Abstract
BackgroundAberrant DNA methylations are significantly associated with esophageal squamous cell carcinoma (ESCC). In this study, we aimed to investigate the DNA methylation-driven genes in ESCC by integrative bioinformatics analysis.MethodsData of DNA methylation and transcriptome profiling were downloaded from TCGA database. DNA methylation-driven genes were obtained by methylmix R package. David database and ConsensusPathDB were used to perform gene ontology (GO) analysis and pathway analysis, respectively. Survival R package was used to analyze overall survival analysis of methylation-driven genes.ResultsTotally 26 DNA methylation-driven genes were identified by the methylmix, which were enriched in molecular function of DNA binding and transcription factor activity. Then, ABCD1, SLC5A10, SPIN3, ZNF69, and ZNF608 were recognized as significant independent prognostic biomarkers from 26 methylation-driven genes. Additionally, a further integrative survival analysis, which combined methylation and gene expression data, was identified that ABCD1, CCDC8, FBXO17 were significantly associated with patients’ survival. Also, multiple aberrant methylation sites were found to be correlated with gene expression.ConclusionIn summary, we studied the DNA methylation-driven genes in ESCC by bioinformatics analysis, offering better understand of molecular mechanisms of ESCC and providing potential biomarkers precision treatment and prognosis detection.
Highlights
Identification of methylation‐driven genes in esophageal squamous cell carcinoma (ESCC) To study methylation-driven genes, a total of 3 normal samples and 96 sample of methylated from The Cancer Genome Atlas (TCGA) were included in our study
EdgR R package was used for identifying the differentially expressed gene (DEG) in ESCC, and DEGs and differentially methylated gene (DMG) were merged
In summary, we found DNA methylation-driven genes involved in ESCC generation and progression by using methylmix technology
Summary
Aberrant DNA methylations are significantly associated with esophageal squamous cell carcinoma (ESCC). Esophageal carcinoma (EC) is one of the most common malignant tumors in the digestive system. It occurs mostly in the esophageal epithelium, and there are no typical clinical symptoms in the early stage of the patient. Roy et al analyzed the lymph node metastasis in esophageal squamous cell carcinoma and built a comprehensive methylation signature for predicting the prognosis of patients [8]. Identification of abnormal methylated genes can explore the redundancy and instability of the esophageal carcinoma genome and provide the basis for risk prediction and targeted therapy
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