Discovery of Novel Epigenetic Regulators of CD8+ T Cell Effector Function

Abstract

CD8+ cytotoxic T lymphocytes (CTLs) play a key role in acquired immunity by killing infected or cancerous cells. Upon antigen recognition and activation, the majority of naïve CD8+ T cells differentiate into potent but short-lived effector CTLs, while a small fraction generates long-lived memory cells that are poised to proliferate rapidly upon antigen re-encounter. While transcriptional control of CD8+ T cell differentiation and effector function has been extensively studied, little is known about epigenetic regulation of these processes. Here we use two screening approaches to uncover novel epigenetic regulators of CD8+ T cell effector function. We first engineered a CRISPR-Cas9 genetic screening platform to reveal epigenetic regulators in tumour-infiltrating CD8+ T cells that could potentially be targeted to improve CD8+ anti-tumour function. This approach identified CARM1 as a strong candidate epigenetic regulator suppressing the accumulation of tumor-specific CD8+ T cells in the pre-clinical B16 melanoma tumour model. We also used a functional pharmacological approach to screen for epigenetic regulators of CD8+ T cell effector function during in vitro T cell activation. We thus identified a novel role of the histone deacetylase HDAC3 as an epigenetic regulator of CD8+ T cell cytotoxicity and persistence. Hdac3-deficient CD8+ T cells transiently acquired augmented cytotoxicity that was associated with early resistance to chronic LCMV infection but did not confer durable disease protection. Mechanistically, HDAC3 inhibited a gene programme of cytotoxicity-associated genes and terminal effector differentiation beginning early during CD8+ T cell activation, and required the transcription factors Runx3 and Blimp-1 as key downstream mediators for its regulation of CD8+ T cell effector function. Targeting HDAC3 activity to epigenetically modulate the balance between a short-lived, potent cytotoxic effector state and a durable, long-lived response could potentially lead to the development of new approaches in adoptive T cell immunotherapy and in therapeutic vaccine development.