Abstract
METHODS
Methylated DNA sequencing (MeD-seq) was used to analyze genome-wide DNA methylation patterns in formalin-fixed paraffin-embedded (FFPE) tonsil samples. Gene set enrichment analysis explored the biological role of DMR associated genes. A literature search of DMR's was performed to compare MeD-seq to other techniques.
RESULTS
Thirty-one analyzed samples (10 HPV + OPSCC, 9 HPV- OPSCC, and 12 controls) revealed 4,962 DMRs. We focused on the top five promoter-region DMRs with the highest fold change per comparison (HPV + vs. HPV-; HPV + vs. controls; HPV - vs. controls). Key DMRs involved IRF4, TCF24, and CLSTN2. IRF4 was hypermethylated in both OPSCC groups compared to controls, while CLSTN2 was hypermethylated in HPV + versus HPV - tumors. Enrichment analysis indicated enrichment of cell cycle-related pathways in HPV + tumors and IGF1R signaling pathways in HPV - tumors. MeD-seq confirmed known methylation patterns and identified novel OPSCC-specific DMRs.
DISCUSSION
This pilot study demonstrates HPV-associated methylation profiles in OPSCC, highlighting MeD-seq as a reliable technique for tumor methylation analysis, confirming existing and identifying novel DMRs. Larger studies are needed to validate potential biomarkers for prognosis and personalized treatment.
INTRODUCTION
Epigenetic modifications, particularly DNA methylation, play a key role in oropharyngeal squamous cell carcinoma (OPSCC). This is the first study to apply genome-wide methylated DNA sequencing (MeD-seq) to identify differentially methylated regions (DMRs) in OPSCC. By comparing HPV-positive and HPV-negative tonsillar carcinomas, we evaluate MeD-seq's applicability to validate known and identify novel DMRs. These findings may support the identification of potential biomarkers for risk stratification and prognostic assessment in OPSCC.