1
|
Papini C, Ullah I, Ranjan AP, Zhang S, Wu Q, Spasov KA, Zhang C, Mothes W, Crawford JM, Lindenbach BD, Uchil PD, Kumar P, Jorgensen WL, Anderson KS. Proof-of-concept studies with a computationally designed M pro inhibitor as a synergistic combination regimen alternative to Paxlovid. Proc Natl Acad Sci U S A 2024; 121:e2320713121. [PMID: 38621119 PMCID: PMC11046628 DOI: 10.1073/pnas.2320713121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/27/2024] [Indexed: 04/17/2024] Open
Abstract
As the SARS-CoV-2 virus continues to spread and mutate, it remains important to focus not only on preventing spread through vaccination but also on treating infection with direct-acting antivirals (DAA). The approval of Paxlovid, a SARS-CoV-2 main protease (Mpro) DAA, has been significant for treatment of patients. A limitation of this DAA, however, is that the antiviral component, nirmatrelvir, is rapidly metabolized and requires inclusion of a CYP450 3A4 metabolic inhibitor, ritonavir, to boost levels of the active drug. Serious drug-drug interactions can occur with Paxlovid for patients who are also taking other medications metabolized by CYP4503A4, particularly transplant or otherwise immunocompromised patients who are most at risk for SARS-CoV-2 infection and the development of severe symptoms. Developing an alternative antiviral with improved pharmacological properties is critical for treatment of these patients. By using a computational and structure-guided approach, we were able to optimize a 100 to 250 μM screening hit to a potent nanomolar inhibitor and lead compound, Mpro61. In this study, we further evaluate Mpro61 as a lead compound, starting with examination of its mode of binding to SARS-CoV-2 Mpro. In vitro pharmacological profiling established a lack of off-target effects, particularly CYP450 3A4 inhibition, as well as potential for synergy with the currently approved alternate antiviral, molnupiravir. Development and subsequent testing of a capsule formulation for oral dosing of Mpro61 in B6-K18-hACE2 mice demonstrated favorable pharmacological properties, efficacy, and synergy with molnupiravir, and complete recovery from subsequent challenge by SARS-CoV-2, establishing Mpro61 as a promising potential preclinical candidate.
Collapse
Affiliation(s)
- Christina Papini
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520-8066
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT06520-8066
| | - Amalendu P. Ranjan
- Department of Microbiology, Immunology and Genetics Graduate School for Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX76107
| | - Shuo Zhang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06520-8066
| | - Qihao Wu
- Department of Chemistry, Yale University, New Haven, CT06520-8107
| | - Krasimir A. Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520-8066
| | - Chunhui Zhang
- Department of Chemistry, Yale University, New Haven, CT06520-8107
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06520-8066
| | | | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06520-8066
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06520-8066
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT06520-8066
| | | | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520-8066
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT06520-8066
| |
Collapse
|
2
|
Di Pietro C, Haberman AM, Lindenbach BD, Smith PC, Bruscia EM, Allore HG, Vander Wyk B, Tyagi A, Zeiss CJ. Prior Influenza Infection Mitigates SARS-CoV-2 Disease in Syrian Hamsters. Viruses 2024; 16:246. [PMID: 38400021 PMCID: PMC10891789 DOI: 10.3390/v16020246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Seasonal infection rates of individual viruses are influenced by synergistic or inhibitory interactions between coincident viruses. Endemic patterns of SARS-CoV-2 and influenza infection overlap seasonally in the Northern hemisphere and may be similarly influenced. We explored the immunopathologic basis of SARS-CoV-2 and influenza A (H1N1pdm09) interactions in Syrian hamsters. H1N1 given 48 h prior to SARS-CoV-2 profoundly mitigated weight loss and lung pathology compared to SARS-CoV-2 infection alone. This was accompanied by the normalization of granulocyte dynamics and accelerated antigen-presenting populations in bronchoalveolar lavage and blood. Using nasal transcriptomics, we identified a rapid upregulation of innate and antiviral pathways induced by H1N1 by the time of SARS-CoV-2 inoculation in 48 h dual-infected animals. The animals that were infected with both viruses also showed a notable and temporary downregulation of mitochondrial and viral replication pathways. Quantitative RT-PCR confirmed a decrease in the SARS-CoV-2 viral load and lower cytokine levels in the lungs of animals infected with both viruses throughout the course of the disease. Our data confirm that H1N1 infection induces rapid and transient gene expression that is associated with the mitigation of SARS-CoV-2 pulmonary disease. These protective responses are likely to begin in the upper respiratory tract shortly after infection. On a population level, interaction between these two viruses may influence their relative seasonal infection rates.
Collapse
Affiliation(s)
- Caterina Di Pietro
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06519, USA; (C.D.P.); (E.M.B.)
| | - Ann M. Haberman
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06519, USA;
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06519, USA;
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06519, USA;
| | - Peter C. Smith
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06519, USA;
| | - Emanuela M. Bruscia
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06519, USA; (C.D.P.); (E.M.B.)
| | - Heather G. Allore
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06519, USA; (H.G.A.); (B.V.W.)
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06519, USA
| | - Brent Vander Wyk
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06519, USA; (H.G.A.); (B.V.W.)
| | - Antariksh Tyagi
- Department of Genetics, Yale Center for Genome Analysis, New Haven, CT 06519, USA;
| | - Caroline J. Zeiss
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06519, USA;
| |
Collapse
|
3
|
Cable J, Denison MR, Kielian M, Jackson WT, Bartenschlager R, Ahola T, Mukhopadhyay S, Fremont DH, Kuhn RJ, Shannon A, Frazier MN, Yuen KY, Coyne CB, Wolthers KC, Ming GL, Guenther CS, Moshiri J, Best SM, Schoggins JW, Jurado KA, Ebel GD, Schäfer A, Ng LFP, Kikkert M, Sette A, Harris E, Wing PAC, Eggenberger J, Krishnamurthy SR, Mah MG, Meganck RM, Chung D, Maurer-Stroh S, Andino R, Korber B, Perlman S, Shi PY, Bárcena M, Aicher SM, Vu MN, Kenney DJ, Lindenbach BD, Nishida Y, Rénia L, Williams EP. Positive-strand RNA viruses-a Keystone Symposia report. Ann N Y Acad Sci 2023; 1521:46-66. [PMID: 36697369 PMCID: PMC10347887 DOI: 10.1111/nyas.14957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Positive-strand RNA viruses have been the cause of several recent outbreaks and epidemics, including the Zika virus epidemic in 2015, the SARS outbreak in 2003, and the ongoing SARS-CoV-2 pandemic. On June 18-22, 2022, researchers focusing on positive-strand RNA viruses met for the Keystone Symposium "Positive-Strand RNA Viruses" to share the latest research in molecular and cell biology, virology, immunology, vaccinology, and antiviral drug development. This report presents concise summaries of the scientific discussions at the symposium.
Collapse
Affiliation(s)
| | - Mark R Denison
- Department of Pediatrics and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; and Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, Tennessee, USA
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - William T Jackson
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University and German Cancer Research Center (DKFZ), Research Division Virus-associated Carcinogenesis, Heidelberg, Germany
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | | | - Daved H Fremont
- Department of Pathology & Immunology; Department of Molecular Microbiology; and Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix Marseille Université, Marseille, France
| | - Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, People's Republic of China
| | - Carolyn B Coyne
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Katja C Wolthers
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Jasmine Moshiri
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Sonja M Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kellie Ann Jurado
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory D Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lisa F P Ng
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR), Singapore City, Singapore
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Peter A C Wing
- Nuffield Department of Medicine and Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology and NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marcus G Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore City, Singapore
| | - Rita M Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Donghoon Chung
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, Texas, USA
| | - Sebastian Maurer-Stroh
- Yong Loo Lin School of Medicine and Department of Biological Sciences, National University of Singapore, Singapore City, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore City, Singapore
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, and Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Montserrat Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sophie-Marie Aicher
- Institut Pasteurgrid, Université de Paris Cité, Virus Sensing and Signaling Unit, Paris, France
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Devin J Kenney
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yukiko Nishida
- Chugai Pharmaceutical, Co., Tokyo, Japan
- Lee Kong Chian School of Medicine and School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Laurent Rénia
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR), Singapore City, Singapore
| | - Evan P Williams
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
| |
Collapse
|
4
|
Wan H, Adams RL, Lindenbach BD, Pyle AM. The In Vivo and In Vitro Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures. J Virol 2022; 96:e0194621. [PMID: 35353000 PMCID: PMC9044954 DOI: 10.1128/jvi.01946-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/24/2022] [Indexed: 01/21/2023] Open
Abstract
Hepatitis C virus (HCV) is a positive-strand RNA virus that remains one of the main contributors to chronic liver disease worldwide. Studies over the last 30 years have demonstrated that HCV contains a highly structured RNA genome and many of these structures play essential roles in the HCV life cycle. Despite the importance of riboregulation in this virus, most of the HCV RNA genome remains functionally unstudied. Here, we report a complete secondary structure map of the HCV RNA genome in vivo, which was studied in parallel with the secondary structure of the same RNA obtained in vitro. Our results show that HCV is folded extensively in the cellular context. By performing comprehensive structural analyses on both in vivo data and in vitro data, we identify compact and conserved secondary and tertiary structures throughout the genome. Genetic and evolutionary functional analyses demonstrate that many of these elements play important roles in the virus life cycle. In addition to providing a comprehensive map of RNA structures and riboregulatory elements in HCV, this work provides a resource for future studies aimed at identifying therapeutic targets and conducting further mechanistic studies on this important human pathogen. IMPORTANCE HCV has one of the most highly structured RNA genomes studied to date, and it is a valuable model system for studying the role of RNA structure in protein-coding genes. While previous studies have identified individual cases of regulatory RNA structures within the HCV genome, the full-length structure of the HCV genome has not been determined in vivo. Here, we present the complete secondary structure map of HCV determined both in cells and from corresponding transcripts generated in vitro. In addition to providing a comprehensive atlas of functional secondary structural elements throughout the genomic RNA, we identified a novel set of tertiary interactions and demonstrated their functional importance. In terms of broader implications, the pipeline developed in this study can be applied to other long RNAs, such as long noncoding RNAs. In addition, the RNA structural motifs characterized in this study broaden the repertoire of known riboregulatory elements.
