Genome-wide Methylation Array Analysis of Saliva for Oral Cancer Diagnosis

Background: Promoter hypermethylation is an epigenetic change that is a critical step in oral carcinogenesis. It is the earliest and most frequent mechanism in silencing cancer-associated genes, and is a promising diagnostic marker. Saliva is an ideal diagnostic fluid for screening patients at risk for oral cancer. To date there have been no methylation array studies evaluating whole genome methylation in the saliva of oral cancer patients.

Objective: To perform a genome-wide methylation array of 807 cancer-associated genes using the saliva of oral cancer patients with the objective of identifying highly positive methylation sites which would hold diagnostic and predictive value as a biomarker.

Methods: We performed the methylation array on DNA extracted from preoperative and postoperative saliva of 13 patients with oral squamous cell carcinoma, and saliva of 10 normal subjects. We identified genes that are highly methylated in preoperative saliva, but not methylated in the postoperative saliva or in normal subjects.

Results: High quality DNA was obtained and the methylation array was successfully run on all samples. We identified significant differences in methylation patterns between the preoperative and postoperative saliva from cancer patients. We identified a suite of 8 genes that showed high methylation in preoperative saliva but were not methylated in postoperative saliva or normal subjects, which could be used as a composite biomarker for oral cancer detection.

Conclusions: As one of only two places in the US running this methylation array we report for the first time genome-wide methylation array analysis in oral cancer. Our strategic methylation biomarker approach demonstrates the proof of principle that methylation array analysis of saliva will produce a suite of cancer-related genes that are specific and can be used as a composite biomarker for the early detection of oral cancer.

Support: NIDCR K12 DE14609