Dynamic chromatin regulatory landscape of human CAR T cell exhaustion

Abstract

Significance T cell exhaustion is a major barrier to cancer immunotherapy. T cell exhaustion is the state of T cell dysfunction after chronic stimulation, and recent studies indicate that exhaustion is epigenetically controlled and associated with unique chromatin profiles. This work reports the genome-wide map of active DNA regulatory elements and their connection to genes in the time course of human chimeric antigen receptor T cell exhaustion. Early chromatin events establish the later program of gene expression, active elements are often human-specific, and exhaustion-associated enhancers can be manipulated to precisely control the level of inhibitory receptors on T cells. Dysfunction in T cells limits the efficacy of cancer immunotherapy. We profiled the epigenome, transcriptome, and enhancer connectome of exhaustion-prone GD2-targeting HA-28z chimeric antigen receptor (CAR) T cells and control CD19-targeting CAR T cells, which present less exhaustion-inducing tonic signaling, at multiple points during their ex vivo expansion. We found widespread, dynamic changes in chromatin accessibility and three-dimensional (3D) chromosome conformation preceding changes in gene expression, notably at loci proximal to exhaustion-associated genes such as PDCD1, CTLA4, and HAVCR2, and increased DNA motif access for AP-1 family transcription factors, which are known to promote exhaustion. Although T cell exhaustion has been studied in detail in mice, we find that the regulatory networks of T cell exhaustion differ between species and involve distinct loci of accessible chromatin and cis-regulated target genes in human CAR T cell exhaustion. Deletion of exhaustion-specific candidate enhancers of PDCD1 suppress the expression of PD-1 in an in vitro model of T cell dysfunction and in HA-28z CAR T cells, suggesting enhancer editing as a path forward in improving cancer immunotherapy.