Integration Of Single Cell Transcriptomics And Epigenomics To Identify New Regulators Of T Cell Development And Function

ab lineage T cells, most of which are CD4+ or CD8+ and recognize MHC I or MHC II-presented antigens, are essential for immune responses and develop from CD4+CD8+ thymocytes. The absence of in vitro models and the heterogeneity of ab thymocytes have hampered analyses of their intrathymic differentiation. Here, combining single-cell RNA- and ATAC- (chromatin accessibility) sequencing, we identified conserved developmental trajectories for both mouse and human ab thymocytes. Integrated analyses of MHC I- and MHC II-signaled cells demonstrated asymmetric emergence of CD4+ and CD8+ lineages. Through computational analysis of single cell data and binding sites for the CD4+-lineage transcription factor Thpok, we inferred transcriptional networks associated with CD4+- or CD8+-lineage differentiation, and with expression of Thpok or of the CD8+-lineage factor Runx3. Finally, we identified Zfp148 and Zfp281 as novel transcription factors that regulate CD4+ T cell development and function via cooperation with the transcription factor Gata3. Our findings provide new insights into the mechanisms of CD4+ and CD8+ T cell differentiation and CD4+ T cell function.