Hemlata Durgapal

Cloning, sequencing, and expression of the hepatitis E virus (HEV) nonstructural open reading frame 1 (ORF1)†

Hepatitis E virus (HEV) causes enterically transmitted epidemic and sporadic viral hepatitis affecting millions of people in the developing world. Different geographical isolates of HEV show a high degree of homology at the nucleotide and amino acid levels. The ∼7.2 kb RNA genome has three open reading frames of which ORF1 is predicted to code for the viral nonstructural polyprotein. The expression, processing and properties of the nonstructural ORF1 polyprotein have not been reported so far. In this study, the complete HEV ORF1 was reconstructed from overlapping fragments amplified by polymerase chain reaction (PCR) of total RNA isolated from the bile fluid of a rhesus monkey experimentally infected with HEV isolate from an epidemic. The complete assembled ORF1 was sequenced using HEV specific primers. The ORF1 polyprotein was expressed in E. coli, in a cell free translation system and in HepG2 cells, and was characterized by western blotting and immunoprecipitation using acute phase patient serum as well as polyclonal antibodies raised against defined parts of the ORF1 polyprotein. The nonstructural polyprotein of HEV was expressed as a 186 kDa protein. No processing was observed into discrete units, either in‐vitro based on a kinetic analysis, or in HepG2 cells based on immunoprecipitation. J. Med. Virol. 60:275–283, 2000.

Study of cellular immune response against Hepatitis E Virus (HEV)

Summary.  Hepatitis E virus infection (HEV) is a major cause of acute viral hepatitis in the developing world. The immunopathology of HEV infections has not yet been elucidated. The virus is noncytopathic, and therefore, liver injury may be attributed to immune‐mediated damage by cytotoxic T cells and natural killer cells. Therefore, we studied the nature of immune cells involved in HEV‐induced liver damage using immunohistochemistry in liver biopsies taken from patients with HEV‐induced acute liver failure and demonstrated a significant infiltration of activated CD8+ T cells containing granzymes. These findings suggest the possible involvement of cytotoxic T cells in disease pathogenesis during HEV infection.

Hepatitis E virus enters liver cells through receptor-dependent clathrin-mediated endocytosis

Summary.  We investigated the virus–host interaction for hepatitis E virus (HEV) by performing competitive binding assays using in vitro assembled virus‐like particles (VLPs). We used Escherichia coli expressed native capsid protein (pORF2) and its mutants with an attached Gly(5)‐Ala (linker) reporter [enhanced green fluorescent protein (EGFP)/firefly luciferase (Fluc)]. Transmission electron microscopy and nanoparticle tracking showed near uniform particles of approximately 30–35 nm in diameter for pORF2 VLPs and 60–100 nm for reporter‐linked VLPs. Binding of reporter‐linked full‐length (1–660aa) and N‐terminal truncated (Δ1–112aa) pORF2 VLPs to Huh7 cell surfaces was found to be specific with 1.92 ± 0.065 × 105 sites per cell. Saturation binding indicated an equilibrium dissociation constant (Kd) of 121.1 ± 23.83 and 123.8 ± 16.15 nm for pORF2‐linker‐EGFP and pORF2‐linker‐Fluc VLPs respectively. A similar binding pattern was observed for Δ1–112aa pORF2‐linker‐EGFP and Δ1–112aa pORF2‐linker‐Fluc VLPs with Kd values of 123.6 ± 10.60 and 135.6 ± 16.19 nm respectively. The affinity (log Ki) of pORF2 binding on Huh7 cells in the presence of EGFP‐tagged and Fluc‐tagged pORF2 VLPs was found to be approximately 2.0. However, no VLP formation or binding was observed with refolded C‐terminal truncated (Δ458–660aa) pORF2. We investigated HEV internalization using fluorescent VLPs (EGFP‐VLPs), which showed vesicle‐mediated uptake starting at 5 min post‐incubation. The uptake of VLPs could be stopped by inhibitors for clathrin‐dependent endocytosis, but not by caveosome inhibitors. No binding and uptake of EGFP‐VLPs were observed on non‐hepatic cell lines (HeLa and SiHa). These findings suggest that HEV attaches to the host cell via a specific high affinity receptor and enters the cytoplasm by clathrin‐mediated endocytosis.

