E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation

Abstract

Significance Following an acute viral infection, the majority of activated virus-specific CD8 T cells die off, while a smaller subset survives and develops into long-lived memory CD8 T cells. The underlying process regulation of this cell fate decision remains incompletely understood. In this study, we identify two main patterns of gene regulatory networks underlying effector and memory CD8 T cell differentiation. Furthermore, enhancer activity correlates with these regulon patterns. Finally, cells destined to become memory CD8 T cells maintain accessibility at enhancers regulating key memory-related genes, and the transcription factor E2A regulates the accessibility of many memory-related enhancers to promote memory cell formation. During an acute viral infection, CD8 T cells encounter a myriad of antigenic and inflammatory signals of variable strength, which sets off individual T cells on their own differentiation trajectories. However, the developmental path for each of these cells will ultimately lead to one of only two potential outcomes after clearance of the infection—death or survival and development into memory CD8 T cells. How this cell fate decision is made remains incompletely understood. In this study, we explore the transcriptional changes during effector and memory CD8 T cell differentiation at the single-cell level. Using single-cell, transcriptome-derived gene regulatory network analysis, we identified two main groups of regulons that govern this differentiation process. These regulons function in concert with changes in the enhancer landscape to confer the establishment of the regulatory modules underlying the cell fate decision of CD8 T cells. Furthermore, we found that memory precursor effector cells maintain chromatin accessibility at enhancers for key memory-related genes and that these enhancers are highly enriched for E2A binding sites. Finally, we show that E2A directly regulates accessibility of enhancers of many memory-related genes and that its overexpression increases the frequency of memory precursor effector cells and accelerates memory cell formation while decreasing the frequency of short-lived effector cells. Overall, our results suggest that effector and memory CD8 T cell differentiation is largely regulated by two transcriptional circuits, with E2A serving as an important epigenetic regulator of the memory circuit.