Identification of SCN7A as the key gene associated with tumor mutation burden in gastric cancer

作者：Wenjie Li, Kezhi Zhou, Mengting Li, Qian Hu, Wanhui Wei, Lan Liu, Qiu Zhao · 发表于：BMC Gastroenterology · 年份：2022 · DOI：10.1186/s12876-022-02112-4 · 被引用次数：10 · 研究领域：Ferroptosis and cancer prognosis、Cancer Immunotherapy and Biomarkers、Immune cells in cancer

OBJECTIVE: Previous 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. METHODS: In 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. RESULTS: In 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 sho...