Collapse
Affiliation(s)
- Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Rebecca L. Adams
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| |
Collapse
|
5
|
Lindenbach BD. Reinventing positive-strand RNA virus reverse genetics. Adv Virus Res 2022; 112:1-29. [PMID: 35840179 PMCID: PMC9273853 DOI: 10.1016/bs.aivir.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Reverse genetics is the prospective analysis of how genotype determines phenotype. In a typical experiment, a researcher alters a viral genome, then observes the phenotypic outcome. Among RNA viruses, this approach was first applied to positive-strand RNA viruses in the mid-1970s and over nearly 50 years has become a powerful and widely used approach for dissecting the mechanisms of viral replication and pathogenesis. During this time the global health importance of two virus groups, flaviviruses (genus Flavivirus, family Flaviviridae) and betacoronaviruses (genus Betacoronavirus, subfamily Orthocoronavirinae, family Coronaviridae), have dramatically increased, yet these viruses have genomes that are technically challenging to manipulate. As a result, several new techniques have been developed to overcome these challenges. Here I briefly review key historical aspects of positive-strand RNA virus reverse genetics, describe some recent reverse genetic innovations, particularly as applied to flaviviruses and coronaviruses, and discuss their benefits and limitations within the larger context of rigorous genetic analysis.
Collapse
|
6
|
Zhang CH, Spasov KA, Reilly RA, Hollander K, Stone EA, Ippolito JA, Liosi ME, Deshmukh MG, Tirado-Rives J, Zhang S, Liang Z, Miller SJ, Isaacs F, Lindenbach BD, Anderson KS, Jorgensen WL. Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency. ACS Med Chem Lett 2021; 12:1325-1332. [PMID: 34408808 PMCID: PMC8291137 DOI: 10.1021/acsmedchemlett.1c00326] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022] Open
Abstract
Non-covalent inhibitors of the main protease (Mpro) of SARS-CoV-2 having a pyridinone core were previously reported with IC50 values as low as 0.018 μM for inhibition of enzymatic activity and EC50 values as low as 0.8 μM for inhibition of viral replication in Vero E6 cells. The series has now been further advanced by consideration of placement of substituted five-membered-ring heterocycles in the S4 pocket of Mpro and N-methylation of a uracil ring. Free energy perturbation calculations provided guidance on the choice of the heterocycles, and protein crystallography confirmed the desired S4 placement. Here we report inhibitors with EC50 values as low as 0.080 μM, while remdesivir yields values of 0.5-2 μM in side-by-side testing with infectious SARS-CoV-2. A key factor in the improvement is enhanced cell permeability, as reflected in PAMPA measurements. Compounds 19 and 21 are particularly promising as potential therapies for COVID-19, featuring IC50 values of 0.044-0.061 μM, EC50 values of ca. 0.1 μM, good aqueous solubility, and no cytotoxicity.
Collapse
Affiliation(s)
- Chun-Hui Zhang
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Krasimir A. Spasov
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Raquel A. Reilly
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Klarissa Hollander
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Elizabeth A. Stone
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joseph A. Ippolito
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Maria-Elena Liosi
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Maya G. Deshmukh
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
- M.D.−Ph.D.
Program, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Julian Tirado-Rives
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Shuo Zhang
- Department
of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, Connecticut 06536-0812, United States
| | - Zhuobin Liang
- Department
of Molecular, Cellular, and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Scott J. Miller
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Farren Isaacs
- Department
of Molecular, Cellular, and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Brett D. Lindenbach
- Department
of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, Connecticut 06536-0812, United States
| | - Karen S. Anderson
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - William L. Jorgensen
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| |
Collapse
|
7
|
Sun Y, Abriola L, Surovtseva YV, Lindenbach BD, Guo JU. Restriction of SARS-CoV-2 Replication by Targeting Programmed -1 Ribosomal Frameshifting In Vitro. bioRxiv 2020:2020.10.21.349225. [PMID: 33106809 PMCID: PMC7587830 DOI: 10.1101/2020.10.21.349225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Translation of open reading frame 1b (ORF1b) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires programmed -1 ribosomal frameshifting (-1 PRF) promoted by an RNA pseudoknot. The extent to which SARS-CoV-2 replication may be sensitive to changes in -1 PRF efficiency is currently unknown. Through an unbiased, reporter-based high-throughput compound screen, we identified merafloxacin, a fluoroquinolone antibacterial, as a -1 PRF inhibitor of SARS-CoV-2. Frameshift inhibition by merafloxacin is robust to mutations within the pseudoknot region and is similarly effective on -1 PRF of other beta coronaviruses. Importantly, frameshift inhibition by merafloxacin substantially impedes SARS-CoV-2 replication in Vero E6 cells, thereby providing the proof of principle of targeting -1 PRF as an effective antiviral strategy for SARS-CoV-2.
Collapse
Affiliation(s)
- Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | | | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Junjie U. Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
8
|
Wei J, Alfajaro MM, DeWeirdt PC, Hanna RE, Lu-Culligan WJ, Cai WL, Strine MS, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Ravindra NG, Gasque V, de Miguel FJ, Patil A, Chen H, Oguntuyo KY, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach BD, Politi K, van Dijk D, Kadoch C, Simon MD, Yan Q, Doench JG, Wilen CB. Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection. Cell 2020; 184:76-91.e13. [PMID: 33147444 PMCID: PMC7574718 DOI: 10.1016/j.cell.2020.10.028] [Citation(s) in RCA: 327] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/11/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
Identification of host genes essential for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may reveal novel therapeutic targets and inform our understanding of coronavirus disease 2019 (COVID-19) pathogenesis. Here we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-CoV-2, Middle East respiratory syndrome CoV (MERS-CoV), bat CoV HKU5 expressing the SARS-CoV-1 spike, and vesicular stomatitis virus (VSV) expressing the SARS-CoV-2 spike. We identified known SARS-CoV-2 host factors, including the receptor ACE2 and protease Cathepsin L. We additionally discovered pro-viral genes and pathways, including HMGB1 and the SWI/SNF chromatin remodeling complex, that are SARS lineage and pan-coronavirus specific, respectively. We show that HMGB1 regulates ACE2 expression and is critical for entry of SARS-CoV-2, SARS-CoV-1, and NL63. We also show that small-molecule antagonists of identified gene products inhibited SARS-CoV-2 infection in monkey and human cells, demonstrating the conserved role of these genetic hits across species. This identifies potential therapeutic targets for SARS-CoV-2 and reveals SARS lineage-specific and pan-CoV host factors that regulate susceptibility to highly pathogenic CoVs.
Collapse
Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William J Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Wesley L Cai
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Vincent R Graziano
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Cameron O Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jennifer S Chen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Madeleine C Mankowski
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Neal G Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Victor Gasque
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Fernando J de Miguel
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Huacui Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kasopefoluwa Y Oguntuyo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Robert C Orchard
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - David van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
9
|
Tallorin L, Villareal VA, Hsia CY, Rodgers MA, Burri DJ, Pfeil MP, Llopis PM, Lindenbach BD, Yang PL. Hepatitis C virus NS3-4A protease regulates the lipid environment for RNA replication by cleaving host enzyme 24-dehydrocholesterol reductase. J Biol Chem 2020; 295:12426-12436. [PMID: 32641492 PMCID: PMC7458815 DOI: 10.1074/jbc.ra120.013455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
Many RNA viruses create specialized membranes for genome replication by manipulating host lipid metabolism and trafficking, but in most cases, we do not know the molecular mechanisms responsible or how specific lipids may impact the associated membrane and viral process. For example, hepatitis C virus (HCV) causes a specific, large-fold increase in the steady-state abundance of intracellular desmosterol, an immediate precursor of cholesterol, resulting in increased fluidity of the membrane where HCV RNA replication occurs. Here, we establish the mechanism responsible for HCV's effect on intracellular desmosterol, whereby the HCV NS3-4A protease controls activity of 24-dehydrocholesterol reductase (DHCR24), the enzyme that catalyzes conversion of desmosterol to cholesterol. Our cumulative evidence for the proposed mechanism includes immunofluorescence microscopy experiments showing co-occurrence of DHCR24 and HCV NS3-4A protease; formation of an additional, faster-migrating DHCR24 species (DHCR24*) in cells harboring a HCV subgenomic replicon RNA or ectopically expressing NS3-4A; and biochemical evidence that NS3-4A cleaves DHCR24 to produce DHCR24* in vitro and in vivo. We further demonstrate that NS3-4A cleaves DHCR24 between residues Cys91 and Thr92 and show that this reduces the intracellular conversion of desmosterol to cholesterol. Together, these studies demonstrate that NS3-4A directly cleaves DHCR24 and that this results in the enrichment of desmosterol in the membranes where NS3-4A and DHCR24 co-occur. Overall, this suggests a model in which HCV directly regulates the lipid environment for RNA replication through direct effects on the host lipid metabolism.
Collapse
Affiliation(s)
- Lorillee Tallorin
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Valerie A Villareal
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chih-Yun Hsia
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Mary A Rodgers
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Dominique J Burri
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Marc-Philipp Pfeil
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Paula Montero Llopis
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale Medical School, New Haven, Connecticut, USA
| | - Priscilla L Yang
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
10
|
Kumar S, Barouch-Bentov R, Xiao F, Schor S, Pu S, Biquand E, Lu A, Lindenbach BD, Jacob Y, Demeret C, Einav S. MARCH8 Ubiquitinates the Hepatitis C Virus Nonstructural 2 Protein and Mediates Viral Envelopment. Cell Rep 2020; 26:1800-1814.e5. [PMID: 30759391 PMCID: PMC7053169 DOI: 10.1016/j.celrep.2019.01.075] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 11/07/2018] [Accepted: 01/18/2019] [Indexed: 02/07/2023] Open
Abstract
The mechanisms that regulate envelopment of HCV and other viruses that bud intracellularly and/or lack late-domain motifs are largely unknown. We reported that K63 polyubiquitination of the HCV nonstructural (NS) 2 protein mediates HRS (ESCRT-0 component) binding and envelopment. Nevertheless, the ubiquitin signaling that governs NS2 ubiquitination remained unknown. Here, we map the NS2 interactome with the ubiquitin proteasome system (UPS) via mammalian cell-based screens. NS2 interacts with E3 ligases, deubiquitinases, and ligase regulators, some of which are candidate proviral or antiviral factors. MARCH8, a RING-finger E3 ligase, catalyzes K63-linked NS2 polyubiquitination in vitro and in HCV-infected cells. MARCH8 is required for infection with HCV, dengue, and Zika viruses and specifically mediates HCV envelopment. Our data reveal regulation of HCV envelopment via ubiquitin signaling and both a viral protein substrate and a ubiquitin K63-linkage of the understudied MARCH8, with potential implications for cell biology, virology, and host-targeted antiviral design. The mechanisms that regulate intracellular viral envelopment are unknown. Kumar et al. report that MARCH8 catalyzes K63-linked polyubiquitination of the HCV nonstructural 2 protein and subsequently ESCRT recruitment and HCV envelopment. MARCH8 is required for infection with other Flaviviridae family members, thereby representing a potential host target for antiviral strategies.
