Abstract 4097: Integrative analysis of epigenetic and transcriptional alterations in head and neck squamous cell carcinomas

Abstract

Abstract Objective: Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide with a 50% patient survival rate 5 years post-diagnosis despite current therapeutic strategies. A direct comprehensive genome wide integrated analysis of epigenetic and transcriptional alteration in primary HNSCC has not been performed before. Such data would greatly enrich our knowledge about HNSCC biology and would be beneficial for the development of the individual targeted therapy. Experimental Design: 44 primary HNSCC and 25 normal mucosal samples were used in the Affymetrix GeneChip Human Exon 1.0 array and for the Illumina Infinium Human Methylation 27 array. To analyze the data we employed a novel screening approach based on Cancer Outlier Profile Analysis (COPA). With use of this approach we determined 81 significant differentially expressed and 37 significant differentially methylated genes with both oncogenic and tumor suppressing properties. Results: Out of total 118 candidate genes we picked 36 candidate tumor suppressing genes with strong correlation between hypermethylation and decrease of expression in tumor samples, such as BANK1, ADFP, MAPK4, ZNF71 and others. 20 genes out of total 36 were validated by bisulfite sequencing in a separate cohort of 32 primary HNSCC tumor and 16 normal mucosal tissues. Out of the total 20 genes, 13 demonstrated at least 40% difference in methylation, most notably for BANK1 81% of tumors were more methylated as compared to normals. 7 of these newly discovered genes out of the 36 belong to Zinc Finger Proteins (ZNF) group and they have never been reported as tumor suppressors in HNSCC before. Bisulfite sequencing and quantitative real time PCR (qRT-PCR) analysis of ZNFs revealed that they are strongly hypermethylated and underexpressed in HNSCC tumor samples. Conclusions: Our new screening approach allowed identification of 36 candidate tumor suppressor genes aberrantly methylated and transcriptionally suppressed in HNSCC. Validation of gene expression and methylation allowed the detection of ZNF genes whose downregulation may play a significant role in HNSCC tumor development. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4097. doi:1538-7445.AM2012-4097