DNA Methylome Distinguishes Oropharyngeal and Oral Cancer from Oral Lesions and Healthy Oral Mucosa

Background: There is a strong need to find new, good biomarkers of head and neck squamous cell carcinoma (HNSCC), because of the prognoses and high mortality of patients. The aim of this study was to identify the potential biomarkers in HNSCC that have differences in their DNA methylome and potentially premalignant oral lesions, in comparison to healthy oral mucosa.Methods: In this study 32 oral samples were tested: 9 healthy oral mucosae, 13 HNSCC and 10 potentially premalignant oral lesions for DNA methylation by Infinium MethylationEPIC BeadChip.Results: Our findings showed a panel of genes significantly hypermethylated in their promoters or specific sites in HNSCC samples in comparison to healthy oral samples, which are mainly oncogenes, receptor and transcription factor genes, or genes included in cell cycle, transformation, apoptosis and autophagy. A group of hypomethylated genes in HNSCC, in comparison to healthy oral mucosa, is mainly involved in the host immune response and transcriptional regulation. The results also showed significant differences in gene methylation between HNSCC and potentially premalignant oral lesions, as well as differently methylated genes that discriminate between oral lesions and healthy mucosa.Conclusions: The given methylation panels point to the possibly early diagnostics of HNSCC as well as potentially premalignant oral lesions and its possible implication in clinical practice.