Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates

Abstract

Naïve CD8 T cells can differentiate into effector (T_EFF), memory (T_MEM), or exhausted (T_EX) CD8 T cells. These developmental pathways are associated with distinct transcriptional and epigenetic changes that endow cells with different functional capacities and therefore therapeutic potential. The molecular circuitry underlying these developmental trajectories and the extent of heterogeneity within T_EFF, T_MEM, T_EX populations remain poorly understood. Here, we used the lymphocytic choriomeningitis virus model of acutely-resolved and chronic infection and addressed these gaps by applying longitudinal scRNA-seq and scATAC-seq analysis. These analyses uncovered new subsets, including a subpopulation of T_EX expressing NK cell-associated genes, as well as multiple distinct TCF1+ stem/progenitor-like subsets in acute and chronic infection. These data also revealed insights into the reshaping of T_EX subsets following PD1 pathway blockade and identified a key role for the cell stress regulator, Btg1, in T_EX differentiation. Finally, these results highlighted how the same biological circuits such as cytotoxicity or stem/progenitor pathways can be used by CD8 T cells with highly divergent underlying chromatin landscapes. Thus, this transcriptional and chromatin accessibility landscape map elucidates developmental biology and underlying mechanisms governing T_EFF, T_MEM, and T_EX differentiation.