METHYLATION PROFILING OF DAPK1, LRPPRC, RAB6C, AND ZNF471 IN SALIVA AND TISSUES AS NOVEL EPIGENETIC MARKERS OF ORAL SQUAMOUS CELL CARCINOMA

Abstract

<h3>Background</h3> Despite rapid progress in the diagnosis and treatment of oral squamous cell carcinoma (OSCC), the survival rates remain poor. Early identification of premalignant lesions is critical in reducing mortality. Epigenetic changes, such as aberrant DNA methylation resulting in altered gene expression, contribute to oral carcinogenesis. <h3>Objective</h3> To identify aberrantly methylated genes in saliva and tissue of OSCC patients as novel biomarkers of patients' prognosis. <h3>Methods</h3> Genome-wide methylation changes were identified by differential methylation hybridization microarray. The results were compared against datasets from TCGA-HNSCC. Promoter sequences of <i>DAPK1, LRPPRC, RAB6C</i>, and <i>ZNF471</i> were validated by bisulfite genome sequencing. The methylation status of these genes was tested in saliva and tissue specimens by targeted next-generation sequence. <h3>Results</h3> Promoter sequences of <i>DAPK1, LRPPRC, RAB6C,</i> and <i>ZNF471</i> were significantly hypermethylated in tumors compared with matched normal tissue (<i>P</i> < .0001). Sensitivity and specificity of methylation markers for detection of OSCC were in the range of 70% to 100%, with AUC 0.83 and above. Salivary DNA methylation levels were higher in premalignant lesions and OSCC in comparison to healthy controls (<i>P</i> < .05). The r-value between premalignant tissue versus saliva and OSCC versus saliva were in the range of 0.6297 to 0.8023 and 0.7823 to 0.9419, respectively. <h3>Conclusions</h3> Our data confirms that the methylation pattern of these candidate genes are significantly higher in premalignant and OSCC tissues and saliva. Thus, the methylation profiling of these candidate genes has the potential to serve as novel non-invasive markers of OSCC.