ArticleBMC gastroenterology2022
Identification of SCN7A as the key gene associated with tumor mutation burden in gastric cancer.
Article in BMC gastroenterology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 10 citations in OpenAlex.
- TMB as a predictive biomarker for ICI response in TNBC: current evidence and future directions for augmented anti-tumor responses.Clinical and experimental medicine · 2025Review
- FAT4 Mutation is Related to Tumor Mutation Burden and Favorable Prognosis in Gastric Cancer.Current genomics · 2024Article
- MFSD2A potentiates gastric cancer response to anti-PD-1 immunotherapy by reprogramming the tumor microenvironment to activate T cell response.Cancer communications (London, England) · 2023Article
- Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer.Journal of advanced research · 2023Article
- Sodium channels and the ionic microenvironment of breast tumours.The Journal of physiology · 2023Article
- Low KCNQ1 expression is associated with unfavorable outcome and metabolism of gastric cancer.American journal of translational research · 2023Article
- Genomic Features of Cervical Cancer in Okinawa, Japan: Preliminary Findings From 23 Patients.Cancer genomics & proteomicsArticle
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
objectivePrevious studies have shown that tumor mutation burden (TMB) in cancer is associated with prognosis. The purpose of this study is to identify TMB related genes in gastric cancer (GC) and to explore their prognostic value.
methodsIn our research, weighted gene coexpression network analysis (WGCNA) algorithm was used to cluster the most relevant TMB modules in the Cancer Genome Atlas (TCGA) database. Limma package was used to screen the differentially expressed genes, and the intersection was identified as hub genes. We used gene expression profiling interactive analysis (GEPIA) and survival algorithm to analyze the clinical characteristics and prognosis of hub genes in tumor and normal tissue samples of TCGA and Gene Expression Omnibus cohort respectively. We also used CIBERSORT algorithm to calculate the proportion of 22 tumor immune cells in the high and low expression subgroups of hub genes. In addition, we used gene set enrichment analysis (GSEA) to predict the biological function of hub genes. P < 0.05 was considered statistically significant.
resultsIn the TCGA cohort, TMB was significantly correlated with the clinical features of GC (P < 0.05). Through WGCNA and differential gene analysis, we identified SCN7A as the hub gene (P < 0.05, |log2fc|> 1, and mm > 0.8). We found that the expression of SCN7A in tumor tissues was lower than that in normal tissues, and its expression level was also related to overall survival rate and tumor stage. GSEA analysis showed that SCN7A low expression group was enriched with "DNA replication", "base extension repair" and "proteasome" gene sets in GC. In addition, we found that there were significant differences in the infiltration degree of 7 kinds of immune cells between the two groups.
conclusionTMB can indicate the prognosis of gastric cancer. SCN7A is a hub gene associated with TMB, and its low expression is associated with better prognosis.
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