Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma

Liu Yang; Song Ye; Xinyi Zhao; Liyan Ji; Yinxin Zhang; Pingyu Zhou; Jun Sun; Yanfang Guan; Yingxin Han; Chao Ni; Xiaoge Hu; Weilong Liu; Haiyan Wang; Boping Zhou; Jian Huang

doi:10.7150/jca.26052

Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma

J Cancer. 2018 Sep 7;9(18):3225-3235. doi: 10.7150/jca.26052. eCollection 2018.

Authors

Liu Yang¹, Song Ye², Xinyi Zhao³, Liyan Ji⁴, Yinxin Zhang⁴, Pingyu Zhou⁵, Jun Sun⁵, Yanfang Guan⁴, Yingxin Han^{6

4}, Chao Ni¹, Xiaoge Hu¹, Weilong Liu⁷, Haiyan Wang⁷, Boping Zhou⁸, Jian Huang^{6

8

7}

Affiliations

¹ Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province and Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical Colleg, Shang Tang Road 158, Hangzhou 310014, Zhejiang, P. R China.
² Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Qing Chun Road 79, Hangzhou 310003, Zhejiang, P. R. China.
³ State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, P. R. China.
⁴ Binhai Genomics Institute, BGI-Tianjin, Tianjin, 300308, China.
⁵ STD Institute, Shanghai Skin Disease Hospital, Tong Ji University, Shanghai, China.
⁶ Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Chinese National Human Genome Center at Shanghai. Shanghai Jiao Tong University, Shanghai, 200240, China.
⁷ Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, 518112, China.
⁸ Shenzhen People's Hospital, Second Clinical Medical College of Jinan University. Shenzhen, 518109, China.

Abstract

Infection by chronic hepatitis B virus (HBV) is one of the major causes of liver cirrhosis and primary hepatocellular carcinoma (HCC). Viral DNA integration into the host cell genome is a key mechanism of hepatocarcinogenesis. However, the molecular characterization and the potential clinical implications of HBV DNA integration into patients suffering from different hepatitis and HCC remain unclear. In this study, we analyzed HBV integrations in patients with hepatitis B and HCC using HBV probe-based capturing and next-generation sequencing. The results revealed that the sizes of the HBV integrations ranged from 28 bp to 3215 bp, including the full-length HBV DNA sequence. The integration breakpoints were preferentially distributed in the viral enhancer, X protein, and core protein regions of the HBV genome. The number of HBV integrations followed an increasing trend from hepatitis to HCC, which was positively correlated with the HBV virus load in patients with hepatitis. The number of HBV integrations in the HBeAg positive chronic hepatitis B group was significantly greater than that in the other hepatitis B groups (P < 0.05). However, the relative abundance of HBV integrations was significantly higher in HCC tissues than in the adjacent liver tissues. Interestingly, 61.6% (8/13) of HBV-human DNA integration fragments could be detected at the RNA level. Our results also showed that HBV integration-targeted genes (ITGs) were significantly enriched in many cancer-related pathways, such as MAPK, extracellular matrix (ECM)-receptor interaction, and the hedgehog signaling pathway. Individuals with HBV integrations exhibited shorter disease-free survival (DFS) and overall survival (OS) than those without HBV integrations in some ITGs including LINC00293 (long intergenic non-protein coding RNA 293; DFS P = 0.008, OS P = 0.009), FSHB (follicle stimulating hormone beta subunit; DFS P = 0.05, OS P = 0.186), and LPHN3 (latrophilin-3; DFS P = 0.493, OS P = 0.033). This study determined the underlying mechanism of HBV DNA integration in liver diseases and laid the foundation for future studies on the pathogenesis of liver cancer.

Keywords: Capture sequencing; Chronic hepatitis B virus; HBV integration.; Hepatocellular carcinoma.