Natural genetic engineering of hepatitis C virus NS5A for immune system counterattack

Cell Therapy and Bioengineering in Experimental Liver Regenerative Medicine: In Vivo Injury Models and Grafting Strategies

Purpose of Review

To describe experimental liver injury models used in regenerative medicine, cell therapy strategies to repopulate damaged livers and the efficacy of liver bioengineering.

Recent Findings

Several animal models have been developed to study different liver conditions. Multiple strategies and modified protocols of cell delivery have been also reported. Furthermore, using bioengineered liver scaffolds has shown promising results that could help in generating a highly functional cell delivery system and/or a whole transplantable liver.

Summary

To optimize the most effective strategies for liver cell therapy, further studies are required to compare among the performed strategies in the literature and/or innovate a novel modifying technique to overcome the potential limitations. Coating of cells with polymers, decellularized scaffolds, or microbeads could be the most appropriate solution to improve cellular efficacy. Besides, overcoming the problems of liver bioengineering may offer a radical treatment for end-stage liver diseases.

Duplication of the V3 domain in hepatitis C virus (1b) NS5A protein: Clonal analysis and physicochemical properties related to hepatocellular carcinoma occurrence

BACKGROUND

Hepatitis C virus non-structural protein 5A is known to play a role in development of hepatocellular carcinoma (HCC) via interactions with host cell pathways.

OBJECTIVES

Hepatitis C virus genotype 1b strains presenting a wide insertion of 31 amino acids in the non-structural protein 5A V3 domain (V3 DI) were studied to determine whether this V3-like additional domain (V3 DII) was associated with HCC occurrence.

STUDY DESIGN

Seventy-four patients' sera were screened for V3 DII presence regarding clinical status.

RESULTS

Three strains with duplicated V3 were detected among patients with progression to HCC (n=28), two strains among patients with liver cirrhosis (Ci, n=27) and none among patients with chronic hepatitis (Chr, n=19). Phylogenetic trees built from V3 DI and V3 DII sequences indicated that the latter clustered separately. In between-group clonal analysis, V3 DII sequences from the HCC group were found to be more distant from HCV-J than V3 DI sequences (p<0.0001). Between-group comparisons showed significant differences in genetic distances from HCV-J, in HCC V3 DI and HCC V3 DII compared to Ci V3 DI and Ci V3 DII sequences (p<0.0001). HCC V3 DII domain and its junction with V3 DI exhibited higher Shannon entropy values and enrichment in disorder-promoting residues.

CONCLUSIONS

Taken together, our results suggest that V3 DII evolution may differ in strains associated with HCC occurrence. The presence of an intrinsically "disordered" V3 duplicate may alter the NS5A protein network. Further investigations are necessary to elucidate the potential impact of V3 duplication in the context of carcinogenesis.

Establishment of two mouse models of autoimmune hepatitis induced by concanavalin A and S-100

AIM: To establish two autoimmune hepatitis (AIH) mouse models by injection of concanavalin A (ConA) and syngeneic S-100, respectively, and to compare the two models.

METHODS: Female Balb/C mice received injection of ConA (15 mg/kg) through the tail vein, whereas control mice were injected with equal volume of sodium chloride. At 6, 12, 24 and 48 h after injection, blood and liver samples were taken. In addition, female C57BL/6 mice were given syngeneic S-100 emulsified with equal volume of Freund's complete adjuvant (CFA) by peritoneal injection at the 1^st and 7^th day, and the mixture of sodium chloride and CFA were given to control mice. Blood and liver samples were taken 4 wk later. Serum levels of alanine transaminase (ALT) and aspartate aminotransferase (AST) were tested using an automatic biochemistry analyzer. Liver pathological changes were observed after hematoxylin and eosin (HE) staining.

