Chromatin organizer ASCL1 governs gene programs in thymic epithelial cells, defining immunological self

Immunological self-tolerance depends on the gene expression program of medullary thymic epithelial cells (mTECs), which ectopically express thousands of tissue-specific self-antigens (TSAs). Although the autoimmune regulator AIRE is essential for this process, it does not fully account for the breadth of TSA expression, suggesting the involvement of additional regulators. Thymomas--epithelial tumors of the thymus frequently associated with autoimmunity-- commonly arise in adults and often retain the capacity to support thymopoiesis, providing a unique model for studying self-tolerance in humans. Using single-cell RNA sequencing of thymic epithelial cells from thymoma patients, we identified ASCL1 as a transcription factor markedly downregulated in tumor mTECs. In mice, deletion of Ascl1 in TECs induced autoimmunity without tumor development. ASCL1 exhibited pioneer factor-like activity, shaping the chromatin landscape to regulate both AIRE-dependent and -independent gene programs. Notably, combined deletion of Ascl1 and Aire in TECs of aged mice led to ectopic thymic B cell follicle formation--a hallmark of both thymoma-associated and idiopathic myasthenia gravis. These findings identify ASCL1 as a key regulator of mTEC gene expression and thymic self-tolerance, with implications for the pathogenesis of autoimmunity.