ArticleNature genetics2017
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.
Article in Nature genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 662 papers, 1 of them a synthesis that pooled it.
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Who cites it
662 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cancer-associated fibroblasts and their prognostic role in colorectal cancer: review and meta-analysis.Frontiers in oncology · 2025Pooled it
- scCADI: Cell-Aware Diffusion Model for Single-Cell RNA-seq Imputation.Interdisciplinary sciences, computational life sciences · 2026Article
- An integrated spatially defined roadmap of normal and cancer-associated colon fibroblasts.Molecular systems biology · 2026Article
- Review
- Adversarial random forests for omics synthesis.bioRxiv : the preprint server for biology · 2026Article
- Single-Nucleus Transcriptomes of Lacrimal Gland Adenoid Cystic Carcinoma With Different Growth Patterns.Head & neck · 2026Article
- Epithelial-mesenchymal transition in carcinoma: navigating phenotypic states to target resistance and metastasis.Cancer metastasis reviews · 2026Review
- Caveola and Its Resident Proteins, Caveolin-1 and -2, Play Critical Roles in the Pathogenesis of nAMD and PCV.Investigative ophthalmology & visual science · 2026Article
- Article
- Cancer-Associated Fibroblasts Promote Epithelial-Mesenchymal Transition and Classical to Basal Subtype Shift in Pancreatic Cancer.Cancer research · 2026Article
- Suppression of the myofibroblastic cancer-associated fibroblast phenotype to enhance anti-PD-1 response.Journal of experimental & clinical cancer research : CR · 2026Article
- Integrating Multi-View Features via Deep Generalized Canonical Correlation Analysis for Single-Cell Clustering.International journal of molecular sciences · 2026Article
- Fusobacterium periodonticum promotes colorectal tumorigenesis via decanoic acid-driven neutrophil chemotaxis.Nature communications · 2026Article
- PI3K and MAPK Signaling Nodes Serve as Divergent Drivers of Phenotypic Plasticity in Cancer-Associated Fibroblasts in Colorectal Cancer.Cancer research · 2026Article
- Molecular cues from distinct neuron classes drive differential myelination in the neocortex.Developmental cell · 2026Article
- Targeting fibroblast TXNDC5 resolves tumor desmoplasia and PD-1 resistance in colorectal cancer with mesenchymal traits.Nature communications · 2026Article
- scKSFD: federated distillation model with knowledge sharing for cell type classification of clinical transcriptome data.BMC bioinformatics · 2026Article
- Joint Low Rank Representation with Symmetric Orthogonal Decomposition for Clustering of scRNA-seq Data.Interdisciplinary sciences, computational life sciences · 2026Article
- Mitochondrial Metabolic Reprogramming in Colorectal Cancer-Associated Fibroblasts: An Up-to-Date Review.Cancers · 2026Review
- E-cadherin inactivation shapes tumor microenvironment specificities in invasive lobular breast cancer.Nature communications · 2026Article
602 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intratumoral heterogeneity is a major obstacle to cancer treatment and a significant confounding factor in bulk-tumor profiling. We performed an unbiased analysis of transcriptional heterogeneity in colorectal tumors and their microenvironments using single-cell RNA-seq from 11 primary colorectal tumors and matched normal mucosa. To robustly cluster single-cell transcriptomes, we developed reference component analysis (RCA), an algorithm that substantially improves clustering accuracy. Using RCA, we identified two distinct subtypes of cancer-associated fibroblasts (CAFs). Additionally, epithelial-mesenchymal transition (EMT)-related genes were found to be upregulated only in the CAF subpopulation of tumor samples. Notably, colorectal tumors previously assigned to a single subtype on the basis of bulk transcriptomics could be divided into subgroups with divergent survival probability by using single-cell signatures, thus underscoring the prognostic value of our approach. Overall, our results demonstrate that unbiased single-cell RNA-seq profiling of tumor and matched normal samples provides a unique opportunity to characterize aberrant cell states within a tumor.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.