Collapse
Affiliation(s)
- Sathish Kumar
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rina Barouch-Bentov
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fei Xiao
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stanford Schor
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Szuyuan Pu
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elise Biquand
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique; Université Paris Diderot, Paris, France
| | - Albert Lu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Yves Jacob
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique; Université Paris Diderot, Paris, France
| | - Caroline Demeret
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique; Université Paris Diderot, Paris, France
| | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
11
|
Inaba JI, Xu K, Kovalev N, Ramanathan H, Roy CR, Lindenbach BD, Nagy PD. Screening Legionella effectors for antiviral effects reveals Rab1 GTPase as a proviral factor coopted for tombusvirus replication. Proc Natl Acad Sci U S A 2019; 116:21739-21747. [PMID: 31591191 PMCID: PMC6815150 DOI: 10.1073/pnas.1911108116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial virulence factors or effectors are proteins targeted into host cells to coopt or interfere with cellular proteins and pathways. Viruses often coopt the same cellular proteins and pathways to support their replication in infected cells. Therefore, we screened the Legionella pneumophila effectors to probe virus-host interactions and identify factors that modulate tomato bushy stunt virus (TBSV) replication in yeast surrogate host. Among 302 Legionella effectors tested, 28 effectors affected TBSV replication. To unravel a coopted cellular pathway in TBSV replication, the identified DrrA effector from Legionella was further exploited. We find that expression of DrrA in yeast or plants blocks TBSV replication through inhibiting the recruitment of Rab1 small GTPase and endoplasmic reticulum-derived COPII vesicles into the viral replication compartment. TBSV hijacks Rab1 and COPII vesicles to create enlarged membrane surfaces and optimal lipid composition within the viral replication compartment. To further validate our Legionella effector screen, we used the Legionella effector LepB lipid kinase to confirm the critical proviral function of PI(3)P phosphoinositide and the early endosomal compartment in TBSV replication. We demonstrate the direct inhibitory activity of LegC8 effector on TBSV replication using a cell-free replicase reconstitution assay. LegC8 inhibits the function of eEF1A, a coopted proviral host factor. Altogether, the identified bacterial effectors with anti-TBSV activity could be powerful reagents in cell biology and virus-host interaction studies. This study provides important proof of concept that bacterial effector proteins can be a useful toolbox to identify host factors and cellular pathways coopted by (+)RNA viruses.
Collapse
Affiliation(s)
- Jun-Ichi Inaba
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546
| | - Kai Xu
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546
| | - Nikolay Kovalev
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546
| | - Harish Ramanathan
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536
| | - Craig R Roy
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536
| | - Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546;
| |
Collapse
|
12
|
Heimer R, Binka M, Koester S, Grund JPC, Patel A, Paintsil E, Lindenbach BD. Recovery of Infectious Hepatitis C Virus From Injection Paraphernalia: Implications for Prevention Programs Serving People Who Inject Drugs. J Infect Dis 2019; 217:466-473. [PMID: 28968665 DOI: 10.1093/infdis/jix427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/18/2017] [Indexed: 01/03/2023] Open
Abstract
Background Controlling hepatitis C virus (HCV) transmission among people who inject drugs (PWID) has focused on preventing sharing syringes and drug preparation paraphernalia, but it is unclear whether HCV incidence linked to sharing paraphernalia reflects contamination of the paraphernalia or syringe-mediated contamination when drugs are shared. Methods In experiments designed to replicate real-world injection practices when drugs are shared, the residual contents of HCV-contaminated syringes with detachable or fixed needled were passed through the "cookers" and filters used by PWID in preparing drugs for injection and then introduced into a second syringe. All items were tested for the presence of infectious HCV using a chimeric HCV with a luciferase gene. Results Hepatitis C virus could not be recovered from cookers regardless of input syringe type or cooker design. Recovery was higher when comparing detachable needles to fixed needles for residue in input syringes (73.8% vs 0%), filters (15.4% vs 1.4%), and receptive syringes (93.8% vs 45.7%). Conclusions Our results, consistent with the hypothesis that sharing paraphernalia does not directly result in HCV transmission but is a surrogate for transmissions resulting from sharing drugs, have important implications for HCV prevention efforts and programs that provide education and safe injection supplies for PWID populations.
Collapse
Affiliation(s)
- Robert Heimer
- Department of the Epidemiology Microbial Diseases, Yale University School of Public Health, New Haven, Connecticut
| | - Mawuena Binka
- Department of the Epidemiology Microbial Diseases, Yale University School of Public Health, New Haven, Connecticut
| | | | - Jean-Paul C Grund
- Addiction Research Centre, Utrecht, the Netherlands.,Department of Addictology, 1st Faculty of Medicine, Charles University and General University Hospital, Prague, the Czech Republic.,Freudenthal Institute for Science and Mathematics Education, Utrecht, the Netherlands
| | - Amisha Patel
- Department of the Epidemiology Microbial Diseases, Yale University School of Public Health, New Haven, Connecticut
| | - Elijah Paintsil
- Department of the Epidemiology Microbial Diseases, Yale University School of Public Health, New Haven, Connecticut.,Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut
| |
Collapse
|
13
|
Bartenschlager R, Baumert TF, Bukh J, Houghton M, Lemon SM, Lindenbach BD, Lohmann V, Moradpour D, Pietschmann T, Rice CM, Thimme R, Wakita T. Critical challenges and emerging opportunities in hepatitis C virus research in an era of potent antiviral therapy: Considerations for scientists and funding agencies. Virus Res 2018; 248:53-62. [PMID: 29477639 DOI: 10.1016/j.virusres.2018.02.016] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/19/2022]
Abstract
The development and clinical implementation of direct-acting antivirals (DAAs) has revolutionized the treatment of chronic hepatitis C. Infection with any hepatitis C virus (HCV) genotype can now be eliminated in more than 95% of patients with short courses of all-oral, well-tolerated drugs, even in those with advanced liver disease and liver transplant recipients. DAAs have proven so successful that some now consider HCV amenable to eradication, and continued research on the virus of little remaining medical relevance. However, given 400,000 HCV-related deaths annually important challenges remain, including identifying those who are infected, providing access to treatment and reducing its costs. Moreover, HCV infection rarely induces sterilizing immunity, and those who have been cured with DAAs remain at risk for reinfection. Thus, it is very unlikely that global eradication and elimination of the cancer risk associated with HCV infection can be achieved without a vaccine, yet research in that direction receives little attention. Further, over the past two decades HCV research has spearheaded numerous fundamental discoveries in the fields of molecular and cell biology, immunology and microbiology. It will continue to do so, given the unique opportunities afforded by the reagents and knowledge base that have been generated in the development and clinical application of DAAs. Considering these critical challenges and new opportunities, we conclude that funding for HCV research must be sustained.
Collapse
Affiliation(s)
- Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Sites Heidelberg and Hannover-Braunschweig, Germany.
| | - Thomas F Baumert
- Institut National de la Santé et de la Recherche Médicale, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France; Université de Strasbourg, Strasbourg, Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Michael Houghton
- Li Ka Shing Institute of Virology, Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
| | - Stanley M Lemon
- Departments of Medicine and Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Darius Moradpour
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Thomas Pietschmann
- German Centre for Infection Research (DZIF), Partner Sites Heidelberg and Hannover-Braunschweig, Germany; Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research (a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI)), Hannover, Germany
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, USA
| | - Robert Thimme
- Center for Medicine, Department of Medicine II, Medical Center - University of Freiburg, Germany
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
14
|
Fink SL, Jayewickreme TR, Molony RD, Iwawaki T, Landis CS, Lindenbach BD, Iwasaki A. IRE1α promotes viral infection by conferring resistance to apoptosis. Sci Signal 2017; 10:eaai7814. [PMID: 28588082 PMCID: PMC5535312 DOI: 10.1126/scisignal.aai7814] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The unfolded protein response (UPR) is an ancient cellular pathway that detects and alleviates protein-folding stresses. The UPR components X-box binding protein 1 (XBP1) and inositol-requiring enzyme 1α (IRE1α) promote type I interferon (IFN) responses. We found that Xbp1-deficient mouse embryonic fibroblasts and macrophages had impaired antiviral resistance. However, this was not because of a defect in type I IFN responses but rather an inability of Xbp1-deficient cells to undergo viral-induced apoptosis. The ability to undergo apoptosis limited infection in wild-type cells. Xbp1-deficient cells were generally resistant to the intrinsic pathway of apoptosis through an indirect mechanism involving activation of the nuclease IRE1α. We observed an IRE1α-dependent reduction in the abundance of the proapoptotic microRNA miR-125a and a corresponding increase in the amounts of the members of the antiapoptotic Bcl-2 family. The activation of IRE1α by the hepatitis C virus (HCV) protein NS4B in XBP1-proficient cells also conferred apoptosis resistance and promoted viral replication. Furthermore, we found evidence of IRE1α activation and decreased miR-125a abundance in liver biopsies from patients infected with HCV compared to those in the livers of healthy controls. Our results reveal a prosurvival role for IRE1α in virally infected cells and suggest a possible target for IFN-independent antiviral therapy.
Collapse
Affiliation(s)
- Susan L Fink
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA.
