ArticleGenome biology2022
Systematic evaluation of colorectal cancer organoid system by single-cell RNA-Seq analysis.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 1 of them a synthesis that pooled it.
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Who cites it
70 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Applications of lung cancer organoids in precision medicine: from bench to bedside.Cell communication and signaling : CCS · 2023Pooled it
- Biomarker-guided responses in patient-derived organoids predict effective therapies in breast cancer.Cell reports. Medicine · 2026Trial
- Epithelial interferon-stimulated gene programs modulate chemotherapy sensitivity in colorectal cancer via EPSTI1.Oncogene · 2026Article
- Single-cell transcriptomic analysis reveals cellular heterogeneity and prognostic subtypes in colorectal cancer.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
- Single-Cell Analysis Identified a Recurrent Malignant-Associated Transcriptional State in Colorectal Cancer.Cancer science · 2026Article
- Chromatin Accessibility in Cancer: Biological Functions, Mechanisms, Therapeutic Potential, and Future Directions.MedComm · 2026Review
- Development and Transformation of Veterinary Experimental In Vitro Models: From 2D Culture to 3D Organoids.Animals : an open access journal from MDPI · 2026Review
- Elemene Augments the Effects of Anti-PD-1 Immunotherapy on Hepatocellular Carcinoma by Regulating the miR-130a-5p/SPP/MHC-I Axis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- An Integrative Roadmap for Advancing Colorectal Cancer Organoid.Biomedicines · 2026Article
- Review
- Application of HepG2-derived organoid and organ-on-a-chip platforms in elucidating selenium-mediated protection against cadmium-induced liver dysfunction.NPJ science of food · 2026Article
- Mitochondrial DNA Mutations in Colorectal Cancer Stem Cells: Implications for Tumor Dynamics and Therapeutic Strategies.Current medicinal chemistry · 2026Review
- Colorectal cancer organoids: a developmental trajectory from Matrigel embedding to AI-empowered precision medicine.Frontiers in oncology · 2026Review
- Tumor organoids for testing metabolic flexibility in precision oncology.Frontiers in oncology · 2026Review
- Single-cell multi-omics characterize colorectal tumors, adjacent healthy tissue and matched (tumor) organoids identifying CRC-unique features.International journal of cancer · 2025Article
- Review
- Tetrabenazine-induced miR-34a-5p suppresses the tumorigenicity of radioresistant colorectal cancer by inhibiting M2 macrophage polarization.Cell communication and signaling : CCS · 2025Article
- Multiscale Construction, Evaluation, and Application of Organoids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Single-cell aneuploidy and chromosomal arm imbalances define subclones with divergent transcriptomic phenotypes.NAR genomics and bioinformatics · 2025Article
- Characterization of stem cell landscape and identification of stemness-related gene ENY2 in colorectal cancer by intergrated transcriptomic analysis.Global medical genetics · 2025Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
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Abstract
backgroundPatient-derived organoid culture is a powerful system for studying the molecular mechanisms of cancers, especially colorectal cancer (CRC), one of the most prevalent cancers worldwide. There are two main types of 3D culture methods for colonic cells, but the similarities and differences between gene expression patterns in different culture media remain largely unexplored.
resultsHere, we establish patient-derived organoids from colorectal cancer patients and perform single-cell RNA-Seq for pairwise samples from seven patients for both organoids and their corresponding tumor and normal tissues in vivo. We find that organoids derived from tumor tissues faithfully recapitulate the main gene expression signatures of cancer cells in vivo. On the other hand, organoids derived from normal tissues exhibited some tumor-like features at the whole transcriptome level but retained normal genomic features, such as CNVs, point mutations, and normal global DNA methylation levels, for both cultural media. More importantly, we show that conditioned medium outperforms chemical-defined medium in long-term culture of tumor epithelial cells. Finally, we mutually exchange the culture medium for the organoids and find that after interchanging the medium, the organoid cells basically maintain the transcriptome characteristics of the original medium.
conclusionsOur work gives a thorough evaluation of both the cultural conditions and the biological features of organoids of CRC patients.
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