The methylation of LHX2, RAPGEFL1, RARB and RYR2 has prognostic significance in head and neck squamous cell carcinoma patients.

Head and neck squamous cell carcinomas (HNSCC) are a group of frequently occurring tumors with a high rate of relapse and 5-year survival of approximately 60%. Novel diagnostic and prognostic biomarkers analyzed in liquid biopsy could improve clinical management of patients and prolong their survival. Thus, the aim of this study was to evaluate the utility of DNA methylation analysis in the clinical management of HNSCC patients. Based on our previous studies and the analysis of TCGA data, we selected six epigenetically regulated genes, which differentiated HNSCC patients from healthy controls. Next, we used a two-step nested MethyLight assay to analyze the DNA methylation of DAPK1, LHX2, MGMT, RAPGEFL1, RARB, and RYR2 in HNSCC tumor samples, which was followed by confirmatory analysis of cfDNA from plasma samples in another cohort of HNSCC patients. We provided evidence for the relevance of DAPK1, LHX2, MGMT, RAPGEFL1, RARB, and RYR2 methylation analysis in HNSCC diagnosis. Importantly, the methylation of RAPGEFL1, RARB, and RYR2 in tumor samples was found to be associated with HNSCC recurrence. The presence of methylation of RARB and LHX2 in cfDNA distinguished HNSCC patients from healthy controls. Overall, we report that LHX2, RAPGEFL1, RARB, and RYR2 are promising candidates for a methylation-based diagnostic tool in HNSCC patients.