Developmental Relationships of Four Exhausted CD8+ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms

Abstract

Highlights d Ly108 and CD69 define four Tex subsets linked in a hierarchical developmental pathway d Two TCF1+ subsets, effector-like and terminally exhausted subsets, are identified d Key transcriptional, epigenetic, and biological changes define subset transitions d TCF1, T-bet, and Tox coordinate Tex subset development and dynamics

A unified atlas of CD8 T cell dysfunctional states in cancer and infection

“…Despite the limited resolution of differential expression analysis for these small subsets of cells, many of the critical marker genes were consistently overexpressed in this cluster when considered independently in d7 acute, d7 chronic, or d35 chronic infection, including many transcription factors and putative drivers of chromatin accessibility changes, such as Tox, Pou2f2, and Ikzf2; the most overexpressed gene in this cluster, Xcl1; the previously described progenitor markers Cxcr5 and Slamf6; and the memory precursor marker Il7r ( Figure 4G,H, Supplementary Figure 13C). This again confirmed the emergence of progenitor-like cells early in chronic infection, together with a small number of similar cells in acute infection, that clustered with dysfunctional progenitor cells, consistent with recent reports (20,54). We independently confirmed the presence of this CD8 T cell subpopulation at d7 in acute infection by reanalysis of three recently published scRNA-seq data sets (30,31,44) and confirmed enrichment of genes Tox, Ikzf2, Cxcr5 in this subpopulation (Supplementary Figure 13D).…”

“…These cluster 10 cells from acute and chronic infection were similar in their genome-wide chromatin accessibility profiles (and thus belonged to the same cluster in scATAC-seq data), in their association with TF activities, including enrichment of Lef1/Tcf7, Nr4a, Nfkb, Nfat, Pou, AP1 family motifs ( Figure 3G), and also in the chromatin accessibility levels at gene loci encoding proteins important for T cell activation and function, including progenitor marker Cxcr5 ( Figure 3I, Supplementary Figure 7A,B), consistent with our observations from bulk ATAC-seq data analysis in progenitor dysfunctional cells ( Figure 1E, Figure 2B,C). This shared cluster suggested that progenitor-like cells, by analogy to memory precursor cells, are established as early as at d7, and may give rise to more differentiated cell states as previously reported for progenitor dysfunctional cells from later time points (18,20,21). However, we also observed evidence of differential accessibility between the progenitor-like and precursor cells in chronic and acute infection ( Figure 3J, Supplementary Figure 7C) and potentially different TF activity ( Figure 3G), suggesting an even earlier divergence between functional and dysfunctional fates.…”

“…Adoptive transfer experiments using sorted progenitor dysfunctional cells have demonstrated their potential to self-renew and give rise to terminally dysfunctional cells in models of melanoma and chronic viral infection (18,20,21). Since single cell chromatin and expression analyses showed that dysfunctional progenitors resemble progenitor-like cells at the plastic stage of T cell dysfunction development as well as the MPEC population in acute infection, we asked whether progenitor cells retain the potential to give rise to effector cells.…”

“…Phenotypic and functional analyses of CD8 T cells in acute and chronic viral infections, cancer, transplantation and "self" tolerance in both experimental animal models and in human patients have offered numerous descriptions of activated effector, long-lived central and short-lived effector memory cells and their precursors, as well as an array of CD8 T cell states with perturbed functionalities dubbed anergic, exhausted, and reversibly or irreversibly dysfunctional (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). Recent characterization of a small subset of exhausted/dysfunctional cells, named "stem cell-like" or progenitor cells, capable of self-renewal, adds further complexity to the topography of CD8 T cell activation and differentiation (6,7,(18)(19)(20)(21)(22)(23)(24)(25)(26). T cell dysfunction therefore presents a challenging case study for resolving gene regulatory programs and differentiation trajectories towards distinct cellular fates.…”

Helpless Priming Sends CD8+ T Cells on the Road to Exhaustion

“…Antigenic stimulation of predysfunctional TCF-1 + CXCR5 + CD8 + T cells can drive their differentiation into TCF-1 − CXCR5 − “terminally exhausted” cells ( 40 , 49 , 69 ). During this differentiation process, predysfunctional cells transiently acquire a more effector-like gene signature ( 49 , 57 , 70 ). Terminally exhausted CD8 + T cells are short-lived and display higher expression of coinhibitory receptors than TCF-1 + predysfunctional cells ( 9 , 42 – 44 ).…”