Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma
Authors
Scott M Langevin, Damaris Kuhnell, Liang Niu, Jacek Biesiada, Yuet-Kin Leung, Ranjan Deka, Aimin Chen, Mario Medvedovic, Karl T Kelsey, Susan Kasper, Xiang Zhang
Institution
University of Cincinnati College of Medicine
Country
United States
Year
2020
Journal
Epigenomics
Abstract
Aim: The goal of this study was to comprehensively interrogate and map DNA methylation across 16 CpG-dense regions previously associated with oral and pharyngeal squamous cell carcinoma (OPSCC). Materials & methods: Targeted multiplex bisulfite amplicon sequencing was performed on four OPSCC cell lines and primary non-neoplastic oral epithelial cells. Real-time quantitative polymerase chain reaction (RT-qPCR) was performed for a subset of associated genes. Results: There was clear differential methylation between one or more OPSCC cell lines and control cells for the majority of CpG-dense regions. Conclusion: Targeted multiplex bisulfite amplicon sequencing allowed us to efficiently map methylation across the entire region of interest with a high degree of sensitivity and helps shed light on novel differentially methylated regions that may have value as biomarkers of OPSCC.