Tissue-embedded CD4 ⁺ plasticity structures mucosal immunity in IBD-related inflammation

Aberrant CD4 ⁺ T helper (Th) cell responses to commensal microbiota are implicated in Inflammatory Bowel Disease (IBD), yet the phenotypic states of human tissue Th cells, their differentiation trajectories across active inflammation and remission, and their coordination with other lymphocytes remain poorly defined. Prior work has emphasized peripheral blood or murine models, leaving a gap in how plastic Th programs coexist and evolve in the human intestinal niche in IBD.

We profiled CD4 ⁺ T cells from ileocolonoscopic biopsies and paired blood of IBD patients and non-IBD controls, combining spectral flow cytometry with functional assays and histology to map subset composition, activation, and spatial relationships across disease activity states. Here we show that IBD exhibits a dynamic, tissue-embedded CD4 ⁺ landscape, characterized by inflammatory expansion, regulatory-Th17 plasticity, branched trajectories toward regulatory and resident fates, coordinated CD4-CD8 networks, and context-dependent cytokine suppression, collectively shaping aberrant mucosal immunity.

Specifically, inflamed mucosa harbored a marked expansion of CD4 ⁺ T cells that contracted in remission. Unbiased t-SNE-based analysis revealed several Th populations and linked a RORγt ⁺ compartment with enhanced T-bet expression to the progression of inflammation. Foxp3 ⁺ cells co-expressing RORγt also emerged within the inflamed niche, indicating regulatory-Th17 plasticity. Trajectory visualization revealed a potential branched differentiation path towards either a regulatory phenotype or a tissue-resident phenotype, with both termini expressing activation/proliferation markers. Correlation network analysis connected pro-inflammatory CD4 ⁺ states to T-bet ⁺ and Granzyme-B ⁺ CD8 ⁺ subsets, indicative of crosstalk between helper and cytotoxic lineages. Histology corroborated this organization, showing frequent interactions between CD4 ⁺ and CD8 ⁺ tissue-resident cells in the lamina propria and epithelial border. In functional assays, TCR stimulation during active disease revealed broad suppression of CD4 ⁺ pro-inflammatory cytokines concomitant with expansion of Foxp3 ⁺ regulatory T cells. Conversely, a memory Th subset co-expressing HLA-DR and CD38 retained multifunctionality, producing elevated levels of IFNγ, IL-21, IL-22 and IL-10.

Together, these results provide insight into how regulatory-effector plasticity, tissue residency, and CD4-CD8 coordination structure the human intestinal immune landscape in IBD, providing a rational for therapies to rebalance resident and regulatory programs while preserving beneficial memory responses.