RESULTS: Serum levels of ALT and AST increased significantly 6 h after ConA injection and reached the peak at 12 h in comparison with the control group. The peak values of ALT and AST were significantly higher than those in the control group (ALT: 1603.40 U/L ± 461.24 U/L vs 66.25 U/L ± 18.66 U/L, AST: 1877.20 U/L ± 623.23 U/L vs 159.50 U/L ± 29.22 U/L, P < 0.01). Liver tissue showed mild congestion, infiltration of few inflammatory cells and hepatocyte degeneration 6 h after ConA injection. Degeneration and necrosis of hepatocytes and inflammatory cell infiltration became more significant and part of liver lobules disappeared at 24 h. Serum levels of ALT and AST in mice injected with syngeneic S-100 were significantly higher than those in the controls (ALT: 156.80 U/L ± 52.86 U/L vs 29.90 U/L ± 8.43 U/L; AST: 317.80 U/L ± 105.80 U/L vs 146.40 U/L ± 30.61 U/L, P < 0.01). The liver cells were arranged irregularly, and local necrosis and massive inflammatory cell infiltration were observed in model mice.

CONCLUSION: Animal models created with S-100 or ConA can be both used as AIH models. ConA model showed an acute course, while S-100 model showed a chronic course. They can be used in different experiments.

Immunoreactivity assessment of hepatitis C virus NS3 protease and NS5A proteins expressed in TOPO cloning system

BACKGROUND

Hepatitis C virus (HCV) is a major cause of acute and chronic liver disease. Numerous screening assays based on the detection of immunoresponses to HCV structural and nonstructural proteins have been designed. Various studies have demonstrated genotype-specific differences in anti-HCV antibody responses to different HCV proteins.

METHODS

Full-length NS3 protease and N-terminally truncated NS5A were expressed using pET TOPO 102/D system. Antigenicity of the purified recombinant proteins was assessed by immunoblotting and indirect enzyme-linked immunosorbent assay (ELISA). Furthermore, anti-HCV antibody responses to the recombinant proteins were evaluated in three prevalent genotypes in Iran.

RESULTS

We were able to express and purify NS5A and NS3 protease using TOPO cloning system. The HCV NS3 protease and NS5A produced in BL21 Star (DE3) was immunoreactive. Our results demonstrate that NS3 protease and NS5A have good immunoreactivity, but they are not sufficient for detecting all HCV-positive sera. No significant genotype-specific differences were detected in immunoresponses to the recombinant proteins.

CONCLUSION

In conclusion, we successfully isolated, expressed, and purified substantial amount of HCV NS3 protease and N-terminally truncated NS5A, and used them as capturing antigens in a screening ELISA assay with high sensitivity, reproducibility, and specificity. Accordingly, it is well confirmed that TOPO cloning system can be used as a dynamic system in order to express higher amount of immunoreactive viral proteins.

Immune mechanisms of Concanavalin A model of autoimmune hepatitis

As a chronic inflammatory disease of the liver, the pa-thogenic mechanisms of autoimmune hepatitis (AIH) have not yet been elucidated, with prognosis and diagnosis remaining unsatisfied. Currently the only viable treatments of AIH are immunosuppressant application and liver transplantation. It is considered that lack of good animal AIH models is the main reason for the shortage of a simple and efficient cure. The Concanavalin A (Con A) model is a typical and well established model for investigating T-cell and macrophage dependent liver injury in mice, which closely mimics the pathogenesis mechanisms and pathological changes of patients, and is regarded as the best experimental model for AIH research so far. In this paper we elucidated the pathogenic mechanisms of AIH and the evolution of relative animal models. We go on to further focus on Con A-induced liver injury from the point of immunological mechanisms and the change of cytokine levels. Finally, we manifested the clinical significance of the AIH animal models and the challenges they would meet during their future development.

Identification of novel conserved functional motifs across most Influenza A viral strains

Background

Influenza A virus poses a continuous threat to global public health. Design of novel universal drugs and vaccine requires a careful analysis of different strains of Influenza A viral genome from diverse hosts and subtypes. We performed a systematic in silico analysis of Influenza A viral segments of all available Influenza A viral strains and subtypes and grouped them based on host, subtype, and years isolated, and through multiple sequence alignments we extrapolated conserved regions, motifs, and accessible regions for functional mapping and annotation.

