ArticleJournal of cancer research and clinical oncology2023
Single-cell RNA-Seq and bulk RNA-Seq reveal reliable diagnostic and prognostic biomarkers for CRC.
Article in Journal of cancer research and clinical oncology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 9 citations in OpenAlex.
- Single-nucleus analysis of menstrual fluid highlights gene expression differences in epithelial cells of endometriosis donors.BMC medicine · 2026Article
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- Integrating Mendelian randomization and multi-omics analysis unravels gut microbiota-driven metabolic mechanisms in sepsis and identifies diagnostic biomarkers through experimental validation.APL bioengineering · 2026Article
- Machine Learning Reveals the Association Between Gene Expression and Immune Infiltration in Colorectal Cancer: A Comprehensive Study From Single-Cell to Survival Analysis.Journal of cellular and molecular medicine · 2026Article
- AI-enabled multi-omics integration in colorectal cancer: from molecular stratification to clinical translation.Frontiers in cell and developmental biology · 2026Review
- Integrating Primary and Metastatic scRNA-Seq and Bulk Data to Develop an Immune-Based Prognosis Signature for Colorectal Cancer.Current issues in molecular biology · 2025Article
- Application of single-cell sequencing in the study of immune cell infiltration in inflammatory bowel disease and colorectal cancer.World journal of gastrointestinal oncology · 2025Review
- Single-cell multi-omics in the study of digestive system cancers.Computational and structural biotechnology journal · 2024Review
- Identification and validation of ferroptosis related markers in erythrocyte differentiation of umbilical cord blood-derived CD34Frontiers in genetics · 2024Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
purposeThe potential role of epithelium-specific genes through the adenoma-carcinoma sequence in the development of colorectal cancer (CRC) remains unknown. Therefore, we integrated single-cell RNA sequencing and bulk RNA sequencing data to select diagnosis and prognosis biomarkers for CRC.
methodsThe CRC scRNA-seq dataset was used to describe the cellular landscape of normal intestinal mucosa, adenoma and CRC and to further select epithelium-specific clusters. Differentially expressed genes (DEGs) of epithelium-specific clusters were identified between intestinal lesion and normal mucosa in the scRNA-seq data throughout the adenoma-carcinoma sequence. Diagnostic biomarkers and prognostic biomarker (the risk score) for CRC were selected in the bulk RNA-seq dataset based on DEGs shared by the adenoma epithelium-specific cluster and the CRC epithelium-specific cluster (shared-DEGs).
resultsAmong the 1063 shared-DEGs, we selected 38 gene expression biomarkers and 3 methylation biomarkers that had promising diagnostic power in plasma. Multivariate Cox regression identified 174 shared-DEGs as prognostic genes for CRC. We combined 1000 times LASSO-Cox regression and two-way stepwise regression to select 10 prognostic shared-DEGs to construct the risk score in the CRC meta-dataset. In the external validation dataset, the 1- and 5-year AUCs of the risk score were higher than those of stage, the pyroptosis-related genes (PRG) score and the cuproptosis-related genes (CRG) score. In addition, the risk score was closely associated with the immune infiltration of CRC.
conclusionThe combined analysis of the scRNA-seq dataset and the bulk RNA-seq dataset in this study provides reliable biomarkers for the diagnosis and prognosis of CRC.
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