Hepatocellular carcinoma (HCC) is one of the most common and lethal malignancies worldwide, accounting for approximately half a million annual deaths globally. HCC is completely asymptomatic in the early stages of the disease; therefore, early detection of HCC in afflicted patients is vital to receive therapeutic benefits from curative surgery. The standard diagnosis of HCC relies upon detection of the serum alpha-fetoprotein (AFP) level in at-risk subjects followed by hepatic ultrasonography to identify suspicious nodules. Accurate levels of AFP are often difficult to detect, and the imaging method to identify nodules is both operator-sensitive and subject to a high false-negative rate. While it is known that hepatocellular carcinoma is a multi-step process that requires altered expression of multiple genes, recent evidence has indicated that epigenetic abnormalities also play an important role in hepatocarcinogenesis. The discovery of reliable and accurate epigenetic biomarkers may open up new avenues for the development of novel diagnostic tools and provide new target for therapeutic interventions. Combining Next Generation Sequencing methods with well-established bisulfite conversation chemistry, a unique genome-wide epigenetic profile for HCC was done in liver tumor and normal tissues. Hypermethylated and hypomethylated gene regions from the genome-wide epigenetic profile were then validated for percent methylation in liver tumor and normal tissues using a streamlined system of methylation-sensitive restriction enzyme (MSRE) digestion combined with real-time PCR. Serum circulated genomic DNA from liver cancer patients were also examined to look for potential epigenetic markers for clinical diagnostic applications. More than one hundred gene loci were identified at differentially methylated regions (DMRs) by comparing several different stage liver tumors with their correspondent normal tissue by the genome wide epigenetic profile. Calculated CT values from combined MSRE digestion and real-time PCR quantitation indicated that percent methylation of the CpG island in the gene ADAM8 was highest in stage IV liver tumor tissue, while percent methylation of the CpG island in CSMD3 was lowest in stage IV tissue compared to normal adjacent tissue. Percent methylation of the CpG island in ZNF783 was high in all stages of HCC tumor liver tissue compared to normal adjacent tissue. Epigenomic profiling and screening with MSRE digestion and real-time PCR identified and validated differences in the CpG island methylation status of three gene loci in different stages of HCC liver tissue and normal tissue. Extensive validation of these gene specific loci in larger numbers of HCC samples is necessary before they can be considered possible epigenetic biomarkers for novel diagnostic tools and therapeutic interventions for HCC.

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 4026. doi:1538-7445.AM2012-4026