Cancer Cell International (Mar 2019)

Identification of DNA methylation-driven genes in esophageal squamous cell carcinoma: a study based on The Cancer Genome Atlas

  • Tong Lu,
  • Di Chen,
  • Yuanyong Wang,
  • Xiao Sun,
  • Shicheng Li,
  • Shuncheng Miao,
  • Yang Wo,
  • Yanting Dong,
  • Xiaoliang Leng,
  • Wenxing Du,
  • Wenjie Jiao

DOI
https://doi.org/10.1186/s12935-019-0770-9
Journal volume & issue
Vol. 19, no. 1
pp. 1 – 13

Abstract

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Abstract Background Aberrant 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. Methods Data 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. Results Totally 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. Conclusion In 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.

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