Genome-Wide Microarray Plafforms Uncover Novel Hypermethylated Genes In An Oral Squamous Cell Carcinoma Case-Control Study: A Phase I Preclinical Biomarker Development Study

Introduction: Panels of hypermethylated genes have been proposed as diagnostic markers in primary head and neck squamous cell carcinoma using a pharmacological unmasking expression microarray approach. Such experiments are performed in cancer cell lines, mostly with poor relevance when extrapolating to primary cancers.Objective: To overcome this lack of relevance we used two unbiased genome-wide DNA methylation platforms that represent 28K CpG Islands and the promoter regions of 14K-17K genes to identify hypermethylated genes in Oral Squamous Cell Carcinoma (OSCC), which also exhibited downregulated expression in the Gene Expression Omnibus (GEO) repository.Methods: DNA isolated from normal, premalignant lesions and squamous cell carcinoma lesions of the oral cavity was: a) bisulfite treated and hybridized to Infinium arrays; b) enriched with Methylated DNA …