The transcription factor Foxo3 sustains the homeostasis of medullary thymic epithelial cells and controls their function in T cell development.

Medullary thymic epithelial cells (mTECs) play a crucial role in central tolerance. While previous studies showed that mTECs rely on genome-protecting pathways, the underlying molecular mechanisms remain elusive. We examined the role of Foxo3 in TECs due to its known involvement in DNA damage response. Mice with specific deletion of Foxo3 in TECs (Foxo3 cKO) showed a disrupted mTEC compartment, particularly affecting the CCL21+ and post-Aire mTEClo subsets. Notably, the simultaneous deletion of Foxo3 and Aire revealed that Foxo3 controlled the homoeostasis of both Aire-dependent and independent mTECs. Functionally, the mutant thymus showed failures in regulatory T cell and iNKT cell development. Moreover, aged Foxo3 cKO mice developed signs of altered immunotolerance, which were aggravated in the Aire-deficient autoimmune background. Mechanistically, Foxo3-deficient mTECs exhibited a molecular signature associated with DNA damage and impaired recovery after radiation-induced injury. Together, our findings highlight the importance of Foxo3 in preserving the genomic stability of mTEC and supporting their role in T-cell development.