Abstract The thymus contains a heterogeneous population of stromal cells which orchestrate T cell development and selection. Recent works highlighted the complexity of thymic stromal cells, and medullary thymic epithelial cells (mTECs) in particular. However, the developmental origin, hierarchy, and function of these subpopulations remain ill-defined. Moreover, the characterization of cortical TECs (cTECs) has been largely restricted to the adult thymus. Here, we compared TEC distribution and gene expression in wild-type (WT) and in mice carrying Rag1 hypomorphic mutations observed in patients with immune deficiency and immune dysregulation. Single cell RNA-seq analysis of TECs isolated from adult Rag1 mutant mice revealed an excess of cTECs, which segregated in different clusters. The mTEC compartment, albeit reduced, showed a similar distribution of previously described subsets (mTEC I–IV), suggesting perturbation of mTEC development rather than mTEC differentiation into functional subsets. To address whether such abnormalities of cTEC and mTEC abundance and subset distribution in Rag1 mutant mice may reflect defects in TEC development, we extended scRNA-seq analysis to TECs from WT mice of neonatal age. A similar pattern was observed in TECs of adult Rag1 mutant mice and WT mice of neonatal age, indicating altered TEC development when Rag1 activity is perturbed. This defect correlates with a decreased number of double-positive thymocytes, suggesting that impaired lymphostromal cross-talk in the thymus of Rag1 mutant mice (and patients with similar defects) is associated with abnormalities of TEC composition which may contribute to altered immune tolerance that is often observed in these conditions.
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