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Triebel S, Lamkiewicz K, Ontiveros N, Sweeney B, Stadler PF, Petrov AI, Niepmann M, Marz M. Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus. Sci Rep 2024; 14:15145. [PMID: 38956134 PMCID: PMC11219754 DOI: 10.1038/s41598-024-62897-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/22/2024] [Indexed: 07/04/2024] Open
Abstract
Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large 'cloud' of RNA genomes (quasispecies) which-by trial and error-comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.
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Affiliation(s)
- Sandra Triebel
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Nancy Ontiveros
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Blake Sweeney
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Peter F Stadler
- European Virus Bioinformatics Center, Friedrich Schiller University Jena, 07743, Jena, Germany
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, 04107, Leipzig, Germany
- German Center for Integrative Biodiversity Research (iDiv), 04103, Leipzig, Germany
| | | | - Michael Niepmann
- Institute for Biochemistry, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany.
- European Virus Bioinformatics Center, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Leibniz Institute on Aging-Fritz Lipmann Institute, 07745, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv), 04103, Leipzig, Germany.
- Michael Stifel Center Jena, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
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2
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Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens 2024; 13:60. [PMID: 38251367 PMCID: PMC10819198 DOI: 10.3390/pathogens13010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.
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Affiliation(s)
| | | | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA; (A.R.Z.); (P.D.)
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3
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Tsopela V, Korakidis E, Lagou D, Kalliampakou KI, Milona RS, Kyriakopoulou E, Mpekoulis G, Gemenetzi I, Stylianaki EA, Sideris CD, Sioli A, Kefallinos D, Sideris DC, Aidinis V, Eliopoulos AG, Kambas K, Vassilacopoulou D, Vassilaki N. L-Dopa decarboxylase modulates autophagy in hepatocytes and is implicated in dengue virus-caused inhibition of autophagy completion. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119602. [PMID: 37778471 DOI: 10.1016/j.bbamcr.2023.119602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 09/13/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
The enzyme L-Dopa Decarboxylase (DDC) synthesizes the catecholamine dopamine and the indolamine serotonin. Apart from its role in the brain as a neurotransmitter biosynthetic enzyme, DDC has been detected also in the liver and other peripheral organs, where it is implicated in cell proliferation, apoptosis, and host-virus interactions. Dengue virus (DENV) suppresses DDC expression at the later stages of infection, during which DENV also inhibits autophagosome-lysosome fusion. As dopamine affects autophagy in neuronal cells, we investigated the possible association of DDC with autophagy in human hepatocytes and examined whether DDC mediates the relationship between DENV infection and autophagy. We performed DDC silencing/overexpression and evaluated autophagic markers upon induction of autophagy, or suppression of autophagosome-lysosome fusion. Our results showed that DDC favored the autophagic process, at least in part, through its biosynthetic function, while knockdown of DDC or inhibition of DDC enzymatic activity prevented autophagy completion. In turn, autophagy induction upregulated DDC, while autophagy reduction by chemical or genetic (ATG14L knockout) ways caused the opposite effect. This study also implicated DDC with the cellular energetic status, as DDC silencing reduced the oxidative phosphorylation activity of the cell. We also report that upon DDC silencing, the repressive effect of DENV on the completion of autophagy was enhanced, and the inhibition of autolysosome formation did not exert an additive effect on viral proliferation. These data unravel a novel role of DDC in the autophagic process and suggest that DENV downregulates DDC expression to inhibit the completion of autophagy, reinforcing the importance of this protein in viral infections.
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Affiliation(s)
- Vassilina Tsopela
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115 21 Athens, Greece
| | - Evangelos Korakidis
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115 21 Athens, Greece
| | - Despoina Lagou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115 21 Athens, Greece
| | | | - Raphaela S Milona
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115 21 Athens, Greece
| | - Eirini Kyriakopoulou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115 21 Athens, Greece
| | - George Mpekoulis
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115 21 Athens, Greece
| | - Ioanna Gemenetzi
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115 21 Athens, Greece
| | - Elli-Anna Stylianaki
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece
| | | | - Aggelina Sioli
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115 21 Athens, Greece
| | - Dionysis Kefallinos
- School of Electrical Engineering and Computer Science, National Technical University of Athens, 157 73 Athens, Greece
| | - Diamantis C Sideris
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 157 01 Athens, Greece
| | - Vassilis Aidinis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece
| | - Aristides G Eliopoulos
- Department of Biology, School of Medicine, NKUA, 115 27 Athens, Greece; Center of Basic Research, Biomedical Research Foundation Academy of Athens, 115 27 Athens, Greece
| | - Konstantinos Kambas
- Laboratory of Molecular Genetics, Department of Immunology, Hellenic Pasteur Institute, 115 21 Athens, Greece
| | - Dido Vassilacopoulou
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 157 01 Athens, Greece
| | - Niki Vassilaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115 21 Athens, Greece.
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4
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Akram F, Waheed HM, Shah FI, Haq IU, Nasir N, Akhtar MT, Farooq Gohar U. Burgeoning therapeutic strategies to curb the contemporary surging viral infections. Microb Pathog 2023; 179:106088. [PMID: 37004965 DOI: 10.1016/j.micpath.2023.106088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
Significant efforts and initiatives were already made in the health care systems, however in the last few years; our world is facing emergences of viral infections which potentially leading to considerable challenges in terms of higher morbidity, mortality, increased and considerable financial loads on the affected populations. Over ten major epidemics or pandemics have been recorded in the twenty-first century, the ongoing coronavirus pandemic being one of them. Viruses being distinct obligate pathogens largely dependent on living beings are considered as one of the prominent causes of death globally. Although effective vaccines and antivirals have led to the eradication of imperative viral pathogens, the emergences of new viral infections as well as novel drug-resistant strains have necessitated the implementation of ingenious and efficient therapeutic approaches to treat viral outbreaks in the future. Nature being a constant source of tremendous therapeutical resources has inspired us to develop multi-target antiviral drugs, overcoming the challenges and limitations faced by pharmaceutical industry. Recent breakthroughs in the understanding of the cellular and molecular mechanisms of viral reproduction have laid the groundwork for potential treatment approaches including antiviral gene therapy relying on the application of precisely engineered nucleic acids for disabling pathogen replication. The development of RNA interference and advancements in genome manipulating tools have proven to be especially significant in this regard. In this review, we discussed mode of actions and pathophysiological events associated with the viral infections; followed by distributions, and advancement made towards the detection strategies for timely diagnosis. In the later section, current approaches to cope up the viral pathogens and their key limitations have also been elaborated. Lastly, we also explored some novel and potential targets to treat such infections, where attentions were made on next generation gene editing technologies.
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Vrazas V, Moustafa S, Makridakis M, Karakasiliotis I, Vlahou A, Mavromara P, Katsani KR. A Proteomic Approach to Study the Biological Role of Hepatitis C Virus Protein Core+1/ARFP. Viruses 2022; 14:v14081694. [PMID: 36016316 PMCID: PMC9518822 DOI: 10.3390/v14081694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis C virus is the major cause of chronic liver diseases and the only cytoplasmic RNA virus known to be oncogenic in humans. The viral genome gives rise to ten mature proteins and to additional proteins, which are the products of alternative translation initiation mechanisms. A protein-known as ARFP (alternative reading frame protein) or Core+1 protein-is synthesized by an open reading frame overlapping the HCV Core coding region in the (+1) frame of genotype 1a. Almost 20 years after its discovery, we still know little of the biological role of the ARFP/Core+1 protein. Here, our differential proteomic analysis of stable hepatoma cell lines expressing the Core+1/Long isoform of HCV-1a relates the expression of the Core+1/Long isoform with the progression of the pathology of HCV liver disease to cancer.
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Affiliation(s)
- Vasileios Vrazas
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (V.V.); (P.M.)
| | - Savvina Moustafa
- Clinical Immunology-Rheumatology Unit, 2nd Department of Medicine and Laboratory, Hippokration General Hospital of Athens, 11527 Athens, Greece;
| | - Manousos Makridakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (A.V.); (M.M.)
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Antonia Vlahou
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (A.V.); (M.M.)
| | - Penelope Mavromara
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (V.V.); (P.M.)
| | - Katerina R. Katsani
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (V.V.); (P.M.)
- Correspondence:
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Hamdy J, Emadeldin N, Hamed MM, Frakolaki E, Katsamakas S, Vassilaki N, Zoidis G, Hirsch AKH, Abdel-Halim M, Abadi AH. Design and Synthesis of Novel Bis-Imidazolyl Phenyl Butadiyne Derivatives as HCV NS5A Inhibitors. Pharmaceuticals (Basel) 2022; 15:632. [PMID: 35631457 PMCID: PMC9146377 DOI: 10.3390/ph15050632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
In today’s global plan to completely eradicate hepatitis C virus (HCV), the essential list of medications used for HCV treatment are direct-acting antivirals (DAAs), as interferon-sparing regimens have become the standard-of-care (SOC) treatment. HCV nonstructural protein 5A (NS5A) inhibitors are a very common component of these regimens. Food and Drug Administration (FDA)-approved NS5A inhibitors, although very potent, do not have the same potency against all eight genotypes of HCV. Therefore, this study aims to synthesize NS5A inhibitor analogues with high potency pan-genotypic activity and high metabolic stability. Starting from an NS5A inhibitor scaffold previously identified by our research group, we made several modifications. Two series of compounds were created to test the effect of changing the length and spatial conformation (para-para vs. meta-meta-positioned bis-imidazole-proline-carbamate), replacing amide groups in the linker with imidazole groups, as well as different end-cap compositions and sizes. The frontrunner inhibits genotype 1b (Con1) replicon, with an EC50 value in the picomolar range, and showed high genotypic coverage with nanomolar range EC50 values against four more genotypes. This together with its high metabolic stability (t½ > 120 min) makes it a potential preclinical candidate.
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Affiliation(s)
- Jehad Hamdy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (J.H.); (N.E.)
| | - Nouran Emadeldin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (J.H.); (N.E.)
| | - Mostafa M. Hamed
- Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)—Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.M.H.); (A.K.H.H.)
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece; (E.F.); (N.V.)
| | - Sotirios Katsamakas
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece;
| | - Niki Vassilaki
- Molecular Virology Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece; (E.F.); (N.V.)
| | - Grigoris Zoidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece;
| | - Anna K. H. Hirsch
- Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)—Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (J.H.); (N.E.)
| | - Ashraf H. Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (J.H.); (N.E.)
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7
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Mpekoulis G, Tsopela V, Chalari A, Kalliampakou KI, Panos G, Frakolaki E, Milona RS, Sideris DC, Vassilacopoulou D, Vassilaki N. Dengue Virus Replication Is Associated with Catecholamine Biosynthesis and Metabolism in Hepatocytes. Viruses 2022; 14:v14030564. [PMID: 35336971 PMCID: PMC8948859 DOI: 10.3390/v14030564] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 12/10/2022] Open
Abstract
Previously, the association between the catecholamine biosynthetic enzyme L-Dopa decarboxylase (DDC) and Dengue virus (DV) replication was demonstrated in liver cells and was found to be mediated at least by the interaction between DDC and phosphoinositide 3-kinase (PI3K). Here, we show that biogenic amines production and uptake impede DV replication in hepatocytes and monocytes, while the virus reduces catecholamine biosynthesis, metabolism, and transport. To examine how catecholamine biosynthesis/metabolism influences DV, first, we verified the role of DDC by altering DDC expression. DDC silencing enhanced virus replication, but not translation, attenuated the negative effect of DDC substrates on the virus and reduced the infection related cell death. Then, the role of the downstream steps of the catecholamine biosynthesis/metabolism was analyzed by chemical inhibition of the respective enzymes, application of their substrates and/or their products; moreover, reserpine, the inhibitor of the vesicular monoamine transporter 2 (VMAT2), was used to examine the role of uptake/storage of catecholamines on DV. Apart from the role of each enzyme/transporter, these studies revealed that the dopamine uptake, and not the dopamine-signaling, is responsible for the negative effect on DV. Accordingly, all treatments expected to enhance the accumulation of catecholamines in the cell cytosol suppressed DV replication. This was verified by the use of chemical inducers of catecholamine biosynthesis. Last, the cellular redox alterations due to catecholamine oxidation were not related with the inhibition of DV replication. In turn, DV apart from its negative impact on DDC, inhibits tyrosine hydroxylase, dopamine beta-hydroxylase, monoamine oxidase, and VMAT2 expression.
