Abstract 46: Validation of potential predictive DNA methylation biomarkers for head and neck squamous cell carcinoma anatomic subsite
Authors: Rivera Bianca L. , Aponte Jaime , Nadal Sol , Oliva Sebastian , Bravo Sebastian , Guerrero Rafael , Trinidad Juan , Baez Adriana 
Published: December 2017

Abstract
Introduction: We previously identified by a genome-wide approach, differentially methylated genes in head and neck squamous cell carcinoma (HNSCC), including genes uniquely methylated in each HNSCC anatomic subsite. To define their potential prognostic value the validation of uniquely methylated genes in a cohort of HNSCC patients, according to the anatomic subsite, is warranted. Thus, here we present validation data of three potential DNA methylation biomarkers in a cohort comprising primary tumors of 54 HNSCC patients.
Methods: Tumor DNA was extracted from HNSCC patients, stratified by the primary tumor anatomic subsite, which included 21 laryngeal cancers, 21 oral cavity cancer, and 12 pharyngeal cancers. The DNA methylation status of three candidate biomarkers, CDH1 for laryngeal cancer, PITX2 for oral cavity cancer, and SFRP1 for pharyngeal cancer were assessed. DNA methylation analysis was performed using qMSP MethyLight assay and quantitative methylation value for each gene was expressed as the Percentage of Methylation Reference (PMR). A PMR value cut-off was established to classify samples as positively or negatively methylated. PMR values &lt;10 were classified as negatively methylated and PMR values of ≥10 were classified as positively methylated for each gene.
Results: Positive methylation (PMR ≥10) was detected in 71% of laryngeal samples for CDH1 and, in pharyngeal cancer, 66% showed positive methylation for SFRP1. 90% of oral cavity samples showed positive methylation for PITX2. No association with clinicopathologic characteristics (stage, differentiation, recurrence) was found. However, high PMR values (PMR ≥20) were observed in early stage tumors (I and II) as for late stage tumors (III and IV) for all candidate genes tested.
Conclusion: HNSCC subsites (larynx, oral cavity and pharynx) show differential DNA methylation patterns for selected genes. Aberrant methylation of CDH1, PITX2 and SFRP1 was established in a high percentage of tumors, suggesting these candidate genes might be useful as molecular classifiers for HNSCC subsite. In addition, aberrant methylation of CDH1, PITX2, and SFRP1 was detected in early stage tumors; which might be indicators of hypermethylation as an early event in HNSCC carcinogenesis, and in association to the anatomic subsite. Analysis of these unique DNA methylation biomarkers for HNSCC may be valuable for an accurate disease prognosis and for design of novel treatments.
Citation Format: Bianca L. Rivera, Jaime Aponte, Sol Nadal, Sebastian Oliva, Sebastian Bravo, Rafael Guerrero, Juan Trinidad, Adriana Baez. Validation of potential predictive DNA methylation biomarkers for head and neck squamous cell carcinoma anatomic subsite [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; April 23-25, 2017; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(23_Suppl):Abstract nr 46.