ArticleNature genetics2022
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer.
Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 284 papers, 1 of them a synthesis that pooled it.
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Who cites it
284 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Clinicopathological and prognostic significance of mucin signatures in lower gastrointestinal cancer-a systematic review and meta-analysis.British journal of cancer · 2026Pooled it
- First-line Nivolumab plus FOLFOXIRI/Bevacizumab in advanced RAS/BRAF-mutated colorectal cancer: efficacy, safety and biomarker discovery from the phase II NIVACOR trial.Nature communications · 2026Trial
- Reframing cancer therapy through tumor plasticity.Nature cancer · 2026Review
- SLC39-driven zinc influx orchestrates pleiotropic tumor-immune system cross-talk to establish immune suppression in colorectal cancer.Science advances · 2026Article
- Single-cell epigenomics of colorectal cancer.Experimental & molecular medicine · 2026Review
- Epithelial interferon-stimulated gene programs modulate chemotherapy sensitivity in colorectal cancer via EPSTI1.Oncogene · 2026Article
- Resolving cell-cell interaction networks and their molecular logic in complex tissues.Nature methods · 2026Article
- An integrated spatially defined roadmap of normal and cancer-associated colon fibroblasts.Molecular systems biology · 2026Article
- Review
- Article
- The Single-Cell and Spatial Transcriptomics Atlas of Epithelial-Fibroblast Interactions in Colorectal Cancer.Digestive diseases and sciences · 2026Article
- Stroma-Dominant Colorectal Cancer Harbors CAF-Rich Spatial Architecture and EMT-Associated Cancer Cell Plasticity Detectable After Dissemination.Biomolecules · 2026Article
- Exceptional treatment responses and molecular markers among 103 colorectal cancer cell lines.Molecular biomedicine · 2026Article
- Article
- Single-cell transcriptomics and functional validation reveal a TUBB4B-associated malignant epithelial state in nasopharyngeal carcinoma.Journal of translational medicine · 2026Article
- Article
- Knowledge-guided learning with curated prior genetic biomarkers for robust model interpretation.Bioinformatics (Oxford, England) · 2026Article
- NF-κB-active tumors with matrix CAFs and suppressive immunity as key resistance mechanisms to chemoradiation in rectal cancer.Experimental & molecular medicine · 2026Article
- Survival of Colon Cancer in a Population-Based Cohort Study: A Comprehensive Analysis of Location of the Primary Tumor.Cancer medicine · 2026Article
- Discovering reference-missing cell types in bulk transcriptomics.Bioinformatics (Oxford, England) · 2026Article
224 more citing papers are in PubMed but not listed here.
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53 authors.
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Abstract
The consensus molecular subtype (CMS) classification of colorectal cancer is based on bulk transcriptomics. The underlying epithelial cell diversity remains unclear. We analyzed 373,058 single-cell transcriptomes from 63 patients, focusing on 49,155 epithelial cells. We identified a pervasive genetic and transcriptomic dichotomy of malignant cells, based on distinct gene expression, DNA copy number and gene regulatory network. We recapitulated these subtypes in bulk transcriptomes from 3,614 patients. The two intrinsic subtypes, iCMS2 and iCMS3, refine CMS. iCMS3 comprises microsatellite unstable (MSI-H) cancers and one-third of microsatellite-stable (MSS) tumors. iCMS3 MSS cancers are transcriptomically more similar to MSI-H cancers than to other MSS cancers. CMS4 cancers had either iCMS2 or iCMS3 epithelium; the latter had the worst prognosis. We defined the intrinsic epithelial axis of colorectal cancer and propose a refined 'IMF' classification with five subtypes, combining intrinsic epithelial subtype (I), microsatellite instability status (M) and fibrosis (F).
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