Whole Genome Sequencing Sheds Light on Hepatitis Virus Integration in Cancer Genome

May 29, 2012

By Allison Proffitt 

May 29, 2012 | Researchers focusing on Asian cancers have used whole-genome sequencing to study the level of hepatitis B virus integration in the genomes of cancer patients and to discover three novel genes associated with recurrent hepatitis B virus integration in hepatocellular carcinoma. The study was published today in Nature Genetics.  

The integration of the hepatitis B virus (HBV) into a host genome is thought to be a major cause of hepatocellular carcinoma (HCC). HBV integration is believed to induce chromosomal instability or alter expression and function of endogenous genes.  

The Asian Cancer Research Group (ACRG)—an independent, not-for-profit company established by Eli Lilly and Company, Merck, and Pfizer and focused on Asian liver, gastric and lung cancers—along with collaborators from BGI, the University of Hong Kong, National University of Singapore, National University Health System (Singapore), and the Genome Institute of Singapore, conducted the research.  

While previous studies of HBV integration into the HCC genome have been limited by technological hurdles and relatively small sample sizes, the current study carried out whole-genome sequencing for 88 HCC patients, including 81 HBV-positive and 7 HBV-negative HCC patients, Hancheng Zheng, primary investigator on this project at BGI, told Bio-IT World. All were Chinese patients diagnosed with HCC who underwent curative primary hepatectomy or liver transplant at Queen Mary Hospital in Hong Kong. All sequencing was done by BGI using Illumina HiSeq 2000 instruments.  

Tumor samples were characterized for genome integration patterns and to determine the prevalence of integrated HBV. Researchers found that HBV integration was a common event in liver tumors and was observed more frequently in tumors (86.4%) than in adjacent normal liver tissues (30.7%).  

In addition to the previously reported TERT and MLL4 genes, researchers discovered three novel genes (CCNE1, SENP5 and ROCK1) associated with recurrent HBV integrations, each of which are known to play an important role in cancer development and progression. 

Researchers also observed that the number of HBV integration events (recurrences) is positively associated with the tumor size and other cancer markers. Patients with no or low numbers (n<3) of detected HBV integrations in their tumor survived longer than those with a high number of HBV integrations (n>3), suggesting that HBV integration events are a negative prognostic indicator in HCC patients. 

“Based on these results, we can better explore the detailed molecular mechanism and clinical impact of HBV integration, promoting the discovery and development of future liver cancer treatments,” said Zheng.   

HBV integration sites are typically found close to or inside of the targeted genes, which may be a mechanism for HBV to control the expression of some oncogenes or tumor suppressor genes. More than 40% of the integrations were observed to break the HBV genome at position 1,800 and integrate into the human genome. This may be due to the fact that the HBV enhancer and the HBV ORF replication sites are found at this locus.  

Moreover, researchers observed that HBV integrations correlated with increased DNA copy number around HBV integration breakpoints, which provides evidence that HBV integration initializes the chromosomal instability of the HCC genome. 

This study provided new insight into mechanisms of HBV integration, which promote liver cancer and affect clinical outcomes,” said Ken Sung, National University of Singapore and Honorary Associate Professor of Hong Kong University, lead author of the study, in a press release. “We expect further investigation may lead to improved diagnosis and treatment of HCC."