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

Abstract

Naive CD8 T cells can differentiate into effector (TEFF), memory (TMEM), or exhausted (TEX) 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 TEFF, TMEM, TEX 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 TEX 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 TEX subsets following PD1 pathway blockade and identified a key role for the cell stress regulator, Btg1, in TEX 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 TEFF, TMEM, and TEX differentiation.

Enhanced STAT5a activation rewires exhausted CD8 T cells during chronic stimulation to acquire a hybrid durable effector like state

“…4D and S4F-G, Table S3 ), similar to a recently described NK-like T EX subset. 26, 44 This subset also had reduced expression of several exhaustion-related genes including Tox and Pdcd1 compared to all other clusters ( Fig. 4D and S4F-G, Table S3 ).…”

“…During the first week of a developing chronic viral infection, Ag-specific CD8 T cells differentiate into either effector-like CD8 T cells or precursors of T EX . 26, 35 Because the potential Stat5a and Tox antagonism observed above was evident by d8p.i., we asked whether Stat5a could impact early CD8 T cell-fate commitment during chronic infection. Congenically distinct P14 cells were transduced with retroviruses (RV) encoding either a constitutively active form of Stat5a (P14 STAT5CA) 36, 37 or a control RV (P14 Empty).…”

“…Commitment of CD8 T cells to exhaustion is associated with acquisition of a distinct epigenetic landscape. 6,26, 40 To investigate whether constitutively active Stat5a altered early epigenetic programming of Ag-specific CD8 T cells, we performed A ssay for T ransposase- A ccessible C hromatin followed by high throughput sequencing (ATACseq) 41 on P14 Empty and P14 STAT5CA cells at d8 of Cl13 infection and compared these data to P14 cells isolated at d8 of Arm infection (T EFF ). Examining all differentially accessible peaks (DAPs; lfc>2, FDR≤0.01), each population of P14 cells was distinct in principal component space ( Fig.…”

“…During the first week of a developing chronic viral infection, Ag-specific CD8 T cells differentiate into either effector-like CD8 T cells or precursors of TEX. 26,35 Because the potential Stat5a and Tox antagonism observed above was evident by d8p.i., we asked whether Stat5a could impact early CD8 T cell-fate commitment during chronic infection.…”

“…1,[16][17][18] Moreover, relieving some inhibition of TEX through PD-1 pathway blockade results in considerable clinical efficacy for some cancers. [19][20][21][22][23][24] Nevertheless, PD-1 pathway blockade fails to induce permanent epigenetic rewiring of TEX 25,26 highlighting the need to identify strategies that can relieve the constraints on (re)differentiation of TEX cells and allow conversion to more durably functional CD8 T cell states.…”