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Affiliation(s)
- George Mpekoulis
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (A.C.); (K.I.K.); (G.P.); (R.S.M.)
| | - Vassilina Tsopela
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (A.C.); (K.I.K.); (G.P.); (R.S.M.)
| | - Anna Chalari
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (A.C.); (K.I.K.); (G.P.); (R.S.M.)
| | - Katerina I. Kalliampakou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (A.C.); (K.I.K.); (G.P.); (R.S.M.)
| | - Georgios Panos
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (A.C.); (K.I.K.); (G.P.); (R.S.M.)
| | - Efseveia Frakolaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (A.C.); (K.I.K.); (G.P.); (R.S.M.)
| | - Raphaela S. Milona
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (A.C.); (K.I.K.); (G.P.); (R.S.M.)
| | - Diamantis C. Sideris
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece; (D.C.S.); (D.V.)
| | - Dido Vassilacopoulou
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece; (D.C.S.); (D.V.)
| | - Niki Vassilaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (A.C.); (K.I.K.); (G.P.); (R.S.M.)
- Correspondence: ; Tel.: +30-210-647-8875
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8
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Abdallah M, Hamed MM, Frakolaki E, Katsamakas S, Vassilaki N, Bartenschlager R, Zoidis G, Hirsch AKH, Abdel-Halim M, Abadi AH. Redesigning of the cap conformation and symmetry of the diphenylethyne core to yield highly potent pan-genotypic NS5A inhibitors with high potency and high resistance barrier. Eur J Med Chem 2021; 229:114034. [PMID: 34959173 DOI: 10.1016/j.ejmech.2021.114034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 11/15/2022]
Abstract
Herein, we report the discovery of several NS5A inhibitors with potency against HCV genotype 1b in the picomolar range. Compounds (15, 33) were of extremely high potency against HCV genotype 1b (EC50 ≈ 1 pM), improved activity against genotype 3a (GT 3a) and good metabolic stability. We studied the impact of changing the cap conformation relative to the diphenylethyne core and/or compound symmetry on both potency and metabolic stability. The analogs obtained exhibited improved potency against HCV genotypes 1a, 1b, 3a and 4a compared to the clinically approved candidate daclatasvir with EC50 values in the low picomolar range and SI50s > 7 orders of magnitude. Compound 15, a symmetrically m-, m'-substituted diphenyl ethyne analog, was 150-fold more potent than daclatasvir against GT 3a, while compound 33, an asymmetrically m-, p-substituted diphenyl ethyne analog, was 35-fold more potent than daclatasvir against GT 3a. In addition, compound 15 exhibited a higher resistance barrier than daclatasvir against genotype 1b.
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Affiliation(s)
- Mennatallah Abdallah
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Mostafa M Hamed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus E8.1, 66123, Saarbrücken, Germany
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521, Athens, Greece
| | - Sotirios Katsamakas
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521, Athens, Greece
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, Germany
| | - Grigoris Zoidis
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece.
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, Saarbrücken, 66123, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt.
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt.
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9
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Mpekoulis G, Tsopela V, Panos G, Siozos V, Kalliampakou KI, Frakolaki E, Sideris CD, Vassiliou AG, Sideris DC, Vassilacopoulou D, Vassilaki N. Association of Hepatitis C Virus Replication with the Catecholamine Biosynthetic Pathway. Viruses 2021; 13:v13112139. [PMID: 34834946 PMCID: PMC8624100 DOI: 10.3390/v13112139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/15/2022] Open
Abstract
A bidirectional negative relationship between Hepatitis C virus (HCV) replication and gene expression of the catecholamine biosynthetic enzyme L-Dopa decarboxylase (DDC) was previously shown in the liver and attributed at least to an association of DDC with phosphatidylinositol 3-kinase (PI3K). Here, we report that the biosynthesis and uptake of catecholamines restrict HCV replication in hepatocytes, while HCV has developed ways to reduce catecholamine production. By employing gene silencing, chemical inhibition or induction of the catecholamine biosynthetic and metabolic enzymes and transporters, and by applying the substrates or the products of the respective enzymes, we unravel the role of the different steps of the pathway in viral infection. We also provide evidence that the effect of catecholamines on HCV is strongly related with oxidative stress that is generated by their autoxidation in the cytosol, while antioxidants or treatments that lower cytosolic catecholamine levels positively affect the virus. To counteract the effect of catecholamines, HCV, apart from the already reported effects on DDC, causes the down-regulation of tyrosine hydroxylase that encodes the rate-limiting enzyme of catecholamine biosynthesis and suppresses dopamine beta-hydroxylase mRNA and protein amounts, while increasing the catecholamine degradation enzyme monoamine oxidase. Moreover, the NS4B viral protein is implicated in the effect of HCV on the ratio of the ~50 kDa DDC monomer and a ~120 kDa DDC complex, while the NS5A protein has a negative effect on total DDC protein levels.
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Affiliation(s)
- George Mpekoulis
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (G.P.); (V.S.); (K.I.K.); (E.F.); (C.D.S.)
| | - Vassilina Tsopela
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (G.P.); (V.S.); (K.I.K.); (E.F.); (C.D.S.)
| | - Georgios Panos
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (G.P.); (V.S.); (K.I.K.); (E.F.); (C.D.S.)
| | - Vasileiοs Siozos
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (G.P.); (V.S.); (K.I.K.); (E.F.); (C.D.S.)
| | - Katerina I. Kalliampakou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (G.P.); (V.S.); (K.I.K.); (E.F.); (C.D.S.)
| | - Efseveia Frakolaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (G.P.); (V.S.); (K.I.K.); (E.F.); (C.D.S.)
| | - Constantinos D. Sideris
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (G.P.); (V.S.); (K.I.K.); (E.F.); (C.D.S.)
| | - Alice G. Vassiliou
- GP Livanos and M Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece;
| | - Diamantis C. Sideris
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece; (D.C.S.); (D.V.)
| | - Dido Vassilacopoulou
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece; (D.C.S.); (D.V.)
| | - Niki Vassilaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.M.); (V.T.); (G.P.); (V.S.); (K.I.K.); (E.F.); (C.D.S.)
- Correspondence: ; Tel.: +30-210-647-8875
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10
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Zakh R, Churkin A, Totzeck F, Parr M, Tuller T, Etzion O, Dahari H, Roggendorf M, Frishman D, Barash D. A Mathematical Analysis of HDV Genotypes: From Molecules to Cells. MATHEMATICS (BASEL, SWITZERLAND) 2021; 9:2063. [PMID: 34540628 PMCID: PMC8445514 DOI: 10.3390/math9172063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hepatitis D virus (HDV) is classified according to eight genotypes. The various genotypes are included in the HDVdb database, where each HDV sequence is specified by its genotype. In this contribution, a mathematical analysis is performed on RNA sequences in HDVdb. The RNA folding predicted structures of the Genbank HDV genome sequences in HDVdb are classified according to their coarse-grain tree-graph representation. The analysis allows discarding in a simple and efficient way the vast majority of the sequences that exhibit a rod-like structure, which is important for the virus replication, to attempt to discover other biological functions by structure consideration. After the filtering, there remain only a small number of sequences that can be checked for their additional stem-loops besides the main one that is known to be responsible for virus replication. It is found that a few sequences contain an additional stem-loop that is responsible for RNA editing or other possible functions. These few sequences are grouped into two main classes, one that is well-known experimentally belonging to genotype 3 for patients from South America associated with RNA editing, and the other that is not known at present belonging to genotype 7 for patients from Cameroon. The possibility that another function besides virus replication reminiscent of the editing mechanism in HDV genotype 3 exists in HDV genotype 7 has not been explored before and is predicted by eigenvalue analysis. Finally, when comparing native and shuffled sequences, it is shown that HDV sequences belonging to all genotypes are accentuated in their mutational robustness and thermodynamic stability as compared to other viruses that were subjected to such an analysis.
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Affiliation(s)
- Rami Zakh
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
| | - Alexander Churkin
- Department of Software Engineering, Sami Shamoon College of Engineering, Beer-Sheva 8410501, Israel
| | - Franziska Totzeck
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Marina Parr
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Ohad Etzion
- Soroka University Medical Center, Ben-Gurion University, Beer-Sheva 8410501, Israel
| | - Harel Dahari
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Michael Roggendorf
- Institute of Virology, Technische Universität München, 81675 Munich, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
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11
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Li HC, Yang CH, Lo SY. Hepatitis C Viral Replication Complex. Viruses 2021; 13:v13030520. [PMID: 33809897 PMCID: PMC8004249 DOI: 10.3390/v13030520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
The life cycle of the hepatitis C virus (HCV) can be divided into several stages, including viral entry, protein translation, RNA replication, viral assembly, and release. HCV genomic RNA replication occurs in the replication organelles (RO) and is tightly linked to ER membrane alterations containing replication complexes (proteins NS3 to NS5B). The amplification of HCV genomic RNA could be regulated by the RO biogenesis, the viral RNA structure (i.e., cis-acting replication elements), and both viral and cellular proteins. Studies on HCV replication have led to the development of direct-acting antivirals (DAAs) targeting the replication complex. This review article summarizes the viral and cellular factors involved in regulating HCV genomic RNA replication and the DAAs that inhibit HCV replication.
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Affiliation(s)
- Hui-Chun Li
- Department of Biochemistry, Tzu Chi University, Hualien 97004, Taiwan;
| | - Chee-Hing Yang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan;
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan;
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
- Correspondence: ; Tel.: +886-3-8565301 (ext. 2322)
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12
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Vassilaki N, Frakolaki E, Kalliampakou KI, Sakellariou P, Kotta-Loizou I, Bartenschlager R, Mavromara P. A Novel Cis-Acting RNA Structural Element Embedded in the Core Coding Region of the Hepatitis C Virus Genome Directs Internal Translation Initiation of the Overlapping Core+1 ORF. Int J Mol Sci 2020; 21:ijms21186974. [PMID: 32972019 PMCID: PMC7554737 DOI: 10.3390/ijms21186974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/04/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) genome translation is initiated via an internal ribosome entry site (IRES) embedded in the 5'-untranslated region (5'UTR). We have earlier shown that the conserved RNA stem-loops (SL) SL47 and SL87 of the HCV core-encoding region are important for viral genome translation in cell culture and in vivo. Moreover, we have reported that an open reading frame overlapping the core gene in the +1 frame (core+1 ORF) encodes alternative translation products, including a protein initiated at the internal AUG codons 85/87 of this frame (nt 597-599 and 603-605), downstream of SL87, which is designated core+1/Short (core+1/S). Here, we provide evidence for SL47 and SL87 possessing a novel cis-acting element that directs the internal translation initiation of core+1/S. Firstly, using a bicistronic dual luciferase reporter system and RNA-transfection experiments, we found that nucleotides 344-596 of the HCV genotype-1a and -2a genomes support translation initiation at the core+1 frame AUG codons 85/87, when present in the sense but not the opposite orientation. Secondly, site-directed mutagenesis combined with an analysis of ribosome-HCV RNA association elucidated that SL47 and SL87 are essential for this alternative translation mechanism. Finally, experiments using cells transfected with JFH1 replicons or infected with virus-like particles showed that core+1/S expression is independent from the 5'UTR IRES and does not utilize the polyprotein initiation codon, but it requires intact SL47 and SL87 structures. Thus, SL47 and SL87, apart from their role in viral polyprotein translation, are necessary elements for mediating the internal translation initiation of the alternative core+1/S ORF.
