Thymic regulatory T cells arise via two distinct developmental programs.

The developmental programs that generate a broad repertoire of regulatory T cells (T cells) able to respond to both self antigens and non-self antigens remain unclear. Here we found that mature T cells were generated through two distinct developmental programs involving CD25 T cell progenitors (CD25 TP cells) and Foxp3 T cell progenitors (Foxp3 TP cells). CD25 TP cells showed higher rates of apoptosis and interacted with thymic self antigens with higher affinity than did Foxp3 TP cells, and had a T cell antigen receptor repertoire and transcriptome distinct from that of Foxp3 TP cells. The development of both CD25 TP cells and Foxp3 TP cells was controlled by distinct signaling pathways and enhancers. Transcriptomics and histocytometric data suggested that CD25 TP cells and Foxp3 TP cells arose by coopting negative-selection programs and positive-selection programs, respectively. T cells derived from CD25 TP cells, but not those derived from Foxp3 TP cells, prevented experimental autoimmune encephalitis. Our findings indicate that T cells arise through two distinct developmental programs that are both required for a comprehensive T cell repertoire capable of establishing immunotolerance.