Genome-wide analysis of DNA methylation in tongue squamous cell carcinoma

Oncol Rep. 2013 May;29(5):1819-26. doi: 10.3892/or.2013.2309. Epub 2013 Feb 27.


Tongue squamous cell carcinoma (TSCC) is one of the most common types of oral cancer; however, its molecular mechanisms remain unclear. In this study, methylated DNA immunoprecipitation (MeDIP) coupled with methylation microarray analysis was performed to screen for aberrantly methylated genes in adjacent normal control and TSCC tissues from 9 patients. Roche NimbleGen Human DNA Methylation 385K Promoter Plus CpG Island Arrays were used to detect 28,226 CpG sites. A total of 1,269 hypermethylated CpG sites covering 330 genes and 1,385 hypomethylated CpG sites covering 321 genes were found in TSCC tissue, compared to the adjacent normal tissue. Furthermore, we chose three candidate genes (FBLN1, ITIH5 and RUNX3) and validated the DNA methylation status by methylation-specific PCR (MS-PCR) and the mRNA expression levels by reverse transcription PCR (RT-PCR). In TSCC tissue, FBLN1 and ITIH5 were shown to be hypermethylated and their expression was found to be decreased, and RUNX3 was shown to be hypomethylated, however, its mRNA expression was found to be increased. In addition, another three genes (BCL2L14, CDCP1 and DIRAS3) were tested by RT-PCR. In TSCC tissue, BCL2L14 and CDCP1 expressions were markedly upregulated, and DIRAS3 expression was significantly downregulated. Our data demonstrated that aberrant DNA methylation is observed in TSCC tissue and plays an important role in the tumorigenesis, development and progression of TSCC.

MeSH terms

  • Antigens, CD / genetics
  • Antigens, Neoplasm
  • Calcium-Binding Proteins / genetics
  • Carcinogenesis / genetics
  • Carcinoma, Squamous Cell / genetics*
  • Carcinoma, Squamous Cell / metabolism
  • Carcinoma, Squamous Cell / pathology
  • Cell Adhesion Molecules / genetics
  • Core Binding Factor Alpha 3 Subunit / genetics
  • CpG Islands
  • DNA Methylation*
  • Disease Progression
  • Genome-Wide Association Study / methods
  • Humans
  • Neoplasm Proteins / genetics
  • Proteinase Inhibitory Proteins, Secretory / genetics
  • RNA, Messenger / genetics
  • Tongue Neoplasms / genetics*
  • Tongue Neoplasms / metabolism
  • Tongue Neoplasms / pathology
  • Up-Regulation
  • bcl-X Protein / genetics
  • rho GTP-Binding Proteins / genetics


  • Antigens, CD
  • Antigens, Neoplasm
  • BCL2L1 protein, human
  • CDCP1 protein, human
  • Calcium-Binding Proteins
  • Cell Adhesion Molecules
  • Core Binding Factor Alpha 3 Subunit
  • DIRAS3 protein, human
  • ITIH5 protein, human
  • Neoplasm Proteins
  • Proteinase Inhibitory Proteins, Secretory
  • RNA, Messenger
  • Runx3 protein, human
  • bcl-X Protein
  • fibulin
  • rho GTP-Binding Proteins