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Affiliation(s)
- Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece; (E.F.); (K.I.K.); (P.S.); (I.K.-L.)
- Correspondence: (N.V.); (P.M.)
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece; (E.F.); (K.I.K.); (P.S.); (I.K.-L.)
| | - Katerina I. Kalliampakou
- Molecular Virology Laboratory, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece; (E.F.); (K.I.K.); (P.S.); (I.K.-L.)
| | - Panagiotis Sakellariou
- Molecular Virology Laboratory, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece; (E.F.); (K.I.K.); (P.S.); (I.K.-L.)
| | - Ioly Kotta-Loizou
- Molecular Virology Laboratory, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece; (E.F.); (K.I.K.); (P.S.); (I.K.-L.)
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany;
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Penelope Mavromara
- Molecular Virology Laboratory, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece; (E.F.); (K.I.K.); (P.S.); (I.K.-L.)
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Thrace, Greece
- Correspondence: (N.V.); (P.M.)
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13
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Genotypic Regulation of Type I Interferon Induction Pathways by Frameshift (F) Proteins of Hepatitis C Virus. J Virol 2020; 94:JVI.00312-20. [PMID: 32434887 DOI: 10.1128/jvi.00312-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) has evolved mechanisms to evade innate immunity that are leading to chronic infections. The immunological function of the HCV frameshift (F) protein, which is a frameshift product of core coding sequences, has not been well characterized. The HCV F protein is produced during natural HCV infections and is found most commonly in genotype 1 HCV. In this study, we investigated whether the F protein plays a role in type I interferon (IFN) induction pathways. We engineered F expression constructs from core coding sequences of 4 genotypes (1a, 2a, 3a, and 4a) of HCV as well as the sequences which would only be able to produce core proteins. The peptide lengths and amino acids sequences of F proteins are highly variable. We hypothesized that F proteins from different genotypes might control the type I IFN production and response differently. We found that both IFN-beta (IFN-β) promoter activities are significantly higher in genotype 1a F protein (F1a)-expressing cells. Conversely, the IFN-β promoter activities are lower in genotype 2a F (F2a) protein-expressing cells. We also used real-time PCR to confirm IFN-β mRNA expression levels. By generating chimera F proteins, we discovered that the effects of F proteins were determined by the amino acid sequence 40 to 57 of genotype 1a. The regulation of type I IFN induction pathway is related but not limited to the activity of F1a to interact with proteasome subunits and to disturb the proteasome activity. Further molecular mechanisms of how F proteins from different genotypes of HCV control these pathways differently remain to be investigated.IMPORTANCE Although naturally present in HCV infection patient serum, the virological or immunological functions of the HCV F protein, which is a frameshift product of core coding sequences, remain unclear. Here, we report the effects of the HCV F protein between genotypes and discuss a potential explanation for the differential responses to type I IFN-based therapy among patients infected with different genotypes of HCV. Our study provides one step forward to understanding the host response during HCV infection and new insights for the prediction of the outcome of IFN-based therapy in HCV patients.
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14
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Abdel Karim SE, Youssef YH, Abdel-Halim M, Frakolaki E, Vassilaki N, Zoidis G, Ahmed NS, Abadi AH. Symmetric benzidine derivatives as anti-HCV agents: Insight into the nature, stereochemistry of the capping amino acid and the size of the terminal capping carbamates. Bioorg Chem 2020; 102:104089. [PMID: 32717691 DOI: 10.1016/j.bioorg.2020.104089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 12/22/2022]
Abstract
Novel symmetric molecules, bearing a benzidine prolinamide core, two terminal carbamate caps of variable sizes and nature, including natural and unnatural amino acids were developed. Several terminal N-carbamate substituents of the core structure, ranging from linear methyl, ethyl and butyl groups to branching isobutyl group; and an aromatic substituent were also synthesized. Series 1 has hydrophobic AA residues, namely S and R phenylglycine and a terminal carbamate capping group, whereas Series 2 bears sulphur containing amino acids, specifically S and R methionine and the natural R methylcysteine. The novel compounds were tested for their inhibitory activity (EC50) and their cytotoxicity (CC50), using an HCV 1b (Con1) reporter replicon cell line. Compound 4 with the unnatural capping residue, bearing d-Phenylglycine amino acid residue and N-isobutyloxycarbonyl capping group, was the most active within the two series, with EC50 = 0.0067 nM. Moreover, it showed high SI50 > 14788524 and was not cytotoxic at the highest tested concentration (100 μΜ), indicating its safety profile. Compound 4 also inhibited HCV genotypes 2a, 3a and 4a. Compared to the clinically approved NS5A inhibitor Daclatasvir, compound 4 shows higher activity against genotypes 1b and 3a, as well as improved safety profile.
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Affiliation(s)
- Shereen E Abdel Karim
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Youssef H Youssef
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Mohammad Abdel-Halim
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, GR-15771 Athens, Greece
| | - Nermin S Ahmed
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Ashraf H Abadi
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt.
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15
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Hepatitis C Virus Translation Regulation. Int J Mol Sci 2020; 21:ijms21072328. [PMID: 32230899 PMCID: PMC7178104 DOI: 10.3390/ijms21072328] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022] Open
Abstract
Translation of the hepatitis C virus (HCV) RNA genome is regulated by the internal ribosome entry site (IRES), located in the 5’-untranslated region (5′UTR) and part of the core protein coding sequence, and by the 3′UTR. The 5′UTR has some highly conserved structural regions, while others can assume different conformations. The IRES can bind to the ribosomal 40S subunit with high affinity without any other factors. Nevertheless, IRES activity is modulated by additional cis sequences in the viral genome, including the 3′UTR and the cis-acting replication element (CRE). Canonical translation initiation factors (eIFs) are involved in HCV translation initiation, including eIF3, eIF2, eIF1A, eIF5, and eIF5B. Alternatively, under stress conditions and limited eIF2-Met-tRNAiMet availability, alternative initiation factors such as eIF2D, eIF2A, and eIF5B can substitute for eIF2 to allow HCV translation even when cellular mRNA translation is downregulated. In addition, several IRES trans-acting factors (ITAFs) modulate IRES activity by building large networks of RNA-protein and protein–protein interactions, also connecting 5′- and 3′-ends of the viral RNA. Moreover, some ITAFs can act as RNA chaperones that help to position the viral AUG start codon in the ribosomal 40S subunit entry channel. Finally, the liver-specific microRNA-122 (miR-122) stimulates HCV IRES-dependent translation, most likely by stabilizing a certain structure of the IRES that is required for initiation.
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16
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Tabata K, Neufeldt CJ, Bartenschlager R. Hepatitis C Virus Replication. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a037093. [PMID: 31570388 DOI: 10.1101/cshperspect.a037093] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Replication and amplification of the viral genome is a key process for all viruses. For hepatitis C virus (HCV), a positive-strand RNA virus, amplification of the viral genome requires the synthesis of a negative-sense RNA template, which is in turn used for the production of new genomic RNA. This process is governed by numerous proteins, both host and viral, as well as distinct lipids and specific RNA elements within the positive- and negative-strand RNAs. Moreover, this process requires specific changes to host cell ultrastructure to create microenvironments conducive to viral replication. This review will focus on describing the processes and factors involved in facilitating or regulating HCV genome replication.
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Affiliation(s)
- Keisuke Tabata
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis, German Cancer Research Center, 69120 Heidelberg, Germany.,German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
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17
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Mohammadi Pour P, Fakhri S, Asgary S, Farzaei MH, Echeverría J. The Signaling Pathways, and Therapeutic Targets of Antiviral Agents: Focusing on the Antiviral Approaches and Clinical Perspectives of Anthocyanins in the Management of Viral Diseases. Front Pharmacol 2019; 10:1207. [PMID: 31787892 PMCID: PMC6856223 DOI: 10.3389/fphar.2019.01207] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/19/2019] [Indexed: 12/31/2022] Open
Abstract
As the leading cause of death worldwide, viruses significantly affect global health. Despite the rapid progress in human healthcare, there are few viricidal and antiviral therapies that are efficient enough. The rapid emergence of resistance, and high costs, as well as the related side effects of synthetic antiviral drugs, raise the need to identify novel, effective, and safe alternatives against viral diseases. Nature has been of the most exceptional help and source of inspiration for developing novel multi-target antiviral compounds, affecting several steps of the viral life cycle and host proteins. For that matter and due to safety and efficacy limitations, as well as high resistance rate of conventional therapies, hundreds of natural molecules are preferred over the synthetic drugs. Besides, natural antiviral agents have shown acceptable antiviral value in both preclinical and clinical trials.This is the first review regarding molecular and cellular pathways of the virus life cycle, treatment strategies, and therapeutic targets of several viral diseases with a particular focus on anthocyanins as promising natural compounds for significant antiviral enhancements. Clinical applications and the need to develop nano-formulation of anthocyanins in drug delivery systems are also considered.
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Affiliation(s)
- Pardis Mohammadi Pour
- Department of Pharmacognosy, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sajad Fakhri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sedigheh Asgary
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hosein Farzaei
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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18
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Emerging Role of l-Dopa Decarboxylase in Flaviviridae Virus Infections. Cells 2019; 8:cells8080837. [PMID: 31387309 PMCID: PMC6721762 DOI: 10.3390/cells8080837] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 12/17/2022] Open
Abstract
l-dopa decarboxylase (DDC) that catalyzes the biosynthesis of bioactive amines, such as dopamine and serotonin, is expressed in the nervous system and peripheral tissues, including the liver, where its physiological role remains unknown. Recently, we reported a physical and functional interaction of DDC with the major signaling regulator phosphoinosite-3-kinase (PI3K). Here, we provide compelling evidence for the involvement of DDC in viral infections. Studying dengue (DENV) and hepatitis C (HCV) virus infection in hepatocytes and HCV replication in liver samples of infected patients, we observed a negative association between DDC and viral replication. Specifically, replication of both viruses reduced the levels of DDC mRNA and the ~120 kDa SDS-resistant DDC immunoreactive functional complex, concomitant with a PI3K-dependent accumulation of the ~50 kDa DDC monomer. Moreover, viral infection inhibited PI3K-DDC association, while DDC did not colocalize with viral replication sites. DDC overexpression suppressed DENV and HCV RNA replication, while DDC enzymatic inhibition enhanced viral replication and infectivity and affected DENV-induced cell death. Consistently, we observed an inverse correlation between DDC mRNA and HCV RNA levels in liver biopsies from chronically infected patients. These data reveal a novel relationship between DDC and Flaviviridae replication cycle and the role of PI3K in this process.