RNA-Seq Based Transcriptome Analysis of Hepatitis E Virus (HEV) and Hepatitis B Virus (HBV) Replicon Transfected Huh-7 Cells

Pathogenesis of hepatitis B virus (HBV) and hepatitis E virus (HEV) infection is as varied as they appear similar; while HBV causes an acute and/or chronic liver disease and hepatocellular carcinoma, HEV mostly causes an acute self-limiting disease. In both infections, host responses are crucial in disease establishment and/or virus clearance. In the wake of worsening prognosis described during HEV super-infection over chronic HBV hepatitis, we investigated the host responses by studying alterations in gene expression in liver cells (Huh-7 cell line) by transfection with HEV replicon only (HEV-only), HBV replicon only (HBV-only) and both HBV and HEV replicons (HBV+HEV). Virus replication was validated by strand-specific real-time RT-PCR for HEV and HBsAg ELISA of the culture supernatants for HBV. Indirect immunofluorescence for the respective viral proteins confirmed infection. Transcription profiling was carried out by RNA Sequencing (RNA-Seq) analysis of the poly-A enriched RNA from the transfected cells. Averages of 600 million bases within 5.6 million reads were sequenced in each sample and ∼15,800 genes were mapped with at least one or more reads. A total of 461 genes in HBV+HEV, 408 in HBV-only and 306 in HEV-only groups were differentially expressed as compared to mock transfection control by two folds (p<0.05) or more. Majority of the significant genes with altered expression clustered into immune-associated, signal transduction, and metabolic process categories. Differential gene expression of functionally important genes in these categories was also validated by real-time RT-PCR based relative gene-expression analysis. To our knowledge, this is the first report of in vitro replicon transfected RNA-Seq based transcriptome analysis to understand the host responses against HEV and HBV.

Hepatitis E virus replication involves alternating negative- and positive-sense RNA synthesis

Hepatitis E virus (HEV) is the major cause of epidemic hepatitis and many outbreaks of sporadic hepatitis. The virus responsible has a single-stranded, positive-sense RNA. Its replication and the regulatory process involved therein are poorly understood. Much of the HEV biology studied has been done by using full-length capped RNA transcripts (replicons) and transient transfections in cell cultures. We investigated replicon replication using negative-sense strand-specific molecular beacons in live cell imaging, and quantifying intracellular viral RNA using strand-specific real-time PCR every 2 h until 24 h post-transfection. A graph of the copy numbers of both positive- and negative-sense RNA at the different time points was plotted. This showed a temporal separation and alternating cycles of negative- and positive-sense RNA formation. As a control, a dysfunctional replicase mutant (GDD→GAA) was used, which showed no increase in copy number. The live cell imaging corroborated the quantitative data, in that the maximal amount of negative-sense RNA was observed at 8 h post-transfection. The real-time-PCR copy-number analysis of the subgenome showed the presence of a single subgenomic RNA. Using fluorescent protein genes mCherry and EGFP fused in-frame to ORF2 and ORF3 in separate constructs and immunofluorescence, we showed the formation of both proteins pORF2 and pORF3 from a single subgenomic RNA. Our study demonstrated cyclical bursts of virus replication and the role of subgenomic RNA in the HEV life cycle.

Immunohistochemistry for the diagnosis of hepatitis E virus infection

Summary.  Hepatitis E virus (HEV) is an emerging pathogen and the most common cause of acute viral hepatitis all over the world. We describe here an immunohistochemical method for the detection of HEV antigens (pORF2 and pORF3) in formalin‐fixed, paraffin‐embedded liver tissues using monoclonal antibodies raised against two of the virus proteins (pORF2 and pORF3). We analysed their specificity and sensitivity in comparison with serology and nucleic acid detection in cases of acute liver failure (ALF). We used this test on 30 liver biopsies collected post‐mortem from the patients of ALF caused by HEV infection. These cases were selected on the basis of positive results for enzyme immunoassay (IgM anti‐HEV). Of the 30 cases taken from the archives of the Department of Pathology, the antibodies successfully stained all. However, only 25 serum samples (83.3%) of these were positive for HEV RNA. Fifteen controls used (Five noninfected liver tissues, five HBV‐ and five hepatitis C virus‐infected liver tissues) were all negative. The immunohistochemical assay described here may prove a valuable tool for the detection of HEV infection in biopsy, autopsy and explant liver tissues and can serve as a link along with other available tests to delineate the extent of HEV‐associated problem worldwide.

