Th40 - Profound abnormalities in thymic epithelial cells in Rag1 mutant mice: implications for immune reconstitution after stem cell transplantation

Thymic epithelial cells (TEC) are a heterogeneous population of stromal cells which orchestrate T cell development and selection. Although recent reports highlighted TEC complexity, their developmental origin, hierarchy and differentiation remain ill-defined. We compared TEC distribution and gene expression in wild-type (WT) mice and in mice carrying Rag1 hypomorphic mutations (Rag1^mut) observed in patients with immunedeficiency and immune dysregulation. Single cell RNA-seq analysis of TECs isolated from Rag1^mutmice revealed an excess of cortical TECs (cTECs). Medullary TECs (mTECs), albeit reduced in number, showed a similar distribution in mature subsets. To address whether TEC abnormalities in Rag1^mut mice might result from a developmental block, we compared them to TECs from neonate WT mice. Indeed, we observed a similar TEC distribution in adult Rag1^mut mice and newborn WT mice, although we identified peculiar features in cTECs of Rag1^mut mice. Transplantation of WT hematopoietic stem cells (HSC) into Rag1^mut mice was able not only to correct thymocyte development, but also to revert TEC phenotype to normalcy. However, in a competitive transplantation setting where 10% of WT and 90% mutant HSCs were used, only partial restoration of thymocyte subsets was observed, associated with incomplete rescue of TEC phenotype. In summary, we show that abnormalities of TEC composition in Rag1 mutant mice correlate with impaired development of thymocytes, highlighting the role of lymphostromal cross-talk in TEC maturation. Moreover, these data point to the need to achieve full donor chimerism after HSC transplantation in order to rescue the thymic compartment and prevent defects of immune tolerance.