DNA Methylation Markers from Negative Surgical Margins Can Predict Recurrence of Oral Squamous Cell Carcinoma

SIMPLE SUMMARY: Up to 30% of oral cavity cancer patients with pathologically negative surgical margins usually exhibit tumor recurrence. Early molecular alterations in the tumor-adjacent normal tissues prior to the onset of cancer phenotype could be important to this event. Therefore, here we aimed to evaluate the DNA methylation patterns of negative surgical margins as a prognostic factor for tumor recurrence. Our results demonstrated that recurrent patients with negative histological margins exhibit differential DNA methylation markers. These markers might be crucial for the identification of individuals at higher risk of developing tumor recurrence and could be clinically explored further to help in decreasing morbidity and improving survival rates of these patients. ABSTRACT: The identification of molecular markers in negative surgical margins of oral squamous cell carcinoma (OSCC) might help in identifying residual molecular aberrations, and potentially improve the prediction of prognosis. We performed an Infinium MethylationEPIC BeadChip array on 32 negative surgical margins stratified based on the status of tumor recurrence in order to identify recurrence-specific aberrant DNA methylation (DNAme) markers. We identified 2512 recurrence-associated Differentially Methylated Positions (DMPs) and 392 Differentially Methylated Regions (DMRs) which were enriched in cell signaling and cancer-related pathways. A set of 14-CpG markers was able to discriminate recurrent and non-recurrent cases with high specificity and sensitivity rates (AUC 0.98, p = 3 × 10(−6); CI: 0.95–1). A risk score based on the 14-CpG marker panel was applied, with cases classified within higher risk scores exhibiting poorer survival. The results were replicated using tumor-adjacent normal HNSCC samples from The Cancer Genome Atlas (TCGA). We identified residual DNAme aberrations in the negative surgical margins of OSCC patients, which could be informative for patient management by improving therapeutic intervention. This study proposes a novel DNAme-based 14-CpG marker panel as a promising predictor for tumor recurrence, which might contribute to improved decision-making for the personalized treatment of OSCC cases.