Hepatitis E virus (HEV) protease: a chymotrypsin-like enzyme that processes both non-structural (pORF1) and capsid (pORF2) protein.

Hepatitis E virus (HEV), a major cause of acute viral hepatitis across the world, is a non-enveloped, plus-strand RNA virus. Its genome codes three proteins, pORF1 (multifunctional polyprotein), pORF2 (capsid protein) and pORF3 (multi-regulatory protein). pORF1 encodes methyltransferase, putative papain-like cysteine protease, helicase and replicase enzymes. Of these, the protease domain has not been characterized. On the basis of sequence analysis, we cloned and expressed a protein covering aa 440-610 of pORF1, expression of which led to cell death in Escherichia coli BL-21 and Huh7 hepatoma cells. Finally, we expressed and purified this protein from E. coli C43 cells (resistant to toxic proteins). The refolded form of this protein showed protease activity in gelatin zymography. Digestion assays showed cleavage of both pORF1 and pORF2 as observed previously. MS revealed digestion of capsid protein at both the N and C termini. N-terminal sequencing of the ~35 kDa methyltransferase, ~35 kDa replicase and ~56 kDa pORF2 proteins released by protease digestion revealed that the cleavage sites were alanine15/isoleucine16, alanine1364/valine1365 in pORF1 and leucine197/valine198 in pORF2. Specificity of these cleavage sites was validated by site-directed mutagenesis. Further characterization of the HEV protease, carried out using twelve inhibitors, showed chymostatin and PMSF to be the most efficient inhibitors, indicating this protein as a chymotrypsin-like protease. The specificity was further confirmed by cleavage of the chymotrypsin-specific fluorogenic peptide N-succinyl-Leu-Leu-Val-Tyr-7-amido-4-methylcoumarin. Mutational analysis of the conserved serine/cysteine/histidine residues suggested that H443 and C472/C481/C483 are possibly the active site residues. To our knowledge, this is the first direct demonstration of HEV protease and its function.

Development of highly sensitive bicistronic vector based non-radioactive antigen-specific cytotoxicity assay

In the absence of a better alternate, (51)Cr release assay, with its several disadvantages is still the most common method for detection of MHC class I restricted T-cell mediated cytotoxicity. We describe a system in which the T-cell mediated cytotoxicity can be assessed using host-derived cells transfected with a bicistronic vector expressing the specific antigen and a quantifiable reporter as target cells. This overcomes the problems associated with use of radioactivity, pre-loading of target cells with reporter/antigen and the MHC restriction. We used HBV core antigen to prove the concept, as it is an established CTL target. Bicistronic vectors containing HBV core and reporter (EGFP/Fluc) gene were generated and further checked for antigen/reporter expression in human HepG2, mouse fibroblast BALB/c.3T3 and mouse lymphoma A20 cell lines. The effector cells to study the cytolytic activity were generated in vivo using BALB/c mice immunized with antigen expressing DNA clone or protein. The target cells (BALB/c.3T3 and A20) transiently transfected with bicistronic constructs were incubated with effector cells (splenocytes) from immunized mice at a different effector to target ratio. Following incubation the CTL activity was calculated by measuring the reporter luciferase in the remaining viable target cells that inversely correlates with the cytolysis of susceptible cells. The percent specific lysis measured in our assay was compared with conventional (51)Cr release assay to validate this approach. This novel bicistronic vector based cytotoxicity assay demonstrated an easy to perform, antigen-specific and non-radioactive method of determining T-cell mediated cytotoxicity.

A self-associating hepatitis B surface antigen-derived peptide that is immunogenic in alum

We previously described an oligomeric synthetic peptide derived from the hepatitis B surface antigen that displayed a limited tendency to form self-associating macromolecular structures in solution. Here it is demonstrated that amino-terminal myristylation of this peptide results in near quantitative aggregation of the oligomeric peptide. The myristylated peptide is highly immunogenic when used in conjunction with alum as adjuvant in both the rabbit and rhesus monkey models. The antibody response generated by peptide also cross-reacted with native antigen and was long-lasting. Collectively the results described in this and previous reports offer an attractive new approach for generating immunogenic peptide mimetics of conformational epitopes that may find application as vaccines.