T cell receptor is required for differentiation but not maintenance of intestinal CD4+ intraepithelial lymphocytes

The gut epithelium is populated by intraepithelial lymphocytes (IELs), a heterogeneous T cell population with cytotoxic and regulatory properties, which can be imprinted on CD4+ T cells at the epithelium. However, the role of the T cell receptor (TCR) in this process remains unclear. Single-cell transcriptomic analyses revealed distinct clonal expansions between cell states, with CD4-IELs being one of the least diverse populations. Conditional deletion of TCR on differentiating CD4+ T cells or of MHCII on intestinal epithelial cells prevented CD4-IEL differentiation. However, TCR ablation on differentiated CD4-IELs, or long-term cognate antigen withdraw, did not affect their maintenance. TCR re-engaging of antigen-specific CD4-IELs during Listeria monocytogenes infection did not alter their state but correlated with reduced bacteria invasion. Thus, local antigen recognition is an essential signal for differentiation of T cells at the epithelium but differentiated CD4-IELs are able to preserve an effector program in the absence of TCR signaling. Full transcriptome profiles of bulk populations and single cells of intraepithelial lymphocytes (IELs) with TCR repertoire of single cells.