Downregulation of chemokine receptor 9 facilitates CD4CD8αα intraepithelial lymphocyte development.

Intestinal intraepithelial lymphocytes (IELs) reside in the gut epithelial layer, where they help in maintaining intestinal homeostasis. Peripheral CD4 T cells can develop into CD4CD8αα IELs upon arrival at the gut epithelium via the lamina propria (LP). Although this specific differentiation of T cells is well established, the mechanisms preventing it from occurring in the LP remain unclear. Here, we show that chemokine receptor 9 (CCR9) expression is low in epithelial CD4CD8αα IELs, but CCR9 deficiency results in CD4CD8αα over-differentiation in both the epithelium and the LP. Single-cell RNA sequencing shows an enriched precursor cell cluster for CD4CD8αα IELs in Ccr9 mice. CD4 T cells isolated from the epithelium of Ccr9 mice also display increased expression of Cbfβ2, and the genomic occupancy modification of Cbfβ2 expression reveals its important function in CD4CD8αα differentiation. These results implicate a link between CCR9 downregulation and Cbfb2 splicing upregulation to enhance CD4CD8αα IEL differentiation.