ArticlePhysiological genomics2021
Drivers of transcriptional variance in human intestinal epithelial organoids.
Article in Physiological genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 39 citations in OpenAlex.
- Culture-specific transcriptional drifts limit the fidelity of organoid infection models.PLoS pathogens · 2026Article
- Equine endometrial organoids preserve tissue structure and cycle-stage transcriptional identity†.Biology of reproduction · 2026Article
- Functional and molecular characterization of equine intestinal organoids across media conditions and intestinal segments.BMC veterinary research · 2026Article
- Gut microbiota-M cell co-culture in inflammatory bowel disease and its therapeutic potential in organoid platforms.Frontiers in pharmacology · 2026Review
- Norovirus replication, host interactions and vaccine advances.Nature reviews. Microbiology · 2025Review
- The differentiation state of small intestinal organoid models influences prediction of drug-induced toxicity.Frontiers in cell and developmental biology · 2025Article
- Intestinal organoids in inflammatory bowel disease: advances, applications, and future directions.Frontiers in cell and developmental biology · 2025Review
- Pig jejunal single-cell RNA landscapes revealing breed-specific immunology differentiation at various domestication stages.Frontiers in immunology · 2025Article
- Analysis of 1,25-dihydroxyvitamin D genomic action in human enteroids and colonoids reveals multiple regulatory effects of vitamin D in human intestinal physiology.Frontiers in endocrinology · 2025Article
- Neutrophils aggravate inflammatory lesions in intestinal organoids from necrotizing enterocolitis.Frontiers in immunology · 2025Article
- Single-cell transcriptomics of rectal organoids from individuals with perianal fistulizing Crohn's disease reveals patient-specific signatures.Scientific reports · 2024Article
- A living organoid biobank of patients with Crohn's disease reveals molecular subtypes for personalized therapeutics.Cell reports. Medicine · 2024Article
- Infant and adult human intestinal enteroids are morphologically and functionally distinct.mBio · 2024Article
- Culture media and format alter cellular composition and barrier integrity of porcine colonoid-derived monolayers.Tissue barriers · 2024Article
- Infant and Adult Human Intestinal Enteroids are Morphologically and Functionally Distinct.bioRxiv : the preprint server for biology · 2024Article
- Monitoring Circadian Oscillations with a Bioluminescence Reporter in Organoids.Journal of visualized experiments : JoVE · 2024Article
- Distribution of P2Y and P2X purinergic receptor expression within the intestine.American journal of physiology. Gastrointestinal and liver physiology · 2024Article
- Divergent responses of human intestinal organoid monolayers using commercial in vitro cytotoxicity assays.PloS one · 2024Article
- Standardization of an antiviral pipeline for human norovirus in human intestinal enteroids demonstrates nitazoxanide has no to weak antiviral activity.Antimicrobial agents and chemotherapy · 2023Article
- Human intestinal organoids as models to study enteric bacteria and viruses.Current opinion in microbiology · 2023Review
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Authors and funding
29 authors at 6 institutions in 1 country.
Funding
Abstract
Human intestinal epithelial organoids (enteroids and colonoids) are tissue cultures used for understanding the physiology of the human intestinal epithelium. Here, we explored the effect on the transcriptome of common variations in culture methods, including extracellular matrix substrate, format, tissue segment, differentiation status, and patient heterogeneity. RNA-sequencing datasets from 276 experiments performed on 37 human enteroid and colonoid lines from 29 patients were aggregated from several groups in the Texas Medical Center. DESeq2 and gene set enrichment analysis (GSEA) were used to identify differentially expressed genes and enriched pathways. PERMANOVA, Pearson's correlation, and dendrogram analysis of the data originally indicated three tiers of influence of culture methods on transcriptomic variation: substrate (collagen vs. Matrigel) and format (3-D, transwell, and monolayer) had the largest effect; segment of origin (duodenum, jejunum, ileum, colon) and differentiation status had a moderate effect; and patient heterogeneity and specific experimental manipulations (e.g., pathogen infection) had the smallest effect. GSEA identified hundreds of pathways that varied between culture methods, such as IL1 cytokine signaling enriched in transwell versus monolayer cultures and E2F target genes enriched in collagen versus Matrigel cultures. The transcriptional influence of the format was furthermore validated in a synchronized experiment performed with various format-substrate combinations. Surprisingly, large differences in organoid transcriptome were driven by variations in culture methods such as format, whereas experimental manipulations such as infection had modest effects. These results show that common variations in culture conditions can have large effects on intestinal organoids and should be accounted for when designing experiments and comparing results between laboratories. Our data constitute the largest RNA-seq dataset interrogating human intestinal epithelial organoids.
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