral infection. Despite clinical efforts to rescue exhaustion, the fundamental mechanisms specifying this state, and the potential for reprogramming exhausted T cells, remain poorly understood. Since the epigenome can govern cell state, we profiled accessible chromatin in exhausted CD8+ T cells. Exhausted cells acquired a state-specific landscape of enhancers that profoundly differed from functional memory. Comparison of mouse cells to those isolated from HCV and HIV infection identified a conserved epigenetic program of exhaustion. Critically, CD8+ tumor infiltrating lymphocytes (TILs) also shared epigenetic and transcriptional features with chronic viral infection, suggesting that T cell exhaustion is a fundamental adaptation to settings of chronic stimulation. Having established that exhausted T cells acquire distinct regulatory regions, we then asked whether that epigenetic state is fixed or plastic following resolution of chronic infection. Longitudinal analysis of HCV-specific CD8+ T cells after curative therapy showed that canonical features of exhaustion, including super-enhancers near key transcription factors, were fixed and did not resolve long-term. Furthermore, anti-PD-1 therapy, which is thought to reinvigorate exhausted TILs by blocking inhibitory signaling, could not reverse the exhausted epigenetic profile. T cell exhaustion is therefore a stable epigenetic state that is not rescued by common treatment modalities. We then sought new strategies to modulate T cell exhaustion. First, we used Cas9-mediated genome editing of an exhaustion-specific enhancer to show its requirement for sustained PD-1 expression. This highlights the potential for tuning regulators of exhaustion through enhancer perturbation. Second, we characterized heterogeneity within exhaustion and found a subpopulation of “progenitor-exhausted” T cells that retained polyfunctionality, were better able to control tumor growth and could uniquely respond to anti-PD-1. Melanoma patients with increased progenitor-exhausted TILs experienced longer responses to checkpoint inhibitors, suggesting that expanding specific subsets of exhausted T cells may improve outcomes. Our studies delineate the epigenetic determinants of T cell exhaustion, including its shared features across disease contexts and the effects of therapeutic intervention. Together, they suggest that ameliorating T cell exhaustion may require novel approaches to increase epigenetic plasticity and/or expand specific subsets of exhausted T cells.