Hepatitis B virus genotype and mutants: risk factors for hepatocellular carcinoma

ncRNA-disease association prediction based on sequence information and tripartite network

Background

Current technology has demonstrated that mutation and deregulation of non-coding RNAs (ncRNAs) are associated with diverse human diseases and important biological processes. Therefore, developing a novel computational method for predicting potential ncRNA-disease associations could benefit pathologists in understanding the correlation between ncRNAs and disease diagnosis, treatment, and prevention. However, only a few studies have investigated these associations in pathogenesis.

Results

This study utilizes a disease-target-ncRNA tripartite network, and computes prediction scores between each disease-ncRNA pair by integrating biological information derived from pairwise similarity based upon sequence expressions with weights obtained from a multi-layer resource allocation technique. Our proposed algorithm was evaluated based on a 5-fold-cross-validation with optimal kernel parameter tuning. In addition, we achieved an average AUC that varies from 0.75 without link cut to 0.57 with link cut methods, which outperforms a previous method using the same evaluation methodology. Furthermore, the algorithm predicted 23 ncRNA-disease associations supported by other independent biological experimental studies.

Conclusions

Taken together, these results demonstrate the capability and accuracy of predicting further biological significant associations between ncRNAs and diseases and highlight the importance of adding biological sequence information to enhance predictions.

The mutation of hepatitis B virus and the prognosis of hepatocellular carcinoma after surgery: a pilot study

Background

Although hepatitis B virus (HBV) is still one of the most common etiological factors for hepatocellular carcinoma (HCC), the association between the HBV mutations and the clinical characteristics and prognosis of HBV-related HCC patients (HBV-HCC) after surgical resection remains largely unknown.

Materials and methods

A cohort of 131 consecutive patients who received hepatectomy for HBV-HCC were retrospectively enrolled. The HBV genotype and 14 genomic mutations, which have been reported to relate to HCC in liver samples, were sequenced. The associations between the genomic mutations and clinical characteristics and outcomes were analyzed.

Results

Both A1762T/G1764A mutation and Pre S deletion related to worse overall survival (OS, p=0.040 and p<0.001, respectively) and disease-free survival (DFS, p=0.040 and p<0.001, respectively), G1899A mutation related to worse OS (p=0.030), A1762T/G1764A mutation correlated with tumor size (r=0.204, p=0.019), G1899A mutation correlated with vascular invasion (r=0.332, p<0.001), and Pre S deletion correlated with alpha-fetoprotein (AFP; r=0.254, p=0.003) positively. Multivariate analysis with Cox proportional hazards model revealed that both A1762T/G1764A mutation and Pre S deletion were independent prognostic factors for OS (hazard ratio [HR]=3.701, 95% CI=1.390–9.855, p=0.009, and HR=4.816, 95% CI=2.311–10.032, p<0.001, respectively) and DFS (HR=3.245, 95% CI=1.400–7.521, p=0.006, and HR=2.437, 95% CI=1.311–4.530, p<0.001, respectively), and patients with dual mutations were found to have the worst OS and DFS (p<0.001 and p<0.001, respectively). Patients with A1762T/G1764A mutation or Pre S deletion were more likely to have early recurrence (p=0.042 and p=0.019, respectively).

Conclusion

HBV DNA genomic mutations in A1762T/G1764A and Pre S deletion were associated with worse prognoses and early recurrence for HBV-HCC patients after surgery.

Proposal of Prognostic Survival Models before and after Liver Resection for Hepatocellular Carcinoma in Potentially Transplantable Patients

BACKGROUND

Transplantable hepatocellular carcinoma (HCC) represents a highly debated issue due to the overlap between indications for liver resection (LR) and transplantation (LT) in patients suitable for both.

STUDY DESIGN

Between January 2000 and December 2012, five hundred and twenty-four transplantable patients affected by HCC were identified among resected patients. Two regression models were constructed to classify patients into 2 groups pre-low and pre-high risk based on preoperative variables and then to reclassify pre-low-risk patients according to postoperative variables into either post-low or post-high-risk. Additionally, a cohort of patients with comparable baseline characteristics who underwent LT were similarly classified into pre-low and pre-high-risk groups and compared with the resected patients in terms of survival.

RESULTS

Cirrhosis, aspartate transaminase, α-fetoprotein, Model for End-Stage Liver Disease score, number of nodules, and diameter of the largest nodule were preoperatively found to be significantly related to overall survival post-LR. Microvascular invasion and satellites were selected to reclassify prognosis in the resulting preoperative low-risk group into post-high risk. The converted group (post-high) demonstrated the same 5-year survival as the pre-high group. Patients undergoing LT had better survival overall than those undergoing LR, with the exception of pre-low LT and post-low LR (confirmed low-risk LR) who had similar outcomes.

