Global Epigenetic Alterations in Head and Neck Squamous Cell Carcinoma
H Zhang, A Stone, C Xie, SA Schichman, C-Y Fan. University of Arkansas for Medical Sciences, Little Rock, AR; John L. McClellan Memorial Veterans Hospital, Little Rock, AR
Background: Head and neck cancer is the most common epithelial malignancy of the upper aerodigestive tract. Despite multimodality treatment regimens of combined surgery and chemoradiation therapies, the overall 5-year survival for head and neck cancer has not exceeded 50% for the past 3 decades. Recently, there is growing evidence that in addition to widespread genetic abnormalities, epigenetic alterations in association with promoter hypermethylation play significant roles in the development and progression of human cancer. In this study, we analyze a global methylation pattern in 4 HNSCC cancer cell lines as compared to normal oral keratinocyte cell line using Illumina DNA methylation microarray.
Design: 4 HNSCC cell lines (CRL1623, HEp2, SQ20B and UMSCC1) treated with or without 5-azacytidine, a DNA demethylating agent and a normal oral keratinocyte cell line (HOK16B) were used for extraction of genomic DNA, followed by sodium bisulfite modification and global promoter methylation analysis using Illumina BeadArray (HumanMethylation27) containing 28,544 target CpG sites, representing a total of 14,956 genes.
Results: Among 14,956 genes, there were 1230 genes that showed increased promoter methylation by 2-fold or greater in all 4 HNSCC cell lines CRL1623, HEp2, SQ20B and UMSCC1) as compared to the normal keratinocyte line (HOK16B). Following the treatment of 5-azacytidine, 42 out of these selected 1230 genes showed decreased methylation in all 4 HNSCC cell lines by at least 10%. Thus, these 42 genes are likely those whose expression is commonly regulated by epigenetic mechanism in HNSCC but not in normal oral keratinocytes. Using these 42 genes for cluster analysis, 4 HNSCC cell lines were clustered closely to one another and the promoter methylation pattern for HNSCC cell lines was distinctively different from that in normal oral keratinocytes.
Conclusions: Using the powerful Illumina DNA methylation microarray, we have identified a small subset of genes that frequently undergo promoter methylation in HNSCC. This information should be invaluable in helping us to identify novel epigenetic markers for early cancer detection or molecular targets for epigenetic therapy in the treatment of HNSCC.
Category: Head & Neck
Monday, March 9, 2009 1:00 PM
Poster Session II # 163, Monday Afternoon