A scalable microarrayed organoid platform for precision modeling of intestinal epithelial damage and recovery
6 affiliations
- 1DOPPL S.A., EPFL Innovation Park, 1015 Lausanne, Switzerland
- 2Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., 1015 Lausanne, Switzerland
- 3Nexco Analytics, EPFL Innovation Park, 1015 Lausanne, Switzerland
- 4Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Société des Produits Nestlé S.A., 1000 Lausanne, Switzerland
- 5Scientific IT and Data Office, Nestlé Research, Société des Produits Nestlé S.A., 1000 Lausanne, Switzerland
- 6Nestlé Product Technology Center, Société des Produits Nestlé S.A., 3510 Konolfingen, Switzerland
Abstract
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.
Related
- Activated macrophages restrict invasive bacterial infection in a human intestinal organoid co-culture model
- Organoid transplantation in the adult endometrium restores fertility and uncovers epithelial lineage plasticity
- SETD3 ACTIN HISTIDINE METHYLTRANSFERASE REGULATES INTESTINAL EPITHELIAL BARRIER INTEGRITY AND MUCOSAL INFLAMMATION
- Campylobacter jejuni Infection Is Associated With Cell-Cycle, Redox, and Metabolic Remodeling of Human Intestinal Epithelial Cells at Single-Cell Resolution
- Integrated transcriptomics, metabolomics, and gut microbiome analysis reveals the association between Rnf43 knockdown and intestinal epithelial hyperproliferation in HFD/AOM/DSS treated mice
BibTeX
@article{meyer2026scalable,
title = {{A scalable microarrayed organoid platform for precision modeling of intestinal epithelial damage and recovery}},
author = {Marine Meyer and Aline Roch and Juliane Dervaux and Laurent Ferrier and Evarist Planet and Julien Duc and Camilla Ceroni and Mariana Costa and Brice Chambrin and Jens Stolte and Sylviane Métairon and Abhilash Kannan and Sylke Hoehnel-Ka and Marine R.-C. Kraus and Patrick Descombes and Nathalie Brandenberg and Mario Noti and Omid Mashinchian},
journal = {Cell Reports Methods},
year = {2026},
month = aug,
doi = {10.1016/j.crmeth.2026.101551},
url = {https://doi.org/10.1016/j.crmeth.2026.101551},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - A scalable microarrayed organoid platform for precision modeling of intestinal epithelial damage and recovery
AU - Marine Meyer
AU - Aline Roch
AU - Juliane Dervaux
AU - Laurent Ferrier
AU - Evarist Planet
AU - Julien Duc
AU - Camilla Ceroni
AU - Mariana Costa
AU - Brice Chambrin
AU - Jens Stolte
AU - Sylviane Métairon
AU - Abhilash Kannan
AU - Sylke Hoehnel-Ka
AU - Marine R.-C. Kraus
AU - Patrick Descombes
AU - Nathalie Brandenberg
AU - Mario Noti
AU - Omid Mashinchian
PY - 2026
DA - 2026/08/14
JO - Cell Reports Methods
DO - 10.1016/j.crmeth.2026.101551
UR - https://doi.org/10.1016/j.crmeth.2026.101551
AB - 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.
SN - 2667-2375
ER -