- Department of Laboratory Medicine, Yale University, New Haven, CT 06520, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Ryan D Molony
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Takao Iwawaki
- Division of Cell Medicine, Department of Life Science, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Charles S Landis
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, CT 06520, USA
- Department of Comparative Medicine, Yale University, New Haven, CT 06520, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20814, USA
| |
Collapse
|
15
|
Yockey LJ, Varela L, Rakib T, Khoury-Hanold W, Fink SL, Stutz B, Szigeti-Buck K, Van den Pol A, Lindenbach BD, Horvath TL, Iwasaki A. Vaginal Exposure to Zika Virus during Pregnancy Leads to Fetal Brain Infection. Cell 2016; 166:1247-1256.e4. [PMID: 27565347 DOI: 10.1016/j.cell.2016.08.004] [Citation(s) in RCA: 301] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 07/29/2016] [Accepted: 08/03/2016] [Indexed: 12/11/2022]
Abstract
Zika virus (ZIKV) can be transmitted sexually between humans. However, it is unknown whether ZIKV replicates in the vagina and impacts the unborn fetus. Here, we establish a mouse model of vaginal ZIKV infection and demonstrate that, unlike other routes, ZIKV replicates within the genital mucosa even in wild-type (WT) mice. Mice lacking RNA sensors or transcription factors IRF3 and IRF7 resulted in higher levels of local viral replication. Furthermore, mice lacking the type I interferon (IFN) receptor (IFNAR) became viremic and died of infection after a high-dose vaginal ZIKV challenge. Notably, vaginal infection of pregnant dams during early pregnancy led to fetal growth restriction and infection of the fetal brain in WT mice. This was exacerbated in mice deficient in IFN pathways, leading to abortion. Our study highlights the vaginal tract as a highly susceptible site of ZIKV replication and illustrates the dire disease consequences during pregnancy.
Collapse
Affiliation(s)
- Laura J Yockey
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - Luis Varela
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - Tasfia Rakib
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - William Khoury-Hanold
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - Susan L Fink
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520 USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - Bernardo Stutz
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - Klara Szigeti-Buck
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - Anthony Van den Pol
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - Tamas L Horvath
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520 USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520 USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, 06520 USA.
| |
Collapse
|
16
|
Donald CL, Brennan B, Cumberworth SL, Rezelj VV, Clark JJ, Cordeiro MT, Freitas de Oliveira França R, Pena LJ, Wilkie GS, Da Silva Filipe A, Davis C, Hughes J, Varjak M, Selinger M, Zuvanov L, Owsianka AM, Patel AH, McLauchlan J, Lindenbach BD, Fall G, Sall AA, Biek R, Rehwinkel J, Schnettler E, Kohl A. Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil. PLoS Negl Trop Dis 2016; 10:e0005048. [PMID: 27706161 PMCID: PMC5051680 DOI: 10.1371/journal.pntd.0005048] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/19/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The outbreak of Zika virus (ZIKV) in the Americas has transformed a previously obscure mosquito-transmitted arbovirus of the Flaviviridae family into a major public health concern. Little is currently known about the evolution and biology of ZIKV and the factors that contribute to the associated pathogenesis. Determining genomic sequences of clinical viral isolates and characterization of elements within these are an important prerequisite to advance our understanding of viral replicative processes and virus-host interactions. METHODOLOGY/PRINCIPAL FINDINGS We obtained a ZIKV isolate from a patient who presented with classical ZIKV-associated symptoms, and used high throughput sequencing and other molecular biology approaches to determine its full genome sequence, including non-coding regions. Genome regions were characterized and compared to the sequences of other isolates where available. Furthermore, we identified a subgenomic flavivirus RNA (sfRNA) in ZIKV-infected cells that has antagonist activity against RIG-I induced type I interferon induction, with a lesser effect on MDA-5 mediated action. CONCLUSIONS/SIGNIFICANCE The full-length genome sequence including non-coding regions of a South American ZIKV isolate from a patient with classical symptoms will support efforts to develop genetic tools for this virus. Detection of sfRNA that counteracts interferon responses is likely to be important for further understanding of pathogenesis and virus-host interactions.
Collapse
Affiliation(s)
- Claire L. Donald
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Benjamin Brennan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | | | - Veronica V. Rezelj
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Jordan J. Clark
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Marli T. Cordeiro
- Fundação Oswaldo Cruz-PE/Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Campus da UFPE-Cidade Universitária, Recife/PE, Brasil
| | - Rafael Freitas de Oliveira França
- Fundação Oswaldo Cruz-PE/Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Campus da UFPE-Cidade Universitária, Recife/PE, Brasil
| | - Lindomar J. Pena
- Fundação Oswaldo Cruz-PE/Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Campus da UFPE-Cidade Universitária, Recife/PE, Brasil
| | - Gavin S. Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Christopher Davis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Martin Selinger
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Luíza Zuvanov
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Ania M. Owsianka
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, United States of America
| | - Gamou Fall
- Pole de Virologie, Unité des arbovirus et virus des fièvres hémorragiques, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou A. Sall
- Pole de Virologie, Unité des arbovirus et virus des fièvres hémorragiques, Institut Pasteur de Dakar, Dakar, Senegal
| | - Roman Biek
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine and Radcliffe Department of Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| |
Collapse
|
17
|
Onorati M, Li Z, Liu F, Sousa AMM, Nakagawa N, Li M, Dell'Anno MT, Gulden FO, Pochareddy S, Tebbenkamp ATN, Han W, Pletikos M, Gao T, Zhu Y, Bichsel C, Varela L, Szigeti-Buck K, Lisgo S, Zhang Y, Testen A, Gao XB, Mlakar J, Popovic M, Flamand M, Strittmatter SM, Kaczmarek LK, Anton ES, Horvath TL, Lindenbach BD, Sestan N. Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia. Cell Rep 2016; 16:2576-2592. [PMID: 27568284 PMCID: PMC5135012 DOI: 10.1016/j.celrep.2016.08.038] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/27/2016] [Accepted: 08/12/2016] [Indexed: 02/08/2023] Open
Abstract
The mechanisms underlying Zika virus (ZIKV)-related microcephaly and other neurodevelopment defects remain poorly understood. Here, we describe the derivation and characterization, including single-cell RNA-seq, of neocortical and spinal cord neuroepithelial stem (NES) cells to model early human neurodevelopment and ZIKV-related neuropathogenesis. By analyzing human NES cells, organotypic fetal brain slices, and a ZIKV-infected micrencephalic brain, we show that ZIKV infects both neocortical and spinal NES cells as well as their fetal homolog, radial glial cells (RGCs), causing disrupted mitoses, supernumerary centrosomes, structural disorganization, and cell death. ZIKV infection of NES cells and RGCs causes centrosomal depletion and mitochondrial sequestration of phospho-TBK1 during mitosis. We also found that nucleoside analogs inhibit ZIKV replication in NES cells, protecting them from ZIKV-induced pTBK1 relocalization and cell death. We established a model system of human neural stem cells to reveal cellular and molecular mechanisms underlying neurodevelopmental defects associated with ZIKV infection and its potential treatment.
Collapse
Affiliation(s)
- Marco Onorati
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Zhen Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Fuchen Liu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Naoki Nakagawa
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Maria Teresa Dell'Anno
- Cellular Neuroscience, Neurodegeneration and Repair Program, Departments of Neurology and Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Forrest O Gulden
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sirisha Pochareddy
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Andrew T N Tebbenkamp
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Wenqi Han
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mihovil Pletikos
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tianliuyun Gao
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ying Zhu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Candace Bichsel
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Luis Varela
- Section of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Klara Szigeti-Buck
- Section of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Steven Lisgo
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE13BZ, UK
| | - Yalan Zhang
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Anze Testen
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Xiao-Bing Gao
- Section of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jernej Mlakar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Mara Popovic
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Marie Flamand
- Department of Virology, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Stephen M Strittmatter
- Cellular Neuroscience, Neurodegeneration and Repair Program, Departments of Neurology and Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Leonard K Kaczmarek
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06510, USA; Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - E S Anton
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Tamas L Horvath
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Section of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Cellular Neuroscience, Neurodegeneration and Repair Program, Departments of Neurology and Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Section of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Departments of Genetics and Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
18
|
Jurado KA, Simoni MK, Tang Z, Uraki R, Hwang J, Householder S, Wu M, Lindenbach BD, Abrahams VM, Guller S, Fikrig E. Zika virus productively infects primary human placenta-specific macrophages. JCI Insight 2016; 1. [PMID: 27595140 DOI: 10.1172/jci.insight.88461] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The strong association of Zika virus infection with congenital defects has led to questions of how a flavivirus is capable of crossing the placental barrier to reach the fetal brain. Here, we demonstrate permissive Zika virus infection of primary human placental macrophages, commonly referred to as Hofbauer cells, and placental villous fibroblasts. We also demonstrate Zika virus infection of Hofbauer cells within the context of the tissue ex vivo using term placental villous explants. In addition to amplifying infectious virus within a usually inaccessible area, the putative migratory activities of Hofbauer cells may aid in dissemination of Zika virus to the fetal brain. Understanding the susceptibility of placenta-specific cell types will aid future work around and understanding of Zika virus-associated pregnancy complications.
Collapse
Affiliation(s)
- Kellie Ann Jurado
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael K Simoni
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Zhonghua Tang
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ryuta Uraki
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jesse Hwang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sarah Householder
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mingjie Wu
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Vikki M Abrahams
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Seth Guller
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| |
Collapse
|
19
|
Affiliation(s)
- Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT
| |
Collapse
|
20
|
Isken O, Langerwisch U, Jirasko V, Rehders D, Redecke L, Ramanathan H, Lindenbach BD, Bartenschlager R, Tautz N. Correction: A Conserved NS3 Surface Patch Orchestrates NS2 Protease Stimulation, NS5A Hyperphosphorylation and HCV Genome Replication. PLoS Pathog 2016; 12:e1005394. [PMID: 26745726 PMCID: PMC4706451 DOI: 10.1371/journal.ppat.1005394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
21
|
Binka M, Paintsil E, Patel A, Lindenbach BD, Heimer R. Correction: Survival of Hepatitis C Virus in Syringes Is Dependent on the Design of the Syringe-Needle and Dead Space Volume. PLoS One 2015; 10:e0146088. [PMID: 26700029 PMCID: PMC4689391 DOI: 10.1371/journal.pone.0146088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
22
|
Binka M, Paintsil E, Patel A, Lindenbach BD, Heimer R. Survival of Hepatitis C Virus in Syringes Is Dependent on the Design of the Syringe-Needle and Dead Space Volume. PLoS One 2015; 10:e0139737. [PMID: 26536599 PMCID: PMC4633215 DOI: 10.1371/journal.pone.0139737] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/15/2015] [Indexed: 11/19/2022] Open
Abstract
Background Many people who inject drugs (PWID) use syringes with detachable needles, which have high dead space (HDS). Contaminated HDS blood may substantially contribute to the transmission of HIV, hepatitis C (HCV), and other blood-borne viruses within this population. Newly designed low dead space (LDS) syringe-needle combinations seek to reduce blood-borne virus transmission among PWID. We evaluated the infectivity of HCV-contaminated residual volumes recovered from two LDS syringe-needle combinations. Methods We tested two different design approaches to reducing the dead space. One added a piston to the plunger; the other reduced the dead space within the needle. The two approaches cannot be combined. Recovery of genotype-2a reporter HCV from LDS syringe-needle combinations was compared to recovery from insulin syringes with fixed needles and standard HDS syringe-needle combinations. Recovery of HCV from syringes was determined immediately following their contamination with HCV-spiked plasma, after storage at 22°C for up to 1 week, or after rinsing with water. Results Insulin syringes with fixed needles had the lowest proportion of HCV-positive syringes before and after storage. HCV recovery after immediate use ranged from 47%±4% HCV-positive 1 mL insulin syringes with 27-gauge ½ inch needles to 98%±1% HCV-positive HDS 2 mL syringes with 23-gauge 1¼ inch detachable needles. LDS combinations yielded recoveries ranging from 65%±5% to 93%±3%. Recovery was lower in combinations containing LDS needles than LDS syringes. After 3 days of storage, as much as 6-fold differences in virus recovery was observed, with HCV recovery being lower in combinations containing LDS needles. Most combinations with detachable needles required multiple rinses to reduce HCV infectivity to undetectable levels whereas a single rinse of insulin syringes was sufficient. Conclusions Our study, the first to assess the infectivity of HCV in residual volumes of LDS syringes and needles available to PWID, demonstrates that LDS syringe-needle combination still has the greater potential for HCV transmission than insulin syringes with fixed needles. Improved LDS designs may be able to further reduce HCV recovery, but based on the designed tested, LDS needles and syringes remain intermediate between fixed-needle syringes and HDS combinations in reducing exposure to HCV.