CONCLUSIONS

The new models were strongly predictive of patients' likelihood of survival after LR for HCC on liver cirrhosis. Liver transplantation offers a survival advantage over LR, except in low-risk groups where both modalities might be comparable.

Deep sequencing of hepatitis B virus basal core promoter and precore mutants in HBeAg-positive chronic hepatitis B patients

Mutants in the basal core promoter (BCP) and precore (PC) regions of hepatitis B virus (HBV) genome are associated with the progression of chronic hepatitis B (CHB) infection. However, quasispecies characteristics of naturally occurring mutants in those regions in HBeAg-positive CHB patients has not been well described, partly limited by quantitative assay. This study aimed to develop an Ion Torrent deep sequencing assay to determine BCP and PC mutant percentages in HBeAg-positive CHB patients who were treatment naïve and correlate them with different viral and host factors. Our results showed that Ion Torrent deep sequencing could achieve high accuracy (R²>0.99) within a dynamic range between 1% and 100%. Twelve hotspots with prevalence of greater than 20% were observed in EnhII/BCP/PC regions. G1719T, T1753V, A1762T and G1764A were genotype C related. BCP A1762T/G1764A double mutants were generally accompanied with PC 1896 wild type or lower PC G1896A mutant percentage. Lower serum HBeAg and HBsAg levels were associated with higher BCP A1762T/G1764A mutant percentages (≥50%). ALT levels were higher in patients with PC G1896A mutant percentage greater than 10%. In conclusion, deep sequencing such as Ion Torrent sequencing could accurately quantify HBV mutants for providing clinical relevant information during HBV infection.

Non-Coding RNAs in Primary Liver Cancer

Hepatocellular carcinoma (HCC) is a primary malignancy of the liver with poor prognosis and limited therapeutic options. Over the past few years, many studies have evaluated the role of non-coding RNAs (ncRNAs) in hepatocarcinogenesis and tumor progression. ncRNAs were shown to have diagnostic, prognostic, and therapeutic potential in HCC. In this manuscript, we review the latest major discoveries concerning microRNAs and long ncRNAs in HCC pathogenesis, and discuss the potentials and the limitations for their use in clinical practice.

Integration of genomic information in the clinical management of HCC

Molecular profiling of hepatocellular carcinoma (HCC) is enabling the advancement of novel approaches to disease diagnosis and management. Accurate prognosis prediction in HCC is specially critical. Clinical staging systems for HCC support clinical decision-making (e.g., BCLC algorithm) might be complemented by molecular-based information in the near future. Molecular signatures derived from tumour and non-tumour samples are associated with patient recurrence an outcome. Single nucleotide polymorphisms have been linked with HCC development. Next generation sequencing studies have brought to light the genomic diversity of this disease. Gens recurrently altered in HCC and susceptible to be targeted belong to signalling pathways including telomere maintenance, cell cycle, chromatin remodelling, Wnt/beta-catenin, RAS/RAF/MAPK and PI3K/AKT/mTOR pathways. Oncogenic loops are unknown but might include some of the already discovered aberrations. Despite the intratumoral heterogeneity observed in HCC tumours, studies including large number of samples can identify key genetic drivers and contribute to the development of novel treatments and a personalized medicine.

Increased expression of iASPP, regulated by hepatitis B virus X protein-mediated NF-κB activation, in hepatocellular carcinoma

BACKGROUND & AIMS

iASPP is an inhibitory member of the ankyrin-repeat-, SH3-domain- and proline-rich-region-containing protein (ASPP) family; iASPP expression is up-regulated in different human tumor types. We explored the molecular mechanism increased expression of iASPP and its role in hepatocellular carcinoma (HCC).

METHODS

iASPP expression levels in human liver samples and cell lines were determined by polymerase chain reaction, immunoblot, and immunohistochemical analyses. Luciferase reporter, chromatin immunoprecipitation, and electrophoretic mobility shift assays were used to measure transcriptional activation by nuclear factor-κB (NF-κB). Effects on tumor growth were characterized with MTS, soft agar colony formation, and flow cytometry analyses. Tumorigenicity of cells was studied in nude mice.

