Identification of a DNA methylome profile of esophageal squamous cell carcinoma and potential plasma epigenetic biomarkers for early diagnosis

PLoS One. 2014 Jul 22;9(7):e103162. doi: 10.1371/journal.pone.0103162. eCollection 2014.


DNA methylation is a critical epigenetic mechanism involved in key cellular processes. Its deregulation has been linked to many human cancers including esophageal squamous cell carcinoma (ESCC). This study was designed to explore the whole methylation status of ESCC and to identify potential plasma biomarkers for early diagnosis. We used Infinium Methylation 450k array to analyze ESCC tissues (n = 4), paired normal surrounding tissues (n = 4) and normal mucosa from healthy individuals (n = 4), and combined these with gene expression data from the GEO database. One hundred and sixty eight genes had differentially methylated CpG sites in their promoter region and a gene expression pattern inverse to the direction of change in DNA methylation. These genes were involved in several cancer-related pathways. Three genes were validated in additional 42 ESCC tissues and paired normal surrounding tissues. The methylation frequency of EPB41L3, GPX3, and COL14A1 were higher in tumor tissues than in normal surrounding tissues (P < 0.017). The higher methylation frequency of EPB41l3 was correlated with large tumor size (P = 0.044) and advanced pT tumor stage (P = 0.001). The higher methylation frequency of GPX3 and COL14A1 were correlated with advanced pN tumor stage (P = 0.001 and P < 0.001). The methylation of EPB41L3, GPX3, and COL14A1 genes were only found in ESCC patients' plasma, but not in normal individuals upon testing 42 ESCC patients and 50 healthy individuals. Diagnostic sensitivity was increased when methylation of any of the 3 genes were counted (64.3% sensitivity and 100% specificity). These differentially methylated genes in plasma may be used as biomarkers for early diagnosis of ESCC.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Carcinoma, Squamous Cell / diagnosis*
  • Carcinoma, Squamous Cell / genetics*
  • Carcinoma, Squamous Cell / pathology
  • Collagen / genetics
  • CpG Islands
  • DNA Methylation*
  • Early Diagnosis
  • Epigenesis, Genetic
  • Esophageal Neoplasms / diagnosis*
  • Esophageal Neoplasms / genetics*
  • Esophageal Neoplasms / pathology
  • Esophageal Squamous Cell Carcinoma
  • Esophagus / metabolism
  • Esophagus / pathology*
  • Female
  • Gene Expression Regulation, Neoplastic*
  • Glutathione Peroxidase / genetics
  • Glycoproteins / genetics
  • Humans
  • Male
  • Microfilament Proteins / genetics
  • Middle Aged
  • Promoter Regions, Genetic


  • COL14A1 protein, human
  • EPB41L3 protein, human
  • Glycoproteins
  • Microfilament Proteins
  • Collagen
  • GPX3 protein, human
  • Glutathione Peroxidase

Grants and funding

This study was supported by a grant from National Natural Science Foundation of China (Grant No. 81202073). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.