Collapse
Affiliation(s)
- Mawuena Binka
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Elijah Paintsil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Departments of Pediatrics & Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Center for Interdisciplinary Research on AIDS, Yale University, New Haven, Connecticut, United States of America
| | - Amisha Patel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Robert Heimer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Center for Interdisciplinary Research on AIDS, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| |
Collapse
|
23
|
Kazakov T, Yang F, Ramanathan HN, Kohlway A, Diamond MS, Lindenbach BD. Hepatitis C virus RNA replication depends on specific cis- and trans-acting activities of viral nonstructural proteins. PLoS Pathog 2015; 11:e1004817. [PMID: 25875808 PMCID: PMC4395149 DOI: 10.1371/journal.ppat.1004817] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/18/2015] [Indexed: 02/07/2023] Open
Abstract
Many positive-strand RNA viruses encode genes that can function in trans, whereas other genes are required in cis for genome replication. The mechanisms underlying trans- and cis-preferences are not fully understood. Here, we evaluate this concept for hepatitis C virus (HCV), an important cause of chronic liver disease and member of the Flaviviridae family. HCV encodes five nonstructural (NS) genes that are required for RNA replication. To date, only two of these genes, NS4B and NS5A, have been trans-complemented, leading to suggestions that other replicase genes work only in cis. We describe a new quantitative system to measure the cis- and trans-requirements for HCV NS gene function in RNA replication and identify several lethal mutations in the NS3, NS4A, NS4B, NS5A, and NS5B genes that can be complemented in trans, alone or in combination, by expressing the NS3-5B polyprotein from a synthetic mRNA. Although NS5B RNA binding and polymerase activities can be supplied in trans, NS5B protein expression was required in cis, indicating that NS5B has a cis-acting role in replicase assembly distinct from its known enzymatic activity. Furthermore, the RNA binding and NTPase activities of the NS3 helicase domain were required in cis, suggesting that these activities play an essential role in RNA template selection. A comprehensive complementation group analysis revealed functional linkages between NS3-4A and NS4B and between NS5B and the upstream NS3-5A genes. Finally, NS5B polymerase activity segregated with a daclatasvir-sensitive NS5A activity, which could explain the synergy of this antiviral compound with nucleoside analogs in patients. Together, these studies define several new aspects of HCV replicase structure-function, help to explain the potency of HCV-specific combination therapies, and provide an experimental framework for the study of cis- and trans-acting activities in positive-strand RNA virus replication more generally.
Collapse
Affiliation(s)
- Teymur Kazakov
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Feng Yang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Harish N. Ramanathan
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Andrew Kohlway
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Michael S. Diamond
- Departments of Medicine, Molecular Microbiology, and Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| |
Collapse
|
24
|
Isken O, Langerwisch U, Jirasko V, Rehders D, Redecke L, Ramanathan H, Lindenbach BD, Bartenschlager R, Tautz N. A conserved NS3 surface patch orchestrates NS2 protease stimulation, NS5A hyperphosphorylation and HCV genome replication. PLoS Pathog 2015; 11:e1004736. [PMID: 25774920 PMCID: PMC4361677 DOI: 10.1371/journal.ppat.1004736] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/06/2015] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a leading cause of liver disease worldwide. The HCV RNA genome is translated into a single polyprotein. Most of the cleavage sites in the non-structural (NS) polyprotein region are processed by the NS3/NS4A serine protease. The vital NS2-NS3 cleavage is catalyzed by the NS2 autoprotease. For efficient processing at the NS2/NS3 site, the NS2 cysteine protease depends on the NS3 serine protease domain. Despite its importance for the viral life cycle, the molecular details of the NS2 autoprotease activation by NS3 are poorly understood. Here, we report the identification of a conserved hydrophobic NS3 surface patch that is essential for NS2 protease activation. One residue within this surface region is also critical for RNA replication and NS5A hyperphosphorylation, two processes known to depend on functional replicase assembly. This dual function of the NS3 surface patch prompted us to reinvestigate the impact of the NS2-NS3 cleavage on NS5A hyperphosphorylation. Interestingly, NS2-NS3 cleavage turned out to be a prerequisite for NS5A hyperphosphorylation, indicating that this cleavage has to occur prior to replicase assembly. Based on our data, we propose a sequential cascade of molecular events: in uncleaved NS2-NS3, the hydrophobic NS3 surface patch promotes NS2 protease stimulation; upon NS2-NS3 cleavage, this surface region becomes available for functional replicase assembly. This model explains why efficient NS2-3 cleavage is pivotal for HCV RNA replication. According to our model, the hydrophobic surface patch on NS3 represents a module critically involved in the temporal coordination of HCV replicase assembly.
Collapse
Affiliation(s)
- Olaf Isken
- Institute of Virology and Cell Biology, University of Lübeck, Germany
| | | | - Vlastimil Jirasko
- Department of Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Dirk Rehders
- Joint Laboratory for Structural Biology of Infection and Inflammation of the University of Hamburg and the University of Lübeck, DESY, Hamburg, Germany
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation of the University of Hamburg and the University of Lübeck, DESY, Hamburg, Germany
| | - Harish Ramanathan
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, United States of America
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, United States of America
| | - Ralf Bartenschlager
- Department of Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Norbert Tautz
- Institute of Virology and Cell Biology, University of Lübeck, Germany
- * E-mail:
| |
Collapse
|
25
|
Binka M, Paintsil E, Patel A, Lindenbach BD, Heimer R. Disinfection of syringes contaminated with hepatitis C virus by rinsing with household products. Open Forum Infect Dis 2015; 2:ofv017. [PMID: 26034767 PMCID: PMC4438897 DOI: 10.1093/ofid/ofv017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/27/2015] [Indexed: 11/14/2022] Open
Abstract
PWID “disinfect” used syringes with readily available household products when new syringes are inaccessible. Household products tested were more effective in fixed-needle syringes (low residual volume) than in syringes with detachable-needles (high residual volume). Bleach was the most effective disinfectant. Background. Hepatitis C virus (HCV) transmission among people who inject drugs (PWID) is associated with the sharing of injection paraphernalia. People who inject drugs often “disinfect” used syringes with household products when new syringes are unavailable. We assessed the effectiveness of these products in disinfecting HCV-contaminated syringes. Methods. A genotype-2a reporter virus assay was used to assess HCV infectivity in syringes postrinsing. Hepatitis C virus-contaminated 1 mL insulin syringes with fixed needles and 1 mL tuberculin syringes with detachable needles were rinsed with water, Clorox bleach, hydrogen peroxide, ethanol, isopropanol, Lysol, or Dawn Ultra at different concentrations. Syringes were either immediately tested for viable virus or stored at 4°C, 22°C, and 37°C for up to 21 days before viral infectivity was determined. Results. Most products tested reduced HCV infectivity to undetectable levels in insulin syringes. Bleach eliminated HCV infectivity in both syringes. Other disinfectants produced virus recovery ranging from high (5% ethanol, 77% ± 12% HCV-positive syringes) to low (1:800 Dawn Ultra, 7% ± 7% positive syringes) in tuberculin syringes. Conclusions. Household disinfectants tested were more effective in fixed-needle syringes (low residual volume) than in syringes with detachable needles (high residual volume). Bleach was the most effective disinfectant after 1 rinse, whereas other diluted household products required multiple rinses to eliminate HCV. Rinsing with water, 5% ethanol (as in beer), and 20% ethanol (as in fortified wine) was ineffective and should be avoided. Our data suggest that rinsing of syringes with household disinfectants may be an effective tool in preventing HCV transmission in PWID when done properly.
