Analysis of Hepatitis B Virus Integration Reveals New Insights of Oncogenic Mechanism in Dysplastic Liver Nodule

Dysplastic nodules (DN) are precursors to cirrhosis-associated malignancy, and the HBV DNA integration in the human genome plays a critical role in tumorigenesis. However, the precise relationship between DN and HBV integration remains unclear. We performed HBV-capture sequencing on 19 cirrhosis patients with HBV infection (DN, 10; RN, 9), out of which 10 subjects (DN, 9; RN, 1) underwent RNA sequencing. In total, 1936 and 1450 HBV integration sites were identified in the DN and RN samples, respectively. The number of HBV integration sites in DN correlated with nodule size. Breakpoints in HBV genome were concentrated within 100 bps toward the 5' or 3' end of involved HBV genes. Furthermore, integration numbers also positively correlated with number of point mutations in DN samples. We identified 53 and 29 recurrent genes containing HBV integrations in ≥ 2 samples in DN and RN samples, respectively. Higher clonality was observed for HBV integrations in recurrent genes than other HBV-integrated genes. The HBV integrations in recurrent genes were predominantly located in intron regions. Notably, among those recurrently HBV-integrated genes in DN samples, SCHIP1, ZDHHC14, YPEL2, RABGAP1L, and SOX5 displayed significant expression alterations. Moreover, clinical indicators revealed significant prolongation of prothrombin time in two DN patients with HBV integrations in SCHIP1 and ZDHHC14. As a new insight regarding HBV integrations in DN stage, our findings suggest a possible role of HBV integration in the transformation of DN to early-stage liver cancer by affecting the expression of key genes.