Line Region Hypomethylation Is Associated with Lifestyle and Differs by Human Papillomavirus Status in Head and Neck Squamous Cell Carcinomas

Abstract

Genomic hypomethylation is a hallmark of essentially all cancers, but the degree of this hypomethylation differs among individual tumors. Little work has explored what leads to these differences and or asked whether they are clinically meaningful. In this study of head and neck squamous cell carcinoma, we assessed hypomethylation in tumors using a semiquantitative fragment analysis approach to determine the relative methylation status of the line retroviral element LRE1 (Line-1.2). Because this is an established marker of genomic methylation status, we examined the relationship between the relative methylation, patient demographics, and other risk factors for head and neck squamous cell carcinoma. We determined relative methylation status for 303 patients, 193 of which had complete data for all variables of interest. Using a generalized linear model, we found that patient body mass index was significantly positively associated with tumor LRE1 methylation level. Smoking duration, particularly in tumors lacking human papillomavirus (HPV) DNA, was significantly negatively associated with relative methylation level. Having previously assessed relative methylation in blood-derived DNA, we compared tumor with the blood DNA methylation level and observed these to be independent. Finally, the lower LRE1 methylation in patients whose tumors were HPV DNA negative was associated with poorer patient survival (hazard ratio, 1.6; 95% confidence interval, 1.0-2.6). These findings suggest that HPVassociated tumors differ molecularly from those arising after heavy tobacco use and that this epigenetic alteration may affect survival in HPV-negative patients already exhibiting a more aggressive disease. (Cancer Epidemiol Biomarkers Prev 2008;17(4):966 -71)

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.…”

“…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. 34 The mean age in HPV-positive tumors was 56.9 compared with 58.4 in HPV-negative tumors.…”

“…Eight studies detected methylation in HPV-positive and HPV-negative primary tumors using formalin-fixed paraffinembedded (FFPE) specimen. 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.…”

“…40 There was a wide variation in percentage of HPV positivity between studies ranging from 7% to 56%. 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. 32,38,39 One study examined both promoter methylation and global methylation, in association with HPV status. 40 Promoter methylation was interpreted differently among studies.…”