HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas

Abstract

High-risk types of human papilloma virus (HPV) are increasingly associated with oropharyngeal squamous cell carcinoma (OPSCC). Strikingly, patients with HPV-positive OPSCC are highly curable with ionizing radiation and have better survival compared with HPV-negative patients, but the underlying molecular mechanisms remain poorly understood. We applied an array-based approach to monitor global changes in CpG island hypermethylation between HPV-negative and HPV-positive OPSCCs and identified a specific pattern of differentially methylated regions that critically depends on the presence of viral transcripts. HPV-related alterations were confirmed for the majority of candidate gene promoters by mass spectrometric, quantitative methylation analysis. There was a significant inverse correlation between promoter hypermethylation of ALDH1A2, OSR2, GATA4, GRIA4, and IRX4 and transcript levels. Interestingly, Kaplan-Meier analysis revealed that a combined promoter methylation pattern of low methylation levels in ALDH1A2 and OSR2 promoters and high methylation levels in GATA4, GRIA4, and IRX4 promoters was significantly correlated with improved survival in 3 independent patient cohorts. ALDH1A2 protein levels, determined by immunohistochemistry on tissue microarrays, confirmed the association with clinical outcome. In summary, our study highlights specific alterations in global gene promoter methylation in HPV-driven OPSCCs and identifies a signature that predicts the clinical outcome in OPSCCs.

Characterization of HPV and host genome interactions in primary head and neck cancers

“…S8 C and D). Recent studies have reported hypermethylation and inversely correlated expression of IRX4 in HPV-driven oropharyngeal tumors compared with non-HPVdriven tumors, and the hypermethylation signature correlated with better clinical outcomes (49). Using Gene Set Enrichment Analysis, we observed differential methylation of genes in the cAMP response element-binding protein (CREB) pathway and differential expression of genes involved in regulation of apoptosis and NF-κB signaling.…”

Differences in methylation profiles between HPV-positive and HPV-negative oropharynx squamous cell carcinoma

“…Seventeen articles met the inclusion criteria and were eligible for further analysis. [28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44] The main reasons for exclusion were duplicates and studies not investigating correlation between HPV status and methylation status in OPSCC.…”

“…Four studies dealt with OPSCC only. 28,33,34,44 In other publications studying overall HNSCC, OPSCC subgroup size ranged from 9% to 80% of the total study population. [29][30][31][32][35][36][37][38][39][40][41][42][43] There was only one study that reported the distribution of average age, nicotine and alcohol consumption between HPV-positive and HPV-negative tumors of which promoter methylation was evaluated.…”

“…28,29,32,[34][35][36][37]40 Six used fresh frozen (FF) tissue or both. 31,38,[41][42][43][44] Three studies did not report used material. 30,33,39 The majority of studies used polymerase chain reaction (PCR) to detect HPV 16 DNA.…”

“…The studies used varying techniques to determine gene methylation; most studies used methylation-specific PCR (MSP), while other studies used combined bisulfite restriction analysis (COBRA), 28,32 pyrosequencing analysis (PMA), 38,39 bead array method (BAM), 29,34,40 or quantitative MSP (qMSP). 33,42,44 Thirteen studies evaluated promoter methylation in selected genes in association with HPV status. [28][29][30][31][33][34][35][36][37][41][42][43][44] Three studies investigated global methylation in association with HPV status.…”