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19
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Leila AR, Mousa MHA, Frakolaki E, Vassilaki N, Bartenschlager R, Zoidis G, Abdel-Halim M, Abadi AH. Symmetric Anti-HCV Agents: Synthesis, Antiviral Properties, and Conformational Aspects of Core Scaffolds. ACS OMEGA 2019; 4:11440-11454. [PMID: 31460249 PMCID: PMC6682128 DOI: 10.1021/acsomega.9b01242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 05/17/2023]
Abstract
As hepatitis C virus (HCV) is one of the major health problems in many countries, interest has been aroused in the design, synthesis, and optimization of novel NS5A inhibitors, outside the chemical space of currently available direct acting antivirals (DAAs). Two series of symmetric molecules with core scaffold 3,3'-(buta-1,3-diyne-1,4-diyl)dianiline or 4,4'-(buta-1,3-diyne-1,4-diyl)dianiline, coupled on its nitrogen as amide with different end caps, were synthesized and tested for their activities against HCV by using cell-based antiviral assays. Molecules with the 3,3'-(buta-1,3-diyne-1,4-diyl)dianiline core were more active than their 4,4'-congeners. Only the 3,3'-derivatives showed noncoplanarity of core phenyls that mostly led to a better interaction with the target protein and appears to be a crucial element for efficient inhibition of HCV replication. Compounds 2f and 2q exhibited potent inhibition of genotype (GT) 1b HCV replication with EC50 values in the picomolar range and selectivity index greater than 6 orders of magnitude. The compounds seem more selective toward GT 1b and 4a. In conclusion, novel symmetric molecules with a 3,3'-(buta-1,3-diyne-1,4-diyl)dianiline core are potent and selective inhibitors that provide new extension to explore the structure-activity relationship of NS5A targeting DAAs.
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Affiliation(s)
- Alaa R.
S. Leila
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Mai H. A. Mousa
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Efseveia Frakolaki
- Molecular
Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece
| | - Niki Vassilaki
- Molecular
Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece
| | - Ralf Bartenschlager
- Department
of Infectious Diseases, Molecular Virology, University of Heidelberg, 69117 Heidelberg, Germany
- German
Center for Infection Research, Heidelberg
Partner Site, 69120 Heidelberg, Germany
| | - Grigoris Zoidis
- School
of Health Sciences, Faculty of Pharmacy, Department of Pharmaceutical
Chemistry, University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Mohammad Abdel-Halim
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Ashraf H. Abadi
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
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20
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Giannakopoulou E, Pardali V, Frakolaki E, Siozos V, Myrianthopoulos V, Mikros E, Taylor MC, Kelly JM, Vassilaki N, Zoidis G. Scaffold hybridization strategy towards potent hydroxamate-based inhibitors of Flaviviridae viruses and Trypanosoma species. MEDCHEMCOMM 2019; 10:991-1006. [PMID: 31303998 DOI: 10.1039/c9md00200f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
Infections with Flaviviridae viruses, such as hepatitis C virus (HCV) and dengue virus (DENV) pose global health threats. Infected individuals are at risk of developing chronic liver failure or haemorrhagic fever respectively, often with a fatal outcome if left untreated. Diseases caused by tropical parasites of the Trypanosoma species, T. brucei and T. cruzi, constitute significant socioeconomic burden in sub-Saharan Africa and continental Latin America, yet drug development is under-funded. Anti-HCV chemotherapy is associated with severe side effects and high cost, while dengue has no clinically approved therapy and antiparasitic drugs are outdated and difficult to administer. Moreover, drug resistance is an emerging concern. Consequently, the need for new revolutionary chemotherapies is urgent. By utilizing a molecular framework combination approach, we combined two distinct chemical entities with proven antiviral and trypanocidal activity into a novel hybrid scaffold attached by an acetohydroxamic acid group (CH2CONHOH), aiming at derivatives with dual activity. The novel spiro-carbocyclic substituted hydantoin analogues were rationally designed, synthesized and evaluated for their potency against three HCV genotypes (1b, 3a, 4a), DENV and two Trypanosoma species (T. brucei, T. cruzi). They exhibited significant EC50 values and remarkable selectivity indices. Several modifications were undertaken to further explore the structure activity relationships (SARs) and confirm the pivotal role of the acetohydroxamic acid metal binding group.
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Affiliation(s)
- Erofili Giannakopoulou
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
| | - Vasiliki Pardali
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
| | - Efseveia Frakolaki
- Molecular Virology Laboratory , Hellenic Pasteur Institute , Vas. Sofias Avenue , GR-11521 , Athens , Greece
| | - Vasileios Siozos
- Molecular Virology Laboratory , Hellenic Pasteur Institute , Vas. Sofias Avenue , GR-11521 , Athens , Greece
| | - Vassilios Myrianthopoulos
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
| | - Emmanuel Mikros
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
| | - Martin C Taylor
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street , London WC1E 7HT , UK
| | - John M Kelly
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street , London WC1E 7HT , UK
| | - Niki Vassilaki
- Molecular Virology Laboratory , Hellenic Pasteur Institute , Vas. Sofias Avenue , GR-11521 , Athens , Greece
| | - Grigoris Zoidis
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
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21
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Vassiliou AG, Siaterli MZ, Frakolaki E, Gkogkosi P, Paspaltsis I, Sklaviadis T, Vassilacopoulou D, Vassilaki N. L-Dopa decarboxylase interaction with the major signaling regulator ΡΙ3Κ in tissues and cells of neural and peripheral origin. Biochimie 2019; 160:76-87. [PMID: 30796964 DOI: 10.1016/j.biochi.2019.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/17/2019] [Indexed: 12/17/2022]
Abstract
L-Dopa decarboxylase (DDC) catalyzes the decarboxylation of L-Dopa to dopamine and 5-hydroxytryptophan (5-HTP) to serotonin. Although DDC has been purified from a variety of peripheral organs, including the liver, kidney and pancreas, the physiological significance of the peripherally expressed enzyme is not yet fully understood. DDC has been considered as a potential novel biomarker for various types of cancer, however, the role of DDC in the development of hepatocellular carcinoma (HCC) remains to be evaluated. Phosphatidylinositol 3-kinase (PI3K), on the other hand, has been shown to play a key role in the tumorigenesis, proliferation, metastasis, apoptosis, and angiogenesis of HCC by regulating gene expression. We initially identified the interaction of DDC with PI3K by means of the phage display methodology. This association was further confirmed in human hepatocellular carcinoma cell lines, human embryonic kidney cells, human neuroblastoma cells, as well as mouse brain, by the use of specific antibodies raised against DDC and PI3K. Functional aspects of the above interaction were studied upon treatment with the DDC inhibitor carbidopa and the PI3K inhibitor LY294002. Interestingly, our data demonstrate the expression of the neuronal type DDC mRNA in HCC cells. The present investigation provides new evidence on the possible link of DDC with the PI3K pathway, underlining the biological significance of this complex enzyme.
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Affiliation(s)
- Alice G Vassiliou
- 1st Department of Critical Care Medicine & Pulmonary Services, GP Livanos and M Simou Laboratories, Evangelismos Hospital, Athens Medical School, National & Kapodistrian University of Athens, Ipsilantou 45-47, 10676, Athens, Greece; Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15701, Athens, Greece
| | - Maria-Zacharenia Siaterli
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15701, Athens, Greece
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias ave., 11521, Athens, Greece
| | - Panayiota Gkogkosi
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15701, Athens, Greece
| | - Ioannis Paspaltsis
- Laboratory of Pharmacology, School of Health Sciences, Department of Pharmacy, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloniki, Greece
| | - Theodoros Sklaviadis
- Laboratory of Pharmacology, School of Health Sciences, Department of Pharmacy, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloniki, Greece
| | - Dido Vassilacopoulou
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15701, Athens, Greece.
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias ave., 11521, Athens, Greece.
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22
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Frakolaki E, Kaimou P, Moraiti M, Kalliampakou KI, Karampetsou K, Dotsika E, Liakos P, Vassilacopoulou D, Mavromara P, Bartenschlager R, Vassilaki N. The Role of Tissue Oxygen Tension in Dengue Virus Replication. Cells 2018; 7:cells7120241. [PMID: 30513781 PMCID: PMC6316080 DOI: 10.3390/cells7120241] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/26/2018] [Accepted: 11/28/2018] [Indexed: 12/18/2022] Open
Abstract
Low oxygen tension exerts a profound effect on the replication of several DNA and RNA viruses. In vitro propagation of Dengue virus (DENV) has been conventionally studied under atmospheric oxygen levels despite that in vivo, the tissue microenvironment is hypoxic. Here, we compared the efficiency of DENV replication in liver cells, monocytes, and epithelial cells under hypoxic and normoxic conditions, investigated the ability of DENV to induce a hypoxia response and metabolic reprogramming and determined the underlying molecular mechanism. In DENV-infected cells, hypoxia had no effect on virus entry and RNA translation, but enhanced RNA replication. Overexpression and silencing approaches as well as chemical inhibition and energy substrate exchanging experiments showed that hypoxia-mediated enhancement of DENV replication depends on the activation of the key metabolic regulators hypoxia-inducible factors 1α/2α (HIF-1α/2α) and the serine/threonine kinase AKT. Enhanced RNA replication correlates directly with an increase in anaerobic glycolysis producing elevated ATP levels. Additionally, DENV activates HIF and anaerobic glycolysis markers. Finally, reactive oxygen species were shown to contribute, at least in part through HIF, both to the hypoxia-mediated increase of DENV replication and to virus-induced hypoxic reprogramming. These suggest that DENV manipulates hypoxia response and oxygen-dependent metabolic reprogramming for efficient viral replication.
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Affiliation(s)
- Efseveia Frakolaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece.
| | - Panagiota Kaimou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece.
| | - Maria Moraiti
- Laboratory of Molecular Virology, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece.
| | | | - Kalliopi Karampetsou
- Laboratory of Cellular Immunology, Hellenic Pasteur Institute, 11521 Athens, Greece.
| | - Eleni Dotsika
- Laboratory of Cellular Immunology, Hellenic Pasteur Institute, 11521 Athens, Greece.
| | - Panagiotis Liakos
- Laboratory of Biochemistry, School of Medicine, University of Thessaly, 41500 Larissa, Greece.
| | - Dido Vassilacopoulou
- Section of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece.
| | - Penelope Mavromara
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Thrace, Greece.
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany.
- German Center for Infection Research, Heidelberg partner site, 69120 Heidelberg, Germany.
| | - Niki Vassilaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute (HPI), 11521 Athens, Greece.
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23
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Bentley K, Cook JP, Tuplin AK, Evans DJ. Structural and functional analysis of the roles of the HCV 5' NCR miR122-dependent long-range association and SLVI in genome translation and replication. PeerJ 2018; 6:e5870. [PMID: 30416884 PMCID: PMC6225842 DOI: 10.7717/peerj.5870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/30/2018] [Indexed: 11/29/2022] Open
Abstract
The hepatitis C virus RNA genome possesses a variety of conserved structural elements, in both coding and non-coding regions, that are important for viral replication. These elements are known or predicted to modulate key life cycle events, such as translation and genome replication, some involving conformational changes induced by long-range RNA–RNA interactions. One such element is SLVI, a stem-loop (SL) structure located towards the 5′ end of the core protein-coding region. This element forms an alternative RNA–RNA interaction with complementary sequences in the 5′ untranslated regions that are independently involved in the binding of the cellular microRNA 122 (miR122). The switch between ‘open’ and ‘closed’ structures involving SLVI has previously been proposed to modulate translation, with lower translation efficiency associated with the ‘closed’ conformation. In the current study, we have used selective 2′-hydroxyl acylation analysed by primer extension to validate this RNA–RNA interaction in the absence and presence of miR122. We show that the long-range association (LRA) only forms in the absence of miR122, or otherwise requires the blocking of miR122 binding combined with substantial disruption of SLVI. Using site-directed mutations introduced to promote open or closed conformations of the LRA we demonstrate no correlation between the conformation and the translation phenotype. In addition, we observed no influence on virus replication compared to unmodified genomes. The presence of SLVI is well-documented to suppress translation, but these studies demonstrate that this is not due to its contribution to the LRA. We conclude that, although there are roles for SLVI in translation, the LRA is not a riboswitch regulating the translation and replication phenotypes of the virus.
