E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation

Abstract

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.

Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usage

“…The major outlier was the central memory cluster, which was almost entirely (>97%) composed of singlet clones. Although it may be possible that some of the cells in this cluster were actually naïve cells, given that naïve and memory T cells share many transcriptomic and epigenetic similarities ( Schauder et al, 2021 ), the splenic CD8 T cells we sequenced were sorted to be CD44 + ( Fig S1B ); these data therefore suggest that central memory CD8 T cells may undergo clonal contraction. In general, splenic CD8 T cell clusters were less clonally expanded than those in the islets, as would be expected given that the islets are the major source of autoantigens in T1D.…”

“…Finally, we identified central memory and anergic cells in the spleen, both of which had limited clonal expansion and predicted differentiation potential. Although the splenocytes we sequenced were sorted on CD44 + cells, it may be possible that the splenic central memory cluster may also contain some naïve CD8 T cells given that naïve and memory CD8 T cells share similar phenotypic and epigenetic profiles ( Schauder et al, 2021 ). Collectively, our data therefore identify previously underappreciated phenotypic heterogeneity among diabetogenic CD8 T cells and show that several different CD8 T-cell populations exist in the islets and spleens of NOD mice during the onset of T1D.…”

New Insights into Epigenetic Regulation of T Cell Differentiation

“…From this report, it is clear that Suv39h1-mediated H3K9me3 deposition creates an epigenetic barrier on the stem/memory gene expression program in the effector cells and thus regulates the fate of T cell differentiation [ 102 ]. To better understand the CD8 + T cell fate decision following activation, another study was performed on antigen-specific CD8 + T cells during an acute infection with LCMV [ 103 ]. scRNA-seq revealed that short-lived effector cells (SLECs) lose accessibility at Tcf7 (Tcf1)- and Tcf3-occupied enhancers, which regulate genes critical for memory T cell differentiation, and these cells are therefore unable to form long-lived memory T cells [ 103 ].…”

“…To better understand the CD8 + T cell fate decision following activation, another study was performed on antigen-specific CD8 + T cells during an acute infection with LCMV [ 103 ]. scRNA-seq revealed that short-lived effector cells (SLECs) lose accessibility at Tcf7 (Tcf1)- and Tcf3-occupied enhancers, which regulate genes critical for memory T cell differentiation, and these cells are therefore unable to form long-lived memory T cells [ 103 ]. On the other hand, memory precursor effector cells (MPECs) sustain chromatin accessibility at enhancers, which are highly enriched for Tcf3 (E2a) binding sites and are important for memory-related gene expression [ 103 ].…”

“…scRNA-seq revealed that short-lived effector cells (SLECs) lose accessibility at Tcf7 (Tcf1)- and Tcf3-occupied enhancers, which regulate genes critical for memory T cell differentiation, and these cells are therefore unable to form long-lived memory T cells [ 103 ]. On the other hand, memory precursor effector cells (MPECs) sustain chromatin accessibility at enhancers, which are highly enriched for Tcf3 (E2a) binding sites and are important for memory-related gene expression [ 103 ]. Another study showed that BH3-only, pro-apoptotic Bcl-2 family member, Bim (Bcl2l11) levels determine T effector memory (T EM ) vs. T central memory (T CM ) cell fate [ 104 ].…”