Tissue-embedded CD4⁺ plasticity defines mucosal immunity in inflammatory bowel disease

Abstract

CD4⁺ T helper (Th) cell responses to commensal microbiota are linked to Inflammatory Bowel Disease (IBD), yet how Th programs coexist and evolve in human tissues remains poorly defined. Here, we profiled CD4⁺ memory T cells in intestinal biopsies using immunological and histological approaches to map phenotypes, functional states, and spatial relationships across disease states. A marked expansion of CD4⁺ T cells concomitant with a RORγt⁺ Th population with elevated T-bet expression was linked to the progression of inflammation. Moreover, Foxp3⁺ cells co-expressing RORγt emerged within the inflamed niche, indicating regulatory–Th17 plasticity. Trajectory visualization revealed a potential branched differentiation path toward regulatory or tissue-resident Th17-like fates, with both termini expressing activation and proliferation markers. Correlation network analysis connected pro-inflammatory CD4⁺ states to T-bet⁺Granzyme-B⁺ CD8⁺ subsets, indicating coordination between helper and cytotoxic lineages. Histology revealed increased T-cell infiltration and spatial segregation of tissue-resident subsets, with CD103⁺CD4⁺ T cells localized mainly in the lamina propria and CD103⁺CD8⁺ T cells near the epithelium. TCR stimulation during active disease revealed broad suppression of CD4⁺ pro-inflammatory cytokines alongside Foxp3⁺ expansion. Conversely, HLA-DR⁺CD38⁺ memory subset retained multifunctionality, producing elevated levels of pro-inflammatory cytokines. Together, these results define a dynamic, tissue-embedded CD4 T-cell landscape in IBD.