1. ¹Molecular Genetics & Oncology Group, School of Dental Sciences, University of Liverpool, Liverpool L69 3GN, UK
2. ²University of Liverpool Cancer Research Centre, Roy Castle Lung Cancer Research Programme, 200 London Rd, Liverpool L3 9TA, UK
3. ³Regional Maxillofacial Unit, University Hospital Aintree, Longmoor Lane, Liverpool L9 7AL, UK

Correspondence: Dr JM Risk, E-mail: j.m.risk@liverpool.ac.uk

Received 1 October 2005; Revised 12 December 2005; Accepted 3 January 2006; Published online 31 January 2006.

Abstract

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, RAR, 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 RAR, 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 RAR (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 RAR 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.