Collapse
Affiliation(s)
- Mawuena Binka
- Department of Epidemiology of Microbial Diseases , Yale School of Public Health , New Haven, Connecticut
| | - Elijah Paintsil
- Department of Epidemiology of Microbial Diseases , Yale School of Public Health , New Haven, Connecticut ; Departments of Pediatrics ; Pharmacology
| | - Amisha Patel
- Department of Epidemiology of Microbial Diseases , Yale School of Public Health , New Haven, Connecticut
| | - Brett D Lindenbach
- Microbial Pathogenesis , Yale School of Medicine , New Haven, Connecticut
| | - Robert Heimer
- Department of Epidemiology of Microbial Diseases , Yale School of Public Health , New Haven, Connecticut
| |
Collapse
|
26
|
Cordek DG, Croom-Perez TJ, Hwang J, Hargittai MRS, Subba-Reddy CV, Han Q, Lodeiro MF, Ning G, McCrory TS, Arnold JJ, Koc H, Lindenbach BD, Showalter SA, Cameron CE. Expanding the proteome of an RNA virus by phosphorylation of an intrinsically disordered viral protein. J Biol Chem 2014; 289:24397-416. [PMID: 25031324 DOI: 10.1074/jbc.m114.589911] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The human proteome contains myriad intrinsically disordered proteins. Within intrinsically disordered proteins, polyproline-II motifs are often located near sites of phosphorylation. We have used an unconventional experimental paradigm to discover that phosphorylation by protein kinase A (PKA) occurs in the intrinsically disordered domain of hepatitis C virus non-structural protein 5A (NS5A) on Thr-2332 near one of its polyproline-II motifs. Phosphorylation shifts the conformational ensemble of the NS5A intrinsically disordered domain to a state that permits detection of the polyproline motif by using (15)N-, (13)C-based multidimensional NMR spectroscopy. PKA-dependent proline resonances were lost in the presence of the Src homology 3 domain of c-Src, consistent with formation of a complex. Changing Thr-2332 to alanine in hepatitis C virus genotype 1b reduced the steady-state level of RNA by 10-fold; this change was lethal for genotype 2a. The lethal phenotype could be rescued by changing Thr-2332 to glutamic acid, a phosphomimetic substitution. Immunofluorescence and transmission electron microscopy showed that the inability to produce Thr(P)-2332-NS5A caused loss of integrity of the virus-induced membranous web/replication organelle. An even more extreme phenotype was observed in the presence of small molecule inhibitors of PKA. We conclude that the PKA-phosphorylated form of NS5A exhibits unique structure and function relative to the unphosphorylated protein. We suggest that post-translational modification of viral proteins containing intrinsic disorder may be a general mechanism to expand the viral proteome without a corresponding expansion of the genome.
Collapse
Affiliation(s)
| | | | - Jungwook Hwang
- the Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul, 133-791, Korea
| | | | - Chennareddy V Subba-Reddy
- the Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, and
| | - Qingxia Han
- From the Department of Biochemistry and Molecular Biology
| | | | - Gang Ning
- the Huck Institutes of the Life Sciences, and
| | | | - Jamie J Arnold
- From the Department of Biochemistry and Molecular Biology
| | - Hasan Koc
- the Department of Pharmaceutical Science and Research, Marshall University School of Pharmacy, Huntington, West Virginia 25755
| | - Brett D Lindenbach
- the Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, and
| | - Scott A Showalter
- the Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | | |
Collapse
|
27
|
Paintsil E, Binka M, Patel A, Lindenbach BD, Heimer R. Hepatitis C virus maintains infectivity for weeks after drying on inanimate surfaces at room temperature: implications for risks of transmission. J Infect Dis 2013; 209:1205-11. [PMID: 24273176 DOI: 10.1093/infdis/jit648] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Healthcare workers may come into contact with fomites that contain infectious hepatitis C virus (HCV) during preparation of plasma or following placement or removal of venous lines. Similarly, injection drugs users may come into contact with fomites. Hypothesizing that prolonged viability of HCV in fomites may contribute significantly to incidence, we determined the longevity of virus infectivity and the effectiveness of antiseptics. METHODS We determined the volume of drops misplaced during transfer of serum or plasma. Aliquots equivalent to the maximum drop volume of plasma spiked with the 2a HCV reporter virus were loaded into 24-well plates. Plates were stored uncovered at 3 temperatures: 4°C, 22°C, and 37°C for up to 6 weeks before viral infectivity was determined in a microculture assay. RESULTS The mean volume of an accidental drop was 29 µL (min-max of 20-33 µL). At storage temperatures 4°C and 22°C, we recovered viable HCV from the low-titer spots for up to 6 weeks of storage. The rank order of HCV virucidal activity of commonly used antiseptics was bleach (1:10) > cavicide (1:10) > ethanol (70%). CONCLUSIONS The hypothesis of potential transmission from fomites was supported by the experimental results. The anti-HCV activity of commercial antiseptics varied.
Collapse
Affiliation(s)
- Elijah Paintsil
- Departments of Pediatrics and Pharmacology, Yale School of Medicine
| | | | | | | | | |
Collapse
|
28
|
Abstract
Hepatitis C virus, a major human pathogen, produces infectious virus particles with several unique features, such as an ability to interact with serum lipoproteins, a dizzyingly complicated process of virus entry, and a pathway of virus assembly and release that is closely linked to lipoprotein secretion. Here, we review these unique features, with an emphasis on recent discoveries concerning virus particle structure, virus entry and virus particle assembly and release.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut 06536, USA
| | | |
Collapse
|
29
|
Abstract
Hepatitis C Virus (HCV) particles exhibit several unusual properties that are not found in other enveloped RNA viruses, most notably their low buoyant density and interaction with serum lipoproteins. With the advent of systems to grow HCV in cell culture, the molecular basis of HCV particle assembly and release can now be addressed. The process of virus assembly involves protein-protein interactions between viral structural and nonstructural proteins and the coordinated action of host factors. This chapter reviews our current understanding of these interactions and factors.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
| |
Collapse
|
30
|
Polyak SJ, Morishima C, Scott JD, Gastaminza P, Cox A, de Araújo ESA, Higgs MR, Loo YM, Golden-Mason L, Lindenbach BD, Baumert TF, Randall G, Gale M. A summary of the 18th International Symposium on Hepatitis C Virus and Related Viruses. Gastroenterology 2012; 142:e1-5. [PMID: 22185796 DOI: 10.1053/j.gastro.2011.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Stephen J Polyak
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD, Pyle AM. Structural insights into RNA recognition by RIG-I. Cell 2011; 147:409-22. [PMID: 22000018 PMCID: PMC3222294 DOI: 10.1016/j.cell.2011.09.023] [Citation(s) in RCA: 301] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 08/02/2011] [Accepted: 09/16/2011] [Indexed: 12/19/2022]
Abstract
Intracellular RIG-I-like receptors (RLRs, including RIG-I, MDA-5, and LGP2) recognize viral RNAs as pathogen-associated molecular patterns (PAMPs) and initiate an antiviral immune response. To understand the molecular basis of this process, we determined the crystal structure of RIG-I in complex with double-stranded RNA (dsRNA). The dsRNA is sheathed within a network of protein domains that include a conserved "helicase" domain (regions HEL1 and HEL2), a specialized insertion domain (HEL2i), and a C-terminal regulatory domain (CTD). A V-shaped pincer connects HEL2 and the CTD by gripping an α-helical shaft that extends from HEL1. In this way, the pincer coordinates functions of all the domains and couples RNA binding with ATP hydrolysis. RIG-I falls within the Dicer-RIG-I clade of the superfamily 2 helicases, and this structure reveals complex interplay between motor domains, accessory mechanical domains, and RNA that has implications for understanding the nanomechanical function of this protein family and other ATPases more broadly.
Collapse
Affiliation(s)
- Dahai Luo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Steve C. Ding
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Adriana Vela
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Andrew Kohlway
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Brett D. Lindenbach
- Section of Microbial Pathogenesis, Yale University, New Haven, Connecticut 06520
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| |
Collapse
|
32
|
Abstract
Hepatitis C virus genome replication occurs in endoplasmic reticulum-derived membrane compartments, but it is unknown how these structures arise. In this issue of Cell Host & Microbe, Reiss and colleagues (2011) show that the virus recruits a specific lipid kinase to replication sites, stimulates its kinase activity, and alters the phospholipid profile of replication compartments.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Section of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, BCMM 354C, New Haven, CT 06536, USA.
| |
Collapse
|
33
|
|
34
|
Paintsil E, He H, Peters C, Lindenbach BD, Heimer R. Survival of hepatitis C virus in syringes: implication for transmission among injection drug users. J Infect Dis 2010; 202:984-90. [PMID: 20726768 DOI: 10.1086/656212] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND We hypothesized that the high prevalence of hepatitis C virus (HCV) among injection drug users might be due to prolonged virus survival in contaminated syringes. METHODS We developed a microculture assay to examine the viability of HCV. Syringes were loaded with blood spiked with HCV reporter virus (Jc1/GLuc2A) to simulate 2 scenarios of residual volumes: low void volume (2 microL) for 1-mL insulin syringes and high void volume (32 microL) for 1-mL tuberculin syringes. Syringes were stored at 4 degrees C, 22 degrees C, and 37 degrees C for up to 63 days before testing for HCV infectivity by using luciferase activity. RESULTS The virus decay rate was biphasic (t1/2alpha= 0.4 h and t1/2beta = 28 hh). Insulin syringes failed to yield viable HCV beyond day 1 at all storage temperatures except 4 degrees , in which 5% of syringes yielded viable virus on day 7. Tuberculin syringes yielded viable virus from 96%, 71%, and 52% of syringes after storage at 4 degrees, 22 degrees, and 37 degrees for 7 days, respectively, and yielded viable virus up to day 63. CONCLUSIONS The high prevalence of HCV among injection drug users may be partly due to the resilience of the virus and the syringe type. Our findings may be used to guide prevention strategies.
Collapse
Affiliation(s)
- Elijah Paintsil
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
| | | | | | | | | |
Collapse
|
35
|
Harding MJ, Lepus CM, Gibson TF, Shepherd BR, Gerber SA, Graham M, Paturzo FX, Rahner C, Madri JA, Bothwell ALM, Lindenbach BD, Pober JS. An implantable vascularized protein gel construct that supports human fetal hepatoblast survival and infection by hepatitis C virus in mice. PLoS One 2010; 5:e9987. [PMID: 20376322 PMCID: PMC2848675 DOI: 10.1371/journal.pone.0009987] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 02/22/2010] [Indexed: 01/16/2023] Open
Abstract
Background Widely accessible small animal models suitable for the study of hepatitis C virus (HCV) in vivo are lacking, primarily because rodent hepatocytes cannot be productively infected and because human hepatocytes are not easily engrafted in immunodeficient mice. Methodology/Principal Findings We report here on a novel approach for human hepatocyte engraftment that involves subcutaneous implantation of primary human fetal hepatoblasts (HFH) within a vascularized rat collagen type I/human fibronectin (rCI/hFN) gel containing Bcl-2-transduced human umbilical vein endothelial cells (Bcl-2-HUVEC) in severe combined immunodeficient X beige (SCID/bg) mice. Maturing hepatic epithelial cells in HFH/Bcl-2-HUVEC co-implants displayed endocytotic activity at the basolateral surface, canalicular microvilli and apical tight junctions between adjacent cells assessed by transmission electron microscopy. Some primary HFH, but not Huh-7.5 hepatoma cells, appeared to differentiate towards a cholangiocyte lineage within the gels, based on histological appearance and cytokeratin 7 (CK7) mRNA and protein expression. Levels of human albumin and hepatic nuclear factor 4α (HNF4α) mRNA expression in gel implants and plasma human albumin levels in mice engrafted with HFH and Bcl-2-HUVEC were somewhat enhanced by including murine liver-like basement membrane (mLBM) components and/or hepatocyte growth factor (HGF)-HUVEC within the gel matrix. Following ex vivo viral adsorption, both HFH/Bcl-2-HUVEC and Huh-7.5/Bcl-2-HUVEC co-implants sustained HCV Jc1 infection for at least 2 weeks in vivo, based on qRT-PCR and immunoelectron microscopic (IEM) analyses of gel tissue. Conclusion/Significance The system described here thus provides the basis for a simple and robust small animal model of HFH engraftment that is applicable to the study of HCV infections in vivo.
