The Emergence and Functional Fitness of Memory CD4+ T Cells Require the Transcription Factor Thpok

Abstract

Memory CD4 + T cells mediate long-term immunity, and their generation is a key objective of vaccination strategies. However, the transcriptional circuitry controlling the emergence of memory cells from early CD4 + antigen-responders remains poorly understood. Here, using single-cell RNA-seq to study the transcriptome of virus-specific CD4 + T cells, we identified a gene signature that distinguishes potential memory precursors from effector cells. We found that both that signature and the emergence of memory CD4 + T cells required the transcription factor Thpok. We further demonstrated that Thpok cellintrinsically protected memory cells from a dysfunctional, effector-like transcriptional program, similar to but distinct from the exhaustion pattern of cells responding to chronic infection. Mechanistically, Thpok-bound genes encoding the transcription factors Blimp1 and Runx3 and acted by antagonizing their expression. Thus, a Thpok-dependent circuitry promotes both memory CD4 + T cells' differentiation and functional fitness, two previously unconnected critical attributes of adaptive immunity.

Protection of bona fide T follicular memory cells during tissue isolation reveals their persistence, plasticity and functional impact

“…(J) Flow cytometric analysis of CCR7, CXCR5 and FR4 on GP-66 specific CD4 memory cells >50 days post infection gated as in Figure 1D. (Boddupalli et al, 2016;Choi et al, 2015;Ciucci et al, 2019;Crawford et al, 2014;Hale et al, 2013;Martinez et al, 2015;Wing et al, 2017;Wu et al, 2012;Zeng et al, 2016). (F) Log-normalized average expression of dysfunction (left) (Ciucci et al, 2019) and exhaustion (right) genes (Martinez et al, 2015).…”

“…TCM and Th1 clusters (4-7) exhibited higher expression of IL-7r, S100a4, S100a6, Selplg and various integrins ( Figures 2B and 2D), while clusters 6 and 7 were enriched for genes strongly associated with Th1 differentiation including Cxcr6, Ccl5, Nkg7 and Id2 (Figures 2B and 2E). Among Th1 clusters, cluster 7 represented the subset highest in Selplg, Ly6c2 and Il7r, while cluster 6 expressed higher levels of Cxcr6 and Id2 and exhibited signatures of dysfunction and exhaustion ( Figures S2D-S2F) (Ciucci et al, 2019;Martinez et al, 2015). Cluster cell-type identities were further confirmed by scoring each cell for signature genes obtained from publicly available datasets and examining the distributions of these scores across clusters ( Figures 2F and S2C).…”

“…al. (Figure 2F) (Ciucci et al, 2019). Clusters 4 and 5 had the highest Ccr7 transcription, which negatively correlated with Cxcr5 across all cells ( Figure 2G).…”

Origins of CD4+ circulating and tissue‐resident memory T‐cells

“…In line with this idea, a recent study by Ciucci et al . utilized single‐cell RNA sequencing to investigate the heterogeneity of antigen‐specific CD4 + effector T‐cells in response to acute LCMV infection.…”

“…In line with this idea, a recent study by Ciucci et al 31 utilized single-cell RNA sequencing to investigate the heterogeneity of antigen-specific CD4 + effector T-cells in response to acute LCMV infection. Visualization with tdistributed stochastic neighbour embedding (t-SNE) of day 7 effector T-cells yielded multiple transcriptionally distinct clusters showcasing the heterogeneity exhibited by T H 1 and T FH effector cells.…”