Abstract 4249: Landscape of DNA methylation status of human hepatocellular carcinoma revealed by Human Methylation BeadChip 450K.

Abstract

Abstract <Background and aim> Global DNA hypomethylation and regional hypermethylation in CpG island has been recognized as common feature of cancer DNA, including that of hepatocellular carcinoma (HCC). However, precise mechanism underlying the alteration of methylation is still unclear. We conducted a genome-wide methylation analysis to elucidate distribution and characteristics of genes that subject to cancer-related DNA methylation in human HCC. <Materials and methods> With written informed consent, 20 HCC and 3 corresponding matched non-cancerous liver tissues were obtained at the time of hepatectomy (2 tumors) or orthotopic living-donor liver transplantation (17 tumors and 3 non-tumors). After bisulfite modification, the converted DNA was subject to hybridization on Infinium Human Methylation BeadChip 450K (Illumina, Inc., San Diego, CA) that contained 485,577 CpGs of the human genome including gene promoters and repetitive DNA elements. The methylation level for each CpG was represented as a beta value according to the fluorescent intensity ratio. In order to identify alteration of methylation profile between HCC and non-tumor liver, difference of average beta values between tumor and non-tumor was calculated. <Results> Of 485,577 CpG loci, differences of average beta values of 460,036 loci (94.7%) were within 30%. These were considered as constitutively methylated or unmethylated. Tumor-specific hypomethylation was found at 18,807 loci. Of these, 65.1% were located outside CpG islands, shore or shelf (so-called ‘open sea’). Tumor-specific demethylation rarely occurred within CpG islands (6.5%). On the other hand, tumor-specific DNA methylation was found at 6734 loci. Of these, 77.6% were located within CpG islands. Interestingly, normally methylated CpGs (average beta value < 0.20) were mainly located in CpG islands (95,943 of 138,081, 69.0%), and many of normally unmethylated or variably methylated CpGs were located in the open sea (165,209 of 347,496, 47.5%). <Conclusion> Tumor-specific methylation occurring at CpG islands, may simply be dependent on the distribution of normally unmethylated CpGs. This finding may help us target epigenetically silenced tumor suppressor genes. Citation Format: Takafumi Nishimura, Yukiko Mori, Naoshi Nishida. Landscape of DNA methylation status of human hepatocellular carcinoma revealed by Human Methylation BeadChip 450K. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4249. doi:10.1158/1538-7445.AM2013-4249