SRA

T cell development in the thymus is essential for cellular immunity and depends on the organotypic thymic epithelial microenvironment. Compared to other organs, the size and cellular composition of the thymus is unusually dynamic, exemplified by rapid growth and high T cell output during early stages of development, followed by a gradual loss of functional thymic epithelial cells and diminished naïve T cell production with age. Single-cell RNA sequencing (scRNA-seq) has uncovered an unexpected heterogeneity of cell types in the thymic epithelium of young and aged adult mice; however, the identities and developmental dynamics of putative pre- and postnatal epithelial progenitors have remained unresolved. Here, we combine scRNA-seq and a novel CRISPR/Cas9-based cellular barcoding system in mice to determine qualitative and quantitative changes in the thymic epithelium over time. This dual approach enabled us to identify two principal progenitor populations: an early bi-potent progenitor type biased towards cortical epithelium, and a postnatal bi-potent progenitor population biased towards medullary epithelium. We further demonstrate that continuous autocrine provision of Fgf7 leads to sustained expansion of thymic microenvironments without exhausting the epithelial progenitor pools, suggesting a strategy to modulate the extent of thymopoietic activity. Overall design: Single cell RNA sequencing was performed on thymic epithelial cells after enzymatic dissociation of the thymi of 4 week old mice from C57BL/6 WT mice as CD45-EpCAM+, UEA1+ as well as Ly51+ cells. Furthermore, scRNA-Seq was also performed on Fgf7-stimulated TECs isolated as CD45-EpCAM+ cells.