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Affiliation(s)
- Kirsten Bentley
- BSRC and School of Biology, University of St Andrews, St Andrews, UK
| | - Jonathan P Cook
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Andrew K Tuplin
- The Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - David J Evans
- BSRC and School of Biology, University of St Andrews, St Andrews, UK
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24
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Hepatitis C Virus core+1/ARF Protein Modulates the Cyclin D1/pRb Pathway and Promotes Carcinogenesis. J Virol 2018; 92:JVI.02036-17. [PMID: 29444947 DOI: 10.1128/jvi.02036-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/06/2018] [Indexed: 02/06/2023] Open
Abstract
Viruses often encompass overlapping reading frames and unconventional translation mechanisms in order to maximize the output from a minimum genome and to orchestrate their timely gene expression. Hepatitis C virus (HCV) possesses such an unconventional open reading frame (ORF) within the core-coding region, encoding an additional protein, initially designated ARFP, F, or core+1. Two predominant isoforms of core+1/ARFP have been reported, core+1/L, initiating from codon 26, and core+1/S, initiating from codons 85/87 of the polyprotein coding region. The biological significance of core+1/ARFP expression remains elusive. The aim of the present study was to gain insight into the functional and pathological properties of core+1/ARFP through its interaction with the host cell, combining in vitro and in vivo approaches. Our data provide strong evidence that the core+1/ARFP of HCV-1a stimulates cell proliferation in Huh7-based cell lines expressing either core+1/S or core+1/L isoforms and in transgenic liver disease mouse models expressing core+1/S protein in a liver-specific manner. Both isoforms of core+1/ARFP increase the levels of cyclin D1 and phosphorylated Rb, thus promoting the cell cycle. In addition, core+1/S was found to enhance liver regeneration and oncogenesis in transgenic mice. The induction of the cell cycle together with increased mRNA levels of cell proliferation-related oncogenes in cells expressing the core+1/ARFP proteins argue for an oncogenic potential of these proteins and an important role in HCV-associated pathogenesis.IMPORTANCE This study sheds light on the biological importance of a unique HCV protein. We show here that core+1/ARFP of HCV-1a interacts with the host machinery, leading to acceleration of the cell cycle and enhancement of liver carcinogenesis. This pathological mechanism(s) may complement the action of other viral proteins with oncogenic properties, leading to the development of hepatocellular carcinoma. In addition, given that immunological responses to core+1/ARFP have been correlated with liver disease severity in chronic HCV patients, we expect that the present work will assist in clarifying the pathophysiological relevance of this protein as a biomarker of disease progression.
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25
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Genetic Analysis of Serum-Derived Defective Hepatitis C Virus Genomes Revealed Novel Viral cis Elements for Virus Replication and Assembly. J Virol 2018; 92:JVI.02182-17. [PMID: 29367245 DOI: 10.1128/jvi.02182-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/08/2018] [Indexed: 12/12/2022] Open
Abstract
Defective viral genomes (DVGs) of hepatitis C virus (HCV) exist, but their biological significances have not been thoroughly investigated. Here, we analyzed HCV DVGs circulating in patient sera that possess deletions in the structural protein-encoding region. About 30% of 41 HCV clinical isolates possess DVGs that originated from the full-length genome in the same patients. No correlation between DVGs, viremia, and alanine aminotransferase (ALT) levels was found. Sequencing analysis of DVGs revealed the existence of deletion hot spots, with upstream sites in E1 and downstream sites in E2 and NS2. Interestingly, the coding sequences for the core protein and the C-terminal protease domain of NS2 were always intact in DVGs despite the fact that both proteins are dispensable for HCV genome replication. Mechanistic studies showed that transmembrane segment 3 (TMS3) of NS2, located immediately upstream of its protease domain, was required for the cleavage of NS2-NS3 and the replication of DVGs. Moreover, we identified a highly conserved secondary structure (SL750) within the core domain 2-coding region that is critical for HCV genome packaging. In summary, our analysis of serum-derived HCV DVGs revealed novel viral cis elements that play important roles in virus replication and assembly.IMPORTANCE HCV DVGs have been identified in vivo and in vitro, but their biogenesis and physiological significances remain elusive. In addition, a conventional packaging signal has not yet been identified on the HCV RNA genome, and mechanisms underlying the specificity in the encapsidation of the HCV genome into infectious particles remain to be uncovered. Here, we identified new viral cis elements critical for the HCV life cycle by determining genetic constraints that define the boundary of serum-derived HCV DVGs. We found that transmembrane segment 3 of NS2, located immediately upstream of its protease domain, was required for the cleavage of NS2-NS3 and the replication of DVGs. We identified a highly conserved secondary structure (SL750) within the core-coding region that is critical for HCV genome packaging. In summary, our analysis of serum-derived HCV DVGs revealed previously unexpected novel cis elements critical for HCV replication and morphogenesis.
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26
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Niepmann M, Shalamova LA, Gerresheim GK, Rossbach O. Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication. Front Microbiol 2018; 9:395. [PMID: 29593672 PMCID: PMC5857606 DOI: 10.3389/fmicb.2018.00395] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/21/2018] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) preferentially replicates in the human liver and frequently causes chronic infection, often leading to cirrhosis and liver cancer. HCV is an enveloped virus classified in the genus Hepacivirus in the family Flaviviridae and has a single-stranded RNA genome of positive orientation. The HCV RNA genome is translated and replicated in the cytoplasm. Translation is controlled by the Internal Ribosome Entry Site (IRES) in the 5' untranslated region (5' UTR), while also downstream elements like the cis-replication element (CRE) in the coding region and the 3' UTR are involved in translation regulation. The cis-elements controlling replication of the viral RNA genome are located mainly in the 5'- and 3'-UTRs at the genome ends but also in the protein coding region, and in part these signals overlap with the signals controlling RNA translation. Many long-range RNA-RNA interactions (LRIs) are predicted between different regions of the HCV RNA genome, and several such LRIs are actually involved in HCV translation and replication regulation. A number of RNA cis-elements recruit cellular RNA-binding proteins that are involved in the regulation of HCV translation and replication. In addition, the liver-specific microRNA-122 (miR-122) binds to two target sites at the 5' end of the viral RNA genome as well as to at least three additional target sites in the coding region and the 3' UTR. It is involved in the regulation of HCV RNA stability, translation and replication, thereby largely contributing to the hepatotropism of HCV. However, we are still far from completely understanding all interactions that regulate HCV RNA genome translation, stability, replication and encapsidation. In particular, many conclusions on the function of cis-elements in HCV replication have been obtained using full-length HCV genomes or near-full-length replicon systems. These include both genome ends, making it difficult to decide if a cis-element in question acts on HCV replication when physically present in the plus strand genome or in the minus strand antigenome. Therefore, it may be required to use reduced systems that selectively focus on the analysis of HCV minus strand initiation and/or plus strand initiation.
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Affiliation(s)
- Michael Niepmann
- Medical Faculty, Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Lyudmila A Shalamova
- Medical Faculty, Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany.,Faculty of Biology and Chemistry, Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Gesche K Gerresheim
- Medical Faculty, Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany.,Faculty of Biology and Chemistry, Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Oliver Rossbach
- Faculty of Biology and Chemistry, Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany
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27
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Kassela K, Karakasiliotis I, Charpantidis S, Koskinas J, Mylopoulou T, Mimidis K, Sarrazin C, Grammatikos G, Mavromara P. High prevalence of antibodies to core+1/ARF protein in HCV-infected patients with advanced cirrhosis. J Gen Virol 2017; 98:1713-1719. [PMID: 28708052 DOI: 10.1099/jgv.0.000851] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) possesses a second open reading frame (ORF) within the core gene encoding an additional protein, known as the alternative reading frame protein (ARFP), F or core+1. The biological significance of the core+1/ARF protein remains elusive. However, several independent studies have shown the presence of core+1/ARFP antibodies in chronically HCV-infected patients. Furthermore, a higher prevalence of core+1/ARFP antibodies was detected in patients with HCV-associated hepatocellular carcinoma (HCC). Here, we investigated the incidence of core+1/ARFPantibodies in chronically HCV-infected patients at different stages of cirrhosis in comparison to chronically HCV-infected patients at earlier stages of disease. Using ELISA, we assessed the prevalence of anti-core+1 antibodies in 30 patients with advanced cirrhosis [model for end-stage liver disease (MELD) ≥15] in comparison with 50 patients with mild cirrhosis (MELD <15) and 164 chronic HCV patients without cirrhosis. 28.7 % of HCV patients with cirrhosis were positive for anti-core+1 antibodies, in contrast with 16.5 % of non-cirrhotic HCV patients. Moreover, there was significantly higher positivity for anti-core+1 antibodies in HCV patients with advanced cirrhosis (36.7 %) compared to those with early cirrhosis (24 %) (P<0.05). These findings, together with the high prevalence of anti-core+1 antibodies in HCV patients with HCC, suggest that core+1 protein may have a role in virus-associated pathogenesis, and provide evidence to suggest that the levels of anti-core+1 antibodies may serve as a marker for disease progression.
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Affiliation(s)
- Katerina Kassela
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece.,Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Medical Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece.,Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens, Greece
| | - Stefanos Charpantidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - John Koskinas
- Department of Internal Medicine, Medical School of Athens, Hippokration Hospital Athens, Greece
| | - Theodora Mylopoulou
- First Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos Mimidis
- First Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christoph Sarrazin
- Medizinische Klinik 1, Universitätsklinikum Frankfurt, Frankfurt am Main, Germany
| | - Georgios Grammatikos
- Medizinische Klinik 1, Universitätsklinikum Frankfurt, Frankfurt am Main, Germany
| | - Penelope Mavromara
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece.,Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens, Greece
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28
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Double Plant Homeodomain Fingers 2 (DPF2) Promotes the Immune Escape of Influenza Virus by Suppressing Beta Interferon Production. J Virol 2017; 91:JVI.02260-16. [PMID: 28404846 DOI: 10.1128/jvi.02260-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/03/2017] [Indexed: 01/12/2023] Open
Abstract
The high mutation rates of the influenza virus genome facilitate the generation of viral escape mutants, rendering vaccines and drugs against influenza virus-encoded targets potentially ineffective. Therefore, we identified host cell determinants dispensable for the host but crucial for virus replication, with the goal of preventing viral escape and finding effective antivirals. To identify these host factors, we screened 2,732 human genes using RNA interference and focused on one of the identified host factors, the double plant homeodomain fingers 2 (DPF2/REQ) gene, for this study. We found that knockdown of DPF2 in cells infected with influenza virus resulted in decreased expression of viral proteins and RNA. Furthermore, production of progeny virus was reduced by two logs in the multiple-cycle growth kinetics assay. We also found that DPF2 was involved in the replication of seasonal influenza A and B viruses. Because DPF2 plays a crucial role in the noncanonical NF-κB pathway, which negatively regulates type I interferon (IFN) induction, we examined the relationship between DPF2 and IFN responses during viral infection. The results showed that knockdown of DPF2 resulted in increased expression of IFN-β and induced phosphorylation of STAT1 in infected cells. In addition, high levels of several cytokines/chemokines (interleukin-8 [IL-8], IP-10, and IL-6) and antiviral proteins (MxA and ISG56) were produced by DPF2 knockdown cells. In conclusion, we identified a novel host factor, DPF2, that is required for influenza virus to evade the host immune response and that may serve as a potential antiviral target.IMPORTANCE Influenza virus is responsible for seasonal epidemics and occasional pandemics and is an ongoing threat to public health worldwide. Influenza virus relies heavily on cellular factors to complete its life cycle. Here we identified a novel host factor, DPF2, which is involved in influenza virus infection. Our results showed that DPF2 plays a crucial role in the replication and propagation of influenza virus. DPF2 functions in the noncanonical NF-κB pathway, which negatively regulates type I IFN induction. Thus, we investigated the relationship between the IFN response and DPF2 in influenza virus infection. Upon influenza virus infection, DPF2 dysregulated IFN-β induction and expression of cytokines/chemokines and antiviral proteins. This study provides evidence that influenza virus utilizes DPF2 to escape host innate immunity.
