Thymocytes trigger self-antigen-controlling pathways in immature medullary thymic epithelial stages.

Interactions of developing T cells with Aire medullary thymic epithelial cells expressing high levels of MHCII molecules (mTEC) are critical for the induction of central tolerance in the thymus. In turn, thymocytes regulate the cellularity of Aire mTEC. However, it remains unknown whether thymocytes control the precursors of Aire mTEC that are contained in mTEC cells or other mTEC subsets that have recently been delineated by single-cell transcriptomic analyses. Here, using three distinct transgenic mouse models, in which antigen presentation between mTECs and CD4 thymocytes is perturbed, we show by high-throughput RNA-seq that self-reactive CD4 thymocytes induce key transcriptional regulators in mTEC and control the composition of mTEC subsets, including Aire mTEC precursors, post-Aire and tuft-like mTECs. Furthermore, these interactions upregulate the expression of tissue-restricted self-antigens, cytokines, chemokines, and adhesion molecules important for T-cell development. This gene activation program induced in mTEC is combined with a global increase of the active H3K4me3 histone mark. Finally, we demonstrate that these self-reactive interactions between CD4 thymocytes and mTECs critically prevent multiorgan autoimmunity. Our genome-wide study thus reveals that self-reactive CD4 thymocytes control multiple unsuspected facets from immature stages of mTECs, which determines their heterogeneity.