Results

Across all species and strains 87 highly conserved regions (conservation percentage > = 90%) and 19 functional motifs (conservation percentage = 100%) were found in PB2, PB1, PA, NP, M, and NS segments. The conservation percentage of these segments ranged between 94 - 98% in human strains (the most conserved), 85 - 93% in swine strains (the most variable), and 91 - 94% in avian strains. The most conserved segment was different in each host (PB1 for human strains, NS for avian strains, and M for swine strains). Target accessibility prediction yielded 324 accessible regions, with a single stranded probability > 0.5, of which 78 coincided with conserved regions. Some of the interesting annotations in these regions included sites for protein-protein interactions, the RNA binding groove, and the proton ion channel.

Conclusions

The influenza virus has evolved to adapt to its host through variations in the GC content and conservation percentage of the conserved regions. Nineteen universal conserved functional motifs were discovered, of which some were accessible regions with interesting biological functions. These regions will serve as a foundation for universal drug targets as well as universal vaccine design.

Prediction of prognostic biomarkers for interferon-based therapy to hepatitis C virus patients: a meta-analysis of the NS5A protein in subtypes 1a, 1b, and 3a

Background

Hepatitis C virus (HCV) is a worldwide health problem with no vaccine and the only approved therapy is Interferon-based plus Ribavarin. Response prediction to treatment has health and economic impacts, and is a multi-factorial problem including both host and viral factors (e.g: age, sex, ethnicity, pre-treatment viral load, and dynamics of the HCV non-structural protein NS5A quasispecies). We implement a novel approach for extracting features including informative markers from mutations in the non-structural 5A protein (NS5A), specifically its Interferon sensitivity determining region (ISDR) and V3 regions, and use a novel bioinformatics approach for pattern recognition on the NS5A protein and its motifs to find biomarkers for response prediction using class association rules and comparing the predictability of the different features.

Results

A total of 58 sequences from sustained responders and 94 from non-responders were downloaded from the HCV LANL database. Site-specific signatures for response prediction from the NS5A protein were extracted from the alignments. Class association rules were generated (e.g.: sustained response is associated with position A2368T in subtype 1a (support 100% and confidence 52.19%); in subtype 1b, response is associated with E2356G/D/K (support 76.3% and confidence 67.3%).

Conclusion

The V3 region was a more accurate biomarker than the ISDR region. Subtype-specific class association rules gave better support and confidence than profile hidden Markov models HMMs scores, genetic distances or number of variable sites, and would thus aid in the prediction of prognostic biomarkers and improve the accuracy of prognosis. Sites-specific class association rules in the V3 region of the NS5A protein have given the best support and confidence.

An integrated methodology for mining promiscuous proteins: a case study of an integrative bioinformatics approach for hepatitis C virus non-structural 5A protein

A methodology for elucidation of structural, functional, and mechanistic knowledge on promiscuous proteins is proposed that constitutes a workflow of integrated bioinformatics analysis. Sequence alignments with closely related homologues can reveal conserved regions which are functionally important. Scanning protein motif databases, along with secondary and surface accessibility predictions integrated with post-translational modification sites (PTMs) prediction reveal functional and protein-binding motifs. Integrating this information about the protein with the GO, SCOP, and CATH annotations of the templates can help to formulate a 3D model with reasonable accuracy even in the case of distant sequence homology. A novel integrative model of the non-structural protein 5A of Hepatitis C virus: a hub promiscuous protein with roles in virus replication and host interactions is proposed. The 3D structure for domain II was predicted based on, the Homo sapiens Replication factor-A protein-1 (RPA1), as a template using consensus meta-servers results. Domain III is an intrinsically unstructured domain with a fold from the retroviral matrix protein, which conducts diverse protein interactions and is involved in viral replication and protein interactions. It also has a single-stranded DNA-binding protein motif (SSDP) signature for pyrimidine binding during viral replication. Two protein-binding motifs with high sequence conservation and disordered regions are proposed; the first corresponds to an Interleukin-8B receptor signature (IL-8R-B), while the second has a lymphotoxin beta receptor (LTβR) high local similarity. A mechanism is proposed to their contribution to NS5A Interferon signaling pathway interception. Lastly, the overlapping between LTβR and SSDP is considered as a sign for NS5A date hubs.