[Personalized treatment of viral hepatitis of the present and the future : Hepatitis B, C, delta, and E]. / Maßgeschneiderte Therapie der Virushepatitis der Gegenwart und Zukunft : Hepatitis B, C, Delta und E.

Precision medicine is also possible for infectious diseases as shown for the treatment of chronic viral hepatitis, especially if different options are available. In hepatitis B virus (HBV) infection, treatment indication as well as the choice of treatment and the decisions to stop treatment are based on viral markers and alanine aminotransferase (ALT) level. Future therapies for HBV infection aiming for functional cure or even virus elimination may be even more personalized and have to take into account the immune status of a given patient. Such treatment modalities might also increase the chance for successful treatment of chronic hepatitis delta where treatment options are still very limited. Some new therapeutic concepts targeting host receptors or host enzymes are promising, but may require individualized approaches. Chronic hepatitis C is a good example for precision medicine based on viral and host factors. However, the main reason for individualized direct-acting antiviral (DAA) treatment is to save costs. As DAAs are effective in more than 95% of patients, elimination of HCV seems to be possible at the level of a given country or even on a global scale. However, owing to high reinfection rates in high-risk groups and limited availability of antiviral therapy in many high endemic countries, it must still be decided whether an HCV vaccine or pre-exposure prophylaxis is required to achieve this goal. Hepatitis E is an emerging topic as this is the most frequent acute hepatitis virus infection. It can result in a chronic infection in immunosuppressed individuals. Treatment options are still limited and individualized management is based on tailoring immunosuppressive therapy and therapy with ribavirin. Thus, personalized therapy of hepatitis E virus infection is still limited.

Low oxygen tension enhances hepatitis C virus replication.

Low oxygen tension exerts a significant effect on the replication of several DNA and RNA viruses in cultured cells. In vitro propagation of hepatitis C virus (HCV) has thus far been studied under atmospheric oxygen levels despite the fact that the liver tissue microenvironment is hypoxic. In this study, we investigated the efficiency of HCV production in actively dividing or differentiating human hepatoma cells cultured under low or atmospheric oxygen tensions. By using both HCV replicons and infection-based assays, low oxygen was found to enhance HCV RNA replication whereas virus entry and RNA translation were not affected. Hypoxia signaling pathway-focused DNA microarray and real-time quantitative reverse transcription-PCR (qRT-PCR) analyses revealed an upregulation of genes related to hypoxic stress, glycolytic metabolism, cell growth, and proliferation when cells were kept under low (3% [vol/vol]) oxygen tension, likely reflecting cell adaptation to anaerobic conditions. Interestingly, hypoxia-mediated enhancement of HCV replication correlated directly with the increase in anaerobic glycolysis and creatine kinase B (CKB) activity that leads to elevated ATP production. Surprisingly, activation of hypoxia-inducible factor alpha (HIF-α) was not involved in the elevation of HCV replication. Instead, a number of oncogenes known to be associated with glycolysis were upregulated and evidence that these oncogenes contribute to hypoxia-mediated enhancement of HCV replication was obtained. Finally, in liver biopsy specimens of HCV-infected patients, the levels of hypoxia and anaerobic metabolism markers correlated with HCV RNA levels. These results provide new insights into the impact of oxygen tension on the intricate HCV-host cell interaction.

Multi-detector fusion and Bayesian smoothing for tracking viral and chromatin structures.

