Abstract 2298: Methylated gene markers discovered in nasopharyngeal carcinoma by differential methylation hybridization (DMH) in high density CpG island DNA chips

Abstract

Abstract Nasopharyngeal carcinoma (NPC) is a prevalent cancer in southern China and south east Asian countries. A variety of tumor suppressor (TS) genes including p16, RASSF1A, EDNRB, DAP-Kinase, RIZ1, E-Cadherin were found to be hypermethylated in NPC. This, however, could only be the tip of an iceberg. We made use of the high throughput differential methylation hybridization (DMH) technique in screening for methylated DNA markers in 244K CpG island DNA chip in three NPC xenografts (C15, C17, 99-186), a NPC tumor cell line (C666) versus an immortalized NP non-cancer cell line (NP69). This DMH screening discovered 100, 213, 372 and 977 genes respectively in 99-186, C17, C15 and C666 with ≥ 5 CpG sites in their gene promotors being methylated. Among these genes, 28 of them were found to have DNA methylation in all the 4 NPC xenografts/ tumor cell line. Bisulphite sequencing was performed in 17 pairs of tumor and normal biopsy samples from 17 NPC patients. This confirmed tumor specific methylation in the promotor regions of 8 gene markers, namely, NRP3, PCDH10, PENK, ADHFE1, IRX4, GSC, PFN2 & GFI1 with positive methylation ratios (+ve MR) in tumor biopsies of 86.7%, 85.7%, 80%, 72.7%, 54.5%, 50%, 41.7% &23.1% respectively and +ve MR of 18.2%, 0%, 0%, 0%, 0%, 37.5%, 12.5% & 0% respectively in normal biopsies. Methylation of CpG sites appears to occur either all or none with 15 to 45 consecutive CpG sites in these genes either all methylated or non-methylated in tumor biopsies probably indicating the need of methylation of a full cluster of CpG sites in order to affect the gene transcription of the discovered genes. Functions of the DMH identified genes includes cell adhesion (PCDH10), signal transduction (PENK), chloride ion binding (NPR3), regulation of DNA dependent transcription (IRX4) and xenobiotic metabolism (ADHFE1). In fact, PCDH10, PENK and GFI1 genes have been reported to be closely associated with NPC/esophageal carcinoma, pancreatic adenocarinoma and T-cell lymphoma respectively. Further analyses in these methylated markers could be useful in the diagnosis and study of etiology of NPC. Citation Format: Wai Wai Cheng, Roger K.C. Ngan, Dora L.W. Kwong, Tim H.M. Huang, Victor W.S. Ma, Stephen C.K. Law, Loretta Tse, Pierre Busson, George S.W. Tsao, Maria Li Lung, Timothy T.C. Yip. Methylated gene markers discovered in nasopharyngeal carcinoma by differential methylation hybridization (DMH) in high density CpG island DNA chips. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2298. doi:10.1158/1538-7445.AM2014-2298