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29
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Functional RNA structures throughout the Hepatitis C Virus genome. Curr Opin Virol 2017; 24:79-86. [PMID: 28511116 DOI: 10.1016/j.coviro.2017.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/21/2017] [Indexed: 12/18/2022]
Abstract
The single-stranded Hepatitis C Virus (HCV) genome adopts a set of elaborate RNA structures that are involved in every stage of the viral lifecycle. Recent advances in chemical probing, sequencing, and structural biology have facilitated analysis of RNA folding on a genome-wide scale, revealing novel structures and networks of interactions. These studies have underscored the active role played by RNA in every function of HCV and they open the door to new types of RNA-targeted therapeutics.
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30
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Lougiakis N, Frakolaki E, Karmou P, Pouli N, Marakos P, Madan V, Bartenschlager R, Vassilaki N. Novel nucleoside analogues targeting HCV replication through an NS5A-dependent inhibition mechanism. Chem Biol Drug Des 2017; 90:352-367. [PMID: 28245093 DOI: 10.1111/cbdd.12966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/20/2017] [Accepted: 02/10/2017] [Indexed: 12/25/2022]
Abstract
A series of new tricyclic nucleosides were synthesized and evaluated as hepatitis C virus (HCV) replication inhibitors. Initial screening in a HCV replicon system, derived from a genotype 1b isolate, identified 9-benzylamino-3-(β-D-ribofuranosyl)-3H-imidazo[4',5':5,6]pyrido[2,3-b]pyrazine (15d) as the most potent analogue. Comparative assessment of 15d activity against HCV full-length viruses or subgenomic replicons derived from genotypes 1 to 4 revealed a specificity of the compound for genotypes 1 and 3. Surprisingly, resistance mutations selected against 15d were mapped to domains II and III of the non-structural protein 5A (NS5A), but not to the RNA-dependent RNA polymerase residing in NS5B. These results argue that compound 15d might represent a lead for the development of a novel class of NS5A inhibitors.
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Affiliation(s)
- Nikolaos Lougiakis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Panagiota Karmou
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Nicole Pouli
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Marakos
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Vanesa Madan
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Heidelberg University, Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
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Bayer K, Banning C, Bruss V, Wiltzer-Bach L, Schindler M. Hepatitis C Virus Is Released via a Noncanonical Secretory Route. J Virol 2016; 90:10558-10573. [PMID: 27630244 PMCID: PMC5110177 DOI: 10.1128/jvi.01615-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/11/2016] [Indexed: 12/12/2022] Open
Abstract
We analyzed hepatitis C virus (HCV) morphogenesis using viral genomes encoding a mCherry-tagged E1 glycoprotein. HCV-E1-mCherry polyprotein expression, intracellular localization, and replication kinetics were comparable to those of untagged HCV, and E1-mCherry-tagged viral particles were assembled and released into cell culture supernatants. Expression and localization of structural E1 and nonstructural NS5A followed a temporospatial pattern with a succinct decrease in the number of replication complexes and the appearance of E1-mCherry punctae. Interaction of the structural proteins E1, Core, and E2 increased at E1-mCherry punctae in a time-dependent manner, indicating that E1-mCherry punctae represent assembled or assembling virions. E1-mCherry did not colocalize with Golgi markers. Furthermore, the bulk of viral glycoproteins within released particles revealed an EndoH-sensitive glycosylation pattern, indicating an absence of viral glycoprotein processing by the Golgi apparatus. In contrast, HCV-E1-mCherry trafficked with Rab9-positive compartments and inhibition of endosomes specifically suppressed HCV release. Our data suggest that assembled HCV particles are released via a noncanonical secretory route involving the endosomal compartment. IMPORTANCE The goal of this study was to shed light on the poorly understood trafficking and release routes of hepatitis C virus (HCV). For this, we generated novel HCV genomes which resulted in the production of fluorescently labeled viral particles. We used live-cell microscopy and other imaging techniques to follow up on the temporal dynamics of virus particle formation and trafficking in HCV-expressing liver cells. While viral particles and viral structural protein were found in endosomal compartments, no overlap of Golgi structures could be observed. Furthermore, biochemical and inhibitor-based experiments support a HCV release route which is distinguishable from canonical Golgi-mediated secretion. Since viruses hijack cellular pathways to generate viral progeny, our results point toward the possible existence of a not-yet-described cellular secretion route.
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Affiliation(s)
- Karen Bayer
- Institute of Virology, Helmholtz Zentrum München-German Research Center for Environmental Health, Munich, Germany
| | - Carina Banning
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Volker Bruss
- Institute of Virology, Helmholtz Zentrum München-German Research Center for Environmental Health, Munich, Germany
| | - Linda Wiltzer-Bach
- University Hospital Tübingen, Institute for Medical Virology and Epidemiology of Viral Diseases, Tübingen, Germany
| | - Michael Schindler
- Institute of Virology, Helmholtz Zentrum München-German Research Center for Environmental Health, Munich, Germany
- University Hospital Tübingen, Institute for Medical Virology and Epidemiology of Viral Diseases, Tübingen, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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32
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Miyamura T, Lemon SM, Walker CM, Wakita T. The HCV Replicase Complex and Viral RNA Synthesis. HEPATITIS C VIRUS I 2016. [PMCID: PMC7122888 DOI: 10.1007/978-4-431-56098-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Replication of hepatitis C virus (HCV) is tightly linked to membrane alterations designated the membranous web, harboring the viral replicase complex. In this chapter we describe the morphology and 3D architecture of the HCV-induced replication organelles, mainly consisting of double membrane vesicles, which are generated by a concerted action of the nonstructural proteins NS3 to NS5B. Recent studies have furthermore identified a number of host cell proteins and lipids contributing to the biogenesis of the membranous web, which are discussed in this chapter. Viral RNA synthesis is tightly associated with these membrane alterations and mainly driven by the viral RNA dependent RNA polymerase NS5B. We summarize our current knowledge of the structure and function of NS5B, the role of cis-acting replication elements at the termini of the genome in regulating RNA synthesis and the contribution of additional viral and host factors to viral RNA synthesis, which is still ill defined.
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Affiliation(s)
- Tatsuo Miyamura
- National Institute of Infectious Diseases, Tokyo, Tokyo Japan
| | - Stanley M. Lemon
- Departments of Medicine and Microbiology & Immunology , The University of North Carolina, Chapel Hill, North Carolina USA
| | - Christopher M. Walker
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio USA
| | - Takaji Wakita
- National Institute of Infectious Diseases, Tokyo, Tokyo Japan
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Vallianou I, Dafou D, Vassilaki N, Mavromara P, Hadzopoulou-Cladaras M. Hepatitis C virus suppresses Hepatocyte Nuclear Factor 4 alpha, a key regulator of hepatocellular carcinoma. Int J Biochem Cell Biol 2016; 78:315-326. [PMID: 27477312 DOI: 10.1016/j.biocel.2016.07.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/20/2016] [Accepted: 07/26/2016] [Indexed: 12/18/2022]
Abstract
Hepatitis C Virus (HCV) infection presents with a disturbed lipid profile and can evolve to hepatic steatosis and hepatocellular carcinoma (HCC). Hepatocyte Nuclear Factor 4 alpha (HNF4α) is the most abundant transcription factor in the liver, a key regulator of hepatic lipid metabolism and a critical determinant of Epithelial to Mesenchymal Transition and hepatic development. We have previously shown that transient inhibition of HNF4α initiates transformation of immortalized hepatocytes through a feedback loop consisting of miR-24, IL6 receptor (IL6R), STAT3, miR-124 and miR-629, suggesting a central role of HNF4α in HCC. However, the role of HNF4α in Hepatitis C Virus (HCV)-related hepatocarcinoma has not been evaluated and remains controversial. In this study, we provide strong evidence suggesting that HCV downregulates HNF4α expression at both transcriptional and translational levels. The observed decrease of HNF4α expression correlated with the downregulation of its downstream targets, HNF1α and MTP. Ectopic overexpression of HCV proteins also exhibited an inhibitory effect on HNF4α levels. The inhibition of HNF4α expression by HCV appeared to be mediated at transcriptional level as HCV proteins suppressed HNF4α gene promoter activity. HCV also up-regulated IL6R, activated STAT3 protein phosphorylation and altered the expression of acute phase genes. Furthermore, as HCV triggered the loss of HNF4α a consequent change of miR-24, miR-629 or miR-124 was observed. Our findings demonstrated that HCV-related HCC could be mediated through HNF4α-microRNA deregulation implying a possible role of HNF4α in HCV hepatocarcinogenesis. HCV inhibition of HNF4α could be sustained to promote HCC.
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Affiliation(s)
- Ioanna Vallianou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Dafou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Penelope Mavromara
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Margarita Hadzopoulou-Cladaras
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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Park SB, Seronello S, Mayer W, Ojcius DM. Hepatitis C Virus Frameshift/Alternate Reading Frame Protein Suppresses Interferon Responses Mediated by Pattern Recognition Receptor Retinoic-Acid-Inducible Gene-I. PLoS One 2016; 11:e0158419. [PMID: 27404108 PMCID: PMC4942120 DOI: 10.1371/journal.pone.0158419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/15/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) actively evades host interferon (IFN) responses but the mechanisms of how it does so are not completely understood. In this study, we present evidence for an HCV factor that contributes to the suppression of retinoic-acid-inducible gene-I (RIG-I)-mediated IFN induction. Expression of frameshift/alternate reading frame protein (F/ARFP) from HCV -2/+1 frame in Huh7 hepatoma cells suppressed type I IFN responses stimulated by HCV RNA pathogen-associated molecular pattern (PAMP) and poly(IC). The suppression occurred independently of other HCV factors; and activation of interferon stimulated genes, TNFα, IFN-λ1, and IFN-λ2/3 was likewise suppressed by HCV F/ARFP. Point mutations in the full-length HCV sequence (JFH1 genotype 2a strain) were made to introduce premature termination codons in the -2/+1 reading frame coding for F/ARFP while preserving the original reading frame, which enhanced IFNα and IFNβ induction by HCV. The potentiation of IFN response by the F/ARFP mutations was diminished in Huh7.5 cells, which already have a defective RIG-I, and by decreasing RIG-I expression in Huh7 cells. Furthermore, adding F/ARFP back via trans-complementation suppressed IFN induction in the F/ARFP mutant. The F/ARFP mutants, on the other hand, were not resistant to exogenous IFNα. Finally, HCV-infected human liver samples showed significant F/ARFP antibody reactivity, compared to HCV-uninfected control livers. Therefore, HCV F/ARFP likely cooperates with other viral factors to suppress type I and III IFN induction occurring through the RIG-I signaling pathway. This study identifies a novel mechanism of pattern recognition receptor modulation by HCV and suggests a biological function of the HCV alternate reading frame in the modulation of host innate immunity.
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Affiliation(s)
- Seung Bum Park
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Scott Seronello
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Wasima Mayer
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - David M. Ojcius
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
- University of the Pacific, Arthur A. Dugoni School of Dentistry, San Francisco, California, United States of America
- * E-mail:
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35
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The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures. Mol Cell 2016; 62:111-20. [PMID: 26924328 DOI: 10.1016/j.molcel.2016.01.024] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 12/22/2015] [Accepted: 01/21/2016] [Indexed: 12/11/2022]
Abstract
RNA is a versatile macromolecule that accommodates functional information in primary sequence and secondary and tertiary structure. We use a combination of chemical probing, RNA structure modeling, comparative sequence analysis, and functional assays to examine the role of RNA structure in the hepatitis C virus (HCV) genome. We describe a set of conserved but functionally diverse structural RNA motifs that occur in multiple coding regions of the HCV genome, and we demonstrate that conformational changes in these motifs influence specific stages in the virus' life cycle. Our study shows that these types of structures can pervade a genome, where they play specific mechanistic and regulatory roles, constituting a "code within the code" for controlling biological processes.
