ArticleGastro hep advances2023
Patient-derived Colonoids From Disease-spared Tissue Retain Inflammatory Bowel Disease-specific Transcriptomic Signatures.
Article in Gastro hep advances, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 9 citations in OpenAlex.
- Early-life colonization withScience (New York, N.Y.) · 2026Article
- Synthetic PEG-4MAL Hydrogels Support Patient-Derived Human Intestinal Enteroid Culture.Cell biomaterials · 2026Article
- Patient-matched transcriptomics of in vivo and in vitro colonic epithelium substantiate organoids as a translational model for ulcerative colitis.Scientific reports · 2026Article
- 3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility.Genome biology · 2025Article
- Ion transport and epithelial barrier dysfunction in experimental models of ulcerative colitis.American journal of physiology. Gastrointestinal and liver physiology · 2025Review
- Intestinal organoids in inflammatory bowel disease: advances, applications, and future directions.Frontiers in cell and developmental biology · 2025Review
- Next-generation non-animal models for inflammatory bowel disease:NAM journal · 2025Review
- Type 1 diabetes human enteroid studies reveal major changes in the intestinal epithelial compartment.Scientific reports · 2024Article
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Authors and funding
18 authors at 1 institution in 1 country.
Funding
Abstract
BACKGROUND AND
aimsA key histopathological feature of inflammatory bowel disease is damage to the mucosa, including breakdown of the epithelial barrier. Human enteroids and colonoids are a critical bench-to-bedside tool for studying the epithelium in inflammatory bowel disease. The goal of the current study was to define transcriptional differences in healthy versus diseased subjects that are sustained in enteroids and colonoids, including from disease-spared tissue.
methodsBiopsies and matching enteroid or colonoid cultures from pediatric patients with ileal Crohn disease (N = 6) and control subjects (N = 17) were subjected to RNA sequencing followed by bioinformatic and machine learning analyses. Late passage enteroids were exposed to cytokines to assess durable transcriptional differences.
resultsWe observed substantial overlap of pathways upregulated in Crohn disease in enteroids and ileal biopsies, as well as colonoids and rectal biopsies. KEGG pathways for cytokine-cytokine receptor interaction, chemokine signaling, protein export, and Toll-like receptor signaling were upregulated in both ileal and rectal biopsies, as well as enteroids and colonoids.
conclusionWe confirmed transcriptional profiles of Crohn disease biopsies are expressed in enteroids and colonoids. Furthermore, transcriptomic data from disease-spared rectal tissue can identify patients with ileal Crohn disease. Our data support the use of patient enteroids and colonoids as critical translational tools for the study of inflammatory bowel disease.
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