Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted

Graham M Poage,E Andres Houseman,John K Wiencke,Karl T Kelsey,John R Clark,Heather H Nelson,Carmen J Marsit,Marshall R Posner,Brock C Christensen,Michael D Mcclean

doi:10.1371/journal.pone.0009651

Abstract

BackgroundSolid tumors, including head and neck squamous cell carcinomas (HNSCC), arise as a result of genetic and epigenetic alterations in a sustained stress environment. Little work has been done that simultaneously examines the spectrum of both types of changes in human tumors on a genome-wide scale and results so far have been limited and mixed. Since it has been hypothesized that epigenetic alterations may act by providing the second carcinogenic hit in gene silencing, we sought to identify genome-wide DNA copy number alterations and CpG dinucleotide methylation events and examine the global/local relationships between these types of alterations in HNSCC.Methodology/Principal FindingsWe have extended a prior analysis of 1,413 cancer-associated loci for epigenetic changes in HNSCC by integrating DNA copy number alterations, measured at 500,000 polymorphic loci, in a case series of 19 primary HNSCC tumors. We have previously demonstrated that local copy number does not bias methylation measurements in this array platform. Importantly, we found that the global pattern of copy number alterations in these tumors was significantly associated with tumor methylation profiles (p<0.002). However at the local level, gene promoter regions did not exhibit a correlation between copy number and methylation (lowest q = 0.3), and the spectrum of genes affected by each type of alteration was unique.Conclusion/SignificanceThis work, using a novel and robust statistical approach demonstrates that, although a “second hit” mechanism is not likely the predominant mode of action for epigenetic dysregulation in cancer, the patterns of methylation events are associated with the patterns of allele loss. Our work further highlights the utility of integrative genomics approaches in exploring the driving somatic alterations in solid tumors.

Highlights

Head and neck squamous cell carcinoma (HNSCC) is the eighth most commonly diagnosed malignancy in males, responsible for over an estimated 11,000 deaths each year in the United States [1]
Epigenetic alterations commonly observed in this disease include promoter hypermethylation, resulting in gene silencing, of CDKN2A, CDH1, DAPK1, RASSF1, and MGMT, which have been shown to be associated with patient outcome [7,8,9]
Evidence has emerged that CDKN2A [10,11], RASSF1 [12], and other genes are regulated both by hypermethylation and allele loss in many solid tumor types [13,14,15] leading to the hypothesis that, in addition to classical Knudson inactivation of tumor suppressors through mutation [16], first and second hits commonly occur in the form of promoter methylation and loss of heterozygosity (LOH) even in the absence of mutation

Summary

Introduction

Head and neck squamous cell carcinoma (HNSCC) is the eighth most commonly diagnosed malignancy in males, responsible for over an estimated 11,000 deaths each year in the United States [1]. Epigenetic alterations commonly observed in this disease include promoter hypermethylation, resulting in gene silencing, of CDKN2A, CDH1, DAPK1, RASSF1, and MGMT, which have been shown to be associated with patient outcome [7,8,9]. Recent large scale array-based studies of epigenetic events have yielded similar insight into the pattern of gene silencing in cancers, in that alterations to promoter methylation status of genes occurs in a highly variable pattern even amongst tumors arising from the same tissue or cell type [19,20,21]. Solid tumors, including head and neck squamous cell carcinomas (HNSCC), arise as a result of genetic and epigenetic alterations in a sustained stress environment. Since it has been hypothesized that epigenetic alterations may act by providing the second carcinogenic hit in gene silencing, we sought to identify genome-wide DNA copy number alterations and CpG dinucleotide methylation events and examine the global/local relationships between these types of alterations in HNSCC

Methods

Results

Conclusion