Promoter methylation of P16, RARbeta, E-cadherin, cyclin A1 and cytoglobin in oral cancer: quantitative evaluation using pyrosequencing

Br J Cancer. 2006 Feb 27;94(4):561-8. doi: 10.1038/sj.bjc.6602972.


Methylation profiling of cancer tissues has identified this mechanism as an important component of carcinogenesis. Epigenetic silencing of tumour suppressor genes through promoter methylation has been investigated by a variety of means, the most recent of which is pyrosequencing. We have investigated quantitative methylation status in oral squamous cell carcinoma patients. Fresh tumour tissue and normal control tissue from resection margin was obtained from 79 consecutive patients undergoing resection of oral squamous cell carcinoma. DNA was extracted and bisulphite treated. PCR primers were designed to amplify 75-200 bp regions of the CpG rich gene promoters of p16, RARbeta, E-cadherin, cytoglobin and cyclinA1. Methylation status of 4-5 CpG sites per gene was determined by pyrosequencing. Significant CpG methylation of gene promoters within tumour specimens was found in 28% for p16, 73% for RARbeta, 42% for E-cadherin, 65% for cytoglobin and 53% for cyclinA1. Promoter methylation was significantly elevated in tumours compared to normal tissue for p16 (P = 0.048), cytoglobin (P = 0.002) and cyclin A1 (P = 0.001) but not in RARbeta (P = 0.088) or E-cadherin (P = 0.347). Concordant methylation was demonstrated in this tumour series (P = 0.03). Significant differences in degree of methylation of individual CpG sites were noted for all genes except RARbeta and these differences were in a characteristic pattern that was reproduced between tumour samples. Cyclin A1 promoter methylation showed an inverse trend with histological grade. Promoter methylation analysis using pyrosequencing reveals valuable quantitative data from several CpG sites. In contrast to qualitative data generated from methylation specific PCR, our data demonstrated p16 promoter methylation in a highly tumour specific pattern. Significant tumour specific methylation of cyclin A1 promoter was also seen. Cytoglobin is a novel candidate tumour suppressor gene highly methylated in upper aero-digestive tract squamous cancer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Base Sequence
  • Cadherins / genetics
  • Carcinoma, Squamous Cell / genetics*
  • Carcinoma, Squamous Cell / pathology
  • Case-Control Studies
  • CpG Islands
  • Cyclin A / biosynthesis
  • Cyclin A / genetics*
  • Cyclin A1
  • Cyclin-Dependent Kinase Inhibitor p16 / genetics
  • Cytoglobin
  • DNA Methylation*
  • Epigenesis, Genetic
  • Female
  • Gene Silencing
  • Globins
  • Humans
  • Male
  • Middle Aged
  • Molecular Sequence Data
  • Mouth Neoplasms / genetics*
  • Mouth Neoplasms / pathology
  • Peroxidases / biosynthesis
  • Peroxidases / genetics*
  • Promoter Regions, Genetic
  • Receptors, Retinoic Acid / genetics
  • Sequence Analysis, DNA


  • CCNA1 protein, human
  • CYGB protein, human
  • Cadherins
  • Cyclin A
  • Cyclin A1
  • Cyclin-Dependent Kinase Inhibitor p16
  • Cytoglobin
  • Receptors, Retinoic Acid
  • retinoic acid receptor beta
  • Globins
  • Peroxidases