Collapse
Affiliation(s)
- Martha J Harding
- Section of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
Since the advent of efficient cell-culture methods for HCV replication and, more recently, infection, there has been a need to efficiently sequence the viral RNA in these systems. This need is especially urgent in light of the error-prone nature of HCV RNA replication, which leads to a variety of interesting mutations. The adaptation of hepatitis C replicons to cell culture, which greatly increased their replication capacity, and the subsequent identification of viral point mutations responsible for this adaptation are prime examples of the type of phenotype-genotype connection that viral RNA sequencing methods can provide. More recently, researchers have used similar sequencing methods to identify changes in replicons that represent viral adaptation to engineered mutations, adaptation to a variety of host cells, and viral evasion of antiviral compound susceptibility. Here, we describe the cloning and isolation of HCV replicon-bearing cells, the extraction of total RNA, the generation of cDNA, and the amplification of specific HCV replicon sequences for sequence analysis. The methods we describe permit rapid and robust determination of HCV RNA sequences from cell culture.
Collapse
|
37
|
Abstract
Recently described systems for efficiently growing HCV in cell culture provide powerful new tools with which to dissect the life cycle of this important human pathogen. This chapter describes methods for measuring the infectivity of HCV produced in cell culture or recovered from animals experimentally infected with the cell culture-produced virus.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
38
|
|
39
|
Abstract
Recently described systems for efficiently growing HCV in cell culture provide powerful new tools with which to dissect the life cycle of this important human pathogen. This chapter describes methods for measuring the infectivity of HCV produced in cell culture or recovered from animals experimentally infected with the cell culture-produced virus.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
40
|
Randall G, Panis M, Cooper JD, Tellinghuisen TL, Sukhodolets KE, Pfeffer S, Landthaler M, Landgraf P, Kan S, Lindenbach BD, Chien M, Weir DB, Russo JJ, Ju J, Brownstein MJ, Sheridan R, Sander C, Zavolan M, Tuschl T, Rice CM. Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A 2007; 104:12884-9. [PMID: 17616579 PMCID: PMC1937561 DOI: 10.1073/pnas.0704894104] [Citation(s) in RCA: 433] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Indexed: 02/06/2023] Open
Abstract
Recently identified hepatitis C virus (HCV) isolates that are infectious in cell culture provide a genetic system to evaluate the significance of virus-host interactions for HCV replication. We have completed a systematic RNAi screen wherein siRNAs were designed that target 62 host genes encoding proteins that physically interact with HCV RNA or proteins or belong to cellular pathways thought to modulate HCV infection. This includes 10 host proteins that we identify in this study to bind HCV NS5A. siRNAs that target 26 of these host genes alter infectious HCV production >3-fold. Included in this set of 26 were siRNAs that target Dicer, a principal component of the RNAi silencing pathway. Contrary to the hypothesis that RNAi is an antiviral pathway in mammals, as has been reported for subgenomic HCV replicons, siRNAs that target Dicer inhibited HCV replication. Furthermore, siRNAs that target several other components of the RNAi pathway also inhibit HCV replication. MicroRNA profiling of human liver, human hepatoma Huh-7.5 cells, and Huh-7.5 cells that harbor replicating HCV demonstrated that miR-122 is the predominant microRNA in each environment. miR-122 has been previously implicated in positively regulating the replication of HCV genotype 1 replicons. We find that 2'-O-methyl antisense oligonucleotide depletion of miR-122 also inhibits HCV genotype 2a replication and infectious virus production. Our data define 26 host genes that modulate HCV infection and indicate that the requirement for functional RNAi for HCV replication is dominant over any antiviral activity this pathway may exert against HCV.
Collapse
Affiliation(s)
- Glenn Randall
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
- Department of Microbiology, University of Chicago, Chicago, IL 60637
| | - Maryline Panis
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
| | - Jacob D. Cooper
- Department of Microbiology, University of Chicago, Chicago, IL 60637
| | | | - Karen E. Sukhodolets
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Sebastien Pfeffer
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021
| | - Markus Landthaler
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021
| | - Pablo Landgraf
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021
| | - Sherry Kan
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
| | - Brett D. Lindenbach
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
| | | | - David B. Weir
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | | | - Jingyue Ju
- Columbia Genome Center, New York, NY 10032
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | | | - Robert Sheridan
- Computational Biology Center, Memorial Sloan–Kettering Cancer Center, New York, NY 10021; and
| | - Chris Sander
- Computational Biology Center, Memorial Sloan–Kettering Cancer Center, New York, NY 10021; and
| | - Mihaela Zavolan
- Biozentrum, Universität Basel, CH-4056 Basel, Switzerland; and
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
| |
Collapse
|
41
|
Lindenbach BD, Prágai BM, Montserret R, Beran RKF, Pyle AM, Penin F, Rice CM. The C terminus of hepatitis C virus NS4A encodes an electrostatic switch that regulates NS5A hyperphosphorylation and viral replication. J Virol 2007; 81:8905-18. [PMID: 17581983 PMCID: PMC1951449 DOI: 10.1128/jvi.00937-07] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus (HCV) nonstructural protein 4A (NS4A) is only 54 amino acids (aa) in length, yet it is a key regulator of the essential serine protease and RNA helicase activities of the NS3-4A complex, as well as a determinant of NS5A phosphorylation. Here we examine the structure and function of the C-terminal acidic region of NS4A through site-directed mutagenesis of a Con1 subgenomic replicon and through biophysical characterization of a synthetic peptide corresponding to this region. Our genetic studies revealed that in 8 of the 15 C-terminal residues of NS4A, individual Ala substitutions or charge reversal substitutions led to severe replication phenotypes, as well as decreased NS5A hyperphosphorylation. By selecting for replication-competent mutants, several second-site changes in NS3 were identified and shown to suppress these defects in replication and NS5A hyperphosphorylation. Circular-dichroism spectroscopy and nuclear magnetic resonance spectroscopy on a peptide corresponding to the C-terminal 19 aa of NS4A revealed that this region can adopt an alpha-helical conformation, but that this folding requires neutralization of a cluster of acidic residues. Taken together, these data suggest that the C terminus of NS4A acts as a dynamic regulator of NS3-4A interaction, NS5A hyperphosphorylation, and HCV replicase activity.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10021, USA.
| | | | | | | | | | | | | |
Collapse
|
42
|
Tscherne DM, Evans MJ, von Hahn T, Jones CT, Stamataki Z, McKeating JA, Lindenbach BD, Rice CM. Superinfection exclusion in cells infected with hepatitis C virus. J Virol 2007; 81:3693-703. [PMID: 17287280 PMCID: PMC1866098 DOI: 10.1128/jvi.01748-06] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Superinfection exclusion is the ability of an established virus infection to interfere with infection by a second virus. In this study, we found that Huh-7.5 cells acutely infected with hepatitis C virus (HCV) genotype 2a (chimeric strain J6/JFH) and cells harboring HCV genotype 1a, 1b, or 2a full-length or subgenomic replicons were resistant to infection with cell culture-produced HCV (HCVcc). Replicon-containing cells became permissive for HCVcc infection after treatment with an HCV-specific protease inhibitor. With the exception of cells harboring a J6/JFH-FLneo replicon, infected or replicon-containing cells were permissive for HCV pseudoparticle (HCVpp) entry, demonstrating a postentry superinfection block downstream of primary translation. The surprising resistance of J6/JFH-FLneo replicon-containing cells to HCVpp infection suggested a defect in virus entry. This block was due to reduced expression of the HCV coreceptor CD81. Further analyses indicated that J6/JFH may be toxic for cells expressing high levels of CD81, thus selecting for a CD81(low) population. CD81 down regulation was not observed in acutely infected cells, suggesting that this may not be a general mechanism of HCV superinfection exclusion. Thus, HCV establishes superinfection exclusion at a postentry step, and this effect is reversible by treatment of infected cells with antiviral compounds.
Collapse
Affiliation(s)
- Donna M Tscherne
- Laboratory of Virology and Infectious Diseases, Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Randall G, Chen L, Panis M, Fischer AK, Lindenbach BD, Sun J, Heathcote J, Rice CM, Edwards AM, McGilvray ID. Silencing of USP18 potentiates the antiviral activity of interferon against hepatitis C virus infection. Gastroenterology 2006; 131:1584-91. [PMID: 17101330 DOI: 10.1053/j.gastro.2006.08.043] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 07/26/2006] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Modulation of the host innate immune response is an attractive means of inhibiting hepatitis C virus (HCV) replication. Having previously determined that expression of the interferon-sensitive gene (ISG)15 protease USP18 is increased in the liver biopsy specimens of patients who do not respond to interferon (IFN)-alfa therapy, we hypothesized that USP18 might hinder the ability of IFN to inhibit HCV replication. METHODS The role of USP18 in IFN antiviral activity was examined using an in vitro model of HCV replication that reproduces the full viral life cycle. USP18 was silenced specifically using small inhibitory RNAs (siRNAs), and the dose response of HCV replication and infectious virus production to IFN-alfa was measured. RESULTS The siRNA knockdown of USP18 in human cells consistently potentiated the ability of IFN to inhibit HCV-RNA replication and infectious virus particle production by a factor of 1-2 log(10). USP18 knockdown also resulted in a number of cellular changes consistent with increased sensitivity to IFN. Decreasing USP18 expression led to increased cellular protein ISGylation in response to exogenous IFN-alfa, prolonged tyrosine phosphorylation of signal transducer and activation of transcription (STAT1), and a general enhancement of IFN-stimulated gene expression. CONCLUSIONS These data suggest that USP18 modulates the anti-HCV type I IFN response, and is a possible therapeutic target for the treatment of HCV infection.
