Natural variation in the activity of RUNX transcription factors pattern the development of effector and memory CD8 T cells 2309563
TL;DR
The three RUNX TFs, and their distinct splice isoforms, likely compete at RUNT motifs, resulting in variation of RUNX activity that directs formation of specific CD8 T cell states.
Abstract
CD8 T cells respond to viral infection and generate memory populations that protect against subsequent encounters with the same antigen. The transcription factor (TF) RUNX3 is required for the formation of circulating and tissue-resident memory CD8 T cells; however, the roles of the co-expressed paralogs RUNX1 and RUNX2 in this process remain poorly defined. We used P14 TCR-transgenic CD8 T cells which recognize LCMV-Armstrong, a virus that produces an acutely resolving infection in mice. Chromatin accessibility at RUNT motifs was assessed by ATAC-seq in RUNX3-depleted P14 cells at day eight post-infection. The three RUNT TFs, or their obligate co-factor CBFβ, were individually depleted by retrovirally delivered shRNAmirs in Tcf7-reporter P14 cells. These experiments were integrated with previously generated scRNA-seq data from day 8 P14 cells. De novo transcriptome assembly of bulk RNA-sequencing data was used to identify expressed RUNX TF splice isoforms. Depletion of RUNX3 resulted in an incomplete loss of chromatin accessibility at RUNT motifs, suggesting compensation by RUNX1 or RUNX2. RUNX1 directed formation of CX3CR1hiKLRG1hi terminal effector cells, whereas RUNX3 counteracted this program to generate a stable CX3CR1intKLRG1int precursor population that gives rise to tissue-resident and central memory CD8 T cells. Depletion of RUNX2 had minimal effects on most effector populations but was required for the formation of Tcf7hiCX3CR1loKLRG1lo central memory precursors. These findings were corroborated by single-cell RNA-sequencing, which revealed variation in RUNX TF activity correlated to distinct transcriptional states. De novo transcriptome assembly further identified differential usage of Runx1 and Runx2 splice isoforms that differed by inclusion of an ETS interaction motif. The three RUNX TFs, and their distinct splice isoforms, likely compete at RUNT motifs, resulting in variation of RUNX activity that directs formation of specific CD8 T cell states. NIH U19AI109976, R01AI095634 , P01AI145815 (M.E.P.) AHA 24PRE1191318 (D.S.A.) Lymphocyte Differentiation and Peripheral Maintenance (LYM)