The impact of DNA demethylation on the upregulation of the NRN1 and TNFAIP3 genes associated with advanced gastric cancer

J Mol Med (Berl). 2020 May;98(5):707-717. doi: 10.1007/s00109-020-01902-1. Epub 2020 Apr 13.


Gastric cancer (GC) is the third leading cause of cancer-related death worldwide. Very few therapeutic options are currently available in this neoplasia. The use of 5-Aza-2'-deoxycytidine (5-AZAdC) was approved for the treatment of myelodysplastic syndromes, and this drug can treat solid tumours at low doses. Epigenetic manipulation of GC cell lines is a useful tool to better understand gene expression regulatory mechanisms for clinical applications. Therefore, we compared the gene expression profile of 5-AZAdC-treated and untreated GC cell lines by a microarray assay. Among the genes identified in this analysis, we selected NRN1 and TNFAIP3 to be evaluated for gene expression by RT-qPCR and DNA methylation by bisulfite DNA next-generation sequencing in 43 and 52 pairs of GC and adjacent non-neoplastic tissue samples, respectively. We identified 83 candidate genes modulated by DNA methylation in GC cell lines. Increased expression of NRN1 and TNFAIP3 was associated with advanced tumours (P < 0.05). We showed that increased NRN1 and TNFAIP3 expression seems to be regulated by DNA demethylation in GC samples: inverse correlations between the mRNA and DNA methylation levels in the promoter of NRN1 (P < 0.05) and the intron of TNFAIP3 (P < 0.05) were detected. Reduced NRN1 promoter methylation was associated with III/IV TNM stage tumours (P = 0.03) and the presence of Helicobacter pylori infection (P = 0.02). The identification of demethylated activated genes in GC may be useful in clinical practice, stratifying patients who are less likely to benefit from 5-AZAdC-based therapies. KEY MESSAGES: Higher expression of NRN1 and TNFAIP3 is associated with advanced gastric cancer (GC). NRN1 promoter hypomethylation contributes to gene upregulation in advanced GC. TNFAIP3 intronic-specific CpG site demethylation contributes to gene upregulation in GC. These findings may be useful to stratify GC patients who are less likely to benefit from DNA demethylating-based therapies.

Keywords: 5-Aza-2′-deoxycytidine; Cancer therapy; DNA methylation; NRN1; TNFAIP3.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Azacitidine / pharmacology
  • Biomarkers, Tumor
  • Cell Line, Tumor
  • Computational Biology / methods
  • CpG Islands
  • DNA Demethylation*
  • DNA Methylation
  • Decitabine / pharmacology
  • Epigenesis, Genetic
  • GPI-Linked Proteins / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • Humans
  • Neoplasm Staging
  • Neuropeptides / genetics*
  • Prognosis
  • Stomach Neoplasms / genetics*
  • Stomach Neoplasms / pathology
  • Transcriptome
  • Tumor Necrosis Factor alpha-Induced Protein 3 / genetics*


  • Biomarkers, Tumor
  • GPI-Linked Proteins
  • NRN1 protein, human
  • Neuropeptides
  • Decitabine
  • TNFAIP3 protein, human
  • Tumor Necrosis Factor alpha-Induced Protein 3
  • Azacitidine