Abstract 1158: Detection of clonally expanded HBV DNA integration sites as a marker for early detection of HBV related HCC.

Abstract

Abstract Hepatocellular carcinoma (HCC), the 5th most frequent cancer worldwide, has a 5-year survival rate of 14% because it is difficult to diagnose at its curative stages. The goal of this project is to determine if the detection of clonally expanded HBV DNA integration sites can be used as a marker for early detection of HBV related HCC (HBV-HCC) in order to improve its prognosis Hepatitis B virus (HBV) infections are associated with over 80% of HCC cases worldwide. Upon infection, the HBV genome integrates into the host chromosome at a random site, thus creating a unique genetic signature for each HBV infected cell. Certain HBV infected cells undergo progressive “uncontrolled clonal expansion” leading to the development of tumors, resulting in an over expansion of the unique HBV integration sites making them the predominant or “major HBV integration sites” (MIS). Cell-free circulating DNA from cancer patients reflects the characteristics of the tumor DNA. We and others have shown that urine contains DNA from the circulation and can be used as a source for cell-free circulating DNA. Successful detection of HBV integration sites in the circulation of HBV-HCC patients has not been demonstrated. In order to detect cell free circulating HBV DNA integration sites, a targeted enriched Next Generation Sequencing (NGS) assay was developed. Targeted enrichment was performed using an in-solution hybridization platform with biotinylated HBV RNA baits surrounding the HBV DNA nucleotide positions 1571 to 1960, the most frequent HBV breakpoint region. The assay was tested using library constructed DNA controls: Hep3B, which contains integrated DNA, and HepG2, which contains no HBV DNA. To determine the amount of captured DNA containing HBV DNA, the captured DNA was quantified for HBV containing DNA and total captured DNA. Almost all captured DNA contained HBV DNA. To confirm targeted capture of integrated HBV DNA, the captured DNA was cloned followed by sequencing. 3 out of 3 clones that were sequenced contain integrated HBV DNA. This assay demonstrated targeted capture and enrichment of HBV integration sites. This assay will be tested for sensitivity in detecting HBV integration sites and used to establish the criteria for the appearance of MIS as a biomarker for HBV-HCC. Overall, if successful, this cancer related HBV DNA marker would offer a high specificity and sensitivity in screening for HBV-HCC. Citation Format: Selena Lin, Surbhi Jain, Timothy Block, Frank Song, Ying Hsiu Su. Detection of clonally expanded HBV DNA integration sites as a marker for early detection of HBV related HCC. [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 1158. doi:10.1158/1538-7445.AM2013-1158