Automatic tracking of viral and intracellular structures displayed as spots with varying sizes in fluorescence microscopy images is an important task to quantify cellular processes. We propose a novel probabilistic tracking approach for multiple particle tracking based on multi-detector and multi-scale data fusion as well as Bayesian smoothing. The approach integrates results from multiple detectors using a novel intensity-based covariance intersection method which takes into account information about the image intensities, positions, and uncertainties. The method ensures a consistent estimate of multiple fused particle detections and does not require an optimization step. Our probabilistic tracking approach performs data fusion of detections from classical and deep learning methods as well as exploits single-scale and multi-scale detections. In addition, we use Bayesian smoothing to fuse information of predictions from both past and future time points. We evaluated our approach using image data of the Particle Tracking Challenge and achieved state-of-the-art results or outperformed previous methods. Our method was also assessed on challenging live cell fluorescence microscopy image data of viral and cellular proteins expressed in hepatitis C virus-infected cells and chromatin structures in non-infected cells, acquired at different spatial-temporal resolutions. We found that the proposed approach outperforms existing methods.

[Molecular mechanisms of hepatitis C virus (HCV) replication - implications for the development of antiviral drugs]. / Die molekularen Mechanismen der Replikation des Hepatitis C Virus - Implikationen für die Entwicklung antiviraler Wirkstoffe.

More than 20 years after the discovery of the hepatitis C virus (HCV), chronic hepatitis C still is a major medical problem. According to the World Health Organisation 120 to 180 million people are chronically infected with HCV, with 5 million infected individuals living in Western Europe. These people have a high risk to develop serious liver disease such as liver cirrhosis and hepatocellular carcinoma (HCC). The standard-of-care therapy is not satisfying and there is no vaccine in sight. Owing to intense research activities, most notably the development of adequate cell culture systems, important insights into the viral replication cycle have been gained and several strategies used by HCV to overcome immune responses have been identified. Adequate cell culture systems also provided the basis for the development of potent and selective antivirals for treatment of chronic hepatitis C and it is expected that NS 3 / 4A protease inhibitors will be approved for clinical use in 2011 / 2012. Nevertheless, important questions are still unanswered and they will keep clinicians and basic researchers busy for the coming years.

Data fusion and smoothing for probabilistic tracking of viral structures in fluorescence microscopy images.

Automatic tracking of viral structures displayed as small spots in fluorescence microscopy images is an important task to determine quantitative information about cellular processes. We introduce a novel probabilistic approach for tracking multiple particles based on multi-sensor data fusion and Bayesian smoothing methods. The approach exploits multiple measurements as in a particle filter, both detection-based measurements and prediction-based measurements from a Kalman filter using probabilistic data association with elliptical sampling. Compared to previous probabilistic tracking methods, our approach exploits separate uncertainties for the detection-based and prediction-based measurements, and integrates them by a sequential multi-sensor data fusion method. In addition, information from both past and future time points is taken into account by a Bayesian smoothing method in conjunction with the covariance intersection algorithm for data fusion. Also, motion information based on displacements is used to improve correspondence finding. Our approach has been evaluated on data of the Particle Tracking Challenge and yielded state-of-the-art results or outperformed previous approaches. We also applied our approach to challenging time-lapse fluorescence microscopy data of human immunodeficiency virus type 1 and hepatitis C virus proteins acquired with different types of microscopes and spatial-temporal resolutions. It turned out, that our approach outperforms existing methods.

Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line.

An estimated 170 million persons worldwide are infected with hepatitis C virus (HCV), a major cause of chronic liver disease. Despite increasing knowledge of genome structure and individual viral proteins, studies on virus replication and pathogenesis have been hampered by the lack of reliable and efficient cell culture systems. A full-length consensus genome was cloned from viral RNA isolated from an infected human liver and used to construct subgenomic selectable replicons. Upon transfection into a human hepatoma cell line, these RNAs were found to replicate to high levels, permitting metabolic radiolabeling of viral RNA and proteins. This work defines the structure of HCV replicons functional in cell culture and provides the basis for a long-sought cellular system that should allow detailed molecular studies of HCV and the development of antiviral drugs.

Phosphorylation and rapid turnover of hepatitis B virus X-protein expressed in HepG2 cells from a recombinant vaccinia virus.

