Comprehensive analysis of DNA methylation in head and neck squamous cell carcinoma indicates differences by survival and clinicopathologic characteristics.
Head and neck squamous cell carcinoma (HNSCC) is the eighth most commonly diagnosed cancer in the United States. The risk of developing HNSCC increases with exposure to tobacco, alcohol and infection with human papilloma virus (HPV). HPV-associated HNSCCs have a distinct risk profile and improved prognosis compared to cancers associated with tobacco and alcohol exposure. Epigenetic changes are an important mechanism in carcinogenic progression, but how these changes differ between viral- and chemical-induced cancers remains unknown. CpG methylation at 1505 CpG sites across 807 genes in 68 well-annotated HNSCC tumor samples from the University of Michigan Head and Neck SPORE patient population were quantified using the Illumina Goldengate Methylation Cancer Panel. Unsupervised hierarchical clustering based on methylation identified 6 distinct tumor clusters, which significantly differed by age, HPV status, and three year survival. Weighted linear modeling was used to identify differentially methylated genes based on epidemiological characteristics. Consistent with previous in vitro findings by our group, methylation of sites in the CCNA1 promoter was found to be higher in HPV(+) tumors, which was validated in an additional sample set of 128 tumors. After adjusting for cancer site, stage, age, gender, alcohol consumption, and smoking status, HPV status was found to be a significant predictor for DNA methylation at an additional 11 genes, including CASP8 and SYBL1. These findings provide insight into the epigenetic regulation of viral vs. chemical carcinogenesis and could provide novel targets for development of individualized therapeutic and prevention regimens based on environmental exposures.
Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA.
Justin A
JA
Colacino
Dana C
DC
Dolinoy
Sonia A
SA
Duffy
Maureen A
MA
Sartor
Douglas B
DB
Chepeha
Carol R
CR
Bradford
Jonathan B
JB
McHugh
Divya A
DA
Patel
Shama
S
Virani
Heather M
HM
Walline
Emily
E
Bellile
Jeffrey E
JE
Terrell
Jay A
JA
Stoerker
Jeremy M G
JM
Taylor
Thomas E
TE
Carey
Gregory T
GT
Wolf
Laura S
LS
Rozek
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001483:Base Sequence; D002294:Carcinoma, Squamous Cell / Q000235:genetics / Q000473:pathology* / Q000821:virology; D016000:Cluster Analysis; D018899:CpG Islands; D019175:DNA Methylation; D017931:DNA Primers; D005260:Female; D006258:Head and Neck Neoplasms / Q000235:genetics / Q000473:pathology* / Q000821:virology; D006801:Humans; D008297:Male; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D016019:Survival Analysis; D055815:Young Adult
D017931:DNA Primers