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Rat thymic epithelium-free areas are specialized medullary niches enriched for mature thymocytes and distinct stromal subsets

ABSTRACT: The rat thymic medulla provides the microenvironment for negative selection, late thymocyte maturation, and thymocyte egress, and is generally characterized by widespread distribution of medullary thymic epithelial cells (mTECs). In contrast, rat thymic medulla contains medullary epithelium-free areas (mEFAs), but the cellular composition and functional significance of these regions remain unclear. Here, we combined spatial transcriptomics, scRNA-seq, and robust cell-type decomposition (RCTD) to characterize mEFAs in Lewis rat thymus. These analyses revealed that mature single-positive thymocytes, including CD4SP, CD8SP, and regulatory T-cell-lineage cells, were preferentially localized in mEFAs, whereas immature SP subsets were enriched in medullary epithelium-containing areas. Rat thymic mesenchymal cell-3 and -4 (TMC3 and TMC4) subsets were also enriched in mEFAs. These subsets were broadly similar to mouse medullary fibroblasts but displayed distinct predicted interactions with SP thymocytes, including costimulatory molecule–receptor, chemokine–receptor, and ECM–integrin axes. In addition, the venous endothelial cells (vECs) expressing portal endothelial cell markers were accumulated in mEFAs. The S1P transporter gene Spns2 was preferentially expressed in both TMC4 and vEC subsets, suggesting increased local concentration in mEFAs. These findings indicate that rat mEFAs are specialized medullary niches linking stromal organization, thymocyte maturation, and thymic egress.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE333693 | GEO | 2026/07/25

REPOSITORIES: GEO

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