The human hepatitis B viral (HBV) genome contains a conserved open reading frame known as the X-gene which is capable of encoding a polypeptide of 16.565 kDa. The corresponding protein has so far not been identified directly in HBV-infected cells, but in transient transfection assays the X-gene encodes a product that functions as a transcriptional transactivator. To characterize the subcellular distribution, stability and post-translational modifications of X-protein in human hepatoma HepG2 cells, we have established a vaccinia virus expression system. As the major X-gene product, a protein with an apparent molecular weight of 16 kDa, and reacting with an X-protein-specific antiserum, was expressed from recombinant vaccinia virus. In indirect immunofluorescence assay, X-protein appeared to be distributed throughout the cells, with a tendency to localize at the nuclear periphery and to accumulate in granules as its levels increased. By subcellular fractionation, we found about one-third of X-protein associated with the fraction defined as the nuclear framework. In pulse-chase experiments, X-protein decayed with a bimodal half-life of 15 min and 3 h. X-protein having a half-life of about 15 min was found associated with the Triton X-100 detergent-soluble fraction of HepG2 cells, while that associated with the insoluble fraction turned over more slowly. By metabolic labeling with [32P] orthophosphate, we show that X-protein is capable of being phosphorylated. Modification by phosphorylation could play an important role in the regulation of X-protein function.

The hepatitis C virus replicon system and its application to molecular studies.

The hepatitis C virus (HCV) was identified as the major causative agent of post-transfusion and sporadic non-A, non-B hepatitis. Approximately 170 million individuals worldwide are afflicted with this infection that in most cases becomes persistent. The clinical outcomes are varied, ranging from an apparently healthy carrier state to liver cirrhosis and even hepatocellular carcinoma. Thus far, no vaccine is available and antiviral treatment is insufficient with only approximately 40% of patients developing a long-term sustained response. These deficits underscore the need for more effective therapies but their development has been severely hampered by the lack of an efficient cell culture system. This impediment has recently been overcome by the development of subgenomic HCV RNA molecules that replicate autonomously in transfected cells. The high level of replication of this system opens new avenues for molecular studies of various aspects of the HCV life-cycle as well as for the development of antiviral drugs.

Novel cell culture systems for the hepatitis C virus.

Infections with the hepatitis C virus (HCV) are a major cause of acute and chronic liver disease. The high prevalence of the virus, the insidious course of the disease and the poor prognosis for long-term persistent infection make this pathogen a serious medical and socioeconomical problem. The identification of the viral genome approximately 10 years ago rapidly led to the delineation of the genomic organization and the structural and biochemical characterization of several virus proteins. However, studies of the viral life cycle as well as the development of antiviral drugs have been difficult because of the lack of a robust and reliable cell culture system. Numerous attempts have been undertaken in the past few years but only recently a highly efficient cell culture model could be developed. This system is based on the self replication of engineered HCV minigenomes (replicons) in a transfected human hepatoma cell line. A summary of the various HCV cell culture models with a focus on the replicon system and its use for drug development is described.

Relation between viral fitness and immune escape within the hepatitis C virus protease.

BACKGROUND: The hepatitis C virus (HCV) mutates within human leucocyte antigen (HLA) class I restricted immunodominant epitopes of the non-structural (NS) 3/4A protease to escape cytotoxic T lymphocyte (CTL) recognition and promote viral persistence. However, variability is not unlimited, and sometimes almost absent, and factors that restrict viral variability have not been defined experimentally. AIMS: We wished to explore whether the variability of the immunodominant CTL epitope at residues 1073-1081 of the NS3 protease was limited by viral fitness. PATIENTS: Venous blood was obtained from six patients (four HLA-A2+) with chronic HCV infection and from one HLA-A2+ patient with acute HCV infection. METHODS: NS3/4A genes were amplified from serum, cloned in a eukaryotic expression plasmid, sequenced, and expressed. CTL recognition of naturally occurring and artificially introduced escape mutations in HLA-A2-restricted NS3 epitopes were determined using CTLs from human blood and genetically immunised HLA-A2-transgenic mice. HCV replicons were used to test the effect of escape mutations on HCV protease activity and RNA replication. RESULTS: Sequence analysis of NS3/4A confirmed low genetic variability. The major viral species had functional proteases with 1073-1081 epitopes that were generally recognised by cross reactive human and murine HLA-A2 restricted CTLs. Introduction of mutations at five positions of the 1073-1081 epitope prevented CTL recognition but three of these reduced protease activity and RNA replication. CONCLUSIONS: Viral fitness can indeed limit the variability of HCV within immunological epitopes. This helps to explain why certain immunological escape variants never appear as a major viral species in infected humans.

