Fundamentals to therapeutics: Epigenetic modulation of CD8+ T Cell exhaustion in the tumor microenvironment

Abstract

In the setting of chronic antigen exposure in the tumor microenvironment (TME), cytotoxic CD8⁺ T cells (CTLs) lose their immune surveillance capabilities and ability to clear tumor cells as a result of their differentiation into terminally exhausted CD8⁺ T cells. Immune checkpoint blockade (ICB) therapies reinvigorate exhausted CD8⁺ T cells by targeting specific inhibitory receptors, thus promoting their cytolytic activity towards tumor cells. Despite exciting results with ICB therapies, many patients with solid tumors still fail to respond to such therapies and patients who initially respond can develop resistance. Recently, through new sequencing technologies such as the assay for transposase-accessible chromatin with sequencing (ATAC-seq), epigenetics has been appreciated as a contributing factor that enforces T cell differentiation toward exhaustion in the TME. Importantly, specific epigenetic alterations and epigenetic factors have been found to control CD8⁺ T cell exhaustion phenotypes. In this review, we will explain the background of T cell differentiation and various exhaustion states and discuss how epigenetics play an important role in these processes. Then we will outline specific epigenetic changes and certain epigenetic and transcription factors that are known to contribute to CD8⁺ T cell exhaustion. We will also discuss the most recent methodologies that are used to study and discover such epigenetic modulations. Finally, we will explain how epigenetic reprogramming is a promising approach that might facilitate the development of novel exhausted T cell-targeting immunotherapies.

Keywords: ATAC-seq; CD8+ T cell; HDAC; PD-1; SLAMF7; TOX; epigenetics; tumor microenvironment.

FIGURE 1

CD8⁺ T cell differentiation in the tumor microenvironment and during acute infection. Naïve T cells can differentiate into various CD8⁺ T cell subsets upon acute antigen exposure, and this varies in comparison to chronic antigen exposure. Effector T cells are capable of secreting cytokines and have cytolytic activity. A portion of effector T cells can differentiate into memory T cells, capable of self-renewal, or undergo cell death. In contrast, exhausted T cell populations lack effector activity and undergo cell death. Progenitor T_ex cells express TCF1 (as well as other markers) and have enhanced proliferation potential. Terminal T_ex cells do not express TCF1 (and increased inhibitory receptor expression) and have reduced proliferation potential. Created with BioRender.com.

FIGURE 2

Common methods for studying epigenetic modifications of chromatin. ATAC-seq, ChIP-seq, and MNase-seq have different mechanisms for DNA isolation, but all result in sequencing of specific DNA structures to identify epigenetic modulations. ATAC-seq involves the use of Tn5 to assess the location and sequence of open chromatin, ChIP-seq assesses the sequence of protein-bound DNA through crosslinking and fragmentation, and MNase identifies protein binding sites on DNA using an MNase enzyme digestion which leaves bound DNA to be isolated and sequenced. These techniques can be completed on bulk cells or single cells as described in this review. Created with Biorender.com and adapted from Chen et al., 2022.

FIGURE 3

A schematic of major epigenetic alterations reinforcing CD8⁺ T cell exhaustion. Hypermethylation is characterized by increased methyl group attachment to DNA on chromatin, making the DNA transcriptionally inactive and closed. Hyperacetylation on the other hand acts in an opposite manner, where acetyl group binding causes chromatin to open and enhanced transcription of DNA. BET targeting to acetyl groups can also modify this transcription. These alterations are manipulated by various targeted drug approaches as listed in this figure. Created with BioRender.com.