Thymic regulatory T cells arise via two distinct developmental programs

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