Systemic Analysis of Patient Derived Esophageal Epithelial Organoid Model Reveals Cell State Heterogeneity and Conservation of Differentiation Hierarchy

IL-13-treated esophageal organoids preserve the epithelial differentiation hierarchy seen in EoE while shifting suprabasal composition and away from terminal differentiation.

• Why it matters: EoE epithelial dysregulation persists despite eosinophilia resolution, and IL-13’s role needs benchmarking against in vivo epithelial states to validate tractable models.
• What they did: The study used scRNA-Seq on control and EoE esophageal biopsies and biopsy-derived organoids with or without IL-13, comparing cell composition, pseudotime trajectories, pathway enrichment, differential expression, and protein-level readouts.
• The result: IL-13 reproduced central EoE transcriptional changes and dysregulated proliferation/differentiation programs, while immune pathway activation occurred in both systems but biopsies showed additional immune and extracellular matrix remodeling not reproduced by IL-13 alone.

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