Celiac disease (CeD) is characterized by villous atrophy, crypt hyperplasia, and chronic intestinal inflammation. Gluten-driven immune activation ultimately leads to the activation of CD8⁺ intraepithelial lymphocytes (IELs), which target the epithelium and contribute to villous atrophy. However, the precise immune–epithelial mechanisms underlying epithelial remodeling remain incompletely understood. To address this, we combined single-cell RNA sequencing of duodenal biopsies with an autologous organoid–IEL co-culture model established from matched patient biopsies.
Single-cell analysis of CeD biopsies revealed marked epithelial remodeling, with loss of mature enterocytes and expansion of transit-amplifying (TA) cells with a pronounced IFNγ-response signature. These TA cells were predicted to interact with IELs, suggesting a link between IEL activity and epithelial stress remodeling. To test this functionally, we generated patient-derived intestinal organoids and matched CD8αβ⁺TCRαβ⁺ IEL lines and studied their interactions in co-culture. Upon IL-15 and IL-21 stimulation, CeD-derived co-cultures showed increased epithelial cell death together with elevated IFNγ secretion. TA-rich epithelial organoids presented a strong IFNγ-associated transcriptional program, recapitulating the epithelial state observed in CeD biopsies. IFNGR1 blockade or genetic knockout in organoids reduced IEL-mediated epithelial cell death, supporting a contribution of epithelial IFNγ signaling to the damage phenotype. Direct IFNγ exposure induced a similar IFNγ program in organoids, but did not increase apoptosis. Instead, prolonged IFNγ stimulation increased organoid growth, consistent with crypt hyperplasia. Accordingly, IFNGR1-deficient organoids were protected from the IFNγ-induced increase in growth.
Together, these findings identify IFNγ as a central mediator of CeD epithelial pathology with a dual role: promoting epithelial injury in the context of IEL activation, while driving epithelial proliferation and crypt hyperplasia upon sustained exposure. The autologous organoid–IEL co-culture model recapitulates key features of CeD and provides a platform to study immune-driven epithelial remodeling and therapeutic targeting of IFNγ signaling.