Collapse
Affiliation(s)
- Glenn Randall
- Center for the Study of Hepatitis C, Rockefeller University, New York, New York, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
von Hahn T, Lindenbach BD, Boullier A, Quehenberger O, Paulson M, Rice CM, McKeating JA. Oxidized low-density lipoprotein inhibits hepatitis C virus cell entry in human hepatoma cells. Hepatology 2006; 43:932-42. [PMID: 16628670 DOI: 10.1002/hep.21139] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cell entry of hepatitis C virus, pseudoparticles (HCVpp) and cell culture grown virus (HCVcc), requires the interaction of viral glycoproteins with CD81 and other as yet unknown cellular factors. One of these is likely to be the scavenger receptor class B type I (SR-BI). To further understand the role of SR-BI, we examined the effect of SR-BI ligands on HCVpp and HCVcc infectivity. Oxidized low-density lipoprotein (oxLDL), but not native LDL, potently inhibited HCVpp and HCVcc cell entry. Pseudoparticles bearing unrelated viral glycoproteins or bovine viral diarrhea virus were not affected. A dose-dependent inhibition was observed for HCVpp bearing diverse viral glycoproteins with an approximate IC50 of 1.5 microg/mL apolipoprotein content, which is within the range of oxLDL reported to be present in human plasma. The ability of lipoprotein components to bind to target cells associated with their antiviral activity, suggesting a mechanism of action which targets a cell surface receptor critical for HCV infection of the host cell. However, binding of soluble E2 to SR-BI or CD81 was not affected by oxLDL, suggesting that oxLDL does not act as a simple receptor blocker. At the same time, oxLDL incubation altered the biophysical properties of HCVpp, suggesting a ternary interaction of oxLDL with both virus and target cells. In conclusion, the SR-BI ligand oxLDL is a potent cell entry inhibitor for a broad range of HCV strains in vitro. These findings suggest that SR-BI is an essential component of the cellular HCV receptor complex.
Collapse
Affiliation(s)
- Thomas von Hahn
- Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10021, USA.
| | | | | | | | | | | | | |
Collapse
|
45
|
Tscherne DM, Jones CT, Evans MJ, Lindenbach BD, McKeating JA, Rice CM. Time- and temperature-dependent activation of hepatitis C virus for low-pH-triggered entry. J Virol 2006; 80:1734-41. [PMID: 16439530 PMCID: PMC1367161 DOI: 10.1128/jvi.80.4.1734-1741.2006] [Citation(s) in RCA: 311] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) is an important human pathogen associated with chronic liver disease. Recently, based on a genotype 2a isolate, tissue culture systems supporting complete replication and infectious virus production have been developed. In this study, we used cell culture-produced infectious HCV to analyze the viral entry pathway into Huh-7.5 cells. Bafilomycin A1 and concanamycin A, inhibitors of vacuolar ATPases, prevented HCV entry when they were present prior to infection and had minimal effect on downstream replication events. HCV entry therefore appears to be pH dependent, requiring an acidified intracellular compartment. For many other enveloped viruses, acidic pH triggers an irreversible conformational change, which promotes virion-endosomal membrane fusion. Such viruses are often inactivated by low pH. In the case of HCV, exposure of virions to acidic pH followed by return to neutral pH did not affect their infectivity. This parallels the observation made for the related pestivirus bovine viral diarrhea virus. Low pH could activate the entry of cell surface-bound HCV but only after prolonged incubation at 37 degrees C. This suggests that there are rate-limiting, postbinding events that are needed to render HCV competent for low-pH-triggered entry. Such events may involve interaction with a cellular coreceptor or other factors but do not require cathepsins B and L, late endosomal proteases that activate Ebola virus and reovirus for entry.
Collapse
Affiliation(s)
- Donna M Tscherne
- Laboratory of Virology and Infectious Diseases, Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | | | | | | | | | | |
Collapse
|
46
|
Lindenbach BD, Meuleman P, Ploss A, Vanwolleghem T, Syder AJ, McKeating JA, Lanford RE, Feinstone SM, Major ME, Leroux-Roels G, Rice CM. Cell culture-grown hepatitis C virus is infectious in vivo and can be recultured in vitro. Proc Natl Acad Sci U S A 2006; 103:3805-9. [PMID: 16484368 PMCID: PMC1533780 DOI: 10.1073/pnas.0511218103] [Citation(s) in RCA: 338] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatitis C virus (HCV) is a major cause of chronic liver disease, frequently progressing to cirrhosis and increased risk of hepatocellular carcinoma. Current therapies are inadequate and progress in the field has been hampered by the lack of efficient HCV culture systems. By using a recently described HCV genotype 2a infectious clone that replicates and produces infectious virus in cell culture (HCVcc), we report here that HCVcc strain FL-J6/JFH can establish long-term infections in chimpanzees and in mice containing human liver grafts. Importantly, virus recovered from these animals was highly infectious in cell culture, demonstrating efficient ex vivo culture of HCV. The improved infectivity of animal-derived HCV correlated with virions of a lower average buoyant density than HCVcc, suggesting that physical association with low-density factors influences viral infectivity. These results greatly extend the utility of the HCVcc genetic system to allow the complete in vitro and in vivo dissection of the HCV life cycle.
Collapse
Affiliation(s)
- Brett D. Lindenbach
- *Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Philip Meuleman
- Center for Vaccinology, Ghent University and Hospital, Building A, First Floor, De Pintelaan 185, 9000 Ghent, Belgium
| | - Alexander Ploss
- *Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Thomas Vanwolleghem
- Center for Vaccinology, Ghent University and Hospital, Building A, First Floor, De Pintelaan 185, 9000 Ghent, Belgium
| | - Andrew J. Syder
- *Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Jane A. McKeating
- Division of Immunity and Infection, Institute of Biomedical Research, University of Birmingham Medical School, Birmingham B15 2TT, United Kingdom
| | - Robert E. Lanford
- Department of Virology and Immunology, Southwest National Primate Research Center and Southwest Foundation for Biomedical Research, 7620 NW Loop 410, San Antonio, TX 78245; and
| | - Stephen M. Feinstone
- Laboratory of Hepatitis Viruses, Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892
| | - Marian E. Major
- Laboratory of Hepatitis Viruses, Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892
| | - Geert Leroux-Roels
- Center for Vaccinology, Ghent University and Hospital, Building A, First Floor, De Pintelaan 185, 9000 Ghent, Belgium
| | - Charles M. Rice
- *Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, The Rockefeller University, 1230 York Avenue, New York, NY 10021
- **To whom correspondence should be addressed. E-mail:
| |
Collapse
|
47
|
Abstract
Since the discovery of the hepatitis C virus over 15 years ago, scientists have raced to develop diagnostics, study the virus and find new therapies. Yet virtually every attempt to dissect this pathogen has met with roadblocks that impeded progress. Its replication was restricted to humans or experimentally infected chimpanzees, and efficient growth of the virus in cell culture failed until very recently. Nevertheless hard-fought progress has been made and the first wave of antiviral drugs is entering clinical trials.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
| | | |
Collapse
|
48
|
Lindenbach BD, Evans MJ, Syder AJ, Wölk B, Tellinghuisen TL, Liu CC, Maruyama T, Hynes RO, Burton DR, McKeating JA, Rice CM. Complete replication of hepatitis C virus in cell culture. Science 2005; 309:623-6. [PMID: 15947137 DOI: 10.1126/science.1114016] [Citation(s) in RCA: 1817] [Impact Index Per Article: 95.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many aspects of the hepatitis C virus (HCV) life cycle have not been reproduced in cell culture, which has slowed research progress on this important human pathogen. Here, we describe a full-length HCV genome that replicates and produces virus particles that are infectious in cell culture (HCVcc). Replication of HCVcc was robust, producing nearly 10(5) infectious units per milliliter within 48 hours. Virus particles were filterable and neutralized with a monoclonal antibody against the viral glycoprotein E2. Viral entry was dependent on cellular expression of a putative HCV receptor, CD81. HCVcc replication was inhibited by interferon-alpha and by several HCV-specific antiviral compounds, suggesting that this in vitro system will aid in the search for improved antivirals.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Lindenbach BD, Evans MJ, Syder AJ, Wölk B, Tellinghuisen TL, Liu CC, Maruyama T, Hynes RO, Burton DR, McKeating JA, Rice CM. Complete replication of hepatitis C virus in cell culture. Science 2005. [PMID: 15947137 DOI: 10.1126/science.1114016.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Many aspects of the hepatitis C virus (HCV) life cycle have not been reproduced in cell culture, which has slowed research progress on this important human pathogen. Here, we describe a full-length HCV genome that replicates and produces virus particles that are infectious in cell culture (HCVcc). Replication of HCVcc was robust, producing nearly 10(5) infectious units per milliliter within 48 hours. Virus particles were filterable and neutralized with a monoclonal antibody against the viral glycoprotein E2. Viral entry was dependent on cellular expression of a putative HCV receptor, CD81. HCVcc replication was inhibited by interferon-alpha and by several HCV-specific antiviral compounds, suggesting that this in vitro system will aid in the search for improved antivirals.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grässer FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T. Identification of microRNAs of the herpesvirus family. Nat Methods 2005; 2:269-76. [PMID: 15782219 DOI: 10.1038/nmeth746] [Citation(s) in RCA: 854] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Accepted: 02/10/2005] [Indexed: 12/15/2022]
Abstract
Epstein-Barr virus (EBV or HHV4), a member of the human herpesvirus (HHV) family, has recently been shown to encode microRNAs (miRNAs). In contrast to most eukaryotic miRNAs, these viral miRNAs do not have close homologs in other viral genomes or in the genome of the human host. To identify other miRNA genes in pathogenic viruses, we combined a new miRNA gene prediction method with small-RNA cloning from several virus-infected cell types. We cloned ten miRNAs in the Kaposi sarcoma-associated virus (KSHV or HHV8), nine miRNAs in the mouse gammaherpesvirus 68 (MHV68) and nine miRNAs in the human cytomegalovirus (HCMV or HHV5). These miRNA genes are expressed individually or in clusters from either polymerase (pol) II or pol III promoters, and share no substantial sequence homology with one another or with the known human miRNAs. Generally, we predicted miRNAs in several large DNA viruses, and we could neither predict nor experimentally identify miRNAs in the genomes of small RNA viruses or retroviruses.
Collapse
Affiliation(s)
- Sébastien Pfeffer
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|