An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Mouse scRNAseq)

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 mouse and human ab thymocyte developmental trajectories. We demonstrated asymmetric emergence of CD4+ and CD8+ lineages, matched differentiation programs of agonist-signaled cells to their MHC specificity, and identified correspondences between mouse and human transcriptomic and epigenomic patterns. 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. Our findings provide insight into the mechanisms of CD4+ and CD8+ T cell differentiation and a foundation for mechanistic investigations of ab T cell development. Overall design: Single cell transcriptomic profiling on CD69+ thymocytes isolated from MHCI or MHCII deficient mice