[Pathogenesis and pathomorphology of chronic viral hepatitis]. / Chronische Virushepatitis--pathogenetische und pathomorphologische Aspekte.

Chronic viral hepatitis represents the most common liver disease worldwide. It can be induced by HBV (eventually as HDV-coinfection) and HCV. From the pathologist's point of view chronic hepatitis represents portal accentuated inflammation of the liver associated with a variable degree of interface hepatitis and acinar damage. Although much research has been done to unravel the mechanisms which cause chronic viral hepatitis, many questions are unanswered. Up to now, liver biopsy is the gold standard for diagnosis of chronic viral hepatitis. On one hand it shows the grade of inflammation and the stage of disease, on the other hand it can highlight additional liver diseases, which might have an adverse influence. Therefore, liver biopsy allows the best prediction of disease progression. In a recent consensus statement, the scoring system of Desmet was recommended for grading and staging of chronic hepatitis.

Candidate targets for hepatitis C virus-specific antiviral therapy.

The hepatitis C virus (HCV) was identified as the major causative agent of posttransfusion and community-acquired non-A, non-B hepatitis throughout the world. It is an enveloped virus with a plus-strand RNA genome encoding a polyprotein of about 3,010 amino acids. This polyprotein is cleaved co- and posttranslationally into mature viral proteins by host cell signal peptidases and 2 viral enzymes designated the NS2-3 proteinase and the NS3/4A proteinase complex. It is assumed that virus replication takes place in a membrane-associated complex containing at least 2 viral enzymatic activities: the NS3 nucleoside triphosphatase (NTPase)/helicase and the NS5B RNA-dependent RNA polymerase (RdRp). Based on their important role for the viral life cycle and the wealth of information available for related cellular and viral proteins, the NS3/4A serine-type proteinase complex, the NS3 NTPase/helicase and the NS5B RdRp are the most attractive targets for development of HCV-specific antiviral therapies. This review will summarize our current knowledge about structure and function of these proteins and describe approaches pursued to identify effective antiviral compounds.

The NS3/4A proteinase of the hepatitis C virus: unravelling structure and function of an unusual enzyme and a prime target for antiviral therapy.

The hepatitis C virus (HCV) is a major causative agent of transfusion-acquired and sporadic non-A, non-B hepatitis worldwide. Infections most often persist and lead, in approximately 50% of all patients, to chronic liver disease. As is characteristic for a member of the family Flaviviridae, HCV has a plus-strand RNA genome encoding a polyprotein, which is cleaved co- and post-translationally into at least 10 different products. These cleavages are mediated, among others, by a virally encoded chymotrypsin-like serine proteinase located in the N-terminal domain of non-structural protein 3 (NS3). Activity of this enzyme requires NS4A, a 54-residue polyprotein cleavage product, to form a stable complex with the NS3 domain. This review will describe the biochemical properties of the NS3/4A proteinase, its X-ray crystal structure and current attempts towards development of efficient inhibitors.

Mechanisms governing hepadnaviral nucleocapsid assembly.

