Tissue-specific emergence of regulatory and intraepithelial T cells from a clonal T cell precursor

Peripheral Foxp3⁺ regulatory T cells (pT_regs) maintain immune homeostasis by controlling potentially harmful effector T cell responses toward dietary and microbial antigens. Although the identity of the T cell receptor (TCR) can impose commitment and functional specialization of T cells, less is known about how TCR identity governs pT_reg development from conventional CD4⁺ T cells. To investigate the extent to which TCR identity dictates pT_reg fate, we used somatic cell nuclear transfer to generate a transnuclear (TN) mouse carrying a monoclonal TCR from a pT_reg (pT_reg TN mice). We found that the pT_reg TCR did not inevitably predispose T cells to become pT_reg but instead allowed for differentiation of noninflammatory CD4⁺CD8αα⁺ intraepithelial lymphocytes (CD4_IELs) in the small intestine. Only when we limited the number of T cell precursors that carried the TN pT_reg TCR did we observe substantial pT_reg development in the mesenteric lymph nodes and small intestine lamina propria of mixed bone marrow chimeras. Small clonal sizes and therefore decreased intraclonal competition were required for pT_reg development. Despite bearing the same TCR, small intestine CD4_IEL developed independently of precursor frequency. Both pT_reg and CD4_IEL development strictly depended on the resident microbiota. A single clonal CD4⁺ T cell precursor can thus give rise to two functionally distinct and anatomically segregated T cell subsets in a microbiota-dependent manner. Therefore, plasticity of the CD4 T cell compartment depends not only on the microbiota but also on specialized environmental cues provided by different tissues.