Extraintestinal Reprogramming of Colon‐Derived CD4+ Intraepithelial Lymphocytes Reveals a Mechanism Underlying the Gut‐Joint Axis

Objective The gut‐joint axis is a central paradigm in spondyloarthritis, yet the cellular mechanisms linking intestinal and joint immunity remain poorly understood. One potential link is TCRαβ + CD4 + intraepithelial lymphocytes in the colon (cIELs) that can traffic to extraintestinal tissues, including the joint. Within an inflamed joint, trafficked cIELs display both regulatory and inflammatory capacity. We sought to determine whether this functional identity is determined by an impaired epithelium or shaped by the joint environment. Methods We combined colonoscopy‐guided photoconversion in KikGR mice with single‐cell multiomic profiling and flow cytometry to trace and characterize CD4 + cIELs in the spleen and joint‐draining lymph nodes. Intestinal perturbation was induced by dextran sodium sulfate (DSS) and epithelial‐specific major histocompatibility complex class II (MHCII) gene deletion. Results Epithelial‐derived CD4 + T cells were enriched for tolerogenic phenotypes, marked by expression of CD73, FR4, and Foxp3. This phenotype persisted despite DSS‐induced intestinal inflammation and was independent of epithelial MHCII expression. However, single cell transcriptomic, epigenetic, and T cell receptor analyses revealed that shared clones undergo tissue‐specific transcriptional reprogramming to more activated states after exiting the epithelium. Conclusions These findings define CD4 + cIELs as mobile T cells that retain tolerogenic phenotypes with functional plasticity to a more activated state determined by extraintestinal microenvironments, indicating that the local environment of the joint‐draining lymph nodes, rather than the gut, is important in determining the function of gut‐trafficked CD4 + T cells.