Reverse transcription of an RNA pregenome is the central step in the replication cycle of the hepatitis B viruses. This reaction takes place within the viral nucleocapsid composed of the core protein, product(s) of the P (pol) gene and the RNA pregenome. As the enzymatic activities required reside in the P-protein it plays a major role in the hepadnaviral life cycle. This article summarizes recent data on structure and function of the hepadnaviral P-protein and discusses its important role in the early steps of nucleocapsid assembly.

Hepadnaviral assembly is initiated by polymerase binding to the encapsidation signal in the viral RNA genome.

Hepadnaviruses, as well as other pararetroviruses, express their pol (P) gene product unfused to the preceding core gene implying that these retroelements have developed a mechanism for initiating assembly and replication that is principally different from the one used by retroviruses and retrotransposons. We have analysed this mechanism for the human hepatitis B virus by using a newly developed, highly sensitive detection method based upon radiolabelling of the P protein at newly introduced target sites for protein kinase A. The results obtained demonstrate that polymerase encapsidation depends on the concomittant encapsidation of the HBV RNA pregenome and that packaging of the viral RNA, in turn, depends on the presence of P protein. Loss of P protein encapsidation by mutations inactivating the HBV RNA encapsidation signal epsilon could be compensated by trans-complementation with recombinant RNA molecules carrying the epsilon sequence. Thus, in contrast to retroviral replication, the interaction of the hepadnaviral P protein and the RNA genome at its packaging signal appears to be crucial for initiating the formation of replication-competent nucleocapsids. Furthermore, RNA control of P protein packaging stringently limits the number of polymerase molecules that can be encapsidated.

The amino-terminal domain of the hepadnaviral P-gene encodes the terminal protein (genome-linked protein) believed to prime reverse transcription.

A series of antisera directed against amino acid sequences from different segments of the duck hepatitis B virus (DHBV) P-gene were shown to immunoprecipitate DHBV DNA molecules that were covalently linked to the DHBV DNA terminal protein. Restriction analysis and sizing after protease treatment demonstrated that the P-gene proteins were bound to the 5'-end of the DHBV DNA minus-strand which was mapped to a G-residue in the centre of the repeat sequence DR1. Resistance to alkali treatment indicated a phosphodiester linkage to tyrosine between protein and DNA. Limited protease treatment prior to immunoprecipitation cleaved C-terminal P-proteins from the viral DNA, indicating that the terminal protein forms a separate domain encoded in the N-terminal part of the P-gene. Functional analysis of a deletion mutant confirmed the notion that a non-essential spacer separates the terminal protein from the polymerase domain residing in the C-terminal half of the P-gene. Thus, the major proteins required for hepadnaviral reverse transcription, namely the primer, DNA polymerase, and possibly also RNase H, appear to be synthesized as a polyprotein precursor which is at least initially linked as such to its first DNA product.

Replication of the hepatitis C virus.

Infection with the hepatitis C virus (HCV) is a major cause of chronic liver disease. HCV is an enveloped plus-strand RNA virus closely related to flavi- and pestiviruses. The first cloning of the HCV genome, about 10 years ago, initiated research efforts leading to the elucidation of the genomic organization and the definition of the functions of most viral proteins. Despite this progress the lack of convenient animal models and appropriate in vitro propagation systems have hampered a full understanding of the way the virus multiplies. This review summarizes our current knowledge about HCV replication and describes attempts pursued in the last few years to establish efficient and reliable cell culture systems.

Expression of the P-protein of the human hepatitis B virus in a vaccinia virus system and detection of the nucleocapsid-associated P-gene product by radiolabelling at newly introduced phosphorylation sites.

