Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade

Abstract

We have recently defined a novel population of PD-1 (programmed cell death 1)+ TCF1 (T cell factor 1)+ virus-specific CD8 T cells that function as resource cells during chronic LCMV infection and provide the proliferative burst seen after PD-1 blockade. Such CD8 T cells have been found in other chronic infections and also in cancer in mice and humans. These CD8 T cells exhibit stem-like properties undergoing self-renewal and also differentiating into the terminally exhausted CD8 T cells. Here we compared the epigenetic signature of stem-like CD8 T cells with exhausted CD8 T cells. ATAC-seq analysis showed that stem-like CD8 T cells had a unique signature implicating activity of HMG (TCF) and RHD (NF-κB) transcription factor family members in contrast to higher accessibility to ETS and RUNX motifs in exhausted CD8 T cells. In addition, regulatory regions of the transcription factorsTcf7andId3were more accessible in stem-like cells whereasPrdm1andId2were more accessible in exhausted CD8 T cells. We also compared the epigenetic signatures of the 2 CD8 T cell subsets from chronically infected mice with effector and memory CD8 T cells generated after an acute LCMV infection. Both CD8 T cell subsets generated during chronic infection were strikingly different from CD8 T cell subsets from acute infection. Interestingly, the stem-like CD8 T cell subset from chronic infection, despite sharing key functional properties with memory CD8 T cells, had a very distinct epigenetic program. These results show that the chronic stem-like CD8 T cell program represents a specific adaptation of the T cell response to persistent antigenic stimulation.

Transient “rest” induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells

“…This is supported by the detection of modest differences in cell fold change, Ki-67 expression, and cleaved PARP (cPARP) between Always ON and RestedD7-11 cells ( Figure S2G and S2H) (Joshi et al, 2007;Rutishauser et al, 2009). Moreover, TCF1 expression, which is associated with a progenitor exhausted cell population that retains anti-tumor functionality and is responsive to checkpoint blockade (Chen et al, 2019c;Im et al, 2016;Jadhav et al, 2019;Utzschneider et al, 2016), was similar in both Always ON and RestedD7-11 conditions and represented approximately 10% of total CD8+ CAR-T cells on D11 ( Figure S2I). Collectively, these observations indicate that transient cessation of CAR signaling prior to exhaustion onset alters the differentiation trajectory of large fraction of CAR-T cell populations rather than inducing outgrowth of a minor subset of highly proliferative, apoptosis-resistant, or TCF1+ progenitor exhausted RestedD7-11 cells.…”

“…Consistent with this, rested CAR-T cell populations exhibited increased accessibility at the Tcf7 locus, enriched Tcf7 binding motifs within accessible regions of the genome, and increased frequency of TCF1+ cells compared to exhausted CAR-T cells ( Figures 6F and 7D, S2I and S6F). However, TCF1+ cells in reinvigorated dasatinib-treated groups did not co-express PD-1 or other immune checkpoint receptors ( Figures 6C and 6D), a canonical feature of progenitor exhausted T cells (Chen et al, 2019c;Im et al, 2016;Jadhav et al, 2019;Miller et al, 2019;Utzschneider et al, 2016).…”

“…Several groups have sought to identify subsets of exhausted T cells that retain the capacity for reversal of the exhaustion program (Im et al, 2016;Miller et al, 2019;Utzschneider et al, 2016;Utzschneider et al, 2013). In murine models of LCMV, "progenitor exhausted" T cells, which are defined by expression of the stemness transcription factor TCF1 (gene name Tcf7), are essential for providing the proliferative burst observed following PD-1 blockade (Chen et al, 2019c;Im et al, 2016;Jadhav et al, 2019;Miller et al, 2019;Utzschneider et al, 2016). Similarly, murine tumor models have revealed that exhaustion reprogrammability is associated with increased accessibility at the Tcf7 locus (Philip et al, 2017).…”

“…Rested D7-15 Rested D11-15 Vehicle EZH2i AP-1 family TF motifs (BATF, BATF3, JUNB, NFATC2), which are known to promote T cell exhaustion (Kurachi et al, 2014;Lynn et al, 2019;Man et al, 2017;Martinez et al, 2015;Scott-Browne et al, 2016), were highly enriched in accessible regions of the Always ON epigenome, but rendered less accessible following rest ( Figures 6E and 6F). TF binding motifs for genes that have been implicated in T cell memory were exclusively accessible in rested conditions (TCF7/TCF7L2, LEF1, RUNX family, FOXO family) (Hu and Chen, 2013;Jadhav et al, 2019;Kratchmarov et al, 2018;Michelini et al, 2013;Milner et al, 2017;Rao et al, 2012;Sullivan et al, 2012;Wang et al, 2018;Xing et al, 2016), whereas those associated with T cell exhaustion (EOMES, TBX21) demonstrated exaggerated inaccessibility compared to Always OFF control cells ( Figure 6F), raising the prospect that T cell rest could induce a unique program to drive the development of memory-like T cells. Gene set enrichment of the genes associated with differentially accessible peaks at D15 revealed biological processes that are enriched (packaging of telomeres, G1 phase) or diminished (Akt signaling, apoptosis, negative regulation of Wnt signaling, chromatin silencing complex) in rested conditions ( Figure S5E), consistent with induction of a quiescent/memory T cell phenotype following rest.…”

Epitherapy and immune checkpoint blockade: using epigenetic reinvigoration of exhausted and dysfunctional T cells to reimburse immunotherapy response

“…In addition to altered epigenetic states between tumor and normal cells, exhausted T cells are now known to have epigenetic patterns distinct from those of effector and memory T cells [23,25,31,35,43]. By comparing functional and exhausted T cells in chronic viral infection, Sen et al [31] established that there was a large difference between their levels of chromatin accessible regions.…”