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36
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Kao CC, Yi G, Huang HC. The core of hepatitis C virus pathogenesis. Curr Opin Virol 2016; 17:66-73. [PMID: 26851516 DOI: 10.1016/j.coviro.2016.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/05/2016] [Accepted: 01/14/2016] [Indexed: 02/06/2023]
Abstract
Capsid proteins form protective shells around viral genomes and mediate viral entry. However, many capsid proteins have additional and important roles for virus infection and in modulating cellular response to infection, with important consequences on pathogenesis. Infection by the Hepatitis C virus (HCV) can lead to liver steatosis, cirrhosis, and hepatocellular carcinoma. Herein, we focus on the role in pathogenesis of Core, the capsid protein of the HCV.
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Affiliation(s)
- C Cheng Kao
- Dept of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States.
| | - Guanghui Yi
- Dept of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States
| | - Hsuan-Cheng Huang
- Inst. of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
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37
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Wang T, Zhao M, Rotgans BA, Strong A, Liang D, Ni G, Limpanont Y, Ramasoota P, McManus DP, Cummins SF. Proteomic Analysis of the Schistosoma mansoni Miracidium. PLoS One 2016; 11:e0147247. [PMID: 26799066 PMCID: PMC4723143 DOI: 10.1371/journal.pone.0147247] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/03/2016] [Indexed: 01/22/2023] Open
Abstract
Despite extensive control efforts, schistosomiasis continues to be a major public health problem in developing nations in the tropics and sub-tropics. The miracidium, along with the cercaria, both of which are water-borne and free-living, are the only two stages in the life-cycle of Schistosoma mansoni which are involved in host invasion. Miracidia penetrate intermediate host snails and develop into sporocysts, which lead to cercariae that can infect humans. Infection of the snail host by the miracidium represents an ideal point at which to interrupt the parasite’s life-cycle. This research focuses on an analysis of the miracidium proteome, including those proteins that are secreted. We have identified a repertoire of proteins in the S. mansoni miracidium at 2 hours post-hatch, including proteases, venom allergen-like proteins, receptors and HSP70, which might play roles in snail-parasite interplay. Proteins involved in energy production and conservation were prevalent, as were proteins predicted to be associated with defence. This study also provides a strong foundation for further understanding the roles that neurohormones play in host-seeking by schistosomes, with the potential for development of novel anthelmintics that interfere with its various life-cycle stages.
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Affiliation(s)
- Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Bronwyn A. Rotgans
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - April Strong
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Di Liang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Guoying Ni
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
- School of Medical Science, Griffith Health Institute, Griffith University, Gold Coast, Queensland, 4222, Australia
| | - Yanin Limpanont
- Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Pongrama Ramasoota
- Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Donald P. McManus
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - Scott F. Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
- * E-mail:
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38
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Xiao W, Zhang Q, Deng XZ, Jiang LF, Zhu DY, Pei JP, Ge CY, Li BJ, Wang CJ, Zhang JH, Zhou ZX, Ding WL, Xu XD, Yue M. HCV F protein amplifies the predictions of IL-28B and CTLA-4 polymorphisms about the susceptibility and outcomes of HCV infection in Southeast China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 34:52-60. [PMID: 26079279 DOI: 10.1016/j.meegid.2015.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 06/01/2015] [Accepted: 06/12/2015] [Indexed: 12/20/2022]
Abstract
Cytotoxic T lymphocyte associated antigen-4(CTLA-4) is an inhibitory receptor with great value in the progression of hepatitis C virus (HCV) infection related diseases. To determine the potential associations of IL-28B rs12979860 and CTLA-4 rs231775, rs3087243 and rs5742909 polymorphisms with the generation of HCV F protein, susceptibility and outcomes of HCV infection, a total of 375 healthy controls, 219 HCV spontaneous recovered patients and 600 chronic HCV patients from Southeast China were recruited and genotyped in this study. And the relative mRNA levels of CTLA-4 in T cells were detected. Logistic regression analysis showed that rs231775 A allele was associated with significantly higher rate of spontaneous viral clearance in anti-HCV F antibody negative patients (adjusted OR=0.512, P=0.008), but allele A was related to higher mRNA level of CTLA-4 with the generation of HCV F protein. And rs5742909 T allele added up to the risk of HCV infection chronicity significantly in patients with the presence of HCV F protein (adjusted OR=2.698, P=0.003). Also, the rs5742909 CC genotype, along with the presence of HCV F protein, indicated a significantly higher CTLA-4 level than that in anti-HCV F antibody negative patients. The AG+AA genotype of rs3087243 significantly increased the susceptibility to HCV infection in subjects over 56 years old (adjusted OR=1.595, P=0.011). Genotype-genotype interaction between IL-28B rs12979860 and CTLA-4 rs3087243 was found to be significantly associated with increased susceptibility to HCV infection (adjusted OR=1.509, P=0.005). Haplotype analysis in CTLA-4 also showed significant association with the generation of HCV F protein. All these results indicated the importance of IL-28B and CTLA-4 polymorphisms and their associations with HCV F protein in the risk and chronicity of HCV infection in Chinese Han population in Southeast China.
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Affiliation(s)
- Wen Xiao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.
| | - Qi Zhang
- Huadong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Xiao Zhao Deng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China; Huadong Research Institute for Medicine and Biotechnics, Nanjing, China.
| | - Long Feng Jiang
- Department of Infectious Diseases, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Dan Yan Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Nanjing Medical University, Nanjing, China
| | - Jia Ping Pei
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Nanjing Medical University, Nanjing, China
| | - Chi Yu Ge
- Jiangsu Food & Pharmaceutical Science College, Huaian, China
| | - Bing Jun Li
- Huadong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Chang Jun Wang
- Huadong Research Institute for Medicine and Biotechnics, Nanjing, China.
| | - Jing Hai Zhang
- Huadong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Zhen Xian Zhou
- Department of Clinical Laboratory, Nanjing Second Hospital, Nanjing, China
| | - Wei Liang Ding
- Department of Clinical Laboratory, Yixing People's Hospital, Yixing, China
| | - Xiao Dong Xu
- Huadong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Ming Yue
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
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39
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Vercauteren K, de Jong YP, Meuleman P. Animal models for the study of HCV. Curr Opin Virol 2015; 13:67-74. [PMID: 26304554 PMCID: PMC4549803 DOI: 10.1016/j.coviro.2015.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 12/18/2022]
Abstract
The development and evaluation of effective therapies and vaccines for the hepatitis C virus (HCV) and the study of its interactions with the mammalian host have been hindered for a long time by the absence of suitable small animal models. Immune compromised mouse models that recapitulate the complete HCV life cycle have been useful to investigate many aspects of the HCV life cycle including antiviral interventions. However, HCV has a high propensity to establish persistence and associated histopathological manifestations such as steatosis, fibrosis, cirrhosis and hepatocellular carcinoma (HCC). Better understanding of these processes requires the development of a permissive and fully immunocompetent small animal model. In this review we summarize the in vivo models that are available for the study of HCV.
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Affiliation(s)
- Koen Vercauteren
- Center for Vaccinology, Dept. of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium; Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, USA
| | - Ype P de Jong
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, USA; Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, USA
| | - Philip Meuleman
- Center for Vaccinology, Dept. of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium.
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Fricke M, Dünnes N, Zayas M, Bartenschlager R, Niepmann M, Marz M. Conserved RNA secondary structures and long-range interactions in hepatitis C viruses. RNA (NEW YORK, N.Y.) 2015; 21:1219-32. [PMID: 25964384 PMCID: PMC4478341 DOI: 10.1261/rna.049338.114] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/07/2015] [Indexed: 05/02/2023]
Abstract
Hepatitis C virus (HCV) is a hepatotropic virus with a plus-strand RNA genome of ∼9.600 nt. Due to error-prone replication by its RNA-dependent RNA polymerase (RdRp) residing in nonstructural protein 5B (NS5B), HCV isolates are grouped into seven genotypes with several subtypes. By using whole-genome sequences of 106 HCV isolates and secondary structure alignments of the plus-strand genome and its minus-strand replication intermediate, we established refined secondary structures of the 5' untranslated region (UTR), the cis-acting replication element (CRE) in NS5B, and the 3' UTR. We propose an alternative structure in the 5' UTR, conserved secondary structures of 5B stem-loop (SL)1 and 5BSL2, and four possible structures of the X-tail at the very 3' end of the HCV genome. We predict several previously unknown long-range interactions, most importantly a possible circularization interaction between distinct elements in the 5' and 3' UTR, reminiscent of the cyclization elements of the related flaviviruses. Based on analogy to these viruses, we propose that the 5'-3' UTR base-pairing in the HCV genome might play an important role in viral RNA replication. These results may have important implications for our understanding of the nature of the cis-acting RNA elements in the HCV genome and their possible role in regulating the mutually exclusive processes of viral RNA translation and replication.
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Affiliation(s)
- Markus Fricke
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Nadia Dünnes
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Margarita Zayas
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Michael Niepmann
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Manja Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany FLI Leibniz Institute for Age Research, 07745 Jena, Germany
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41
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Abstract
Hepatitis C virus (HCV) infects over 170 million people worldwide and is a leading cause of liver disease and cancer. The virus has a 9,650-nt, single-stranded, messenger-sense RNA genome that is infectious as an independent entity. The RNA genome has evolved in response to complex selection pressures, including the need to maintain structures that facilitate replication and to avoid clearance by cell-intrinsic immune processes. Here we used high-throughput, single-nucleotide resolution information to generate and functionally test data-driven structural models for three diverse HCV RNA genomes. We identified, de novo, multiple regions of conserved RNA structure, including all previously characterized cis-acting regulatory elements and also multiple novel structures required for optimal viral fitness. Well-defined RNA structures in the central regions of HCV genomes appear to facilitate persistent infection by masking the genome from RNase L and double-stranded RNA-induced innate immune sensors. This work shows how structure-first comparative analysis of entire genomes of a pathogenic RNA virus enables comprehensive and concise identification of regulatory elements and emphasizes the extensive interrelationships among RNA genome structure, viral biology, and innate immune responses.
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42
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Tuplin A, Struthers M, Cook J, Bentley K, Evans DJ. Inhibition of HCV translation by disrupting the structure and interactions of the viral CRE and 3' X-tail. Nucleic Acids Res 2015; 43:2914-26. [PMID: 25712095 PMCID: PMC4357731 DOI: 10.1093/nar/gkv142] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A phylogenetically conserved RNA structure within the NS5B coding region of hepatitis C virus functions as a cis-replicating element (CRE). Integrity of this CRE, designated SL9266 (alternatively 5BSL3.2), is critical for genome replication. SL9266 forms the core of an extended pseudoknot, designated SL9266/PK, involving long distance RNA–RNA interactions between unpaired loops of SL9266 and distal regions of the genome. Previous studies demonstrated that SL9266/PK is dynamic, with ‘open’ and ‘closed’ conformations predicted to have distinct functions during virus replication. Using a combination of site-directed mutagenesis and locked nucleic acids (LNA) complementary to defined domains of SL9266 and its interacting regions, we have explored the influence of this structure on genome translation and replication. We demonstrate that LNAs which block formation of the closed conformation inhibit genome translation. Inhibition was at least partly independent of the initiation mechanism, whether driven by homologous or heterologous internal ribosome entry sites or from a capped message. Provision of SL9266/PK in trans relieved translational inhibition, and mutational analysis implied a mechanism in which the closed conformation recruits a cellular factor that would otherwise suppresses translation. We propose that SL9266/PK functions as a temporal switch, modulating the mutually incompatible processes of translation and replication.
