Multi-omics uncovers transcriptional programs of gut-resident memory CD4+ T cells in Crohn's disease

Tissue-resident memory T cells (TRM) remain in nonlymphatic barrier tissues for extended periods and are deeply involved in immune memory at the site of inflammation. Here, we employed multilayered single-cell analytic approaches including chromatin, gene, and protein profiling to characterize a unique CD4+ TRM subset present in the inflamed gut mucosa of Crohn's disease patients. We identified two key transcription factors, RUNX2 and BHLHE40, as regulators of pathologically relevant CD4+ TRM. These transcriptional regulators work together to induce distinct cellular properties of disease-specific TRM, such as cytotoxicity, T helper 1-effector activity, and tissue retention. Downregulation of RUNX2 and BHLHE40 in patient-derived gut CD4+ T cells resulted in the mitigation of the pathogenic phenotype of these cells. Conversely, the ectopic overexpression of both transcription factors in healthy donor-derived CD4+ T cells drove IFN-γ pathways and enhanced tissue residency. Our findings illuminate the transcriptional programs driving disease-specific T cell formation in Crohn's disease.