ArticleScientific reports2021
Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 22 citations in OpenAlex.
- Using Brain Organoids to Explore Human Neurobiology.Cellular and molecular neurobiology · 2026Review
- Recent advancements and limitations of intestinal organoids for clinical applications.Progress in biomedical engineering (Bristol, England) · 2026Review
- Protocol for culture, drug treatment, and dissociation of patient-derived 3D ovarian cancer microspheroids for flow cytometry.STAR protocols · 2026Article
- Culture-specific transcriptional drifts limit the fidelity of organoid infection models.PLoS pathogens · 2026Article
- Characterization of jejunal enteroids in human obesity; a model for studying GLP-1 cells.International journal of obesity (2005) · 2026Article
- Equine endometrial organoids preserve tissue structure and cycle-stage transcriptional identity†.Biology of reproduction · 2026Article
- Fetal reversion from diverse lineages sustains the intestinal stem cell pool and confers stress resilience.Communications biology · 2026Article
- Immunosenescence and organoids: pathophysiology and therapeutic opportunities.Immunity & ageing : I & A · 2025Review
- A Novel Cultivation System for Germ Cell Proliferation and Sustaining Whole Testicular Niche.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Epithelial genetic muscarinic receptor 3 ablation induces sex-specific modulation of colonic intestinal progenitor cells and response to intestinal injury.Journal of Crohn's & colitis · 2025Article
- Review
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- Enteroids to Study Pediatric Intestinal Drug Transport.Molecular pharmaceutics · 2024Article
- Advanced 3D imaging and organoid bioprinting for biomedical research and therapeutic applications.Advanced drug delivery reviews · 2024Review
- AI-organoid integrated systems for biomedical studies and applications.Bioengineering & translational medicine · 2024Review
- HIV-1 transmission: modelling and direct visualization in the third dimension.Microscopy (Oxford, England) · 2023Review
- Precision oncology using organoids of a secretory carcinoma of the salivary gland treated with TRK-inhibitors.Oral oncology · 2023Article
- Breaking bad: necroptosis in the pathogenesis of gastrointestinal diseases.Frontiers in immunology · 2023Review
- Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes.EMBO molecular medicine · 2022Article
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Organoids culture provides unique opportunities to study human diseases and to complement animal models. Several organs and tissues can be in vitro cultured in 3D structures resembling in vivo tissue organization. Organoids culture contains most of the cell types of the original tissue and are maintained by growth factors mimicking the in vivo state. However, the system is yet not fully understood, and specific in vivo features especially those driven by cell-extrinsic factors may be lost in culture. Here we show a comprehensive transcriptome-wide characterization of mouse gut organoids derived from different intestinal compartments and from mice of different gender and age. RNA-seq analysis showed that the in vitro culture strongly influences the global transcriptome of the intestinal epithelial cells (~ 60% of the total variance). Several compartment-, age- and gender-related transcriptome features are lost after culturing indicating that they are driven by niche or systemic factors. However, certain intrinsic transcriptional programs, for example, some compartment-related features and a minority of gender- and aging- related features are maintained in vitro which suggested possibilities for these features to be studied in this system. Moreover, our study provides knowledge about the cell-extrinsic or cell-intrinsic origin of intestinal epithelial transcriptional programs. We anticipated that our characterization of this in vitro system is an important reference for scientists and clinicians using intestinal organoids as a research model.
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