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Affiliation(s)
- Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Madeleine Struthers
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jonathan Cook
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Kirsten Bentley
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - David J Evans
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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43
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Expression of the novel hepatitis C virus core+1/ARF protein in the context of JFH1-based replicons. J Virol 2015; 89:5164-70. [PMID: 25694591 DOI: 10.1128/jvi.02351-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 02/09/2015] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus contains a second open reading frame within the core gene, designated core+1/ARF. Here we demonstrate for the first time expression of core+1/ARF protein in the context of a bicistronic JFH1-based replicon and report the production of two isoforms, core+1/L (long) and core+1/S (short), with different kinetics.
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Afzal MS, Alsaleh K, Farhat R, Belouzard S, Danneels A, Descamps V, Duverlie G, Wychowski C, Zaidi NUSS, Dubuisson J, Rouillé Y. Regulation of core expression during the hepatitis C virus life cycle. J Gen Virol 2015; 96:311-321. [DOI: 10.1099/vir.0.070433-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Muhammad Sohail Afzal
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
- Center for Infection & Immunity of Lille (CIIL), Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Khaled Alsaleh
- Center for Infection & Immunity of Lille (CIIL), Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Rayan Farhat
- Center for Infection & Immunity of Lille (CIIL), Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Sandrine Belouzard
- Center for Infection & Immunity of Lille (CIIL), Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Adeline Danneels
- Center for Infection & Immunity of Lille (CIIL), Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Véronique Descamps
- EA4294, Unité de Virologie Clinique et Fondamentale, CHU d’Amiens, University of Picardie Jules Verne, Amiens, France
| | - Gilles Duverlie
- EA4294, Unité de Virologie Clinique et Fondamentale, CHU d’Amiens, University of Picardie Jules Verne, Amiens, France
| | - Czeslaw Wychowski
- Center for Infection & Immunity of Lille (CIIL), Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Najam us Sahar Sadaf Zaidi
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Jean Dubuisson
- Center for Infection & Immunity of Lille (CIIL), Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Yves Rouillé
- Center for Infection & Immunity of Lille (CIIL), Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
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Sagan SM, Chahal J, Sarnow P. cis-Acting RNA elements in the hepatitis C virus RNA genome. Virus Res 2015; 206:90-8. [PMID: 25576644 DOI: 10.1016/j.virusres.2014.12.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/12/2014] [Accepted: 12/24/2014] [Indexed: 12/22/2022]
Abstract
Hepatitis C virus (HCV) infection is a rapidly increasing global health problem with an estimated 170 million people infected worldwide. HCV is a hepatotropic, positive-sense RNA virus of the family Flaviviridae. As a positive-sense RNA virus, the HCV genome itself must serve as a template for translation, replication and packaging. The viral RNA must therefore be a dynamic structure that is able to readily accommodate structural changes to expose different regions of the genome to viral and cellular proteins to carry out the HCV life cycle. The ∼ 9600 nucleotide viral genome contains a single long open reading frame flanked by 5' and 3' non-coding regions that contain cis-acting RNA elements important for viral translation, replication and stability. Additional cis-acting RNA elements have also been identified in the coding sequences as well as in the 3' end of the negative-strand replicative intermediate. Herein, we provide an overview of the importance of these cis-acting RNA elements in the HCV life cycle.
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Affiliation(s)
- Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Jasmin Chahal
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States.
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Vercauteren K, de Jong YP, Meuleman P. HCV animal models and liver disease. J Hepatol 2014; 61:S26-33. [PMID: 25443343 DOI: 10.1016/j.jhep.2014.07.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/07/2014] [Accepted: 07/10/2014] [Indexed: 01/08/2023]
Abstract
The development and evaluation of effective therapies and vaccines for the hepatitis C virus (HCV) and the study of its interactions with the mammalian host have been hindered for a long time by the absence of suitable small animal models. Due to the narrow host tropism of HCV, the development of mice that can be robustly engrafted with human hepatocytes was a major breakthrough since they recapitulate the complete HCV life cycle. This model has been useful to investigate many aspects of the HCV life cycle, including antiviral interventions. However, studies of cellular immunity, immunopathogenesis and resulting liver diseases have been hampered by the lack of a small animal model with a functional immune system. In this review, we summarize the evolution of in vivo models for the study of HCV.
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Affiliation(s)
- Koen Vercauteren
- Center for Vaccinology, Ghent University Hospital, Ghent University, Gent, Belgium
| | - Ype P de Jong
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, USA; Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, USA
| | - Philip Meuleman
- Center for Vaccinology, Ghent University Hospital, Ghent University, Gent, Belgium.
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Khawaja A, Vopalensky V, Pospisek M. Understanding the potential of hepatitis C virus internal ribosome entry site domains to modulate translation initiation via their structure and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:211-24. [PMID: 25352252 PMCID: PMC4361049 DOI: 10.1002/wrna.1268] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 08/31/2014] [Accepted: 09/02/2014] [Indexed: 12/16/2022]
Abstract
Translation initiation in the hepatitis C virus (HCV) occurs through a cap-independent mechanism that involves an internal ribosome entry site (IRES) capable of interacting with and utilizing the eukaryotic translational machinery. In this review, we focus on the structural configuration of the different HCV IRES domains and the impact of IRES primary sequence variations on secondary structure conservation and function. In some cases, multiple mutations, even those scattered across different domains, led to restoration of the translational activity of the HCV IRES, although the individual occurrences of these mutations were found to be deleterious. We propose that such observation may be attributed to probable long-range inter- and/or intra-domain functional interactions. The precise functioning of the HCV IRES requires the specific interaction of its domains with ribosomal subunits and a subset of eukaryotic translation initiation factors (eIFs). The structural conformation, sequence preservation and variability, and translational machinery association with the HCV IRES regions are also thoroughly discussed, along with other factors that can affect and influence the formation of translation initiation complexes. WIREs RNA 2015, 6:211–224. doi: 10.1002/wrna.1268
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Affiliation(s)
- Anas Khawaja
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
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Ren Q, Au HHT, Wang QS, Lee S, Jan E. Structural determinants of an internal ribosome entry site that direct translational reading frame selection. Nucleic Acids Res 2014; 42:9366-82. [PMID: 25038250 PMCID: PMC4132737 DOI: 10.1093/nar/gku622] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The dicistrovirus intergenic internal ribosome entry site (IGR IRES) directly recruits the ribosome and initiates translation using a non-AUG codon. A subset of IGR IRESs initiates translation in either of two overlapping open reading frames (ORFs), resulting in expression of the 0 frame viral structural polyprotein and an overlapping +1 frame ORFx. A U–G base pair adjacent to the anticodon-like pseudoknot of the IRES directs +1 frame translation. Here, we show that the U-G base pair is not absolutely required for +1 frame translation. Extensive mutagenesis demonstrates that 0 and +1 frame translation can be uncoupled. Ribonucleic acid (RNA) structural probing analyses reveal that the mutant IRESs adopt distinct conformations. Toeprinting analysis suggests that the reading frame is selected at a step downstream of ribosome assembly. We propose a model whereby the IRES adopts conformations to occlude the 0 frame aminoacyl-tRNA thereby allowing delivery of the +1 frame aminoacyl-tRNA to the A site to initiate translation of ORFx. This study provides a new paradigm for programmed recoding mechanisms that increase the coding capacity of a viral genome.
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Affiliation(s)
- Qian Ren
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Hilda H T Au
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Qing S Wang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Seonghoon Lee
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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Li HC, Ma HC, Yang CH, Lo SY. Production and pathogenicity of hepatitis C virus core gene products. World J Gastroenterol 2014; 20:7104-7122. [PMID: 24966583 PMCID: PMC4064058 DOI: 10.3748/wjg.v20.i23.7104] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/05/2013] [Accepted: 04/03/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is a major cause of chronic liver diseases, including steatosis, cirrhosis and hepatocellular carcinoma, and its infection is also associated with insulin resistance and type 2 diabetes mellitus. HCV, belonging to the Flaviviridae family, is a small enveloped virus whose positive-stranded RNA genome encoding a polyprotein. The HCV core protein is cleaved first at residue 191 by the host signal peptidase and further cleaved by the host signal peptide peptidase at about residue 177 to generate the mature core protein (a.a. 1-177) and the cleaved peptide (a.a. 178-191). Core protein could induce insulin resistance, steatosis and even hepatocellular carcinoma through various mechanisms. The peptide (a.a. 178-191) may play a role in the immune response. The polymorphism of this peptide is associated with the cellular lipid drop accumulation, contributing to steatosis development. In addition to the conventional open reading frame (ORF), in the +1 frame, an ORF overlaps with the core protein-coding sequence and encodes the alternative reading frame proteins (ARFP or core+1). ARFP/core+1/F protein could enhance hepatocyte growth and may regulate iron metabolism. In this review, we briefly summarized the current knowledge regarding the production of different core gene products and their roles in viral pathogenesis.
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Xu X, Yue M, Jiang L, Deng X, Zhang Y, Zhang Y, Zhu D, Xiao W, Zhou Z, Yao W, Kong J, Yu X, Wei J. Genetic variants in human leukocyte antigen-DP influence both hepatitis C virus persistence and hepatitis C virus F protein generation in the Chinese Han population. Int J Mol Sci 2014; 15:9826-43. [PMID: 24897020 PMCID: PMC4100124 DOI: 10.3390/ijms15069826] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/19/2014] [Accepted: 05/21/2014] [Indexed: 12/16/2022] Open
Abstract
Chronic hepatitis C is a serious liver disease that often results in cirrhosis or hepatocellular carcinoma. The aim of this study was to assess the association of human leukocyte antigen-DP (HLA-DP) variants with risk of chronic hepatitis C virus (HCV) or anti-F antibody generation. We selected two single nucleotide polymorphisms (SNPs) in a region including HLA-DPA1 (rs3077) and HLA-DPB1 (rs9277534) and genotyped SNPs in 702 cases and 342 healthy controls from the Chinese population using TaqMan SNP genotyping assay. Moreover, the exon 2 of the HLA-DPA1 and HLA-DPB1 genes were amplified and determined by sequencing-based typing (SBT). The results showed that rs3077 significantly increased the risk of chronic HCV infection in additive models and dominant models (odds ratio (OR) = 1.32 and 1.53). The rs3077 also contributed to decrease the risk of anti-F antibody generation in additive models and dominant models (OR = 0.46 and 0.56). Subsequent analyses revealed the risk haplotypes (DPA1*0103-DPB1*0501 and DPA1*0103-DPB1*0201) and protective haplotypes (DPA1*0202-DPB1*0501 and DPA1*0202-DPB1*0202) to chronic HCV infection. Moreover, we also found that the haplotype of DPA1*0103-DPB1*0201 and DPA1*0202-DPB1*0202 were associated with the anti-F antibody generation. Our findings show that genetic variants in HLA-DP gene are associated with chronic HCV infection and anti-F antibody generation.
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Affiliation(s)
- Xiaodong Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Nanjing Medical University, Nanjing 210029, China.
| | - Ming Yue
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
| | - Longfeng Jiang
- Department of Infectious Diseases, the First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China.
| | - Xiaozhao Deng
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Nanjing Medical University, Nanjing 210029, China.
| | - Yongxiang Zhang
- Department of Infectious Diseases, the First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China.
| | - Yun Zhang
- Institute of Disease Control and Prevention, Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, China.
| | - Danyan Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Nanjing Medical University, Nanjing 210029, China.
| | - Wen Xiao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
| | - Zhenxian Zhou
- Department of Clinical Laboratory, Nanjing Second Hospital, Nanjing 210003, China.
| | - Wenjuan Yao
- Department of Pharmacology, Nantong University Medical College, Nantong 226019, China.
| | - Jing Kong
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Xiaojie Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Nanjing Medical University, Nanjing 210029, China.
| | - Juan Wei
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Nanjing Medical University, Nanjing 210029, China.
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