Targeting epithelial IFN-I signaling restores barrier integrity in anti-TNF refractory Crohn’s disease

Abstract

Abstract Background and Aims Type I interferons (IFN-Is) are central regulators of intestinal epithelial homeostasis, yet their role in driving epithelial dysfunction and therapeutic non-response in Crohn’s disease (CD) remains poorly defined. Here, we investigated epithelial tumor necrosis factor (TNF)–IFN-I crosstalk as a previously unrecognized contributor to anti-TNF non-response in CD. Methods We analyzed human intestinal biopsies, single-cell RNA sequencing data from CD donors, and used murine TNFR1-deficient and patient-derived organoids exposed to inflammatory cytokines and clinically relevant treatments. Results Colonic epithelia from anti-TNF non-responders (NR-CD) showed enrichment of IFN-I genes associated with epithelial stress, impaired regeneration, and inflammatory cytokine production. Using patient-derived and murine TNFR1-deficient organoids, we demonstrated that TNF signaling sustains epithelial IFN-I responses linked to immune regulation and antiviral pathways, establishing a mechanistic connection between chronic TNF signaling and epithelial barrier failure. Low-dose butyrate (0.1 mM) suppressed cytokine-induced IFN-I genes and enhanced epithelial turnover in non-IBD and responder CD (R-CD) organoids but did not rescue the apoptosis and defective repair characteristic of NR-CD organoids. Notably, anti-IFN-I antibody treatment selectively attenuated IFN-I signaling and restored epithelial integrity in NR-CD organoids, identifying epithelial IFN-I blockade as a novel therapeutic rescue strategy for anti-TNF refractory disease. Conclusions TNF–IFN-I crosstalk drives epithelial dysfunction in CD. Elevated epithelial IFN-I genes distinguish anti-TNF non-responders and underlie differential therapeutic responses. Together, this work supports integration of epithelial IFN-I gene expression and patient-derived ex vivo functional testing into treatment decisions for CD patients.