Identification and validation of a seven‐gene prognostic marker in colon cancer based on single‐cell transcriptome analysis

Abstract

Colon cancer (CC) is one of the most commonly diagnosed tumours worldwide. Single‐cell RNA sequencing (scRNA‐seq) can accurately reflect the heterogeneity within and between tumour cells and identify important genes associated with cancer development and growth. In this study, scRNA‐seq was used to identify reliable prognostic biomarkers in CC. ScRNA‐seq data of CC before and after 5‐fluorouracil treatment were first downloaded from the Gene Expression Omnibus database. The data were pre‐processed, and dimensionality reduction was performed using principal component analysis and t‐distributed stochastic neighbour embedding algorithms. Additionally, the transcriptome data, somatic variant data, and clinical reports of patients with CC were obtained from The Cancer Genome Atlas database. Seven key genes were identified using Cox regression analysis and the least absolute shrinkage and selection operator method to establish signatures associated with CC prognoses. The identified signatures were validated on independent datasets, and somatic mutations and potential oncogenic pathways were further explored. Based on these features, gene signatures, and other clinical variables, a more effective predictive model nomogram for patients with CC was constructed, and a decision curve analysis was performed to assess the utility of the nomogram. A prognostic signature consisting of seven prognostic‐related genes, including CAV2 , EREG , NGFRAP1 , WBSCR22 , SPINT2 , CCDC28A , and BCL10 , was constructed and validated. The proficiency and credibility of the signature were verified in both internal and external datasets, and the results showed that the seven‐gene signature could effectively predict the prognosis of patients with CC under various clinical conditions. A nomogram was then constructed based on features such as the RiskScore, patients' age, neoplasm stage, and tumor (T), nodes (N), and metastases (M) classification, and the nomogram had good clinical utility. Higher RiskScores were associated with a higher tumour mutational burden, which was confirmed to be a prognostic risk factor. Gene set enrichment analysis showed that high‐score groups were enriched in ‘cytoplasmic DNA sensing’, ‘Extracellular matrix receptor interactions’, and ‘focal adhesion’, and low‐score groups were enriched in ‘natural killer cell‐mediated cytotoxicity’, and ‘T‐cell receptor signalling pathways’, among other pathways. A robust seven‐gene marker for CC was identified based on scRNA‐seq data and was validated in multiple independent cohort studies. These findings provide a new potential marker to predict the prognosis of patients with CC.

Identification of gut microbes-related molecular subtypes and their biomarkers in colorectal cancer

“…Xia et al reported frequent mutations in BCL10 signaling mediators, which chronically activate the CBM signaling amplification complex, thereby contributing to an unfavorable outcome in activated B-cell-like diffuse large B-cell lymphoma (ABC-DLBCL) [ 62 ]. Similarly, Zhou et al demonstrated a significant positive correlation between higher expression levels of BCL10 and favorable survival outcomes in colon cancer patients [ 65 ]. Furthermore, Borthakur et al found that carrageenan, a high molecular weight sulfated polygalactan, significantly increases BCL10 secretion in patients with IBD [ 66 ].…”

A Comprehensive Prognostic Model for Colon Adenocarcinoma Depending on Nuclear-Mitochondrial-Related Genes

“…In current research, numerous biomarker models associated with cancer-associated fibroblast-derived genes, 65 metastasis-associated genes, 66 immune-related gene, 67 lipid metabolism-associated genes 68 have been utilized for predicting the diagnosis and treatment of CRC. Studies on the role of mitochondria-associated genes in predicting COAD prognosis are still insufficient.…”

Intratumor microbiome derived glycolysis-lactate signatures depicts immune heterogeneity in lung adenocarcinoma by integration of microbiomic, transcriptomic, proteomic and single-cell data

“…The expression of the CCDC28A gene changes in low-grade and highgrade gliomas, which may be related to the development of these diseases (Gahoi et al, 2020). A recent study also found that the CCDC28A gene is a significant prognostic marker for patients with colon cancer (Zhou et al, 2022). The gene ISCU encodes a protein that plays a key role in the biosynthesis of iron-sulfur (Fe-S) clusters.…”