Fine mapping of hepatitis B virus pre-S deletion and its association with hepatocellular carcinoma.

Background Naturally occurring pre-S deletion mutants have been identified in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Aims This study investigated whether specific deletions within the pre-S region were associated with HCC development. Methods The virologic characteristics of 56 HBV chronic carriers and 112 age-matched patients with HBV-related HCC were examined. Results The HCC patients had a significantly higher frequency of high viral load, basal core promoter mutation and pre-S deletion than chronic carriers. Sequencing analysis showed that the deleted regions were clustered mainly in the C terminus of pre-S1 (70.5%) and the N terminus of pre-S2 (72.7%) in HCC patients. Immuno-epitope mapping of these pre-S deletion sequences showed that all the deletion regions encompassed T- and B- cell epitopes and the B-cell epitope at amino acid 1–6 of pre-S2 was significantly deleted in HCC patients (60.0% vs. 0.0%; P = 0.036). Functional mapping of these deletion mutants showed that most of HCC patients lost one or more functional sites and the deletion of site for viral secretion (aa 1–5 of pre-S2 domain) was significantly detected in HCC patients than chronic carriers (62.5% vs. 0.0%; P = 0.029). Computational protein function prediction indicated that these mutants may have different molecular functions and participate in other biological processes compared with wild-type pre-S. Conclusions Deletion of B-cell epitope at amino acid 1–6 of pre-S2 region and the site for virion secretion are significantly associated with the development of HCC in HBV carriers.