Marine Meyer, Aline Roch, Juliane Dervaux, Laurent Ferrier, Evarist Planet, Julien Duc, Camilla Ceroni, Mariana Costa, Brice Chambrin, Jens Stolte, Sylviane Métairon, Abhilash Kannan, Sylke Hoehnel-Ka, Marine R-C Kraus, Patrick Descombes, Nathalie Brandenberg, Mario Noti, Omid Mashinchian
Chronic inflammatory bowel diseases (IBDs), including Crohn's disease, are characterized by relapsing-remitting intestinal inflammation associated with epithelial barrier dysfunction. Existing preclinical models of IBD have limited capacity to quantitatively capture dynamic epithelial damage and recovery, which hinders the translation of research findings into new therapeutic approaches. Here, we establish a scalable, microarrayed 3D human intestinal organoid platform enabling high-throughput, single-organoid-resolution phenotyping of cytokine-induced epithelial injury and recovery. By integrating time-resolved morphological imaging, transcriptomics, permeability assays, and the intestinal organoid recovery score (IORS), we quantify injury-recovery trajectories and identify responder organoids following preventive or therapeutic intervention. CytoMix-challenged organoids display epithelial inflammatory programs with transcriptional overlap to Crohn's disease biopsy signatures. Dexamethasone, nicotinamide, and β-hydroxybutyrate improved epithelial recovery, with dexamethasone and nicotinamide modulating distinct inflammatory and barrier-associated pathways. Collectively, this single-organoid-resolution approach establishes a standardized platform for modeling epithelial inflammatory damage and recovery, enabling phenotype-driven precision medicine applications in gastrointestinal disease.