Hepatitis B virus (HBV) contains a particle-associated DNA polymerase/reverse transcriptase activity encoded by the P (pol) open reading frame. Due to its low abundance, the corresponding protein has so far escaped direct detection and structural analysis. As a first step to overcome these difficulties, a series of recombinant vaccinia viruses was constructed and used for the synthesis in human hepatoma cells of both the authentic full length protein and of its functional domains. Pulse chase experiments demonstrated that the P-proteins had very short half lives in striking contrast to the viral core protein expressed in parallel with the same system. No evidence was obtained for a specific proteolytic processing of the P-protein as occurring with retroviral pol gene products. Overexpression of P-protein by recombinant vaccinia viruses was then employed to develop a highly sensitive detection method based on the in vitro phosphorylation of newly introduced target sites for protein kinase A. The usefulness of this method was demonstrated in the analysis of encapsidated P-gene products that were transiently expressed from an appropriately modified HBV genome. The results obtained indicate that the P-protein acts unprocessed, at least during the initial steps of nucleocapsid assembly and reverse transcription, and that a fraction of the P-protein molecules is linked as such to the viral DNA. Direct detection of the hepadnaviral P-protein by in vitro phosphorylation should greatly facilitate future analyses on P-protein structure and function.

Determinants of substrate specificity in the NS3 serine proteinase of the hepatitis C virus.

Processing of the nonstructural polyprotein of the hepatitis C virus (HCV) requires the serine-type proteinase located in the amino-terminal domain of NS3. To identify residues within NS3 determining substrate specificity, a mutation analysis was performed. Using sequence alignments and three-dimensional structure predictions, amino acids assumed to be important for specificity were replaced and the enzymes were tested in an intracellular trans-processing assay for their effects on cleavage of an NS4B-5B substrate. For some of the substitutions at positions 133, 134, 135, 136, 138, 152, 155, 157, and 169, slightly reduced processing efficiencies were observed but in no case was the substrate specificity altered. In contrast, substitutions of the phenylalanine at position 154 resulted in a modified cleavage pattern, suggesting an important role for this residue in substrate specificity. To substantiate this assumption, a panel of NS4B-5B substrates carrying different P1 residues at the NS4B/5A site were tested for cleavage by these altered proteinases. We found that substitution of Phe-154 by alanine, by valine, and particularly by threonine generated enzymes with the following affinities for aliphatic P1 residues: C > L > I > V for 154 F --> A, C = L > I > V for 154 F --> V and L > C > I > V for 154 F --> T. Neither leucine nor isoleucine nor valine was accepted by the parental NS3 proteinase, showing that Phe-154 is an important determinant for substrate specificity. Furthermore, we present evidence that Ala-157 plays an additional but minor role for this property.

Modulation of hepatitis C virus NS5A hyperphosphorylation by nonstructural proteins NS3, NS4A, and NS4B.

NS5A of the hepatitis C virus (HCV) is a highly phosphorylated protein involved in resistance against interferon and required most likely for replication of the viral genome. Phosphorylation of this protein is mediated by a cellular kinase(s) generating multiple proteins with different electrophoretic mobilities. In the case of the genotype 1b isolate HCV-J, in addition to the basal phosphorylated NS5A (designated pp56), a hyperphosphorylated form (pp58) was found on coexpression of NS4A (T. Kaneko, Y. Tanji, S. Satoh, M. Hijikata, S. Asabe, K. Kimura, and K. Shimotohno, Biochem. Biophys. Res. Commun. 205:320-326, 1994). Using a comparative analysis of two full-length genomes of genotype 1b, competent or defective for NS5A hyperphosphorylation, we investigated the requirements for this NS5A modification. We found that hyperphosphorylation occurs when NS5A is expressed as part of a continuous NS3-5A polyprotein but not when it is expressed on its own or trans complemented with one or several other viral proteins. Results obtained with chimeras of both genomes show that single amino acid substitutions within NS3 that do not affect polyprotein cleavage can enhance or reduce NS5A hyperphosphorylation. Furthermore, mutations in the central or carboxy-terminal NS4A domain as well as small deletions in NS4B can also reduce or block hyperphosphorylation without affecting polyprotein processing. These requirements most likely reflect the formation of a highly ordered NS3-5A multisubunit complex responsible for the differential phosphorylation of NS5A and probably also for modulation of its biological activities.