RESULTS

Compared with normal liver cells or tissues, iASPP was expressed at significantly higher levels in HCC cell lines (9/14) and liver samples from patients with HCC, cirrhosis, or hepatitis B virus infection. Increased expression of iASPP was significantly associated with time to recurrence and survival time of patients with HCC. NF-κB activation increased the expression of iASPP through p65/p50 binding to a putative NF-κB-binding site in the iASPP promoter; hepatitis B virus X gene product might up-regulate expression of iASPP. Transgenic expression of iASPP promoted tumor cell proliferation and resistance to chemotherapeutic drugs in vitro and in vivo.

CONCLUSIONS

iASPP is up-regulated in HCC; it is a direct transcription target of NF-κB. Increased iASPP expression contributes to tumor progression by proliferative and antiapoptotic effects. iASPP might be developed as an HCC therapeutic target or to sensitize cancer cells to chemotherapeutic drugs; it might also be used as a prognostic factor.

Hepatocellular carcinoma: novel molecular approaches for diagnosis, prognosis, and therapy

The genomic era is changing the understanding of cancer, although translation of the vast amount of data available into decision-making algorithms is far from reality. Molecular profiling of hepatocellular carcinoma (HCC), the most common cause of death among cirrhotic patients and a fast-growing malignancy in Western countries, is enabling the advancement of novel approaches to disease diagnosis and management. Most HCCs arise on a cirrhotic liver, and predictably, an accurate genomic characterization will allow the identification of procarcinogenic signals amenable to selective targeting by chemopreventive strategies. Molecular diagnosis is currently feasible for small tumors, but it has not yet been formalized by scientific guidelines. Molecular treatment is a reality: Sorafenib confers unprecedented survival benefits in patients at advanced stages. Genomic information from tumor and nontumoral tissue will aid prognosis prediction and facilitate the identification of oncogene addiction loops, providing the opportunity for more personalized medicine.

Molecular classification and novel targets in hepatocellular carcinoma: recent advancements

Hepatocellular carcinoma (HCC) is one of most lethal cancers worldwide. Strategic decisions for the advancement of molecular therapies in this neoplasm require a clear understanding of its molecular classification. Studies indicate aberrant activation of signaling pathways involved in cellular proliferation (e.g., epidermal growth factor and RAS/mitogen-activated protein kinase pathways), survival (e.g., Akt/mechanistic target of rapamycin pathway), differentiation (e.g., Wnt and Hedgehog pathways), and angiogenesis (e.g., vascular endothelial growth factor and platelet-derived growth factor), which is heterogeneously presented in each tumor. Integrative analysis of accumulated genomic datasets has revealed a global scheme of molecular classification of HCC tumors observed across diverse etiologic factors and geographic locations. Such a framework will allow systematic understanding of the frequently co-occurring molecular aberrations to design treatment strategy for each specific subclass of tumors. Accompanied by a growing number of clinical trials of molecular targeted drugs, diagnostic and prognostic biomarker development will be facilitated with special attention on study design and with new assay technologies specialized for archived fixed tissues. A new class of genomic information, microRNA dysregulation and epigenetic alterations, will provide insight for more precise understanding of disease mechanism and expand the opportunity of biomarker/therapeutic target discovery. These efforts will eventually enable personalized management of HCC.

[Hepatitis B virus genetic diversity and mutant]

Hepatitis B virus (HBV) is a partially double stranded DNA virus with genetic diversity represented by eight genotypes (A to H). Natural course and response to treatment could be affected by HBV genotypes. HBV shows high rates of turn over in the absence of proof-reading ability. As a result, large amounts of quasispecies are produced naturally or antiviral-associated. HBV consists of four open reading frames, namely preS/S gene, precore/core gene, polymerase gene, and X gene. Mutations on preS gene can result in undetectable HBsAg even in case that HBV is replicating. Surface gene mutation leads to decreased binding affinity to anti-HBs, which is associated with a vaccine escape mutant. Precore mutation abolishes HBeAg whereas mutations on basal core promoter gene down-regulate the HBeAg production. Mutations on basal core promoter are associated with increased HBV replication and high incidence of progressive liver diseases such as liver cirrhosis and hepatocellular carcinoma. Mutations on polymerase genes are often induced by antiviral therapy. Emergence of antiviral-resistant mutation is the major cause of treatment failure. Furthermore, existence of prior antiviral-resistant mutations limits the options of subsequent antiviral agents. Therefore, judicious use of antivirals and selection of the most potent drug with the lowest resistance rate are of the utmost importance for the prevention of antiviral-associated mutants. Detailed knowledge and understanding of HBV genetic diversity and mutant would be critical to establish strategies for the diagnosis and management of HBV infection.