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

Baccarella, A.; Zhou, Y.; Karakasheva, T. A.; Gautam, R.; Lal, M.; Beers, J.; Mrozek, Z.; Semeao, A.; Mirchandani, L.; Teranishi, R.; Itami, T.; Kennedy, K.; Mahon, M.; Ogbolu, E.; Kelsen, J. R.; Whelan, K. A.; Wechsler, J.; Muir, A.; Ruffner, M. A.

doi:10.64898/2026.10.29.762343

bioRxiv · 10.64898/2026.10.29.762343

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

Baccarella, A.·Zhou, Y.·Karakasheva, T. A.·Gautam, R.·Lal, M.·Beers, J.·Mrozek, Z.·Semeao, A.·Mirchandani, L.·Teranishi, R.·Itami, T.·Kennedy, K.·Mahon, M.·Ogbolu, E.·Kelsen, J. R.·Whelan, K. A.·Wechsler, J.·Muir, A.·Ruffner, M. A.

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Abstract

Background and Aims: Eosinophilic esophagitis (EoE) features prominent epithelial dysregulation that persists despite resolution of eosinophilia. Interleukin-13 (IL-13) is known to be a key upstream driver of epithelial abnormalities in EoE. We sought to benchmark an IL-13 esophageal organoid model against the in vivo epithelial state in EoE at a single cell resolution, to define in the role of IL-13 in aberrant epithelial development and inflammation in EoE, and to validate the IL-13 organoid as a model system to study the epithelial changes seen in EoE. Methods: We performed scRNA-Seq on esophageal biopsies from control and EoE patients, and esophageal biopsy-derived organoids with or without IL-13. We compared cellular composition, differentiation trajectories, pathway enrichment, and differential gene expression within both systems, and assessed findings at a protein level. Results: Seven distinct epithelial cell clusters were identified and preserved in both biopsies and organoids. EoE biopsies demonstrated expansion of cycling cells, whereas IL-13-treated organoids showed shift in the composition of the suprabasal compartments. Pseudotime topology was preserved across tissues, with a shift away from terminal differentiation in both EoE biopsies and IL-13-treated organoids. IL-13 reproduced changes in the transcription of central EoE genes and the dysregulation of epithelial proliferation and differentiation pathways seen in EoE. There was broad activation of immune related pathways within both EoE biopsies and IL-13-treated organoids, however, biopsies additionally showed activation in several immune and extracellular matrix remodeling programs that IL-13 alone did not reproduce. Conclusion: IL-13-treated esophageal organoids replicate key epithelial features of EoE including dysregulated epithelial development, impaired cornification, and inflammatory signals, while preserving lineage architecture, providing a tractable platform for epithelial-targeted mechanistic and therapeutic studies.

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Baccarella, A., Zhou, Y., Karakasheva, T. A., Gautam, R., Lal, M., Beers, J., Mrozek, Z., Semeao, A., Mirchandani, L., Teranishi, R., Itami, T., Kennedy, K., Mahon, M., Ogbolu, E., Kelsen, J. R., Whelan, K. A., Wechsler, J., Muir, A., Ruffner, M. A.. 2026-10-30. Systemic Analysis of Patient Derived Esophageal Epithelial Organoid Model Reveals Cell State Heterogeneity and Conservation of Differentiation Hierarchy. https://doi.org/10.64898/2026.10.29.762343

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